John Mattick

Genome-wide analysis of long noncoding RNA stability.

Publisher: Cold Spring Harbor Laboratory

Date: 09-03-2012

DOI: 10.1101/GR.131037.111

Abstract: Transcriptomic analyses have identified tens of thousands of intergenic, intronic, and cis -antisense long noncoding RNAs (lncRNAs) that are expressed from mammalian genomes. Despite progress in functional characterization, little is known about the post-transcriptional regulation of lncRNAs and their half-lives. Although many are easily detectable by a variety of techniques, it has been assumed that lncRNAs are generally unstable, but this has not been examined genome-wide. Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs in the mouse Neuro-2a cell line. We find only a minority of lncRNAs are unstable. LncRNA half-lives vary over a wide range, comparable to, although on average less than, that of mRNAs, suggestive of complex metabolism and widespread functionality. Combining half-lives with comprehensive lncRNA annotations identified hundreds of unstable (half-life 2 h) intergenic, cis -antisense, and intronic lncRNAs, as well as lncRNAs showing extreme stability (half-life 16 h). Analysis of lncRNA features revealed that intergenic and cis -antisense RNAs are more stable than those derived from introns, as are spliced lncRNAs compared to unspliced (single exon) transcripts. Subcellular localization of lncRNAs indicated widespread trafficking to different cellular locations, with nuclear-localized lncRNAs more likely to be unstable. Surprisingly, one of the least stable lncRNAs is the well-characterized paraspeckle RNA Neat1 , suggesting Neat1 instability contributes to the dynamic nature of this subnuclear domain. We have created an online interactive resource ( stability.matticklab.com ) that allows easy navigation of lncRNA and mRNA stability profiles and provides a comprehensive annotation of ∼7200 mouse lncRNAs.

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

Publisher: Springer Science and Business Media LLC

Date: 13-11-2012

DOI: 10.1038/NBT.2024

Retinoic acid-dependent upregulation of mouse folate receptor-alpha expression in embryonic stem cells, and conservation of alternative splicing patterns.

Publisher: Elsevier BV

Date: 04-1999

DOI: 10.1016/S0378-1119(99)00081-5

The extent of functionality in the human genome

Publisher: Springer Science and Business Media LLC

Date: 15-07-2013

DOI: 10.1186/1877-6566-7-2

Non-coding RNAs: Regulators of disease

Publisher: Wiley

Date: 30-10-2010

DOI: 10.1002/PATH.2638

Abstract: For 50 years the term 'gene' has been synonymous with regions of the genome encoding mRNAs that are translated into protein. However, recent genome-wide studies have shown that the human genome is pervasively transcribed and produces many thousands of regulatory non-protein-coding RNAs (ncRNAs), including microRNAs, small interfering RNAs, PIWI-interacting RNAs and various classes of long ncRNAs. It is now clear that these RNAs fulfil critical roles as transcriptional and post-transcriptional regulators and as guides of chromatin-modifying complexes. Here we review the biology of ncRNAs, focusing on the fundamental mechanisms by which ncRNAs facilitate normal development and physiology and, when dysfunctional, underpin disease. We also discuss evidence that intergenic regions associated with complex diseases express ncRNAs, as well as the potential use of ncRNAs as diagnostic markers and therapeutic targets. Taken together, these observations emphasize the need to move beyond the confines of protein-coding genes and highlight the fact that continued investigation of ncRNA biogenesis and function will be necessary for a comprehensive understanding of human disease.

The Ras target AF-6 is a substrate of the fam deubiquitinating enzyme.

Publisher: Rockefeller University Press

Date: 24-08-1998

DOI: 10.1083/JCB.142.4.1053

Abstract: The Ras target AF-6 has been shown to serve as one of the peripheral components of cell–cell adhesions, and is thought to participate in cell–cell adhesion regulation downstream of Ras. We here purified an AF-6-interacting protein with a molecular mass of ∼220 kD (p220) to investigate the function of AF-6 at cell–cell adhesions. The peptide sequences of p220 were identical to the amino acid sequences of mouse Fam. Fam is homologous to a deubiquitinating enzyme in Drosophila, the product of the fat facets gene. Recent genetic analyses indicate that the deubiquitinating activity of the fat facets product plays a critical role in controlling the cell fate. We found that Fam accumulated at the cell–cell contact sites of MDCKII cells, but not at free ends of plasma membranes. Fam was partially colocalized with AF-6 and interacted with AF-6 in vivo and in vitro. We also showed that AF-6 was ubiquitinated in intact cells, and that Fam prevented the ubiquitination of AF-6.

Widespread purifying selection on RNA structure in mammals

Publisher: Oxford University Press (OUP)

Date: 11-07-2013

DOI: 10.1093/NAR/GKT596

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

Publisher: Elsevier BV

Date: 05-2016

DOI: 10.1016/J.CELL.2016.04.028

Response from Mattick and Alm: common architecture of type 4 fimbriae and complexes involved in macromolecular traffic

Publisher: Elsevier BV

Date: 11-1995

DOI: 10.1016/S0966-842X(00)88990-8

The RNA modification landscape in human disease

Publisher: Cold Spring Harbor Laboratory

Date: 30-08-2017

DOI: 10.1261/RNA.063503.117

Abstract: RNA modifications have been historically considered as fine-tuning chemo-structural features of infrastructural RNAs, such as rRNAs, tRNAs, and snoRNAs. This view has changed dramatically in recent years, to a large extent as a result of systematic efforts to map and quantify various RNA modifications in a transcriptome-wide manner, revealing that RNA modifications are reversible, dynamically regulated, far more widespread than originally thought, and involved in major biological processes, including cell differentiation, sex determination, and stress responses. Here we summarize the state of knowledge and provide a catalog of RNA modifications and their links to neurological disorders, cancers, and other diseases. With the advent of direct RNA-sequencing technologies, we expect that this catalog will help prioritize those RNA modifications for transcriptome-wide maps.

The location and nucleotide sequence of the thymidine kinase gene of bovine herpesvirus type 1.2

Publisher: Microbiology Society

Date: 10-1990

DOI: 10.1099/0022-1317-71-10-2417

Escherichia coli contains a set of genes homologous to those involved in protein secretion, DNA uptake and the assembly of type-4 fimbriae in other bacteria.

Publisher: Elsevier BV

Date: 12-1994

DOI: 10.1016/0378-1119(94)90851-6

The state of long non-coding RNA biology

Publisher: MDPI AG

Date: 10-08-2018

DOI: 10.3390/NCRNA4030017

Abstract: Transcriptomic studies have demonstrated that the vast majority of the genomes of mammals and other complex organisms is expressed in highly dynamic and cell-specific patterns to produce large numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Despite well characterized ex les, their scaling with developmental complexity, and many demonstrations of their association with cellular processes, development and diseases, lncRNAs are still to be widely accepted as major players in gene regulation. This may reflect an underappreciation of the extent and precision of the epigenetic control of differentiation and development, where lncRNAs appear to have a central role, likely as organizational and guide molecules: most lncRNAs are nuclear-localized and chromatin-associated, with some involved in the formation of specialized subcellular domains. I suggest that a reassessment of the conceptual framework of genetic information and gene expression in the 4-dimensional ontogeny of spatially organized multicellular organisms is required. Together with this and further studies on their biology, the key challenges now are to determine the structure–function relationships of lncRNAs, which may be aided by emerging evidence of their modular structure, the role of RNA editing and modification in enabling epigenetic plasticity, and the role of RNA signaling in transgenerational inheritance of experience.

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

Publisher: Cold Spring Harbor Laboratory

Date: 05-01-2010

DOI: 10.1101/GR.095273.109

Abstract: MicroRNAs (miRNAs) are short (20–23 nt) RNAs that are sequence-specific mediators of transcriptional and post-transcriptional regulation of gene expression. Modern high-throughput technologies enable deep sequencing of such RNA species on an unprecedented scale. We find that the analysis of small RNA deep-sequencing libraries can be affected by cross-mapping, in which RNA sequences originating from one locus are inadvertently mapped to another. Similar to cross-hybridization on microarrays, cross-mapping is prevalent among miRNAs, as they tend to occur in families, are similar or derived from repeat or structural RNAs, or are post-transcriptionally modified. Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In contrast to previous reports, our analysis suggests that RNA editing in mature miRNAs is rare in animals.

Seq and you will find

Publisher: Bentham Science Publishers Ltd.

Date: 16-06-2016

DOI: 10.2174/1566523216666160524144159

Abstract: The human genome sequence is freely available, nearly complete and is providing a foundation of research opportunities that are overturning our current understanding of human biology. The advent of next generation sequencing has revolutionized the way we can interrogate the genome and its transcriptional products and how we analyze, diagnose, monitor and even treat human disease. Personal genetic profiles are increasing dramatically in medical value as researchers accumulate more and more knowledge about the interaction between genetic and environmental factors that contribute to the onset of common disorders. As the cost of sequencing plummets, whole genome sequencing of in iduals is becoming a reality and the field of personalized genomic medicine is rapidly developing. Now there is great need for accurate annotation of all functionally important sequences in the human genome and the variations within them that contribute to health and disease. The vast majority of our genome gives rise to RNA transcripts. This extraordinarily versatile molecule not only encodes protein information but also has great structural dynamics and plasticity, capacity for DNA/RNA rotein interactions and catalytic activity. It is a key regulator of biological networks with clear links to human disease and a more comprehensive understanding of its function is needed to maximise its use in medical practice. This review focuses on the complexity of our genome and the impact of sequencing technologies in understanding its many products and functions in health and disease.

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

Publisher: Springer Science and Business Media LLC

Date: 05-09-2011

DOI: 10.1186/1471-2164-12-441

The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion.

Publisher: American Association for Cancer Research (AACR)

Date: 31-05-2011

DOI: 10.1158/0008-5472.CAN-10-4460

Abstract: The identification of cancer-associated long noncoding RNAs (lncRNAs) and the investigation of their molecular and biological functions are important to understand the molecular biology of cancer and its progression. Although the functions of lncRNAs and the mechanisms regulating their expression are largely unknown, recent studies are beginning to unravel their importance in human health and disease. Here, we report that a number of lncRNAs are differentially expressed in melanoma cell lines in comparison to melanocytes and keratinocyte controls. One of these lncRNAs, SPRY4-IT1 (GenBank accession ID AK024556), is derived from an intron of the SPRY4 gene and is predicted to contain several long hairpins in its secondary structure. RNA-FISH analysis showed that SPRY4-IT1 is predominantly localized in the cytoplasm of melanoma cells, and SPRY4-IT1 RNAi knockdown results in defects in cell growth, differentiation, and higher rates of apoptosis in melanoma cell lines. Differential expression of both SPRY4 and SPRY4-IT1 was also detected in vivo, in 30 distinct patient s les, classified as primary in situ, regional metastatic, distant metastatic, and nodal metastatic melanoma. The elevated expression of SPRY4-IT1 in melanoma cells compared to melanocytes, its accumulation in cell cytoplasm, and effects on cell dynamics, including increased rate of wound closure on SPRY4-IT1 overexpression, suggest that the higher expression of SPRY4-IT1 may have an important role in the molecular etiology of human melanoma. Cancer Res 71(11) 3852–62. ©2011 AACR.

Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms

Publisher: Wiley

Date: 17-09-2003

DOI: 10.1002/BIES.10332

Identification of major antigenic proteins of bovine herpesvirus 1 and their correlation with virus neutralizing activity.

Publisher: Elsevier BV

Date: 02-1988

DOI: 10.1016/0378-1135(88)90035-1

Type IV pili and twitching motility.

Publisher: Annual Reviews

Date: 10-2002

DOI: 10.1146/ANNUREV.MICRO.56.012302.160938

Abstract: ▪ Abstract Twitching motility is a flagella-independent form of bacterial translocation over moist surfaces. It occurs by the extension, tethering, and then retraction of polar type IV pili, which operate in a manner similar to a grappling hook. Twitching motility is equivalent to social gliding motility in Myxococcus xanthus and is important in host colonization by a wide range of plant and animal pathogens, as well as in the formation of biofilms and fruiting bodies. The biogenesis and function of type IV pili is controlled by a large number of genes, almost 40 of which have been identified in Pseudomonas aeruginosa. A number of genes required for pili assembly are homologous to genes involved in type II protein secretion and competence for DNA uptake, suggesting that these systems share a common architecture. Twitching motility is also controlled by a range of signal transduction systems, including two-component sensor-regulators and a complex chemosensory system.

A new paradigm for developmental biology.

Publisher: The Company of Biologists

Date: 05-2007

DOI: 10.1242/JEB.005017

Abstract: It is usually thought that the development of complex organisms is controlled by protein regulatory factors and morphogenetic signals exchanged between cells and differentiating tissues during ontogeny. However, it is now evident that the majority of all animal genomes is transcribed, apparently in a developmentally regulated manner, suggesting that these genomes largely encode RNA machines and that there may be a vast hidden layer of RNA regulatory transactions in the background. I propose that the epigenetic trajectories of differentiation and development are primarily programmed by feed-forward RNA regulatory networks and that most of the information required for multicellular development is embedded in these networks, with cell–cell signalling required to provide important positional information and to correct stochastic errors in the endogenous RNA-directed program.

Small regulatory RNAs in mammals.

Publisher: Oxford University Press (OUP)

Date: 15-04-2005

DOI: 10.1093/HMG/DDI101

Characterization of a gene, pilU, required for twitching motility but not phage sensitivity in Pseudomonas aeruginosa.

Publisher: Wiley

Date: 09-1994

DOI: 10.1111/J.1365-2958.1994.TB00499.X

The functional genomics of noncoding RNA.

Publisher: American Association for the Advancement of Science (AAAS)

Date: 02-09-2005

DOI: 10.1126/SCIENCE.1117806

Abstract: Large numbers of noncoding RNA transcripts (ncRNAs) are being revealed by complementary DNA cloning and genome tiling array studies in animals. The big and as yet largely unanswered question is whether these transcripts are relevant. A paper by Willingham et al . shows the way forward by developing a strategy for large-scale functional screening of ncRNAs, involving small interfering RNA knockdowns in cell-based screens, which identified a previously unidentified ncRNA repressor of the transcription factor NFAT. It appears likely that ncRNAs constitute a critical hidden layer of gene regulation in complex organisms, the understanding of which requires new approaches in functional genomics.

Long noncoding RNAs in cell biology

Publisher: Elsevier BV

Date: 06-2011

DOI: 10.1016/J.SEMCDB.2011.01.001

Abstract: Whole genome transcriptomic analyses have identified large numbers of dynamically expressed long non-protein-coding RNAs (lncRNAs) in mammals and other animals whose functions are, as yet, largely unknown. Here we summarize the growing evidence that lncRNAs, like mRNAs, can be trafficked to and function in a wide variety of subcellular locations. Investigation of the subcellular distribution of lncRNAs has the potential to greatly expand our knowledge not only of the function of lncRNAs but also of cell biology by identifying previously unknown subcellular structures and novel constituents of known cellular organelles.

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

Publisher: Springer Science and Business Media LLC

Date: 19-12-2022

DOI: 10.1038/S41592-022-01714-W

Abstract: RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore 3′ end-capture sequencing (Nano3P-seq), a method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition, and tail length dynamics at per-read resolution. By employing a template-switching-based sequencing protocol, Nano3P-seq can sequence RNA molecule from its 3′ end, regardless of its polyadenylation status, without the need for PCR lification or ligation of RNA adapters. We demonstrate that Nano3P-seq provides quantitative estimates of RNA abundance and tail lengths, and captures a wide ersity of RNA biotypes. We find that, in addition to mRNA and long non-coding RNA, polyA tails can be identified in 16S mitochondrial ribosomal RNA in both mouse and zebrafish models. Moreover, we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform-specific level, correlating with mRNA decay. Finally, we demonstrate the ability of Nano3P-seq in capturing non-A bases within polyA tails of various lengths, and reveal their distribution during vertebrate embryogenesis. Overall, Nano3P-seq is a simple and robust method for accurately estimating transcript levels, tail lengths, and tail composition heterogeneity in in idual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.

A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs

Publisher: Wiley

Date: 15-06-2023

DOI: 10.1002/BIES.202300080

Abstract: Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non‐functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection introns repetitive sequences a complex epigenome lack of scaling of (protein‐coding) genes and increase in ‘noncoding’ sequences with developmental complexity genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information. Also see the video abstract here: youtu.be/qxeGwahBANw

Genome-sequencing anniversary. The genomic foundation is shifting.

Publisher: American Association for the Advancement of Science (AAAS)

Date: 18-02-2011

DOI: 10.1126/SCIENCE.1203703

Abstract: The most important outcome of the human genome project has been to expose the fallacy that most genetic information is expressed as proteins.

tonB3 is required for normal twitching motility and extracellular assembly of type IV pili.

Publisher: American Society for Microbiology

Date: 07-2004

DOI: 10.1128/JB.186.13.4387-4389.2004

Abstract: Three mutants with Tn 5 -B21 insertion in tonB3 (PA0406) of Pseudomonas aeruginosa exhibited defective twitching motility and reduced assembly of extracellular pili. These defects could be complemented with wild-type tonB3 .

Characterization of a five-gene cluster required for the biogenesis of type 4 fimbriae in Pseudomonas aeruginosa.

Publisher: Wiley

Date: 05-1995

DOI: 10.1111/J.1365-2958.1995.TB02414.X

Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions

Publisher: Frontiers Media SA

Date: 12-04-2019

DOI: 10.3389/FGENE.2019.00309

Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage.

Publisher: Cold Spring Harbor Laboratory

Date: 21-12-2013

DOI: 10.1261/RNA.036202.112

Abstract: Adenosine to inosine (A I) RNA editing, which is catalyzed by the ADAR family of proteins, is one of the fundamental mechanisms by which transcriptomic ersity is generated. Indeed, a number of genome-wide analyses have shown that A I editing is not limited to a few mRNAs, as originally thought, but occurs widely across the transcriptome, especially in the brain. Importantly, there is increasing evidence that A I editing is essential for animal development and nervous system function. To more efficiently characterize the complete catalog of ADAR events in the mammalian transcriptome we developed a high-throughput protocol to identify A I editing sites, which exploits the capacity of glyoxal to protect guanosine, but not inosine, from RNAse T1 treatment, thus facilitating extraction of RNA fragments with inosine bases at their termini for high-throughput sequencing. Using this method we identified 665 editing sites in mouse brain RNA, including most known sites and suite of novel sites that include nonsynonymous changes to protein-coding genes, hyperediting of genes known to regulate p53, and alterations to non-protein-coding RNAs. This method is applicable to any biological system for the de novo discovery of A I editing sites, and avoids the complicated informatic and practical issues associated with editing site identification using traditional RNA sequencing data. This approach has the potential to substantially increase our understanding of the extent and function of RNA editing, and thereby to shed light on the role of transcriptional plasticity in evolution, development, and cognition.

Genome-wide discovery of human splicing branchpoints

Publisher: Cold Spring Harbor Laboratory

Date: 05-01-2015

DOI: 10.1101/GR.182899.114

Abstract: During the splicing reaction, the 5′ intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in ,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3′ splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide ersity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit ergent usage in vertebrate lineages and associate with other splicing elements and distinct intron–exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome

Publisher: Elsevier BV

Date: 07-2017

DOI: 10.1016/J.TIG.2017.04.004

Abstract: The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and ersity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing. These features are consistent with their role as modular epigenetic regulators. We describe here the key studies and technological advances that have shaped our understanding of the dimensions, dynamics, and biological relevance of the mammalian noncoding transcriptome.

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

Publisher: Springer Science and Business Media LLC

Date: 09-03-2015

DOI: 10.1038/NMETH.3321

Abstract: We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and novel coding exons across 20 human tissues. CaptureSeq was superior for the detection and quantification of genes with low expression, showed little technical variation and accurately measured differential expression. This approach expands and refines previous annotations and simultaneously generates an expression atlas.

Characterisation of a Pseudomonas aeruginosa twitching motility gene and evidence for a specialised protein export system widespread in eubacteria.

Publisher: Elsevier BV

Date: 05-1991

DOI: 10.1016/0378-1119(91)90221-V

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

Publisher: Proceedings of the National Academy of Sciences

Date: 23-02-2015

DOI: 10.1073/PNAS.1420955112

Abstract: MicroRNAs (miRNAs) are small ∼22-nt RNAs that are important regulators of posttranscriptional gene expression. Since their initial discovery, they have been shown to be involved in many cellular processes, and their misexpression is associated with disease etiology. Currently, nearly 2,800 human miRNAs are annotated in public repositories. A key question in miRNA research is how many miRNAs are harbored by the human genome. To answer this question, we examined 1,323 short RNA sequence s les and identified 3,707 novel miRNAs, many of which are human-specific and tissue-specific. Our findings suggest that the human genome expresses a greater number of miRNAs than has previously been appreciated and that many more miRNA molecules may play key roles in disease etiology.

Regulation of Epidermal Growth Factor Receptor Signaling in Human Cancer Cells by MicroRNA-7

Publisher: Elsevier BV

Date: 02-2009

DOI: 10.1074/JBC.M804280200

RNA lights up

Publisher: Springer Science and Business Media LLC

Date: 10-2011

DOI: 10.1038/NBT.2003

Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing the integration of genome sequencing with clinical records and data from the internet of things will transform health care

Publisher: AMPCo

Date: 09-04-2018

DOI: 10.5694/MJA17.01176

Non-coding RNA.

Publisher: Oxford University Press (OUP)

Date: 15-04-2006

DOI: 10.1093/HMG/DDL046

Abstract: The term non-coding RNA (ncRNA) is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. Although it has been generally assumed that most genetic information is transacted by proteins, recent evidence suggests that the majority of the genomes of mammals and other complex organisms is in fact transcribed into ncRNAs, many of which are alternatively spliced and/or processed into smaller products. These ncRNAs include microRNAs and snoRNAs (many if not most of which remain to be identified), as well as likely other classes of yet-to-be-discovered small regulatory RNAs, and tens of thousands of longer transcripts (including complex patterns of interlacing and overlapping sense and antisense transcripts), most of whose functions are unknown. These RNAs (including those derived from introns) appear to comprise a hidden layer of internal signals that control various levels of gene expression in physiology and development, including chromatin architecture/epigenetic memory, transcription, RNA splicing, editing, translation and turnover. RNA regulatory networks may determine most of our complex characteristics, play a significant role in disease and constitute an unexplored world of genetic variation both within and between species.

The future of molecular pathology

Publisher: Springer New York

Date: 2017

DOI: 10.1007/978-1-4939-6643-1_16

A global view of genomic information - moving beyond the gene and the master regulator

Publisher: Elsevier BV

Date: 2010

DOI: 10.1016/J.TIG.2009.11.002

Abstract: The current view of gene regulation in complex organisms holds that gene expression is largely controlled by the combinatoric actions of transcription factors and other regulatory proteins, some of which powerfully influence cell type. Recent large-scale studies have confirmed that cellular differentiation involves many different regulatory factors. However, other studies indicate that the genome is pervasively transcribed to produce a variety of short and long non-protein-coding RNAs, including those derived from retrotransposed sequences, which also play important roles in the epigenetic regulation of gene expression. The evidence suggests that ontogenesis requires interplay between state-specific regulatory proteins, multitasked effector complexes and target-specific RNAs that recruit these complexes to their sites of action. Moreover, the semi-continuous nature of the transcriptome prompts the reassessment of 'genes' as discrete entities and indicates that the mammalian genome might be more accurately viewed as islands of protein-coding information in a sea of cis- and trans-acting regulatory sequences.

Molecular characterisation of Australian bovine enteroviruses.

Publisher: Elsevier BV

Date: 08-1999

DOI: 10.1016/S0378-1135(99)00062-0

Abstract: In this study we report the full length (7.4 kb) sequence of two Australian bovine enterovirus (BEV) isolates, K2577 and SL305 and the partial sequence of a third isolate, 66/27, which are the prototypes of the three major serological groups of BEV in Australia. Australian BEV isolates have not previously been related to the international classification of BEV into the major serotypes BEV-1 and BEV-2. The sequences of the three representative Australian isolates were compared to the full length sequence of a Northern Ireland isolate (VG527) classified as BEV-1, as well as two partial sequences of isolates from the United States and the United Kingdom classified as BEV-2. All three Australian isolates were classified as BEV-1 on the basis of closer nucleotide and amino acid similarity to the 5'-UTR and capsid proteins of VG527 than to the BEV-2 isolates (79-81% versus 76-77% nucleotide identity in the 5-UTR, and 86-98% versus 65-77% amino acid identity in the capsid proteins). These results indicate that most if not all Australian BEV are BEV-1. The remainder of the genome, which encodes non-structural proteins involved in viral replication, showed high sequence homology as has been observed among such genes in other enteroviruses. A system for full-length lification of BEV isolates was also developed and the K2577 isolate was cloned to obtain a full-length, infectious DNA copy of the BEV genome. When RNA transcripts of BEV lification products were transfected into MDBK cells infectious particles were produced. These virus particles were identical to the original virus isolates. This system can be used as a basis for the development of BEV-vectored vaccines as well in further molecular studies of bovine enteroviruses.

UHT processing--effect on process energy requirements.

Publisher: Wiley

Date: 05-1984

DOI: 10.1111/J.1365-2621.1984.TB13262.X

The rise of regulatory RNA

Publisher: Springer Science and Business Media LLC

Date: 29-04-2014

DOI: 10.1038/NRG3722

Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease

Publisher: Springer Science and Business Media LLC

Date: 17-09-2018

DOI: 10.1038/S41593-018-0223-0

Long non-coding RNAs: definitions, functions, challenges and recommendations

Publisher: Springer Science and Business Media LLC

Date: 03-01-2023

DOI: 10.1038/S41580-022-00566-8

The action of structural analogues of ethidium bromide on the mitochondrial genome of yeast.

Publisher: Springer Science and Business Media LLC

Date: 12-1977

DOI: 10.1007/BF00808386

A 'one tube reaction' for synthesis and amplification of total cDNA from small numbers of cells.

Publisher: Oxford University Press (OUP)

Date: 1993

DOI: 10.1093/NAR/21.3.783

Expression and Function of the Protein Tyrosine Phosphatase Receptor J (PTPRJ) in Normal Mammary Epithelial Cells and Breast Tumors

Publisher: Public Library of Science (PLoS)

Date: 17-07-2012

DOI: 10.1371/JOURNAL.PONE.0040742

RNAs as extracellular signaling molecules

Publisher: Bioscientifica

Date: 16-01-2008

DOI: 10.1677/JME-07-0160

Abstract: RNA is emerging as a major component of the regulatory circuitry that underpins the development and physiology of complex organisms. Here we review recent evidence that suggests that RNA may supplement endocrine and paracrine signaling by small molecules and proteins, and act as an efficient and evolutionarily flexible source of sequence-specific information transfer between cells, both locally and systemically. As such, RNA signaling may play a central but previously hidden role in multicellular ontogeny, homeostasis, and transmitted epigenetic memory.

The lethal toxin from Australian funnel-web spiders is encoded by an intronless gene

Publisher: Public Library of Science (PLoS)

Date: 22-08-2012

DOI: 10.1371/JOURNAL.PONE.0043699

Raising the estimate of functional human sequences.

Publisher: Cold Spring Harbor Laboratory

Date: 09-08-2007

DOI: 10.1101/GR.6406307

Abstract: While less than 1.5% of the mammalian genome encodes proteins, it is now evident that the vast majority is transcribed, mainly into non-protein-coding RNAs. This raises the question of what fraction of the genome is functional, i.e., composed of sequences that yield functional products, are required for the expression (regulation or processing) of these products, or are required for chromosome replication and maintenance. Many of the observed noncoding transcripts are differentially expressed, and, while most have not yet been studied, increasing numbers are being shown to be functional and/or trafficked to specific subcellular locations, as well as exhibit subtle evidence of selection. On the other hand, analyses of conservation patterns indicate that only ∼5% (3%–8%) of the human genome is under purifying selection for functions common to mammals. However, these estimates rely on the assumption that reference sequences (usually ancient transposon-derived sequences) have evolved neutrally, which may not be the case, and if so would lead to an underestimate of the fraction of the genome under evolutionary constraint. These analyses also do not detect functional sequences that are evolving rapidly and/or have acquired lineage-specific functions. Indeed, many regulatory sequences and known functional noncoding RNAs, including many microRNAs, are not conserved over significant evolutionary distances, and recent evidence from the ENCODE project suggests that many functional elements show no detectable level of sequence constraint. Thus, it is likely that much more than 5% of the genome encodes functional information, and although the upper bound is unknown, it may be considerably higher than currently thought.

Exploring the epitranscriptome by native RNA sequencing

Publisher: Cold Spring Harbor Laboratory

Date: 14-09-2022

DOI: 10.1261/RNA.079404.122

Abstract: Chemical RNA modifications, collectively referred to as the “epitranscriptome,” are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely due to the advent of high-throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m 6 A), pseudouridine (Ψ), and inosine (I). However, the signal modulations caused by most RNA modifications are yet to be determined. A global effort is needed to determine the signatures of the full range of RNA modifications to avoid the technical biases that have so far limited our understanding of the epitranscriptome.

Complex architecture and regulated expression of the Sox2ot locus during vertebrate development.

Publisher: Cold Spring Harbor Laboratory

Date: 18-09-2009

DOI: 10.1261/RNA.1705309

Abstract: The Sox2 gene is a key regulator of pluripotency embedded within an intron of a long noncoding RNA (ncRNA), termed Sox2 overlapping transcript ( Sox2ot ), which is transcribed in the same orientation. However, this ncRNA remains uncharacterized. Here we show that Sox2ot has multiple transcription start sites associated with genomic features that indicate regulated expression, including highly conserved elements (HCEs) and chromatin marks characteristic of gene promoters. To identify biological processes in which Sox2ot may be involved, we analyzed its expression in several developmental systems, compared to expression of Sox2 . We show that Sox2ot is a stable transcript expressed in mouse embryonic stem cells, which, like Sox2 , is down-regulated upon induction of embryoid body (EB) differentiation. However, in contrast to Sox2 , Sox2ot is up-regulated during EB mesoderm-lineage differentiation. In adult mouse, Sox2ot isoforms were detected in tissues where Sox2 is expressed, as well as in different tissues, supporting independent regulation of expression of the ncRNA. Sox2dot , an isoform of Sox2ot transcribed from a distal HCE located kb upstream of Sox2 , was detected exclusively in the mouse brain, with enrichment in regions of adult neurogenesis. In addition, Sox2ot isoforms are transcribed from HCEs upstream of Sox2 in other vertebrates, including in several regions of the human brain. We also show that Sox2ot is dynamically regulated during chicken and zebrafish embryogenesis, consistently associated with central nervous system structures. These observations provide insight into the structure and regulation of the Sox2ot gene, and suggest conserved roles for Sox2ot orthologs during vertebrate development.

The central role of RNA in human development and cognition

Publisher: Wiley

Date: 06-05-2011

DOI: 10.1016/J.FEBSLET.2011.05.001

Abstract: It appears that the genetic programming of humans and other complex organisms has been misunderstood for the past 50 years, due to the assumption that most genetic information is transacted by proteins. However, the human genome contains only about 20,000 protein-coding genes, similar in number and with largely orthologous functions as those in nematodes that have only 1000 somatic cells. By contrast, the extent of non-protein-coding DNA increases with increasing complexity, reaching 98.8% in humans. The majority of these sequences are dynamically transcribed, mainly into non-protein-coding RNAs, with tens if not hundreds of thousands that show specific expression patterns and subcellular locations, as well as many classes of small regulatory RNAs. The emerging evidence indicates that these RNAs control the epigenetic states that underpin development, and that many are dysregulated in cancer and other complex diseases. Moreover it appears that animals, particularly primates, have evolved plasticity in these RNA regulatory systems, especially in the brain. Thus, it appears that what was dismissed as 'junk' because it was not understood holds the key to understanding human evolution, development, and cognition.

Evolution, biogenesis and function of promoter-associated RNAs.

Publisher: Informa UK Limited

Date: 08-2009

DOI: 10.4161/CC.8.15.9154

Abstract: Transcription initiation is a tightly controlled process that involves chromatin modifications and nucleosome remodelling, transcription factor binding, and the assembly and recruitment of the RNA Polymerase II (RNAPII) complex. Recent studies have reported a ersity of long and short RNAs derived from eukaryotic promoters, which may be involved in transcription regulation. Here we review these species with particular attention to the features and biogenesis of transcription initiation RNAs (tiRNAs), a class of 18 nucleotide small RNA conserved from insects to mammals. We also report and discuss the observation that tiRNAs are not present in plants and are not clearly expressed in the nematode C. elegans. We suggest that tiRNAs may be intimately connected RNAPII backtracking, nucleosome marking, and gene regulation.

MicroRNAs in beta-Cell Biology, Insulin Resistance, Diabetes and Its Complications

Publisher: American Diabetes Association

Date: 20-06-2011

DOI: 10.2337/DB11-0171

RNA as the substrate for epigenome-environment interactions: RNA guidance of epigenetic processes and the expansion of RNA editing in animals underpins development, phenotypic plasticity, learning, and cognition

Publisher: Wiley

Date: 28-06-2010

DOI: 10.1002/BIES.201000028

Identification of a gene, pilF, required for type 4 fimbrial biogenesis and twitching motility in Pseudomonas aeruginosa.

Publisher: Elsevier BV

Date: 1996

DOI: 10.1016/S0378-1119(96)00403-9

Abstract: Many bacterial pathogens produce a class of surface structures called type 4 fimbriae. In Pseudomonas aeruginosa these fimbriae are responsible for adhesion and translocation across host epithelial surfaces. We have identified a novel gene involved in the complex process of type 4 fimbrial biogenesis. This gene, termed pilF, is located on SpeI fragment S at 30 min on the P. aeruginosa genomic map, which is the sixth region on the chromosome shown to contain a fimbrial-associated gene. The PilF protein has a predicted M(r) of 22402, and together with a highly homologous upstream ORF shares a chromosomal arrangement similar to that found in Haemophilus influenzae. A pilF mutant is blocked in the export/assembly of the fimbrial subunit PilA, and accumulates this protein in the membrane fraction. Complementation studies indicate that the cloned pilF gene is able to restore the expression of surface fimbriae, twitching motility and susceptibility to fimbrial-specific bacteriophage.

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network

Publisher: Springer Science and Business Media LLC

Date: 16-10-2013

DOI: 10.1038/SREP02962

Abstract: Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for ex le, TERC , which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2 and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles and by integrating these data with RNA-seq data obtained from melanoma cells, we have identified a co-expression network of differentially methylated genes with significance for cancer related functions. Focused assays of melanoma patient tissue s les for CpG island methylation near the noncoding RNA gene SNORD-10 demonstrated high specificity.

The molecular genetics of type-4 fimbriae in Pseudomonas aeruginosa--a review.

Publisher: Elsevier BV

Date: 1996

DOI: 10.1016/S0378-1119(96)00441-6

Abstract: Type-4 fimbriae (or pili) are filaments found at the poles of a wide range of bacterial pathogens, including Neisseria gonorrhoeae, Moraxella bovis, Dichelobacter nodosus and Pseudomonas aeruginosa. They are composed of a small subunit which is highly conserved among different species and appear to mediate adhesion and translocation across epithelial surfaces via a phenomenon termed "twitching motility'. These fimbriae are key host colonisation factors and important protective antigens. We have analysed the genetics and biosynthesis of type-4 fimbriae in P. aeruginosa, which is an opportunistic pathogen of compromised in iduals, including those suffering cystic fibrosis, AIDS or burns. A library of P. aeruginosa transposon mutants was constructed which exhibited loss of twitching motility, as determined by altered colony morphology. Analysis of these mutants, and of similar collections by other groups, have revealed that there are at least 22 genes involved in type-4 fimbrial assembly and function. A large number (pilA, B, C, D, E, M, N, O, P, Q, T, U, V and Z) appear to be involved in the biogenesis of the fimbriae and to represent a subset of a supersystem involved in the assembly of surface-associated protein complexes. Homologs of at least some of these genes have subsequently been identified in other type-4 fimbriate bacteria. In P. aeruginosa, the system is also regulated via two signal transduction pathways-a classic sensor-regulator system (encoded by pilS, pilR and rpoN) which controls transcription of the fimbrial subunit, presumably in response to host cues, and a chemotactic system (encoded by pilG, H, I, J, K and L) which may be involved in the directional or rate control of twitching motility in response to local environmental variables.

Morphogenetic expression of Bacteroides nodosus fimbriae in Pseudomonas aeruginosa

Publisher: American Society for Microbiology

Date: 1987

DOI: 10.1128/JB.169.1.33-41.1987

Abstract: Type 4 fimbriae are found in a range of pathogenic bacteria, including Bacteroides nodosus, Moraxella bovis, Neisseria gonorrhoeae, and Pseudomonas aeruginosa. The structural subunits of these fimbriae all contain a highly conserved hydrophobic amino-terminal sequence preceding a variable hydrophilic carboxy-terminal region. We show here that recombinant P. aeruginosa cells containing the B. nodosus fimbrial subunit gene under the control of a strong promoter (pL, from bacteriophage lambda) produced large amounts of fimbriae that were structurally and antigenically indistinguishable from those produced by B. nodosus. This was demonstrated by fimbrial isolation and purification, electrophoretic and Western transfer analyses, and immunogold labeling and electron microscopy. These results suggest that type 4 fimbriated bacteria use a common mechanism for fimbrial assembly and that the structural subunits are interchangeable, thereby providing a basis for the development of multivalent vaccines.

Somatic retrotransposition alters the genetic landscape of the human brain

Publisher: Springer Science and Business Media LLC

Date: 30-10-2011

DOI: 10.1038/NATURE10531

RNA regulation of epigenetic processes

Publisher: Wiley

Date: 2009

DOI: 10.1002/BIES.080099

Abstract: There is increasing evidence that dynamic changes to chromatin, chromosomes and nuclear architecture are regulated by RNA signalling. Although the precise molecular mechanisms are not well understood, they appear to involve the differential recruitment of a hierarchy of generic chromatin modifying complexes and DNA methyltransferases to specific loci by RNAs during differentiation and development. A significant fraction of the genome-wide transcription of non-protein coding RNAs may be involved in this process, comprising a previously hidden layer of intermediary genetic information that underpins developmental ontogeny and the differences between species, ecotypes and in iduals. It is also evident that RNA editing is a primary means by which hardwired genetic information in animals can be altered by environmental signals, especially in the brain, indicating a dynamic RNA-mediated interplay between the transcriptome, the environment and the epigenome. Moreover, RNA-directed regulatory processes may also transfer epigenetic information not only within cells but also between cells and organ systems, as well as across generations.

Effects of substitution of aspartate-440 and tryptophan-487 in the thiamin diphosphate binding region of pyruvate decarboxylase from Zymomonas mobilis.

Publisher: Wiley

Date: 13-01-1992

DOI: 10.1016/0014-5793(92)80411-9

Abstract: A tryptophan residue at position 487 in Zymomonas mobilis pyruvate decarboxylase was altered to leucine by site-directed mutagenesis. This modified Z. mobilis pyruvate decarboxylase was active when expressed in Escherichia coli and had unchanged kinetics towards pyruvate. The enzyme showed a decreased affinity for the cofactors with the half-saturating concentrations increasing from 0.64 to 9.0 microM for thiamin diphosphate and from 4.21 to 45 microM for Mg2+. Unlike the wild-type enzyme, there was little quenching of tryptophan fluorescence upon adding cofactors to this modified form. The data suggest that tryptophan-487 is close to the cofactor binding site but is not required absolutely for pyruvate decarboxylase activity. Substitution of asparagine, threonine or glycine for aspartate-440, a residue which is conserved between many thiamin diphosphate-dependent enzymes, completely abolishes enzyme activity.

Genetic Variations of Ultraconserved Elements in the Human Genome

Publisher: Mary Ann Liebert Inc

Date: 11-2019

DOI: 10.1089/OMI.2019.0156

Stringent Programming of DNA Methylation in Humans

Publisher: Cambridge University Press (CUP)

Date: 10-2010

DOI: 10.1375/TWIN.13.5.405

Abstract: We describe a PCR-based method called Amplified Methylation Polymorphism (AMP) for scanning genomes for DNA methylation changes. AMP detects tissue-specific DNA methylation signatures often representing junctions between methylated and unmethylated DNA close to intronexon junctions and/or associated with CpG islands. Identical AMP profiles are detected for healthy, young, monozygotic twins.

An analysis of the organization and evolution of type 4 fimbrial (MePhe) subunit proteins.

Publisher: Springer Science and Business Media LLC

Date: 07-1987

DOI: 10.1007/BF02100020

In grateful recognition of our Editorial Board

Publisher: Wiley

Date: 14-11-2012

DOI: 10.1002/BIES.201290056

Long non-coding RNAs: Insights into functions

Publisher: Springer Science and Business Media LLC

Date: 03-2009

DOI: 10.1038/NRG2521

Abstract: In mammals and other eukaryotes most of the genome is transcribed in a developmentally regulated manner to produce large numbers of long non-coding RNAs (ncRNAs). Here we review the rapidly advancing field of long ncRNAs, describing their conservation, their organization in the genome and their roles in gene regulation. We also consider the medical implications, and the emerging recognition that any transcript, regardless of coding potential, can have an intrinsic function as an RNA.

Mapping of mitochondrial RNA-protein interactions by digital rnase footprinting

Publisher: Elsevier BV

Date: 11-2013

DOI: 10.1016/J.CELREP.2013.09.036

Abstract: Human mitochondrial DNA is transcribed as long polycistronic transcripts that encompass each strand of the genome and are processed subsequently into mature mRNAs, tRNAs, and rRNAs, necessitating widespread posttranscriptional regulation. Here, we establish methods for massively parallel sequencing and analyses of RNase-accessible regions of human mitochondrial RNA and thereby identify specific regions within mitochondrial transcripts that are bound by proteins. This approach provides a range of insights into the contribution of RNA-binding proteins to the regulation of mitochondrial gene expression.

Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome

Publisher: Cold Spring Harbor Laboratory

Date: 06-2003

DOI: 10.1101/GR.1015703

Abstract: The chromodomain is 40–50 amino acids in length and is conserved in a wide range of chromatic and regulatory proteins involved in chromatin remodeling. Chromodomain-containing proteins can be classified into families based on their broader characteristics, in particular the presence of other types of domains, and which correlate with different subclasses of the chromodomains themselves. Hidden Markov model (HMM)-generated profiles of different subclasses of chromodomains were used here to identify sequences encoding chromodomain-containing proteins in the mouse transcriptome and genome. A total of 36 different loci encoding proteins containing chromodomains, including 17 novel loci, were identified. Six of these loci (including three apparent pseudogenes, a novel HP1 ortholog, and two novel Msl-3 transcription factor-like proteins) are not present in the human genome, whereas the human genome contains four loci (two CDY orthologs and two apparent CDY pseudogenes) that are not present in mouse. A number of these loci exhibit alternative splicing to produce different isoforms, including 43 novel variants, some of which lack the chromodomain. The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family.

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci

Publisher: Oxford University Press (OUP)

Date: 05-06-2013

DOI: 10.1093/BIOINFORMATICS/BTT315

Abstract: Summary: At the heart of many modern biotechnological and therapeutic applications lies the need to target specific genomic loci with pinpoint accuracy. Although landmark experiments demonstrate technological maturity in manufacturing and delivering genetic material, the genomic sequence analysis to find suitable targets lags behind. We provide a computational aid for the sophisticated design of sequence-specific ligands and selection of appropriate targets, taking gene location and genomic architecture into account. Availability: Source code and binaries are downloadable from www.bioinformatics.org.au/triplexator/inspector. Contact: t.bailey@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.

Long noncoding RNAs in cell and developmental biology

Publisher: Elsevier BV

Date: 06-2011

DOI: 10.1016/J.SEMCDB.2011.05.002

Transcription of the fimbrial subunit gene and an associated transfer RNA gene of Pseudomonas aeruginosa.

Publisher: Elsevier BV

Date: 02-1988

DOI: 10.1016/0378-1119(88)90560-4

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes.

Publisher: Oxford University Press (OUP)

Date: 07-10-2012

DOI: 10.1093/BIOINFORMATICS/BTS582

Abstract: Motivation: Comparing transcriptomic data with proteomic data to identify protein-coding sequences is a long-standing challenge in molecular biology, one that is exacerbated by the increasing size of high-throughput datasets. To address this challenge, and thereby to improve the quality of genome annotation and understanding of genome biology, we have developed an integrated suite of programs, called Pinstripe. We demonstrate its application, utility and discovery power using transcriptomic and proteomic data from publicly available datasets. Results: To demonstrate the efficacy of Pinstripe for large-scale analysis, we applied Pinstripe’s reverse peptide mapping pipeline to a transcript library including de novo assembled transcriptomes from the human Illumina Body Atlas (IBA2) and GENCODE v10 gene annotations, and the EBI Proteomics Identifications Database (PRIDE) peptide database. This analysis identified 736 canonical open reading frames (ORFs) supported by three or more PRIDE peptide fragments that are positioned outside any known coding DNA sequence (CDS). Because of the unfiltered nature of the PRIDE database and high probability of false discovery, we further refined this list using independent evidence for translation, including the presence of a Kozak sequence or functional domains, synonymous/non-synonymous substitution ratios and ORF length. Using this integrative approach, we observed evidence of translation from a previously unknown let7e primary transcript, the archetypical lncRNA H19, and a homolog of RD3. Reciprocally, by exclusion of transcripts with mapped peptides or significant ORFs (& codon), we identify 32 187 loci with RNAs longer than 2000 nt that are unlikely to encode proteins. Availability and implementation: Pinstripe (pinstripe.matticklab.com) is freely available as source code or a Mono binary. Pinstripe is written in C# and runs under the Mono framework on Linux or Mac OS X, and both under Mono and .Net under Windows. Contact: m.dinger@garvan.org.au or j.mattick@garvan.org.au Supplementary information: Supplementary data are available at Bioinformatics online.

Small RNAs derived from snoRNAs

Publisher: Cold Spring Harbor Laboratory

Date: 27-05-2009

DOI: 10.1261/RNA.1528909

Abstract: Small nucleolar RNAs (snoRNAs) guide RNA modification and are localized in nucleoli and Cajal bodies in eukaryotic cells. Components of the RNA silencing pathway associate with these structures, and two recent reports have revealed that a human and a protozoan snoRNA can be processed into miRNA-like RNAs. Here we show that small RNAs with evolutionary conservation of size and position are derived from the vast majority of snoRNA loci in animals (human, mouse, chicken, fruit fly), Arabidopsis , and fission yeast. In animals, sno-derived RNAs (sdRNAs) from H/ACA snoRNAs are predominantly 20–24 nucleotides (nt) in length and originate from the 3′ end. Those derived from C/D snoRNAs show a bimodal size distribution at ∼17–19 nt and nt and predominantly originate from the 5′ end. SdRNAs are associated with AGO7 in Arabidopsis and Ago1 in fission yeast with characteristic 5′ nucleotide biases and show altered expression patterns in fly loquacious and Dicer-2 and mouse Dicer1 and Dgcr8 mutants. These findings indicate that there is interplay between the RNA silencing and snoRNA-mediated RNA processing systems, and that sdRNAs comprise a novel and ancient class of small RNAs in eukaryotes.

Development and trial of a bovine herpesvirus 1-thymidine kinase deletion virus as a vaccine.

Publisher: Wiley

Date: 03-1994

DOI: 10.1111/J.1751-0813.1994.TB03329.X

The genetic signatures of noncoding RNAs.

Publisher: Public Library of Science (PLoS)

Date: 24-04-2009

DOI: 10.1371/JOURNAL.PGEN.1000459

Nucleotide and predicted amino acid sequence of a cDNA clone encoding part of human transketolase.

Publisher: Elsevier BV

Date: 03-1992

DOI: 10.1016/S0006-291X(05)80312-2

Noncoding RNA in development

Publisher: Springer Science and Business Media LLC

Date: 08-2008

DOI: 10.1007/S00335-008-9136-7

Genome-wide identification of long noncoding RNAs in CD8⁺ T cells

Publisher: The American Association of Immunologists

Date: 15-06-2009

DOI: 10.4049/JIMMUNOL.0900603

Abstract: Previous research into the molecular mechanisms that underlie Ag-specific CD8+ T cell differentiation and function has largely focused on the role of proteins. However, it is now apparent that the mammalian genome expresses large numbers of long (& nt) nonprotein-coding RNAs (ncRNAs), and there is increasing evidence that these RNAs have important regulatory functions, particularly in the regulation of epigenetic processes underpinning cell differentiation. In this study, we show that CD8+ T cells express hundreds of long ncRNAs, many of which are lymphoid-specific and/or change dynamically with lymphocyte differentiation or activation. Numerous ncRNAs surround or overlap immunologically important protein-coding genes and can be predicted to function via a range of regulatory mechanisms. The overlap of many long ncRNAs expressed in CD8+ T cells with microRNAs and small interfering RNAs further suggests that long ncRNAs may be processed into and exert their effects via smaller functional species. Finally, we show that the majority of long ncRNAs expressed in CD8+ T cells harbor signatures of evolutionary conservation, secondary structures, and/or regulated promoters, further supporting their functionality. Taken together, our findings represent the first systematic discovery of long ncRNAs expressed in CD8+ T cells and suggest that many of these transcripts are likely to play a role in adaptive immunity.

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

Publisher: Cold Spring Harbor Laboratory

Date: 06-07-2020

DOI: 10.1101/2020.07.06.189969

Abstract: A broad ersity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular responses to external signals and environmental circumstances. A major difficulty in studying these modifications, however, is the need of tailored protocols to map each modification type in idually. Here, we present a new approach that uses direct RNA nanopore sequencing to identify and quantify RNA modifications present in native RNA molecules. First, we show that each RNA modification type results in a distinct and characteristic base-calling ‘error’ signature, which we validate using a battery of genetic strains lacking either pseudouridine (Y) or 2’-O-methylation (Nm) modifications. We then demonstrate the value of these signatures for de novo prediction of Y modifications transcriptome-wide, confirming known Y-modified sites as well as uncovering novel Y sites in mRNAs, ncRNAs and rRNAs, including a previously unreported Pus4-dependent Y modification in yeast mitochondrial rRNA, which we validate using orthogonal methods. To explore the dynamics of pseudouridylation across environmental stresses, we treat the cells with oxidative, cold and heat stresses, finding that yeast ribosomal rRNA modifications do not change upon environmental exposures, contrary to the general belief. By contrast, our method reveals many novel heat-sensitive Y-modified sites in snRNAs, snoRNAs and mRNAs, in addition to recovering previously reported sites. Finally, we develop a novel software, nanoRMS , which we show can estimate per-site modification stoichiometries from in idual RNA molecules by identifying the reads with altered current intensity and trace profiles, and quantify the RNA modification stoichiometry changes between two conditions. Our work demonstrates that Y RNA modifications can be predicted de novo and in a quantitative manner using native RNA nanopore sequencing.

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins

Publisher: Cold Spring Harbor Laboratory

Date: 25-10-2011

DOI: 10.1261/RNA.029405.111

Abstract: Human mitochondrial long noncoding RNAs (lncRNAs) have not been described to date. By analysis of deep-sequencing data we have identified three lncRNAs generated from the mitochondrial genome and confirmed their expression by Northern blotting and strand-specific qRT–PCR. We show that the abundance of these lncRNAs is comparable to their complementary mRNAs and that nuclear-encoded mitochondrial proteins involved in RNA processing regulate their expression. We also identify the 5′ and 3′ transcript ends of the three lncRNAs and show that mitochondrial RNase P protein 1 (MRPP1) is important for the processing of these transcripts. Finally, we show that mitochondrial lncRNAs form intermolecular duplexes and that their abundance is cell- and tissue-specific, suggesting a functional role in the regulation of mitochondrial gene expression.

RNA regulation: A new genetics?

Publisher: Springer Science and Business Media LLC

Date: 04-2004

DOI: 10.1038/NRG1321

Western blot (immunoblot) analysis of the fimbrial antigens of Bacteroides nodosus

Publisher: American Society for Microbiology

Date: 09-1987

DOI: 10.1128/JB.169.9.4018-4023.1987

Abstract: The roles of the fimbrial subunit and the putative basal protein antigens in the serological classification of Bacteroides nodosus have been examined by Western blot (immunoblot)-antibody binding studies of fimbriae isolated from a wide range of strains representative of different serogroups and serotypes. Fimbrial subunits were recognized by antiserum against the homologous serogroup but not generally by heterologous antisera, whereas recognition of the basal antigen was independent of serological classification. Secondary cross-reaction patterns among fimbrial subunits indicated that some serogroups may be more closely related than others. Ex les include serogroups C and G and serogroups D and H. Similar analyses of isolates classified within serotypes A1 and A2, with serotype-specific antisera, showed that this sub ision is also determined by the fimbrial subunit and that significant variation does occur even at this level. These studies suggest that the various serogroups and serotypes of B. nodosus comprise a series of overlapping sets of antigenically related strains.

FimX, a Multidomain Protein Connecting Environmental Signals to Twitching Motility in Pseudomonas aeruginosa

Publisher: American Society for Microbiology

Date: 15-12-2003

DOI: 10.1128/JB.185.24.7068-7076.2003

Abstract: Twitching motility is a form of surface translocation mediated by the extension, tethering, and retraction of type IV pili. Three independent Tn 5 -B21 mutations of Pseudomonas aeruginosa with reduced twitching motility were identified in a new locus which encodes a predicted protein of unknown function annotated PA4959 in the P. aeruginosa genome sequence. Complementation of these mutants with the wild-type PA4959 gene, which we designated fimX , restored normal twitching motility. fimX mutants were found to express normal levels of pilin and remained sensitive to pilus-specific bacteriophages, but they exhibited very low levels of surface pili, suggesting that normal pilus function was impaired. The fimX gene product has a molecular weight of 76,000 and contains four predicted domains that are commonly found in signal transduction proteins: a putative response regulator (CheY-like) domain, a PAS-PAC domain (commonly involved in environmental sensing), and DUF1 (or GGDEF) and DUF2 (or EAL) domains, which are thought to be involved in cyclic di-GMP metabolism. Red fluorescent protein fusion experiments showed that FimX is located at one pole of the cell via sequences adjacent to its CheY-like domain. Twitching motility in fimX mutants was found to respond relatively normally to a range of environmental factors but could not be stimulated by tryptone and mucin. These data suggest that fimX is involved in the regulation of twitching motility in response to environmental cues.

Improved definition of the mouse transcriptome via targeted RNA sequencing

Publisher: Cold Spring Harbor Laboratory

Date: 05-2016

DOI: 10.1101/GR.199760.115

Abstract: Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.

Genes involved in the biogenesis and function of type-4 fimbriae in Pseudomonas aeruginosa.

Publisher: Elsevier BV

Date: 06-1997

DOI: 10.1016/S0378-1119(96)00805-0

Dynamics of hepatic gene expression profile in a rat cecal ligation and puncture model

Publisher: Elsevier BV

Date: 08-2012

DOI: 10.1016/J.JSS.2011.11.1031

Specific expression of long noncoding RNAs in the mouse brain

Publisher: Proceedings of the National Academy of Sciences

Date: 15-01-2008

DOI: 10.1073/PNAS.0706729105

Abstract: A major proportion of the mammalian transcriptome comprises long RNAs that have little or no protein-coding capacity (ncRNAs). Only a handful of such transcripts have been examined in detail, and it is unknown whether this class of transcript is generally functional or merely artifact. Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Examination of their genomic context revealed that the ncRNAs were expressed from erse places including intergenic, intronic, and imprinted loci and that many overlap with, or are transcribed antisense to, protein-coding genes of neurological importance. Comparisons between the expression profiles of ncRNAs and their associated protein-coding genes revealed complex relationships that, in combination with the specific expression profiles exhibited at both regional and subcellular levels, are inconsistent with the notion that they are transcriptional noise or artifacts of chromatin remodeling. Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs.

Understanding the regulatory and transcriptional complexity of the genome through structure

Publisher: Cold Spring Harbor Laboratory

Date: 07-2013

DOI: 10.1101/GR.156612.113

Abstract: An expansive functionality and complexity has been ascribed to the majority of the human genome that was unanticipated at the outset of the draft sequence and assembly a decade ago. We are now faced with the challenge of integrating and interpreting this complexity in order to achieve a coherent view of genome biology. We argue that the linear representation of the genome exacerbates this complexity and an understanding of its three-dimensional structure is central to interpreting the regulatory and transcriptional architecture of the genome. Chromatin conformation capture techniques and high-resolution microscopy have afforded an emergent global view of genome structure within the nucleus. Chromosomes fold into complex, territorialized three-dimensional domains in concert with specialized subnuclear bodies that harbor concentrations of transcription and splicing machinery. The signature of these folds is retained within the layered regulatory landscapes annotated by chromatin immunoprecipitation, and we propose that genome contacts are reflected in the organization and expression of interweaved networks of overlapping coding and noncoding transcripts. This pervasive impact of genome structure favors a preeminent role for the nucleoskeleton and RNA in regulating gene expression by organizing these folds and contacts. Accordingly, we propose that the local and global three-dimensional structure of the genome provides a consistent, integrated, and intuitive framework for interpreting and understanding the regulatory and transcriptional complexity of the human genome.

Identification of a novel gene, pilZ, essential for type 4 fimbrial biogenesis in Pseudomonas aeruginosa

Publisher: American Society for Microbiology

Date: 1996

DOI: 10.1128/JB.178.1.46-53.1996

Abstract: The opportunistic pathogen Pseudomonas aeruginosa produces type 4 fimbriae which promote adhesion to epithelial cells and are associated with a form of surface translocation called twitching motility. We have used transposon mutagenesis to identify loci required for fimbrial assembly or function by screening for mutants that lack the spreading colony morphology characteristic of twitching motility. A subset of these mutants is resistant to fimbria-specific phage. One of these mutants (R270) was found to contain a transposon insertion in a new gene, termed pilZ, which is located on chromosomal SpeI fragment I at about 40 min on the P. aeruginosa map, a position remote from other loci involved in fimbrial biogenesis. pilZ appears to be linked to and possibly forms an operon with a gene, holB*, which is homologous to the gene encoding the delta' subunit of Escherichia coli DNA polymerase III. The product of the pilZ gene is a protein of 118 amino acids (predicted molecular weight, 12,895) which probably has a cytoplasmic location. PilZ appears to be a new class of protein which has not hitherto been represented in the sequence databases, and its function is unknown. Complementation studies indicate that pilZ is able to restore the expression of fimbriae on the surface of P. aeruginosa, as well as twitching motility and sensitivity to fimbria-specific phage when provided in trans to the R270 mutant.

Construction of a gentamicin resistance gene probe for epidemiological studies.

Publisher: American Society for Microbiology

Date: 07-1985

DOI: 10.1128/AAC.28.1.96

Abstract: A 7.7-kilobase BamHI fragment was cloned from the transconjugant of a clinical isolate of Escherichia coli containing a 120-kilobase multiresistance IncC plasmid. The recombinant plasmid conferred resistance to kanamycin, gentamicin, tobramycin, sulfamethoxazole, and trimethoprim. This clone was used to generate a series of subclones from which a 2.0-kilobase BamHI-HindIII probe containing a gentamicin 2''-O-adenylyltransferase [AAD(2'')] gene was obtained. This probe hybridized specifically in both colony and Southern hybridizations with the AAD(2'') gene but not with other resistance genes, including other aminoglycoside-modifying genes, or with a reference IncC plasmid lacking the AAD(2'') gene. The AAD(2'') gene may be part of a transposon, since hybridization occurred with both nonconjugative plasmids and the chromosome in some isolates.

The isolation and characterization of fatty-acid synthetase mRNA from rat mammary gland.

Publisher: Wiley

Date: 03-1981

DOI: 10.1111/J.1432-1033.1981.TB05192.X

Structure and function of long noncoding RNAs in epigenetic regulation

Publisher: Springer Science and Business Media LLC

Date: 03-2013

DOI: 10.1038/NSMB.2480

Abstract: Genomes of complex organisms encode an abundance and ersity of long noncoding RNAs (lncRNAs) that are expressed throughout the cell and fulfill a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass sensory, guiding, scaffolding and allosteric capacities, derive from folded modular domains in lncRNAs. In this erse functional repertoire, we focus on the well-characterized ability for lncRNAs to function as epigenetic modulators. Many lncRNAs bind to chromatin-modifying proteins and recruit their catalytic activity to specific sites in the genome, thereby modulating chromatin states and impacting gene expression. Considering this regulatory potential in combination with the abundance of lncRNAs suggests that lncRNAs may be part of a broad epigenetic regulatory network.

RNA: Networks & Imaging

Publisher: EMBO

Date: 2006

DOI: 10.1038/MSB4100086

Noncoding RNAs: A Regulatory Role?

Publisher: Wiley

Date: 27-01-2006

DOI: 10.1038/NPG.ELS.0005985

A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells

Publisher: Cold Spring Harbor Laboratory

Date: 20-04-2010

DOI: 10.1261/RNA.2019810

Abstract: In humans, more than 30,000 chimeric transcripts originating from 23,686 genes have been identified. The mechanisms and association of chimeric transcripts arising from chromosomal rearrangements with cancer are well established, but much remains unknown regarding the biogenesis and importance of other chimeric transcripts that arise from nongenomic alterations. Recently, a SLC45A3 – ELK4 chimera has been shown to be androgen-regulated, and is overexpressed in metastatic or high-grade prostate tumors relative to local prostate cancers. Here, we characterize the expression of a KLK4 cis sense–antisense chimeric transcript, and show other ex les in prostate cancer. Using non-protein-coding microarray analyses, we initially identified an androgen-regulated antisense transcript within the 3′ untranslated region of the KLK4 gene in LNCaP cells. The KLK4 cis -NAT was validated by strand-specific linker-mediated RT-PCR and Northern blotting. Characterization of the KLK4 cis -NAT by 5′ and 3′ rapid lification of cDNA ends (RACE) revealed that this transcript forms multiple fusions with the KLK4 sense transcript. Lack of KLK4 antisense promoter activity using reporter assays suggests that these transcripts are unlikely to arise from a trans -splicing mechanism. 5′ RACE and analyses of deep sequencing data from LNCaP cells treated ±androgens revealed six high-confidence sense–antisense chimeras of which three were supported by the cDNA databases. In this study, we have shown complex gene expression at the KLK4 locus that might be a hallmark of cis sense–antisense chimeric transcription.

'Touchdown' PCR to circumvent spurious priming during gene amplification.

Publisher: Oxford University Press (OUP)

Date: 1991

DOI: 10.1093/NAR/19.14.4008

Expression of Transposable Elements in Neural Tissues during Xenopus Development

Publisher: Public Library of Science (PLoS)

Date: 26-07-2011

DOI: 10.1371/JOURNAL.PONE.0022569

An RNA recognition motif in Wilms' tumour protein (WT1) revealed by structural modelling.

Publisher: Springer Science and Business Media LLC

Date: 03-1996

DOI: 10.1038/NG0396-329

Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms.

Publisher: Wiley

Date: 31-12-2015

DOI: 10.1111/NYAS.12608

UNCL, the mammalian homologue of UNC-50, is an inner nuclear membrane RNA-binding protein11Published on the World Wide Web on 10 August 2000.

Publisher: Elsevier BV

Date: 09-2000

DOI: 10.1016/S0006-8993(00)02692-5

Abstract: We isolated a mammalian homologue of the C. elegans gene unc-50 that we have named UNCL. The 777 kb rat UNCL cDNA encodes a 259 amino acid protein that is expressed in a wide variety of tissues with highest mRNA levels in brain, kidney and testis. Hydropathy plot analysis and in vitro translation experiments with microsomal membranes indicate that UNCL is a transmembrane protein. Hemagglutinin tagged UNCL was stably transfected into SaOS-2 osteosarcoma cells and exhibited a nuclear rim staining pattern which was retained following extraction with 1% Triton X-100, suggesting that UNCL localizes to the inner nuclear membrane. UNCL-HA was extractable in 350 mM NaCl, suggesting that UNCL is not associated with the nuclear matrix. Homopolymer RNA-binding assays performed on in vitro translated UNCL protein and 'structural modeling by homology' suggest that UNCL binds RNA via an amino-terminal RNA Recognition-like Motif. Since unc-50 is required for expression of assembled muscle-type nicotinic receptors in the nematode we investigated whether UNCL had a similar function for mammalian nicotinic receptors. When UNCL was co-expressed with neural nicotinic receptors in Xenopus oocytes or COS cells it increased expression of functional cell surface receptors up to 1. 6-fold. We conclude that UNCL is a novel inner nuclear membrane protein that associates with RNA and is involved in the cell-surface expression of neuronal nicotinic receptors. UNCL plays a broader role because UNCL homologues are present in two yeast and a plant species, none of which express nicotinic receptors and it is also found in tissues that lack nicotinic receptors.

Long noncoding RNAs and the genetics of cancer.

Publisher: Springer Science and Business Media LLC

Date: 09-05-2013

DOI: 10.1038/BJC.2013.233

Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver

Publisher: Springer Science and Business Media LLC

Date: 25-03-2014

DOI: 10.1186/1471-2105-15-83

Abstract: The circadian clock is a critical regulator of biological functions controlling behavioral, physiological and biochemical processes. Because the liver is the primary regulator of metabolites within the mammalian body and the disruption of circadian rhythms in liver is associated with severe illness, circadian regulators would play a strong role in maintaining liver function. However, the regulatory structure that governs circadian dynamics within the liver at a transcriptional level remains unknown. To explore this aspect, we analyzed hepatic transcriptional dynamics in Sprague-Dawley rats over a period of 24 hours to assess the genome-wide responses. Using an unsupervised consensus clustering method, we identified four major gene expression clusters, corresponding to central carbon and nitrogen metabolism, membrane integrity, immune function, and DNA repair, all of which have dynamics which suggest regulation in a circadian manner. With the assumption that transcription factors (TFs) that are differentially expressed and contain CLOCK:BMAL1 binding sites on their proximal promoters are likely to be clock-controlled TFs, we were able to use promoter analysis to putatively identify additional clock-controlled TFs besides PARF and RORA families. These TFs are both functionally and temporally related to the clusters they regulate. Furthermore, we also identified significant sets of clock TFs that are potentially transcriptional regulators of gene clusters. All together, we were able to propose a regulatory structure for circadian regulation which represents alternative paths for circadian control of different functions within the liver. Our prediction has been affirmed by functional and temporal analyses which are able to extend for similar studies.

Multiple Evolutionary Rate Classes in Animal Genome Evolution

Publisher: Oxford University Press (OUP)

Date: 02-12-2009

DOI: 10.1093/MOLBEV/MSP299

Abstract: The proportion of functional sequence in the human genome is currently a subject of debate. The most widely accepted figure is that approximately 5% is under purifying selection. In Drosophila, estimates are an order of magnitude higher, though this corresponds to a similar quantity of sequence. These estimates depend on the difference between the distribution of genomewide evolutionary rates and that observed in a subset of sequences presumed to be neutrally evolving. Motivated by the widening gap between these estimates and experimental evidence of genome function, especially in mammals, we developed a sensitive technique for evaluating such distributions and found that they are much more complex than previously apparent. We found strong evidence for at least nine well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least seven classes in an alignment of four mammals, including human. We also identified at least three rate classes in human ancestral repeats. By positing that the largest of these ancestral repeat classes is neutrally evolving, we estimate that the proportion of nonneutrally evolving sequence is 30% of human ancestral repeats and 45% of the aligned portion of the genome. However, we also question whether any of the classes represent neutrally evolving sequences and argue that a plausible alternative is that they reflect variable structure-function constraints operating throughout the genomes of complex organisms.

Escherichia coli gpt as a positive and negative selectable marker in embryonal stem cells.

Publisher: Elsevier BV

Date: 06-1994

DOI: 10.1016/0167-4781(94)90005-1

Gene sequences and comparison of the fimbrial subunits representative of Bacteroides nodosus serotypes A to I: class I and class II strains.

Publisher: Wiley

Date: 03-1991

DOI: 10.1111/J.1365-2958.1991.TB00727.X

Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease

Publisher: American Physiological Society

Date: 07-2007

DOI: 10.1152/PHYSREV.00036.2006

Abstract: The progressive maturation and functional plasticity of the nervous system in health and disease involve a dynamic interplay between the transcriptome and the environment. There is a growing awareness that the previously unexplored molecular and functional interface mediating these complex gene-environmental interactions, particularly in brain, may encompass a sophisticated RNA regulatory network involving the twin processes of RNA editing and multifaceted actions of numerous subclasses of non-protein-coding RNAs. The mature nervous system encompasses a wide range of cell types and interconnections. Long-term changes in the strength of synaptic connections are thought to underlie memory retrieval, formation, stabilization, and effector functions. The evolving nervous system involves numerous developmental transitions, such as neurulation, neural tube patterning, neural stem cell expansion and maintenance, lineage elaboration, differentiation, axonal path finding, and synaptogenesis. Although the molecular bases for these processes are largely unknown, RNA-based epigenetic mechanisms appear to be essential for orchestrating these precise and versatile biological phenomena and in defining the etiology of a spectrum of neurological diseases. The concerted modulation of RNA editing and the selective expression of non-protein-coding RNAs during seminal as well as continuous state transitions may comprise the plastic molecular code needed to couple the intrinsic malleability of neural network connections to evolving environmental influences to establish erse forms of short- and long-term memory, context-specific behavioral responses, and sophisticated cognitive capacities.

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

Publisher: Cold Spring Harbor Laboratory

Date: 22-09-2021

DOI: 10.1101/2021.09.22.461331

Abstract: RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here, we develop Nanopore 3’ end-capture sequencing (Nano3P-seq), a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition and tail length dynamics at per-read resolution. By employing a template switching-based sequencing protocol, Nano3P-seq can sequence any given RNA molecule from its 3’ end, regardless of its polyadenylation status, without the need for PCR lification or ligation of RNA adapters. We demonstrate that Nano3P-seq captures a wide ersity of RNA biotypes, providing quantitative estimates of RNA abundance and tail lengths in mRNA, lncRNA, sn/snoRNA, scaRNA, and rRNA molecules. We find that, in addition to mRNA and lncRNA, polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover, we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform-specific level, correlating with mRNA decay. Finally, we identify non-A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall, Nano3P-seq is a simple and robust method for accurately estimating transcript levels, tail lengths, and tail composition heterogeneity in in idual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.

Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent.

Publisher: Springer Science and Business Media LLC

Date: 25-05-2010

DOI: 10.1007/S00438-010-0543-6

Abstract: The epidermal compartment is complex and organized into several strata composed of keratinocytes (KCs), including basal, spinous, granular, and cornified layers. The continuous process of self-renewal and barrier formation is dependent on a homeostatic balance achieved amongst KCs involving proliferation, differentiation, and cell death. To determine genes responsible for initiating and maintaining a cornified epidermis, organotypic cultures comprised entirely of stratified KCs creating epidermal equivalents (EE) were raised from a submerged state to an air/liquid (A/L) interface. Compared to the array profile of submerged cultures containing KCs predominantly in a proliferative (relatively undifferentiated) state, EEs raised to an A/L interface displayed a remarkably consistent and distinct profile of mRNAs. Cultures lifted to an A/L interface triggered the induction of gene groups that regulate proliferation, differentiation, and cell death. Next, differentially expressed microRNAs (miRNAs) and long non-coding (lncRNA) RNAs were identified in EEs. Several differentially expressed miRNAs were validated by qRT-PCR and Northern blots. miRNAs 203, 205 and Let-7b were up-regulated at early time points (6, 18 and 24 h) but down-regulated by 120 h. To study the lncRNA regulation in EEs, we profiled lncRNA expression by microarray and validated the results by qRT-PCR. Although the differential expression of several lncRNAs is suggestive of a role in epidermal differentiation, their biological functions remain to be elucidated. The current studies lay the foundation for relevant model systems to address such fundamentally important biological aspects of epidermal structure and function in normal and diseased human skin.

Isolation and characterization of a new nucleolar protein, Nrap, that is conserved from yeast to humans.

Publisher: Wiley

Date: 02-2002

DOI: 10.1046/J.1356-9597.2001.00507.X

Universal Alternative Splicing of Noncoding Exons

Publisher: Elsevier BV

Date: 02-2018

DOI: 10.1016/J.CELS.2017.12.005

Abstract: The human transcriptome is so large, erse, and dynamic that, even after a decade of investigation by RNA sequencing (RNA-seq), we have yet to resolve its true dimensions. RNA-seq suffers from an expression-dependent bias that impedes characterization of low-abundance transcripts. We performed targeted single-molecule and short-read RNA-seq to survey the transcriptional landscape of a single human chromosome (Hsa21) at unprecedented resolution. Our analysis reaches the lower limits of the transcriptome, identifying a fundamental distinction between protein-coding and noncoding gene content: almost every noncoding exon undergoes alternative splicing, producing a seemingly limitless variety of isoforms. Analysis of syntenic regions of the mouse genome shows that few noncoding exons are shared between human and mouse, yet human splicing profiles are recapitulated on Hsa21 in mouse cells, indicative of regulation by a deeply conserved splicing code. We propose that noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.

Construction of improved vectors for protein production in Pseudomonas aeruginosa.

Publisher: Elsevier BV

Date: 1996

DOI: 10.1016/0378-1119(96)00026-1

Ultraconserved elements in the human genome.

Publisher: American Association for the Advancement of Science (AAAS)

Date: 28-05-2004

DOI: 10.1126/SCIENCE.1098119

Abstract: There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.

Spliced synthetic genes as internal controls in RNA sequencing experiments

Publisher: Springer Science and Business Media LLC

Date: 08-08-2016

DOI: 10.1038/NMETH.3958

Abstract: RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and ersity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNA-seq analysis. We have developed a set of spike-in RNA standards, termed 'sequins' (sequencing spike-ins), that represent full-length spliced mRNA isoforms. Sequins have an entirely artificial sequence with no homology to natural reference genomes, but they align to gene loci encoded on an artificial in silico chromosome. The combination of multiple sequins across a range of concentrations emulates alternative splicing and differential gene expression, and it provides scaling factors for normalization between s les. We demonstrate the use of sequins in RNA-seq experiments to measure s le-specific biases and determine the limits of reliable transcript assembly and quantification in accompanying human RNA s les. In addition, we have designed a complementary set of sequins that represent fusion genes arising from rearrangements of the in silico chromosome to aid in cancer diagnosis. RNA sequins provide a qualitative and quantitative reference with which to navigate the complexity of the human transcriptome.

Representing genetic variation with synthetic DNA standards

Publisher: Springer Science and Business Media LLC

Date: 08-08-2016

DOI: 10.1038/NMETH.3957

Abstract: The identification of genetic variation with next-generation sequencing is confounded by the complexity of the human genome sequence and by biases that arise during library preparation, sequencing and analysis. We have developed a set of synthetic DNA standards, termed 'sequins', that emulate human genetic features and constitute qualitative and quantitative spike-in controls for genome sequencing. Sequencing reads derived from sequins align exclusively to an artificial in silico reference chromosome, rather than the human reference genome, which allows them them to be partitioned for parallel analysis. Here we use this approach to represent common and clinically relevant genetic variation, ranging from single nucleotide variants to large structural rearrangements and copy-number variation. We validate the design and performance of sequin standards by comparison to ex les in the NA12878 reference genome, and we demonstrate their utility during the detection and quantification of variants. We provide sequins as a standardized, quantitative resource against which human genetic variation can be measured and diagnostic performance assessed.

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

Publisher: Springer Science and Business Media LLC

Date: 11-07-2010

DOI: 10.1038/NSMB.1841

Abstract: We have recently shown that transcription initiation RNAs (tiRNAs) are derived from sequences immediately downstream of transcription start sites. Here, using cytoplasmic and nuclear small RNA high-throughput sequencing datasets, we report the identification of a second class of nuclear-specific approximately 17- to 18-nucleotide small RNAs whose 3' ends map precisely to the splice donor site of internal exons in animals. These splice-site RNAs (spliRNAs) are associated with highly expressed genes and show evidence of developmental stage- and region-specific expression. We also show that tiRNAs are localized to the nucleus, are enriched at chromatin marks associated with transcription initiation and possess a 3'-nucleotide bias. Additionally, we find that microRNA-offset RNAs (moRNAs), the miR-15/16 cluster previously linked to oncosuppression and most small nucleolar RNA (snoRNA)-derived small RNAs (sdRNAs) are enriched in the nucleus, whereas most miRNAs and two H/ACA sdRNAs are cytoplasmically enriched. We propose that nuclear-localized tiny RNAs are involved in the epigenetic regulation of gene expression.

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

Publisher: Springer Science and Business Media LLC

Date: 04-04-2014

DOI: 10.1038/NPROT.2014.058

Abstract: RNA sequencing (RNAseq) s les the majority of expressed genes infrequently, owing to the large size, complex splicing and wide dynamic range of eukaryotic transcriptomes. This results in sparse sequencing coverage that can hinder robust isoform assembly and quantification. RNA capture sequencing (CaptureSeq) addresses this challenge by using oligonucleotide probes to capture selected genes or regions of interest for targeted sequencing. Targeted RNAseq provides enhanced coverage for sensitive gene discovery, robust transcript assembly and accurate gene quantification. Here we describe a detailed protocol for all stages of RNA CaptureSeq, from initial probe design considerations and capture of targeted genes to final assembly and quantification of captured transcripts. Initial probe design and final analysis can take less than 1 d, whereas the central experimental capture stage requires ∼7 d.

Identification of a novel gene, fimV, involved in twitching motility in Pseudomonas aeruginosa

Publisher: Microbiology Society

Date: 06-2000

DOI: 10.1099/00221287-146-6-1321

Abstract: Transposon mutagenesis was used to identify a new locus required for twitching motility in Pseudomonas aeruginosa. Four Tn5-B21 mutants which lacked twitching motility and a fifth which exhibited impaired motility were found to map to the same KPN:I restriction fragment at approximately 40 min on the P. aeruginosa genome. Cloning and sequencing studies showed that all five transposon insertions occurred within the same 2.8 kb ORF, which was termed fimV. The product of this gene has a putative peptidoglycan-binding domain, predicted transmembrane domains, a highly acidic C terminus and anomalous electrophoretic migration, indicating unusual primary or secondary structure. The P. aeruginosa genome also possesses a paralogue of fimV. Homologues of fimV were also found in the sequenced genomes of the other type-IV-fimbriated bacteria Neisseria gonorrhoeae, Neisseria meningitidis, Legionella pneumophila and Vibrio cholerae, but not in those of other bacteria which lack type IV fimbriae. A fimV homologue was also found in the genome sequence of Shewanella putrefaciens, along with many other homologues of type IV fimbrial genes, indicating that this bacterium is also likely to produce type IV fimbriae. Wild-type twitching motility was restored to fimV mutants by complementation in a dosage-dependent manner. Overexpression of fimV resulted in an unusual phenotype where the cells were massively elongated and migrated in large convoys at the periphery of the colony. It is suggested that FimV may be involved in remodelling of the peptidoglycan layer to enable assembly of the type IV fimbrial structure and machinery.

DotAligner: identification and clustering of RNA structure motifs

Publisher: Springer Science and Business Media LLC

Date: 12-2017

DOI: 10.1186/S13059-017-1371-3

Long non-coding RNAs in nervous system function and disease

Publisher: Elsevier BV

Date: 06-2010

DOI: 10.1016/J.BRAINRES.2010.03.110

Understanding the Chemical Diversity of Spider Venoms Using a Combined Genomic, Transcriptomic and Proteomic Approach

Publisher: Elsevier BV

Date: 08-2012

DOI: 10.1016/J.TOXICON.2012.04.060

Topology and Dynamics of Signaling Networks: In Search of Transcriptional Control of the Inflammatory Response

Publisher: Annual Reviews

Date: 11-07-2013

DOI: 10.1146/ANNUREV-BIOENG-071812-152425

Abstract: Over the past several decades, to develop a fundamental understanding of inflammation's progression, research has focused on extracellular mediators, such as cytokines, as characteristic components of inflammatory response. These efforts have recently been complemented by advances in proteomics that allow analysis of multiple signaling proteins in parallel, to provide more complete mechanistic models of inflammation. In this review, we discuss various techniques for assessing protein activity, as well as computational techniques that are well suited for interpreting large amounts of proteomic data to generate signaling networks or for modeling the dynamics of known network interactions. We also discuss ex les that explore these experimental and computational techniques in tandem to generate signaling networks under various conditions and that link those networks to transcriptional activity. Further advancements in this field will likely provide an explicit description of inflammatory response, paving the way for better diagnostics and therapies in clinic.

Long Noncoding RNAs in Cardiac Development and Pathophysiology

Publisher: Ovid Technologies (Wolters Kluwer Health)

Date: 26-10-2012

DOI: 10.1161/CIRCRESAHA.112.268953

Abstract: Heart function requires sophisticated regulatory networks to orchestrate organ development, physiological responses, and environmental adaptation. Until recently, it was thought that these regulatory networks are composed solely of protein-mediated transcriptional control and signaling systems consequently, it was thought that cardiac disease involves perturbation of these systems. However, it is becoming evident that RNA, long considered to function primarily as the platform for protein production, may in fact play a major role in most, if not all, aspects of gene regulation, especially the epigenetic processes that underpin organogenesis. These include not only well-validated classes of regulatory RNAs, such as microRNAs, but also tens of thousands of long noncoding RNAs that are differentially expressed across the entire genome of humans and other animals. Here, we review this emerging landscape, summarizing what is known about their functions and their role in cardiac biology, and provide a toolkit to assist in exploring this previously hidden layer of gene regulation that may underpin heart adaptation and complex heart diseases.

Video Q&A: Non-coding RNAs and eukaryotic evolution - a personal view

Publisher: Springer Science and Business Media LLC

Date: 16-07-2010

DOI: 10.1186/1741-7007-8-67

Morphogenetic expression of Moraxella bovis fimbriae (Pili) in Pseudomonas aeruginosa

Publisher: American Society for Microbiology

Date: 05-1990

DOI: 10.1128/JB.172.5.2601-2607.1990

Abstract: Type 4 fimbriae (pili) are found in a wide variety of gram-negative bacteria and are composed of small structural subunits which share significant sequence homology among different species, especially at their amino-terminal ends. Previous studies demonstrating morphogenetic expression of Bacteroides nodosus fimbriae from cloned subunit genes in Pseudomonas aeruginosa suggested that there is a common mechanism for type 4 fimbriae assembly and that the structural subunits are interchangeable (J. S. Mattick et al., J. Bacteriol. 169:33-41, 1987). Here we have examined the expression of Moraxella bovis fimbrial subunits in P. aeruginosa. M. bovis subunits were assembled into extracellular fimbriae in this host, in some cases as a homopolymer but in others as a mosaic with the indigenous subunit, indicating structural equivalence. This result contrasts with other studies in which recombinant P. aeruginosa expressing different subunits produced fimbriae composed almost exclusively of one subunit or the other (T. C. Elleman and J. E. Peterson, Mol. Microbiol. 1:377-380, 1987). Both observations can be explained by reversibility of subunit-subunit interactions at the site of assembly, with the forward equilibrium favoring chain extension between compatible subunits.

GONOME: Measuring correlations between GO terms and genomic positions

Publisher: Springer Science and Business Media LLC

Date: 25-02-2006

DOI: 10.1186/1471-2105-7-94

Abstract: Current methods to find significantly under- and over-represented gene ontology (GO) terms in a set of genes consider the genes as equally probable "balls in a bag", as may be appropriate for transcripts in micro-array data. However, due to the varying length of genes and intergenic regions, that approach is inappropriate for deciding if any GO terms are correlated with a set of genomic positions. We present an algorithm – GONOME – that can determine which GO terms are significantly associated with a set of genomic positions given a genome annotated with (at least) the starts and ends of genes. We show that certain GO terms may appear to be significantly associated with a set of randomly chosen positions in the human genome if gene lengths are not considered, and that these same terms have been reported as significantly over-represented in a number of recent papers. This apparent over-representation disappears when gene lengths are considered, as GONOME does. For ex le, we show that, when gene length is taken into account, the term "development" is not significantly enriched in genes associated with human CpG islands, in contradiction to a previous report. We further demonstrate the efficacy of GONOME by showing that occurrences of the proteosome-associated control element (PACE) upstream activating sequence in the S. cerevisiae genome associate significantly to appropriate GO terms. An extension of this approach yields a whole-genome motif discovery algorithm that allows identification of many other promoter sequences linked to different types of genes, including a large group of previously unknown motifs significantly associated with the terms 'translation' and 'translational elongation'. GONOME is an algorithm that correctly extracts over-represented GO terms from a set of genomic positions. By explicitly considering gene size, GONOME avoids a systematic bias toward GO terms linked to large genes. Inappropriate use of existing algorithms that do not take gene size into account has led to erroneous or suspect conclusions. Reciprocally GONOME may be used to identify new features in genomes that are significantly associated with particular categories of genes.

Discovery and annotation of long noncoding RNAs

Publisher: Springer Science and Business Media LLC

Date: 2015

DOI: 10.1038/NSMB.2942

Abstract: Recent advances in RNA-sequencing technologies have led to the discovery of thousands of previously unannotated noncoding transcripts, including many long noncoding RNAs (lncRNAs) whose functions remain largely unknown. Here we discuss considerations and best practices in lncRNA identification and annotation, which we hope will foster functional and mechanistic exploration.

RNA, the Epicenter of Genetic Information

Publisher: CRC Press

Date: 25-08-2022

DOI: 10.1201/9781003109242

Structural venomics reveals evolution of a complex venom by duplication and diversification of an ancient peptide-encoding gene.

Publisher: Proceedings of the National Academy of Sciences

Date: 12-05-2020

DOI: 10.1073/PNAS.1914536117

Abstract: Spiders are one of the most successful venomous animals, with more than 48,000 described species. Most spider venoms are dominated by cysteine-rich peptides with a erse range of pharmacological activities. Some spider venoms contain thousands of unique peptides, but little is known about the mechanisms used to generate such complex chemical arsenals. We used an integrated transcriptomic, proteomic, and structural biology approach to demonstrate that the lethal Australian funnel-web spider produces 33 superfamilies of venom peptides and proteins. Twenty-six of the 33 superfamilies are disulfide-rich peptides, and we show that 15 of these are knottins that contribute % of the venom proteome. NMR analyses revealed that most of these disulfide-rich peptides are structurally related and range in complexity from simple to highly elaborated knottin domains, as well as double-knot toxins, that likely evolved from a single ancestral toxin gene.

The central role of RNA in the genetic programming of complex organisms.

Publisher: FapUNIFESP (SciELO)

Date: 12-2010

DOI: 10.1590/S0001-37652010000400016

Abstract: Notwithstanding lineage-specific variations, the number and type of protein-coding genes remain relatively static across the animal kingdom. By contrast there has been a massive expansion in the extent of genomic non-proteincoding sequences with increasing developmental complexity. These non-coding sequences are, in fact, transcribed in a regulated manner to produce large numbers of large and small non-protein-coding RNAs that control gene expression at many levels including chromatin architecture, post-transcriptional processing and translation. Moreover, many RNAs are edited, especially in the nervous system, which may be the basis of epigenome-environment interactions and the function of the brain.

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

Publisher: Springer Science and Business Media LLC

Date: 13-05-2021

DOI: 10.1038/S41587-021-00915-6

Abstract: Nanopore RNA sequencing shows promise as a method for discriminating and identifying different RNA modifications in native RNA. Expanding on the ability of nanopore sequencing to detect N

MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

Publisher: Cold Spring Harbor Laboratory

Date: 22-12-2008

DOI: 10.1101/GR.087775.108

Abstract: Studies of the transcriptional output of the human and mouse genomes have revealed that there are many more transcripts produced than can be accounted for by predicted protein-coding genes. Using a custom microarray, we have identified 184 non-coding RNAs that exhibit more than twofold up- or down-regulation upon differentiation of C2C12 myoblasts into myotubes. Here, we focus on the Men ε/β locus, which is up-regulated 3.3-fold during differentiation. Two non-coding RNA isoforms are produced from a single RNA polymerase II promoter, differing in the location of their 3′ ends. Men ε is a 3.2-kb polyadenylated RNA, whereas Men β is an ∼20-kb transcript containing a genomically encoded poly(A)-rich tract at its 3′-end. The 3′-end of Men β is generated by RNase P cleavage. The Men ε/β transcripts are localized to nuclear paraspeckles and directly interact with NONO. Knockdown of MEN ε/β expression results in the disruption of nuclear paraspeckles. Furthermore, the formation of paraspeckles, after release from transcriptional inhibition by DRB treatment, was suppressed in MEN ε/β -depleted cells. Our findings indicate that the MEN ε/β non-coding RNAs are essential structural/organizational components of paraspeckles.

Phosphorylation of the Pseudomonas aeruginosa response regulator AlgR is essential for type IV fimbria-mediated twitching motility.

Publisher: American Society for Microbiology

Date: 15-08-2002

DOI: 10.1128/JB.184.16.4544-4554.2002

Abstract: The response regulator AlgR is required for both alginate biosynthesis and type IV fimbria-mediated twitching motility in Pseudomonas aeruginosa . In this study, the roles of AlgR signal transduction and phosphorylation in twitching motility and biofilm formation were examined. The predicted phosphorylation site of AlgR (aspartate 54) and a second aspartate (aspartate 85) in the receiver domain of AlgR were mutated to asparagine, and mutant algR alleles were introduced into the chromosome of P. aeruginosa strains PAK and PAO1. Assays of these mutants demonstrated that aspartate 54 but not aspartate 85 of AlgR is required for twitching motility and biofilm initiation. However, strains expressing AlgR D85N were found to be hyperfimbriate, indicating that both aspartate 54 and aspartate 85 are involved in fimbrial biogenesis and function. algD mutants were observed to have wild-type twitching motility, indicating that AlgR control of twitching motility is not mediated via its role in the control of alginate biosynthesis. In vitro phosphorylation assays showed that AlgR D54N is not phosphorylated by the enteric histidine kinase CheA. These findings indicate that phosphorylation of AlgR most likely occurs at aspartate 54 and that aspartate 54 and aspartate 85 of AlgR are required for the control of the molecular events governing fimbrial biogenesis, twitching motility, and biofilm formation in P. aeruginosa .

Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA

Publisher: Informa UK Limited

Date: 2006

DOI: 10.4161/RNA.3.1.2789

Abstract: Several recent studies indicate that mammals and other organisms produce large numbers of RNA transcripts that do not correspond to known genes. It has been suggested that these transcripts do not encode proteins, but may instead function as RNAs. However, discrimination of coding and non-coding transcripts is not straightforward, and different laboratories have used different methods, whose ability to perform this discrimination is unclear. In this study, we examine ten bioinformatic methods that assess protein-coding potential and compare their ability and congruency in the discrimination of non-coding from coding sequences, based on four underlying principles: open reading frame size, sequence similarity to known proteins or protein domains, statistical models of protein-coding sequence, and synonymous versus non-synonymous substitution rates. Despite these different approaches, the methods show broad concordance, suggesting that coding and non-coding transcripts can, in general, be reliably discriminated, and that many of the recently discovered extra-genic transcripts are indeed non-coding. Comparison of the methods indicates reasons for unreliable predictions, and approaches to increase confidence further. Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts.

Organization of the fimbrial gene region of Bacteroides nodosus: class I and class II strains.

Publisher: Wiley

Date: 03-1991

DOI: 10.1111/J.1365-2958.1991.TB00726.X

Noncoding RNAs in long-term memory formation

Publisher: SAGE Publications

Date: 16-11-2008

DOI: 10.1177/1073858408319187

Abstract: Current research exploring the molecular basis of memory focuses mainly on proteins despite recent genomic studies reporting the abundant transcription of non-protein-coding RNA (ncRNA). Although ncRNAs are involved in a erse range of biological processes, they are particularly prevalent within the nervous system, where they contribute towards the complexity and function of the mammalian brain. In this review, we apply recent advances in ncRNA biology to predict a critical role for ncRNAs in the molecular mechanisms underlying memory formation and maintenance. We describe the role of ncRNAs in regulating the translation, stability, and editing of mRNA populations in response to synaptic activity during memory formation and the role of ncRNAs in the epigenetic and transcriptional programs that underlie long-term memory storage. We also consider ncRNAs acting as an additional avenue of communication between neurons by their intercellular trafficking. Taken together, the emerging evidence suggests a central role for ncRNAs in memory formation and provokes novel research directions in this field. NEUROSCIENTIST 14(5):434—445, 2008. DOI: 10.1177/1073858408319187

Functional expression of heterologous type 4 fimbriae in Pseudomonas aeruginosa.

Publisher: Elsevier BV

Date: 10-1996

DOI: 10.1016/0378-1119(96)00140-0

RNA Networks as Digital Control Circuits of Nuclear Functions

Publisher: Wiley

Date: 14-11-2011

DOI: 10.1002/9783527639991.CH14

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

Publisher: Springer Science and Business Media LLC

Date: 25-01-2017

DOI: 10.1186/S40168-016-0224-8

Delineating slowly and rapidly evolving fractions of the Drosophila genome.

Publisher: Mary Ann Liebert Inc

Date: 05-2008

DOI: 10.1089/CMB.2007.0173

Abstract: Evolutionary conservation is an important indicator of function and a major component of bioinformatic methods to identify non-protein-coding genes. We present a new Bayesian method for segmenting pairwise alignments of eukaryotic genomes while simultaneously classifying segments into slowly and rapidly evolving fractions. We also describe an information criterion similar to the Akaike Information Criterion (AIC) for determining the number of classes. Working with pairwise alignments enables detection of differences in conservation patterns among closely related species. We analyzed three whole-genome and three partial-genome pairwise alignments among eight Drosophila species. Three distinct classes of conservation level were detected. Sequences comprising the most slowly evolving component were consistent across a range of species pairs, and constituted approximately 62-66% of the D. melanogaster genome. Almost all (>90%) of the aligned protein-coding sequence is in this fraction, suggesting much of it (comprising the majority of the Drosophila genome, including approximately 56% of non-protein-coding sequences) is functional. The size and content of the most rapidly evolving component was species dependent, and varied from 1.6% to 4.8%. This fraction is also enriched for protein-coding sequence (while containing significant amounts of non-protein-coding sequence), suggesting it is under positive selection. We also classified segments according to conservation and GC content simultaneously. This analysis identified numerous sub-classes of those identified on the basis of conservation alone, but was nevertheless consistent with that classification. Software, data, and results available at www.maths.qut.edu.au/-keithj/. Genomic segments comprising the conservation classes available in BED format.

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

Publisher: Informa UK Limited

Date: 15-10-2009

DOI: 10.4161/CC.8.20.9916

Abstract: Nucleosome positioning is constrained at eukaryotic transcription start sites and implicated in transcriptional regulation. Moreover, recent observations indicate that chromatin structure, transcription and splicing are functionally intertwined, and that modified nucleosomes with trimethylation of lysine 36 in histone subunit 3 (H3K36me3) are enriched at internal exons and the downstream flanking intronic regions of highly expressed genes. However, the position of nucleosomes in the interior of genes has been thought to be largely random. Here we show, by analysis of data sets from human sperm and T cells and medaka (Japanese killifish, Oryzias latipes) blastulae, that internal exons of genes are characterized by sharply elevated average nucleosome occupancy in comparison to flanking intronic sequences. We also show that the preferential positioning of nucleosomes at internal exons is independent of their modification status, and of the GC content, conservation or the expression level of the exon. These findings show that the location of exons is recorded in the chromatin structure and may be inherited across generations. Such embedded information may underpin transcriptionally coupled exon recognition and splice site selection.

Non-coding RNAs: the architects of eukaryotic complexity.

Publisher: EMBO

Date: 11-2001

DOI: 10.1093/EMBO-REPORTS/KVE230

Abstract: Around 98% of all transcriptional output in humans is non‐coding RNA. RNA‐mediated gene regulation is widespread in higher eukaryotes and complex genetic phenomena like RNA interference, co‐suppression, transgene silencing, imprinting, methylation, and possibly position‐effect variegation and transvection, all involve intersecting pathways based on or connected to RNA signaling. I suggest that the central dogma is incomplete, and that intronic and other non‐coding RNAs have evolved to comprise a second tier of gene expression in eukaryotes, which enables the integration and networking of complex suites of gene activity. Although proteins are the fundamental effectors of cellular function, the basis of eukaryotic complexity and phenotypic variation may lie primarily in a control architecture composed of a highly parallel system of trans ‐acting RNAs that relay state information required for the coordination and modulation of gene expression, via chromatin remodeling, RNA–DNA, RNA–RNA and RNA–protein interactions. This system has interesting and perhaps informative analogies with small world networks and dataflow computing.

Transposon-free regions in mammalian genomes.

Publisher: Cold Spring Harbor Laboratory

Date: 19-12-2006

DOI: 10.1101/GR.4624306

Abstract: Despite the presence of over 3 million transposons separated on average by ∼500 bp, the human and mouse genomes each contain almost 1000 transposon-free regions (TFRs) over 10 kb in length. The majority of human TFRs correlate with orthologous TFRs in the mouse, despite the fact that most transposons are lineage specific. Many human TFRs also overlap with orthologous TFRs in the marsupial opossum, indicating that these regions have remained refractory to transposon insertion for long evolutionary periods. Over 90% of the bases covered by TFRs are noncoding, much of which is not highly conserved. Most TFRs are not associated with unusual nucleotide composition, but are significantly associated with genes encoding developmental regulators, suggesting that they represent extended regions of regulatory information that are largely unable to tolerate insertions, a conclusion difficult to reconcile with current conceptions of gene regulation.

An interactive web-based Pseudomonas aeruginosa genome database: Discovery of new genes, pathways and structures

Publisher: Microbiology Society

Date: 10-2000

DOI: 10.1099/00221287-146-10-2351

Expression of active yeast pyruvate decarboxylase in Escherichia coli

Publisher: Microbiology Society

Date: 12-1991

DOI: 10.1099/00221287-137-12-2811

The Non-Coding RNA Journal Club: Highlights on Recent Papers

Publisher: MDPI AG

Date: 17-06-2015

DOI: 10.3390/NCRNA1010087

Abstract: The number of papers dealing with new modus operandi or new biological functions of non-coding RNAs published in recent years has indeed exploded. A simple search for ‘non-coding RNA’ in Pubmed on 10 June 2015 yielded 128,649 articles, half of which were published in the last 10 years [1]. Every researcher in this field knows that he has something to learn and can discover new ideas, new concepts or new tools from studies made in models others than the ones used in its lab. The Scientific board of Non-Coding RNA publishes here its first Journal Club and highlights, in about hundred words, a selection of the most interesting papers published recently. We hope we will tease your curiosity and encourage you to read full papers outside of your research area that you may not have read otherwise. [...]

Cloning and expression analysis of a novel mouse gene with sequence similarity to the Drosophila fat facets gene.

Publisher: Elsevier BV

Date: 04-1997

DOI: 10.1016/S0925-4773(97)00672-2

High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs

Publisher: Springer Science and Business Media LLC

Date: 27-09-2021

DOI: 10.1186/S13072-021-00419-2

Abstract: It is established that protein-coding exons are preferentially localized in nucleosomes. To examine whether the same is true for non-coding exons, we analysed nucleosome occupancy in and adjacent to internal exons in genes encoding long non-coding RNAs (lncRNAs) in human CD4+ T cells and K562 cells. We confirmed that internal exons in lncRNAs are preferentially associated with nucleosomes, but also observed an elevated signal from H3K4me3-marked nucleosomes in the sequences upstream of these exons. Examination of 200 genomic lncRNA loci chosen at random across all chromosomes showed that high-density regions of H3K4me3-marked nucleosomes, which we term ‘slabs’, are associated with genomic regions exhibiting intron retention. These retained introns occur in over 50% of lncRNAs examined and are mostly first introns with an average length of just 354 bp, compared to the average length of all human introns of 6355 and 7987 bp in mRNAs and lncRNAs, respectively. Removal of short introns from the dataset abrogated the high upstream H3K4me3 signal, confirming that the association of slabs and short lncRNA introns with intron retention holds genome-wide. The high upstream H3K4me3 signal is also associated with alternatively spliced exons, known to be prominent in lncRNAs. This phenomenon was not observed with mRNAs. There is widespread intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs, which raises intriguing questions about the relationship of IR to lncRNA function and chromatin organization.

The promise of personalised medicine

Publisher: Elsevier BV

Date: 2016

DOI: 10.1016/S0140-6736(16)00176-8

The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization

Publisher: Springer Science and Business Media LLC

Date: 03-08-2011

DOI: 10.1186/1756-8935-4-13

Abstract: Transcription initiation RNAs (tiRNAs) are nuclear localized 18 nucleotide RNAs derived from sequences immediately downstream of RNA polymerase II (RNAPII) transcription start sites. Previous reports have shown that tiRNAs are intimately correlated with gene expression, RNA polymerase II binding and behaviors, and epigenetic marks associated with transcription initiation, but not elongation. In the present work, we show that tiRNAs are commonly found at genomic CCCTC-binding factor (CTCF) binding sites in human and mouse, and that CTCF sites that colocalize with RNAPII are highly enriched for tiRNAs. To directly investigate the relationship between tiRNAs and CTCF we examined tiRNAs originating near the intronic CTCF binding site in the human tumor suppressor gene, p21 (cyclin-dependent kinase inhibitor 1A gene, also known as CDKN1A ). Inhibition of CTCF-proximal tiRNAs resulted in increased CTCF localization and increased p21 expression, while overexpression of CTCF-proximal tiRNA mimics decreased CTCF localization and p21 expression. We also found that tiRNA-regulated CTCF binding influences the levels of trimethylated H3K27 at the alternate upstream p21 promoter, and affects the levels of alternate p21 ( p21 alt ) transcripts. Extending these studies to another randomly selected locus with conserved CTCF binding we found that depletion of tiRNA alters nucleosome density proximal to sites of tiRNA biogenesis. Taken together, these data suggest that tiRNAs modulate local epigenetic structure, which in turn regulates CTCF localization.

Introns: evolution and function.

Publisher: Elsevier BV

Date: 12-1994

DOI: 10.1016/0959-437X(94)90066-3

Biogenesis of mitochondria. 43. A comparative study of petite induction and inhibition of mitochondrial DNA replication in yeast by ethidium bromide and berenil.

Publisher: Springer Science and Business Media LLC

Date: 12-1975

DOI: 10.1007/BF00331451

A meta-analysis of the genomic and transcriptomic composition of complex life

Publisher: Informa UK Limited

Date: 07-2013

DOI: 10.4161/CC.25134

The double life of RNA

Publisher: Elsevier BV

Date: 11-2011

DOI: 10.1016/S0300-9084(11)00355-5

Molecular evolution of the HBII-52 snoRNA cluster.

Publisher: Elsevier BV

Date: 09-2008

DOI: 10.1016/J.JMB.2008.06.057

Abstract: HBII-52 is a human brain-specific C/D box snoRNA that potentially regulates the editing and/or alternative splicing of the serotonin receptor. Forty-two nearly identical copies of the HBII-52 gene are located immediately downstream of the SNRPN protein-coding gene in an imprinted locus associated with Prader-Willi syndrome. Other eutherian mammals, with genomic assemblies covering the corresponding locus, also have multiple orthologous copies of HBII-52. The SNRPB gene, which is known to have given rise to SNRPN through gene duplication, expresses a C/D box snoRNA, SNORD119, from its fifth intron. Here we show that, despite the fact that they lie in different positions relative to the orthologous SNRPB/SNRPN coding sequences, there are significant sequence similarities between SNORD119 and HBII-52, including the antisense element and the stem-forming regions. By analysing these snoRNAs in marsupial and eutherian mammal genomes, we reconstruct the likely evolutionary history of the HBII-52 cluster and SNORD119 and suggest that they have evolved from a common ancestor.

The alginate regulator AlgR and an associated sensor FimS are required for twitching motility in Pseudomonas aeruginosa.

Publisher: Proceedings of the National Academy of Sciences

Date: 03-09-1996

DOI: 10.1073/PNAS.93.18.9839

Abstract: Mucoid strains of Pseudomonas aeruginosa isolated from the lungs of cystic fibrosis patients produce large amounts of the exopolysaccharide alginate. AlgR has long been considered a key regulator of alginate production, but its cognate sensor has not been identified. Here we show that AlgR is required for twitching motility, which is a form of bacterial surface translocation mediated by type 4 fimbriae. Adjacent to algR we have identified a sensor gene (fimS), which is also required for twitching motility. However, FimS does not appear to be required for alginate production in mucoid strains. FimS and AlgR are representative of a new subclass of two-component transmitter-receiver regulatory systems. The alternative sigma factor AlgU also affects both alginate production and twitching motility. Therefore, these two virulence determinants appear to be closely associated and coordinately regulated.

Deconstructing the dogma: a new view of the evolution and genetic programming of complex organisms.

Publisher: Wiley

Date: 10-2009

DOI: 10.1111/J.1749-6632.2009.04991.X

Abstract: Since the birth of molecular biology it has been generally assumed that most genetic information is transacted by proteins, and that RNA plays an intermediary role. This led to the subsidiary assumption that the vast tracts of noncoding sequences in the genomes of higher organisms are largely nonfunctional, despite the fact that they are transcribed. These assumptions have since become articles of faith, but they are not necessarily correct. I propose an alternative evolutionary history whereby developmental and cognitive complexity has arisen by constructing sophisticated RNA-based regulatory networks that interact with generic effector complexes to control gene expression patterns and the epigenetic trajectories of differentiation and development. Environmental information can also be conveyed into this regulatory system via RNA editing, especially in the brain. Moreover, the observations that RNA-directed epigenetic changes can be inherited raises the intriguing question: has evolution learnt how to learn?

The Long Noncoding RNA SPRIGHTLY Regulates Cell Proliferation in Primary Human Melanocytes

Publisher: Elsevier BV

Date: 04-2016

DOI: 10.1016/J.JID.2016.01.018

The impact of genomics on the future of medicine and health.

Publisher: AMPCo

Date: 07-2014

DOI: 10.5694/MJA13.10920

A re-examination of twitching motility in Pseudomonas aeruginosa

Publisher: Microbiology Society

Date: 10-1999

DOI: 10.1099/00221287-145-10-2863

Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock.

Publisher: Oxford University Press (OUP)

Date: 02-01-2008

DOI: 10.1093/MOLBEV/MSM268

Abstract: Mammalian genomes contain millions of highly conserved noncoding sequences, many of which are regulatory. The most extreme ex les are the 481 ultraconserved elements (UCEs) that are identical over at least 200 bp in human, mouse, and rat and show 96% identity with chicken, which erged approximately 310 MYA. If the substitution rate in UCEs remained constant, these elements should also be present with a high level of identity in fish (approximately 450 Myr), but this is not the case, suggesting that many appeared in the amniotes or tetrapods or that the molecular clock has slowed down in these lineages, or both. Taking advantage of the availability of multiple genomes, we identified 13,736 UCEs in the human genome that are identical over at least 100 bp in at least 3 of 5 placental mammals, including 2,189 sequences over at least 200 bp, thereby greatly expanding the repertoire of known UCEs, and investigated the evolution of these sequences in opossum, chicken, frog, and fish. We conclude that there was a massive genome-wide acquisition and expansion of UCEs during tetrapod and then amniote evolution, accompanied by a slowdown of the molecular clock, particularly in the amniotes, a process consistent with their functional exaptation in these lineages. The majority of tetrapod-specific UCEs are noncoding and associated with genes involved in regulation of transcription and development. In contrast, fish genomes contain relatively few UCEs, the majority of which are common to all bony vertebrates. These elements are different from other conserved noncoding elements and appear to be important regulatory innovations that became fixed following the emergence of vertebrates from the sea to the land.

Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective.

Publisher: Oxford University Press (OUP)

Date: 05-2013

DOI: 10.1093/BFGP/ELT016

Abstract: Cells and organisms are subject to challenges and perturbations in their environment and physiology in all stages of life. The molecular response to such changes, including insulting conditions such as pathogen infections, involves coordinated modulation of gene expression programmes and has not only homeostatic but also ecological and evolutionary importance. Although attention has been primarily focused on signalling pathways and protein networks, non-coding RNAs (ncRNAs), which comprise a significant output of the genomes of prokaryotes and especially eukaryotes, are increasingly implicated in the molecular mechanisms of these responses. Long and short ncRNAs not only regulate development and cell physiology, they are also involved in disease states, including cancers, in host-pathogen interactions, and in a variety of stress responses. Indeed, regulatory RNAs are part of genetically encoded response networks and also underpin epigenetic processes, which are emerging as key mechanisms of adaptation and transgenerational inheritance. Here we present the growing evidence that ncRNAs are intrinsically involved in cellular and organismal adaptation processes, in both robustness and protection to stresses, as well as in mechanisms generating evolutionary change.

The characterisation of an esterase derived from Babesia bovis and its use as a vaccine.

Publisher: Springer Science and Business Media LLC

Date: 1983

DOI: 10.1007/BF00927420

Homologous mammalian brain cell lysate system for the initiation and translation of exogenous mRNAs.

Publisher: Wiley

Date: 08-1981

DOI: 10.1111/J.1471-4159.1981.TB00459.X

Serotype-specific glycoprotein of simian 11 rotavirus: coding assignment and gene sequence.

Publisher: Proceedings of the National Academy of Sciences

Date: 05-1983

DOI: 10.1073/PNAS.80.10.3091

Abstract: Cloned DNA copies of the double-stranded RNA genomic segments of simian 11 rotavirus have been used to determine the coding assignment for VP7, the type-specific antigen of this virus. Translation of hybrid-selected mRNAs in an in vitro system supplemented with canine pancreatic microsomes permitted VP7 to be assigned to segment 9 and the two nonstructural viral proteins NCVP4 and NCVP3, to segments 7 and 8, respectively. Hybridization of cloned DNA probes for segments 7-9 with the corresponding segments of human rotavirus Wa confirmed these assignments. The complete nucleotide sequence of gene 9 has been determined. The deduced amino acid sequence reveals VP7 to be 326 amino acids in length with two NH2-terminal hydrophobic regions and a single glycosylation site at residues 69-71.

Proteome analysis of extracellular proteins regulated by the las and rhl quorum sensing systems in Pseudomonas aeruginosa PAO1

Publisher: Microbiology Society

Date: 05-2003

DOI: 10.1099/MIC.0.25967-0

Abstract: The las and rhl quorum sensing (QS) systems regulate the expression of several genes in response to cell density changes in Pseudomonas aeruginosa . Many of these genes encode surface-associated or secreted virulence factors. Proteins from stationary phase culture supernatants were collected from wild-type and P. aeruginosa PAO1 mutants deficient in one or more of the lasRI , rhlRI and vfr genes and analysed using two-dimensional gel electrophoresis. All mutants released significantly lower amounts of protein than the wild-type. Protein spot patterns from each strain were compared using image analysis and visible spot differences were identified using mass spectrometry. Several previously unknown QS-regulated proteins were characterized, including an aminopeptidase (PA2939), an endoproteinase (PrpL) and a unique ‘hypothetical’ protein (PA0572), which could not be detected in the culture supernatants of Δ las mutants, although they were unaffected in Δ rhl mutants. Chitin-binding protein (CbpD) and a hypothetical protein (PA4944) with similarity to host factor I (HF-I) could not be detected when any of the lasRI or rhlRI genes were disrupted. Fourteen proteins were present at significantly greater levels in the culture supernatants of QS mutants, suggesting that QS may also negatively control the expression of some genes. Increased levels of two-partner secretion exoproteins (PA0041 and PA4625) were observed and may be linked to increased stability of their cognate transporters in a QS-defective background. Known QS-regulated extracellular proteins, including elastase ( lasB ), LasA protease ( lasA ) and alkaline metalloproteinase ( aprA ) were also detected.

The evolution of RNAs with multiple functions.

Publisher: Elsevier BV

Date: 11-2011

DOI: 10.1016/J.BIOCHI.2011.07.018

Abstract: Increasing numbers of transcripts have been reported to transmit both protein-coding and regulatory information. Apart from challenging our conception of the gene, this observation raises the question as to what extent this phenomenon occurs across the genome and how and why such dual encoding of function has evolved in the eukaryotic genome. To address this question, we consider the evolutionary path of genes in the earliest forms of life on Earth, where it is generally regarded that proteins evolved from a cellular machinery based entirely within RNA. This led to the domination of protein-coding genes in the genomes of microorganisms, although it is likely that RNA never lost its other capacities and functionalities, as evidenced by cis-acting riboswitches and UTRs. On the basis that the subsequent evolution of a more sophisticated regulatory architecture to provide higher levels of epigenetic control and accurate spatiotemporal expression in developmentally complex organisms is a complicated task, we hypothesize: (i) that mRNAs have been and remain subject to secondary selection to provide trans-acting regulatory capability in parallel with protein-coding functions (ii) that some and perhaps many protein-coding loci, possibly as a consequence of gene duplication, have lost protein-coding functions en route to acquiring more sophisticated trans-regulatory functions (iii) that many transcripts have become subject to secondary processing to release different products and (iv) that novel proteins have emerged within loci that previously evolved functionality as regulatory RNAs. In support of the idea that there is a dynamic flux between different types of informational RNAs in both evolutionary and real time, we review recent observations that have arisen from transcriptomic surveys of complex eukaryotes and reconsider how these observations impact on the notion that apparently discrete loci may express transcripts with more than one function. In conclusion, we posit that many eukaryotic loci have evolved the capacity to transact a multitude of overlapping and potentially independent functions as both regulatory and protein-coding RNAs.

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

Publisher: Oxford University Press (OUP)

Date: 22-03-2011

DOI: 10.1093/NAR/GKR110

Effects of a Novel Long Noncoding RNA, lncUSMycN, on N-Myc Expression and Neuroblastoma Progression

Publisher: Oxford University Press (OUP)

Date: 06-2014

DOI: 10.1093/JNCI/DJU113

Abstract: Patients with neuroblastoma due to the lification of a 130-kb genomic DNA region containing the MYCN oncogene have poor prognoses. Bioinformatics data were used to discover a novel long noncoding RNA, lncUSMycN, at the 130-kb licon. RNA-protein pull-down assays were used to identify proteins bound to lncUSMycN RNA. Kaplan-Meier survival analysis, multivariable Cox regression, and two-sided log-rank test were used to examine the prognostic value of lncUSMycN and NonO expression in three cohorts of neuroblastoma patients (n = 47, 88, and 476, respectively). Neuroblastoma-bearing mice were treated with antisense oligonucleotides targeting lncUSMycN (n = 12) or mismatch sequence (n = 13), and results were analyzed by multiple comparison two-way analysis of variance. All statistical tests were two-sided. Bioinformatics data predicted lncUSMycN gene and RNA, and reverse-transcription polymerase chain reaction confirmed its three exons and two introns. The lncUSMycN gene was co lified with MYCN in 88 of 341 human neuroblastoma tissues. lncUSMycN RNA bound to the RNA-binding protein NonO, leading to N-Myc RNA upregulation and neuroblastoma cell proliferation. High levels of lncUSMycN and NonO expression in human neuroblastoma tissues independently predicted poor patient prognoses (lncUSMycN: hazard ratio [HR] = 1.87, 95% confidence interval [CI] = 1.06 to 3.28, P = .03 NonO: HR = 2.48, 95% CI = 1.34 to 4.57, P = .004). Treatment with antisense oligonucleotides targeting lncUSMycN in neuroblastoma-bearing mice statistically significantly hindered tumor progression (P < .001). Our data demonstrate the important roles of lncUSMycN and NonO in regulating N-Myc expression and neuroblastoma oncogenesis and provide the first evidence that lification of long noncoding RNA genes can contribute to tumorigenesis.

Extracellular Vesicles from Neural Stem Cells Transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells

Publisher: Elsevier BV

Date: 11-2014

DOI: 10.1016/J.MOLCEL.2014.11.009

Erratum

Publisher: Oxford University Press (OUP)

Date: 29-10-2014

DOI: 10.1093/JNCI/DJU359

The hidden genetic program of complex organisms

Publisher: Springer Science and Business Media LLC

Date: 10-2004

DOI: 10.1038/SCIENTIFICAMERICAN1004-60

Publisher Correction: Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease

Publisher: Springer Science and Business Media LLC

Date: 17-12-2018

DOI: 10.1038/S41593-018-0277-Z

Abstract: In the version of this article initially published, the legends for Supplementary Figs. 4-8 and 10-14 contained errors. The Supplementary Figure legends have been corrected in the HTML and PDF versions of the article.

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells

Publisher: Elsevier BV

Date: 10-2014

DOI: 10.1016/J.MOLCEL.2014.08.020

Saccharopolyspora erythraea’sgenome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch

Publisher: Springer Science and Business Media LLC

Date: 16-01-2013

DOI: 10.1186/1471-2164-14-15

Abstract: Actinobacteria form a major bacterial phylum that includes numerous human pathogens. Actinobacteria are primary contributors to carbon cycling and also represent a primary source of industrial high value products such as antibiotics and biopesticides. Consistent with other members of the actinobacterial phylum, Saccharopolyspora erythraea undergo a transitional switch. This switch is characterized by numerous metabolic and morphological changes. We performed RNA sequencing to analyze the transcriptional changes that occur during growth of Saccharopolyspora erythraea in batch culture. By sequencing RNA across the fermentation time course, at a mean coverage of 4000X, we found the vast majority of genes to be prominently expressed, showing that we attained close to saturating sequencing coverage of the transcriptome. During the metabolic switch, global changes in gene expression influence the metabolic machinery of Saccharopolyspora erythraea, resetting an entirely novel gene expression program. After the switch, global changes include the broad repression of half the genes regulated by complex transcriptional mechanisms. Paralogous transposon clusters, delineate these transcriptional programs. The new transcriptional program is orchestrated by a bottleneck event during which mRNA levels are severely restricted by targeted mRNA degradation. Our results, which attained close to saturating sequencing coverage of the transcriptome, revealed unanticipated transcriptional complexity with almost one third of transcriptional content originating from un-annotated sequences. We showed that the metabolic switch is a sophisticated mechanism of transcriptional regulation capable of resetting and re-synchronizing gene expression programs at extraordinary speed and scale.

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

Publisher: Cold Spring Harbor Laboratory

Date: 12-12-2006

DOI: 10.1101/GR.4200206

Abstract: Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did not contain an apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-mRNA contamination during library construction, or alternatively represent nonspecific “transcriptional noise.” Here we show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts of unknown function whose expression appears to be regulated. The ncRNA transcripts have larger exons and fewer introns than protein-coding transcripts. Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following lipopolysaccharide stimulation. Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome.

Differentiating protein-coding and noncoding RNA: Challenges and ambiguities

Publisher: Public Library of Science (PLoS)

Date: 28-11-2008

DOI: 10.1371/JOURNAL.PCBI.1000176

Widespread formation of double-stranded RNAs in testis

Publisher: Cold Spring Harbor Laboratory

Date: 22-06-2021

DOI: 10.1101/GR.265603.120

Abstract: The testis transcriptome is highly complex and includes RNAs that potentially hybridize to form double-stranded RNA (dsRNA). We isolated dsRNA using the monoclonal J2 antibody and deep-sequenced the enriched s les from testes of juvenile Dicer1 knockout mice, age-matched controls, and adult animals. Comparison of our data set with recently published data from mouse liver revealed that the dsRNA transcriptome in testis is markedly different from liver: In testis, dsRNA-forming transcripts derive from mRNAs including promoters and immediate downstream regions, whereas in somatic cells they originate more often from introns and intergenic transcription. The genes that generate dsRNA are significantly expressed in isolated male germ cells with particular enrichment in pachytene spermatocytes. dsRNA formation is lower on the sex (X and Y) chromosomes. The dsRNA transcriptome is significantly less complex in juvenile mice as compared to adult controls and, possibly as a consequence, the knockout of Dicer1 has only a minor effect on the total number of transcript peaks associated with dsRNA. The comparison between dsRNA-associated genes in testis and liver with a reported set of genes that produce endogenous siRNAs reveals a significant overlap in testis but not in liver. Testis dsRNAs also significantly associate with natural antisense genes—again, this feature is not observed in liver. These findings point to a testis-specific mechanism involving natural antisense transcripts and the formation of dsRNAs that feed into the RNA interference pathway, possibly to mitigate the mutagenic impacts of recombination and transposon mobilization.

The Functional Characterization of Long Noncoding RNASPRY4-IT1in Human Melanoma Cells

Publisher: Impact Journals, LLC

Date: 26-03-2014

DOI: 10.18632/ONCOTARGET.1863

Abstract: Expression of the long noncoding RNA (lncRNA) SPRY4-IT1 is low in normal human melanocytes but high in melanoma cells. siRNA knockdown of SPRY4-IT1 blocks melanoma cell invasion and proliferation, and increases apoptosis. To investigate its function further, we affinity purified SPRY4-IT1 from melanoma cells and used mass spectrometry to identify the protein lipin 2, an enzyme that converts phosphatidate to diacylglycerol (DAG), as a major binding partner. SPRY4-IT1 knockdown increases the accumulation of lipin2 protein and upregulate the expression of diacylglycerol O-acyltransferase 2 (DGAT2) an enzyme involved in the conversion of DAG to triacylglycerol (TAG). When SPRY4-IT1 knockdown and control melanoma cells were subjected to shotgun lipidomics, an MS-based assay that permits the quantification of changes in the cellular lipid profile, we found that SPRY4-IT1 knockdown induced significant changes in a number of lipid species, including increased acyl carnitine, fatty acyl chains, and triacylglycerol (TAG). Together, these results suggest the possibility that SPRY4-IT1 knockdown may induce apoptosis via lipin 2-mediated alterations in lipid metabolism leading to cellular lipotoxicity.

RNAdb 2.0--an expanded database of mammalian non-coding RNAs

Publisher: Oxford University Press (OUP)

Date: 03-01-2007

DOI: 10.1093/NAR/GKL926

ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome.

Publisher: Springer Science and Business Media LLC

Date: 04-2000

DOI: 10.1038/74153

Genome research.

Publisher: Springer Science and Business Media LLC

Date: 08-1990

DOI: 10.1038/346604C0

The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation.

Publisher: Springer Science and Business Media LLC

Date: 26-05-2016

DOI: 10.1038/SREP26657

Abstract: Thousands of sense-antisense mRNA-lncRNA gene pairs occur in the mammalian genome. While there is usually little doubt about the function of the coding transcript, the function of the lncRNA partner is mostly untested. Here we examine the function of the homeotic Evx1 - Evx1as gene locus. Expression is tightly co-regulated in posterior mesoderm of mouse embryos and in embryoid bodies. Expression of both genes is enhanced by BMP4 and WNT3A, and reduced by Activin. We generated a suite of deletions in the locus by CRISPR-Cas9 editing. We show EVX1 is a critical downstream effector of BMP4 and WNT3A with respect to patterning of posterior mesoderm. The lncRNA, Evx1as arises from alternative promoters and is difficult to fully abrogate by gene editing or siRNA approaches. Nevertheless, we were able to generate a large 2.6 kb deletion encompassing the shared promoter with Evx1 and multiple additional exons of Evx1as. This led to an identical dorsal-ventral patterning defect to that generated by micro-deletion in the DNA-binding domain of EVX1. Thus, Evx1as has no function independent of EVX1, and is therefore unlikely to act in trans . We predict many antisense lncRNAs have no specific trans function, possibly only regulating the linked coding genes in cis .

The retroelement Lx9 puts a brake on the immune response to virus infection

Publisher: Springer Science and Business Media LLC

Date: 10-08-2022

DOI: 10.1038/S41586-022-05054-9

Abstract: The notion that mobile units of nucleic acid known as transposable elements can operate as genomic controlling elements was put forward over six decades ago

Effect of site-specific mutations in different phosphotransfer domains of the chemosensory protein ChpA on Pseudomonas aeruginosa motility.

Publisher: American Society for Microbiology

Date: 15-12-2006

DOI: 10.1128/JB.00157-06

Abstract: The virulence of Pseudomonas aeruginosa and other surface pathogens involves the coordinate expression of a wide range of virulence determinants, including type IV pili. These surface filaments are important for the colonization of host epithelial tissues and mediate bacterial attachment to, and translocation across, surfaces by a process known as twitching motility. This process is controlled in part by a complex signal transduction system whose central component, ChpA, possesses nine potential sites of phosphorylation, including six histidine-containing phosphotransfer (HPt) domains, one serine-containing phosphotransfer domain, one threonine-containing phosphotransfer domain, and one CheY-like receiver domain. Here, using site-directed mutagenesis, we show that normal twitching motility is entirely dependent on the CheY-like receiver domain and partially dependent on two of the HPt domains. Moreover, under different assay conditions, point mutations in several of the phosphotransfer domains of ChpA give rise to unusual “swarming” phenotypes, possibly reflecting more subtle perturbations in the control of P. aeruginosa motility that are not evident from the conventional twitching stab assay. Together, these results suggest that ChpA plays a central role in the complex regulation of type IV pilus-mediated motility in P. aeruginosa .

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

Publisher: Cold Spring Harbor Laboratory

Date: 18-06-2008

DOI: 10.1101/GR.078378.108

Abstract: The transcriptional networks that regulate embryonic stem (ES) cell pluripotency and lineage specification are the subject of considerable attention. To date such studies have focused almost exclusively on protein-coding transcripts. However, recent transcriptome analyses show that the mammalian genome contains thousands of long noncoding RNAs (ncRNAs), many of which appear to be expressed in a developmentally regulated manner. The functions of these remain untested. To identify ncRNAs involved in ES cell biology, we used a custom-designed microarray to examine the expression profiles of mouse ES cells differentiating as embryoid bodies (EBs) over a 16-d time course. We identified 945 ncRNAs expressed during EB differentiation, of which 174 were differentially expressed, many correlating with pluripotency or specific differentiation events. Candidate ncRNAs were identified for further characterization by an integrated examination of expression profiles, genomic context, chromatin state, and promoter analysis. Many ncRNAs showed coordinated expression with genomically associated developmental genes, such as Dlx1 , Dlx4 , Gata6 , and Ecsit . We examined two novel developmentally regulated ncRNAs, Evx1as and Hoxb5/6as , which are derived from homeotic loci and share similar expression patterns and localization in mouse embryos with their associated protein-coding genes. Using chromatin immunoprecipitation, we provide evidence that both ncRNAs are associated with trimethylated H3K4 histones and histone methyltransferase MLL1, suggesting a role in epigenetic regulation of homeotic loci during ES cell differentiation. Taken together, our data indicate that long ncRNAs are likely to be important in processes directing pluripotency and alternative differentiation programs, in some cases through engagement of the epigenetic machinery.

CNS cell type-specific gene profiling of P301S tau transgenic mice identifies genes dysregulated by progressive tau accumulation

Publisher: Elsevier BV

Date: 09-2019

DOI: 10.1074/JBC.RA118.005263

The Reality of Pervasive Transcription

Publisher: Public Library of Science (PLoS)

Date: 12-07-2011

DOI: 10.1371/JOURNAL.PBIO.1000625

RNA as the substrate for epigenome-environment interactions

Publisher: Wiley

Date: 28-06-2010

DOI: 10.1002/BIES.201090026

Touchdown PCR for increased specificity and sensitivity in PCR amplification.

Publisher: Springer Science and Business Media LLC

Date: 21-08-2008

DOI: 10.1038/NPROT.2008.133

Abstract: Touchdown (TD) PCR offers a simple and rapid means to optimize PCRs, increasing specificity, sensitivity and yield, without the need for lengthy optimizations and/or the redesigning of primers. TD-PCR employs an initial annealing temperature above the projected melting temperature (T(m)) of the primers being used, then progressively transitions to a lower, more permissive annealing temperature over the course of successive cycles. Any difference in T(m) between correct and incorrect annealing will produce an exponential advantage of twofold per cycle. TD-PCR has found wide applicability in standard PCR protocols, including reverse transcriptase-dependent PCR, as well as in the generation of cDNA libraries and single nucleotide polymorphism screening. TD-PCR is particularly useful for templates that are difficult to lify but can also be standardly used to enhance specificity and product formation. The procedure takes between 90 and 120 min, depending on the template length.

Long Noncoding RNA-Directed Epigenetic Regulation of Gene Expression Is Associated With Anxiety-like Behavior in Mice

Publisher: Elsevier BV

Date: 12-2015

DOI: 10.1016/J.BIOPSYCH.2015.02.004

Characterization of G3BPs: tissue specific expression, chromosomal localisation and rasGAP(120) binding studies.

Publisher: Wiley

Date: 07-12-2001

DOI: 10.1002/JCB.1277

Chromosomal location of the human transketolase gene

Publisher: S. Karger AG

Date: 1992

DOI: 10.1159/000133421

Abstract: The gene encoding the human transketolase enzyme (TKT) was localized by fluorescence in situ hybridization to normal and FRA3B human chromosomes. Southern blot analysis of a series of human × mouse and human × hamster hybrid cell lines confirmed this localisation. TKT maps to 3p 14 and distal to FRA3B, localizing TKT to 3p14.3.

RNAdb--a comprehensive mammalian noncoding RNA database

Publisher: Oxford University Press (OUP)

Date: 17-12-2004

DOI: 10.1093/NAR/GKI089

Co-localization of FAM and AF-6, the mammalian homologues of Drosophila faf and canoe, in mouse eye development.

Publisher: Elsevier BV

Date: 03-2000

DOI: 10.1016/S0925-4773(99)00294-4

Variation in the structural subunit and basal protein antigens of Bacteroides nodosus fimbriae

Publisher: American Society for Microbiology

Date: 05-1986

DOI: 10.1128/JB.166.2.453-460.1986

Abstract: The fimbriae of Bacteroides nodosus play a major role in protective immunity against ovine footrot and are an important determinant in the serological classification system that ides field isolates into at least eight serogroups and 16 serotypes. Purified fimbriae contain two polypeptide antigens, the structural subunit of the fimbrial strand (molecular weight about 17,000) and a basal protein (molecular weight about 80,000), both of which exhibit structural variation. Fimbriae were prepared from all prototype strains, as well as from a number of other isolates representative of each of the B. nodosus serotypes, and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Substantial variation was observed in the electrophoretic mobility of the fimbrial subunits from the prototypes of each of the eight serogroups. With the exception of serogroup H, which is an unusual case, the apparent molecular weights of the fimbrial subunits ranged from about 16,500 in serogroup D to 19,000 in serogroup F (serotype 1) in serogroup A, B, C and E, the apparent molecular weights were clustered in the range of 17,000 to 17,500, whereas serogroup G was about 18,500. Serogroup H fimbriae appeared to consist of two smaller polypeptides, which in the prototype (H1) had apparent molecular weights of about 6,000 and 10,000 and which seem to have arisen as a consequence of an internal proteolytic nick in the original subunit. Electrophoretic variation in the fimbrial subunit was also observed between different serotypes, although with the exceptions of serogroups F and H, this was not as pronounced as between the serogroups. Examination of a number of isolates classified within the same serotypes showed that some variation, although minor, also occurred at this level. The basal antigen exhibited significant variation at all levels of the serotypic hierarchy in a manner apparently unrelated to the classification system. Among the range of isolates examined, the apparent molecular weight of this antigen varied from about 77,000 to 88,000.

Macropodid herpesvirus 1 encodes genes for both thymidylate synthase and ICP34.5.

Publisher: Springer Science and Business Media LLC

Date: 2002

DOI: 10.1023/A:1015396430131

Splicing bypasses 3′ end formation signals to allow complex gene architectures

Publisher: Elsevier BV

Date: 11-2007

DOI: 10.1016/J.GENE.2007.08.012

Abstract: Many genes are arranged in complex overlapping and interlaced patterns in eukaryotic genomes. It is unclear whether or how such genes can avoid interference from each other's RNA processing signals and retain distinct identities. This puzzle applies particularly to 3' end formation sites, which inherently terminate the transcript, and thus act as boundaries between adjacent genes. We hypothesise that the transcript processing machinery can bypass 3' end formation sites by splicing out an intron surrounding the site. We confirm a prediction of this hypothesis: the likelihood of transcripts extending beyond 3' end sites depends on the strength of 3' end formation signals located in exons in the mature transcript, but not of those in introns that are spliced out of the transcript. This bypassing mechanism permits nested and interleaved gene architectures, as well as fusion transcripts that combine exons from adjacent genes.

FAM deubiquitylating enzyme is essential for preimplantation mouse embryo development.

Publisher: Elsevier BV

Date: 12-2001

DOI: 10.1016/S0925-4773(01)00551-2

Structural and functional annotation of long noncoding RNAs

Publisher: Springer New York

Date: 29-11-2017

DOI: 10.1007/978-1-4939-6613-4_4

Abstract: Protein-coding RNAs represent only a small fraction of the transcriptional output in higher eukaryotes. The remaining RNA species encompass a broad range of molecular functions and regulatory roles, a consequence of the structural polyvalence of RNA polymers. Albeit several classes of small noncoding RNAs are relatively well characterized, the accessibility of affordable high-throughput sequencing is generating a wealth of novel, unannotated transcripts, especially long noncoding RNAs (lncRNAs) that are derived from genomic regions that are antisense, intronic, intergenic, and overlapping protein-coding loci. Parsing and characterizing the functions of noncoding RNAs-lncRNAs in particular-is one of the great challenges of modern genome biology. Here we discuss concepts and computational methods for the identification of structural domains in lncRNAs from genomic and transcriptomic data. In the first part, we briefly review how to identify RNA structural motifs in in idual lncRNAs. In the second part, we describe how to leverage the evolutionary dynamics of structured RNAs in a computationally efficient screen to detect putative functional lncRNA motifs using comparative genomics.

Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs

Publisher: Elsevier BV

Date: 09-2010

DOI: 10.1016/J.YGENO.2010.05.006

Abstract: Non-protein-coding DNA comprises the majority of animal genomes but its functions are largely unknown. We identified over 17,000 different tetranucleotide pairs in the Drosophila melanogaster genome that are over-represented at distances up to 100nt in conserved non-exonic sequences. Those exhibiting the highest information content in surrounding nucleotides were classified into five groups: tRNAs, motifs associated with histone genes, Suppressor-of-Hairy-wing binding sites, and two sets of previously unrecognized motifs (DLM3 and DLM4). There are hundreds to thousands of copies of DLM3 and DLM4, respectively, in the genome, located almost exclusively in non-coding regions. They have similar copy numbers among drosophilids, but are largely absent in other insects. DLM3 is likely a cis-regulatory element, whereas DLM4 sequences are capable of forming a short hairpin structure and are expressed as approximately 80nt RNAs. This work reports the existence of Drosophila genus-specific sequence motifs, and suggests that many more novel functional elements may be discovered in genomes using the general approach outlined herein.

Linc-ing Long noncoding RNAs and enhancer function.

Publisher: Elsevier BV

Date: 10-2010

DOI: 10.1016/J.DEVCEL.2010.10.003

Abstract: Enhancers are distal regulatory sequences that control gene expression in development. Ørom et al. now report in Cell that some long noncoding RNAs have functional properties of enhancers. Known enhancers are also transcribed in cells in which they are active, suggesting that noncoding RNAs are integral to enhancer action.

Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs

Publisher: Public Library of Science (PLoS)

Date: 28-04-2006

DOI: 10.1371/JOURNAL.PGEN.0020037

Protection of sheep against footrot with a recombinant DNA-based fimbrial vaccine.

Publisher: Elsevier BV

Date: 09-1987

DOI: 10.1016/0378-1135(87)90030-7

Accelerating, hyperaccelerating, and decelerating networks

Publisher: American Physical Society (APS)

Date: 20-07-2005

DOI: 10.1103/PHYSREVE.72.016123

Factors affecting resistance to heat and recovery of heat-injuried bacteria.

Publisher: American Dairy Science Association

Date: 05-1969

DOI: 10.3168/JDS.S0022-0302(69)86615-4

Abstract: Nursing scientists have long been interested in complex, context-dependent questions addressing in idual- and population-level challenges in health and illness. These critical questions require multilevel data (e.g., genetic, physiologic, biologic, behavioral, affective, and social). Advances in data-gathering methods have resulted in the collection of large sets of complex, multifaceted, and often non-comparable data. Scientific visualization is a powerful methodological tool for facilitating understanding of these multidimensional data sets. Our purpose is to demonstrate the utility of scientific visualization as a method for identifying associations, patterns, and trends in multidimensional data as exemplified in two studies. We describe a brief history of visual analysis, processes involved in scientific visualization, and opportunities and challenges in the use of visualization methods. Scientific visualization can play a crucial role in helping nurse scientists make sense of the structure and underlying patterns in their data to answer vital questions in the field.

Pseudomonas aeruginosa fimL regulates multiple virulence functions by intersecting with Vfr-modulated pathways.

Publisher: Wiley

Date: 04-02-2005

DOI: 10.1111/J.1365-2958.2005.04479.X

Erratum: Tiny RNAs associated with transcription start sites in animals (Nature Genetics (2009) 41 (572-578)).

Publisher: Springer Science and Business Media LLC

Date: 07-2009

DOI: 10.1038/NG0709-859A

Pervasive transcription of the eukaryotic genome: Functional indices and conceptual implications

Publisher: Oxford University Press (OUP)

Date: 21-09-2009

DOI: 10.1093/BFGP/ELP038

Abstract: Genome-wide analyses of the eukaryotic transcriptome have revealed that the majority of the genome is transcribed, producing large numbers of non-protein-coding RNAs (ncRNAs). This surprising observation challenges many assumptions about the genetic programming of higher organisms and how information is stored and organized within the genome. Moreover, the rapid advances in genomics have given little opportunity for biologists to integrate these emerging findings into their intellectual and experimental frameworks. This problem has been compounded by the perception that genome-wide studies often generate more questions than answers, which in turn has led to confusion and controversy. In this article, we address common questions associated with the phenomenon of pervasive transcription and consider the indices that can be used to evaluate the function (or lack thereof) of the resulting ncRNAs. We suggest that many lines of evidence, including expression profiles, conservation signatures, chromatin modification patterns and examination of increasing numbers of in idual cases, argue in favour of the widespread functionality of non-coding transcription. We also discuss how informatic and experimental approaches used to analyse protein-coding genes may not be applicable to ncRNAs and how the general perception that protein-coding genes form the main informational output of the genome has resulted in much of the misunderstanding surrounding pervasive transcription and its potential significance. Finally, we present the conceptual implications of the majority of the eukaryotic genome being functional and describe how appreciating this perspective will provide considerable opportunity to further understand the molecular basis of development and complex diseases.

Tiny RNAs associated with transcription start sites in animals

Publisher: Springer Science and Business Media LLC

Date: 19-04-2009

DOI: 10.1038/NG.312

Abstract: It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. In conjunction with the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within -60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5' ends of tiRNAs show peak density 10-30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes.

Quorum sensing is not required for twitching motility in Pseudomonas aeruginosa.

Publisher: American Society for Microbiology

Date: 07-2002

DOI: 10.1128/JB.184.13.3598-3604.2002

Abstract: It has been reported that mutations in the quorum-sensing genes lasI and rhlI in Pseudomonas aeruginosa result in, among many other things, loss of twitching motility (A. Glessner, R. S. Smith, B. H. Iglewski, and J. B. Robinson, J. Bacteriol. 181:1623-1629, 1999). We constructed knockouts of lasI and rhlI and the corresponding regulatory genes lasR and rhlR and found no effect on twitching motility. However, twitching-defective variants accumulated during culturing of lasI and rhlI mutants. Further analysis showed that the stable twitching-defective variants of lasI and rhlI mutants had arisen as a consequence of secondary mutations in vfr and algR , respectively, both of which encode key regulators affecting a variety of phenotypes, including twitching motility. In addition, when grown in shaking broth culture, lasI and rhlI mutants, but not the wild-type parent, also accumulated unstable variants that lacked both twitching motility and swimming motility and appeared to be identical in phenotype to the S1 and S2 variants that were recently reported to occur at high frequencies in P. aeruginosa strains grown as a biofilm or in static broth culture (E. Deziel, Y. Comeau, and R. Villemur, J. Bacteriol. 183:1195-1204, 2001). These results indicate that mutations in one regulatory system may create distortions that select during subsequent culturing for compensatory mutations in other regulatory genes within the cellular network. This problem may have compromised some past studies of regulatory hierarchies controlled by quorum sensing and of bacterial regulatory systems in general.

Genomics down under. A talk with John Mattick Director of the Australian Genome Research Facility, and Co-Director of the Institute for Molecular Bioscience. Interview by Holger Breithaupt.

Publisher: EMBO

Date: 09-2000

DOI: 10.1093/EMBO-REPORTS/KVD060

Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing

Publisher: Cold Spring Harbor Laboratory

Date: 17-05-2005

DOI: 10.1101/GR.3545105

Abstract: Recently, we identified a large number of ultraconserved (uc) sequences in noncoding regions of human, mouse, and rat genomes that appear to be essential for vertebrate and amniote ontogeny. Here, we used similar methods to identify ultraconserved genomic regions between the insect species Drosophila melanogaster and Drosophila pseudoobscura , as well as the more distantly related Anopheles gambiae. As with vertebrates, ultraconserved sequences in insects appear to occur primarily in intergenic and intronic sequences, and at intron-exon junctions. The sequences are significantly associated with genes encoding developmental regulators and transcription factors, but are less frequent and are smaller in size than in vertebrates. The longest identical, nongapped orthologous match between the three genomes was found within the homothorax ( hth ) gene. This sequence spans an internal exon-intron junction, with the majority located within the intron, and is predicted to form a highly stable stem-loop RNA structure. Real-time quantitative PCR analysis of different hth splice isoforms and Northern blotting showed that the conserved element is associated with a high incidence of intron retention in hth pre-mRNA, suggesting that the conserved intronic element is critically important in the post-transcriptional regulation of hth expression in Diptera .

The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms.

Publisher: Oxford University Press (OUP)

Date: 09-2001

DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A003951

MicroRNAs in the shoot apical meristem of soybean

Publisher: Oxford University Press (OUP)

Date: 19-04-2011

DOI: 10.1093/JXB/ERQ437

Abstract: Plant microRNAs (miRNAs) play crucial regulatory roles in various developmental processes. In this study, we characterize the miRNA profile of the shoot apical meristem (SAM) of an important legume crop, soybean, by integrating high-throughput sequencing data with miRNA microarray analysis. A total of 8423 non-redundant sRNAs were obtained from two libraries derived from micro-dissected SAM or mature leaf tissue. Sequence analysis allowed the identification of 32 conserved miRNA families as well as 8 putative novel miRNAs. Subsequent miRNA profiling with microarrays verified the expression of the majority of these conserved and novel miRNAs. It is noteworthy that several miRNAs* were expressed at a level similar to or higher than their corresponding mature miRNAs in SAM or mature leaf, suggesting a possible biological function for the star species. In situ hybridization analysis revealed a distinct spatial localization pattern for a conserved miRNA, miR166, and its star speciessuggesting that they serve different roles in regulating leaf development. Furthermore, localization studies showed that a novel soybean miRNA, miR4422a, was nuclear-localized. This study also indicated a novel expression pattern of miR390 in soybean. Our approach identified potential key regulators and provided vital spatial information towards understanding the regulatory circuits in the SAM of soybean during shoot development.

Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination

Publisher: American Association for the Advancement of Science (AAAS)

Date: 02-06-2017

DOI: 10.1126/SCIADV.1700731

Abstract: Alternative splicing in chromatin-modifying genes is associated with temperature-dependent sex in ergent reptile lineages.

Rocking the foundations of molecular genetics.

Publisher: Proceedings of the National Academy of Sciences

Date: 27-09-2012

DOI: 10.1073/PNAS.1214129109

Inherent size constraints on prokaryote gene networks due to accelerating growth

Publisher: Springer Science and Business Media LLC

Date: 15-04-2005

DOI: 10.1016/J.THBIO.2005.02.002

Accelerating Networks

Publisher: American Association for the Advancement of Science (AAAS)

Date: 11-02-2005

DOI: 10.1126/SCIENCE.1103737

Digital RNA regulation of complex organisms

Publisher: Brill

Date: 12-2004

DOI: 10.1163/1568558043967517

The first disulphide loop of the rabbit growth hormone receptor is required for binding to the hormone.

Publisher: Bioscientifica

Date: 12-1992

DOI: 10.1677/JME.0.0090213

Abstract: Residues within the first disulphide loop of the GH receptor are highly conserved, and the two cysteines forming this motif are conserved across many cytokine receptors. We have used site-directed mutagenesis and the polymerase chain reaction with splicing by overlap extension to show that these residues are essential for binding of bovine (b)GH and human (h)GH to the rabbit GH receptor. When all residues within this loop were replaced with an equivalent polyalanine sequence, hormone binding was abolished. Conversion of Arg 39 within the loop to aspartate (R39D) decreased affinity for bGH by up to 20-fold. Conversion of Glu 42 to lysine (E42K) also resulted in a fivefold loss of affinity for bGH. However, charge reversals at Lys 37, Glu 44 and the conversion of Leu 43 to an arginine (as in the human receptor) were without a major effect on bGH binding. The lack of effect of the L43R mutation on bGH affinity, despite a significant (threefold) decrease in hGH affinity, argues against a role for Arg 43 as a residue conferring primate GH-binding specificity on the human receptor. Examination of the affinities of poly Ala, R39D and E42K mutants for a variety of hormone-binding-site directed and other monoclonal antibodies (MAbs) to the GH receptor revealed that these mutations were without a major effect on tertiary structure. It is of interest that the epitopes for the hormone-binding inhibitory MAbs 263 and 7 are located within this first loop, since the poly Ala mutation abolished the binding of both MAbs, and the R39D mutation abolished binding of MAb 7. In conclusion, residues within the first disulphide loop of the GH receptor are critical for hormone binding, and are epitopes for the binding of inhibitory MAbs. These findings may be applicable to other cytokine receptors.

Branched‐chain amino acid supplementation: impact on signaling and relevance to critical illness

Publisher: Wiley

Date: 29-03-2013

DOI: 10.1002/WSBM.1219

SVMtm: Support Vector Machines to Predict Transmembrane Segments

Publisher: Wiley

Date: 15-01-2004

DOI: 10.1002/JCC.10411

Abstract: A new method has been developed for prediction of transmembrane helices using support vector machines. Different coding schemes of protein sequences were explored, and their performances were assessed by crossvalidation tests. The best performance method can predict the transmembrane helices with sensitivity of 93.4% and precision of 92.0%. For each predicted transmembrane segment, a score is given to show the strength of transmembrane signal and the prediction reliability. In particular, this method can distinguish transmembrane proteins from soluble proteins with an accuracy of approximately 99%. This method can be used to complement current transmembrane helix prediction methods and can be used for consensus analysis of entire proteomes. The predictor is located at genet.imb.uq.edu.au redictors/SVMtm.

Q pili enhance the attachment of Moraxella bovis to bovine corneas in vitro.

Publisher: Wiley

Date: 1993

DOI: 10.1111/J.1365-2958.1993.TB01119.X

lncRNAdb: a reference database for long noncoding RNAs

Publisher: Oxford University Press (OUP)

Date: 25-11-2010

DOI: 10.1093/NAR/GKQ1138

Mitochondrial DNA replication in petite mutants of yeast: resistance to inhibition by ethidium bromide, berenil and euflavine.

Publisher: Springer Science and Business Media LLC

Date: 1977

DOI: 10.1007/BF00693081

RNA processing in human mitochondria

Publisher: Informa UK Limited

Date: 09-2011

DOI: 10.4161/CC.10.17.17060

Abstract: Mammalian mitochondrial DNA is transcribed as precursor polycistronic transcripts containing 13 mRNAs, 2 rRNAs, punctuated by 22 tRNAs. The mechanisms involved in the excision of mitochondrial tRNAs from these polycistronic transcripts have remained largely unknown. We have investigated the roles of ELAC2, mitochondrial RNase P proteins 1 and 3, and pentatricopeptide repeat domain protein 1 in the processing of mitochondrial polycistronic transcripts. We used a deep sequencing approach to characterize the 5' and 3' ends of processed mitochondrial transcripts and provide a detailed map of mitochondrial tRNA processing sites affected by these proteins. We show that MRPP1 and MRPP3 process the 5' ends of tRNAs and the 5' unconventional, non tRNA containing site of the CO1 transcript. By contrast, we find that ELAC2 and PTCD1 affect the 3' end processing of tRNAs. Finally, we found that MRPP1 is essential for transcript processing, RNA modification, translation and mitochondrial respiration.

Comparative studies of the effects of acridines and other petite inducing drugs on the mitochondrial genome of Saccharomyces cerevisiae.

Publisher: Springer Science and Business Media LLC

Date: 1977

DOI: 10.1007/BF00693080

Prediction of protein solvent accessibility using support vector machines.

Publisher: Wiley

Date: 25-06-2002

DOI: 10.1002/PROT.10176

Reactivation of a macropodid herpesvirus from the eastern grey kangaroo (Macropus giganteus) following corticosteroid treatment.

Publisher: Elsevier BV

Date: 08-1999

DOI: 10.1016/S0378-1135(99)00061-9

Nucleotide and amino acid sequence analysis of the thymidine kinase gene of a bovine encephalitis herpesvirus.

Publisher: Springer Science and Business Media LLC

Date: 09-1991

DOI: 10.1007/BF01310670

Identification of two genes with prepilin-like leader sequences involved in type 4 fimbrial biogenesis in Pseudomonas aeruginosa

Publisher: American Society for Microbiology

Date: 07-1996

DOI: 10.1128/JB.178.13.3809-3817.1996

Abstract: Type 4 fimbriae are surface filaments produced by a range of bacterial pathogens for colonization of host epithelial surfaces. In Pseudomonas aeruginosa, they are involved in adhesion as well as in a form of surface translocation called twitching motility, and sensitivity to infection by fimbria-specific bacteriophage. Analysis of the 2.5-kb intergenic region between the previously defined pilR and pilV genes on P. aeruginosa genomic SpeI fragment E has identified three new genes, fimT, fimU, and dadA*. The predicted 18.5-kDa products of the fimT and fimU genes contain prepilin-like leader sequences, whereas the third gene, dadA*, encodes a protein similar to the D-amino acid dehydrogenase of Escherichia coli. Isogenic mutants constructed by allelic exchange demonstrated that the fimU gene was required for fimbrial biogenesis and twitching motility, whereas the fimT and dada* mutants retained wild-type phenotypes. However, overexpression of the fimT gene was found to be able to functionally replace the lack of a fimU gene product, suggesting a subtle role in fimbrial biogenesis. The identification of these proteins increases the similarity between type 4 fimbrial biogenesis and the supersystems involved in macromolecular traffic, such as extracellular protein secretion and DNA uptake, all of which now possess multiple protein species that possess prepilin-like leader sequences.

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation

Publisher: Springer Science and Business Media LLC

Date: 05-02-2010

DOI: 10.1186/1471-2202-11-14

Abstract: Long non-protein-coding RNAs (ncRNAs) are emerging as important regulators of cellular differentiation and are widely expressed in the brain. Here we show that many long ncRNAs exhibit dynamic expression patterns during neuronal and oligodendrocyte (OL) lineage specification, neuronal-glial fate transitions, and progressive stages of OL lineage elaboration including myelination. Consideration of the genomic context of these dynamically regulated ncRNAs showed they were part of complex transcriptional loci that encompass key neural developmental protein-coding genes, with which they exhibit concordant expression profiles as indicated by both microarray and in situ hybridization analyses. These included ncRNAs associated with differentiation-specific nuclear subdomains such as Gomafu and Neat1 , and ncRNAs associated with developmental enhancers and genes encoding important transcription factors and homeotic proteins. We also observed changes in ncRNA expression profiles in response to treatment with trichostatin A, a histone deacetylase inhibitor that prevents the progression of OL progenitors into post-mitotic OLs by altering lineage-specific gene expression programs. This is the first report of long ncRNA expression in neuronal and glial cell differentiation and of the modulation of ncRNA expression by modification of chromatin architecture. These observations explicitly link ncRNA dynamics to neural stem cell fate decisions, specification and epigenetic reprogramming and may have important implications for understanding and treating neuropsychiatric diseases.

Evidence for a functional association of DNA synthesis with the membrane in mitochondria of Saccharomyces cerevisiae.

Publisher: Springer Science and Business Media LLC

Date: 07-1975

DOI: 10.1007/BF00357539

Probing the phenomics of noncoding RNA Genetic knockout experiments on mice confirm that some long noncoding RNA molecules have developmental functions.

Publisher: eLife Sciences Publications, Ltd

Date: 31-12-2013

DOI: 10.7554/ELIFE.01968

Abstract: Genetic knockout experiments on mice confirm that some long noncoding RNA molecules have developmental functions.

DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements

Publisher: Springer Science and Business Media LLC

Date: 23-06-2013

DOI: 10.1038/NG.2677

Initiating an undiagnosed diseases program in the Western Australian public health system

Publisher: Springer Science and Business Media LLC

Date: 03-05-2017

DOI: 10.1186/S13023-017-0619-Z

Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein-secretion apparatus: a general system for the formation of surface-associated protein complexes.

Publisher: Wiley

Date: 10-1993

DOI: 10.1111/J.1365-2958.1993.TB01949.X

Potential in vivo roles of nucleic acid triple-helices

Publisher: Informa UK Limited

Date: 05-2011

DOI: 10.4161/RNA.8.3.14999

Improved diagnosis and care for rare diseases through implementation of precision public health framework

Publisher: Springer International Publishing

Date: 2017

DOI: 10.1007/978-3-319-67144-4_4

Abstract: Public health relies on technologies to produce and analyse data, as well as effectively develop and implement policies and practices. An ex le is the public health practice of epidemiology, which relies on computational technology to monitor the health status of populations, identify disadvantaged or at risk population groups and thereby inform health policy and priority setting. Critical to achieving health improvements for the underserved population of people living with rare diseases is early diagnosis and best care. In the rare diseases field, the vast majority of diseases are caused by destructive but previously difficult to identify protein-coding gene mutations. The reduction in cost of genetic testing and advances in the clinical use of genome sequencing, data science and imaging are converging to provide more precise understandings of the 'person-time-place' triad. That is: who is affected (people) when the disease is occurring (time) and where the disease is occurring (place). Consequently we are witnessing a paradigm shift in public health policy and practice towards 'precision public health'.Patient and stakeholder engagement has informed the need for a national public health policy framework for rare diseases. The engagement approach in different countries has produced highly comparable outcomes and objectives. Knowledge and experience sharing across the international rare diseases networks and partnerships has informed the development of the Western Australian Rare Diseases Strategic Framework 2015-2018 (RD Framework) and Australian government health briefings on the need for a National plan.The RD Framework is guiding the translation of genomic and other technologies into the Western Australian health system, leading to greater precision in diagnostic pathways and care, and is an ex le of how a precision public health framework can improve health outcomes for the rare diseases population.Five vignettes are used to illustrate how policy decisions provide the scaffolding for translation of new genomics knowledge, and catalyze transformative change in delivery of clinical services. The vignettes presented here are from an Australian perspective and are not intended to be comprehensive, but rather to provide insights into how a new and emerging 'precision public health' paradigm can improve the experiences of patients living with rare diseases, their caregivers and families.The conclusion is that genomic public health is informed by the in idual and family needs, and the population health imperatives of an early and accurate diagnosis which is the portal to best practice care. Knowledge sharing is critical for public health policy development and improving the lives of people living with rare diseases.

Differential Regulation of Twitching Motility and Elastase Production by Vfr in Pseudomonas aeruginosa

Publisher: American Society for Microbiology

Date: 07-2002

DOI: 10.1128/JB.184.13.3605-3613.2002

Abstract: Vfr, a homolog of Escherichia coli cyclic AMP (cAMP) receptor protein, has been shown to regulate quorum sensing, exotoxin A production, and regA transcription in Pseudomonas aeruginosa . We identified a twitching motility-defective mutant that carries a transposon insertion in vfr and confirmed that vfr is required for twitching motility by construction of an independent allelic deletion-replacement mutant of vfr that exhibited the same phenotype, as well as by the restoration of normal twitching motility by complementation of these mutants with wild-type vfr . Vfr-null mutants exhibited severely reduced twitching motility with barely detectable levels of type IV pili, as well as loss of elastase production and altered pyocyanin production. We also identified reduced-twitching variants of quorum-sensing mutants (PAK lasI ::Tc) with a spontaneous deletion in vfr (S. A. Beatson, C. B. Whitchurch, A. B. T. Semmler, and J. S. Mattick, J. Bacteriol., 184:3598-3604, 2002), the net result of which was the loss of five residues (EQERS) from the putative cAMP-binding pocket of Vfr. This allele (VfrΔEQERS) was capable of restoring elastase and pyocyanin production to wild-type levels in vfr -null mutants but not their defects in twitching motility. Furthermore, structural analysis of Vfr and VfrΔEQERS in relation to E. coli CRP suggests that Vfr is capable of binding both cAMP and cyclic GMP whereas VfrΔEQERS is only capable of responding to cAMP. We suggest that Vfr controls twitching motility and quorum sensing via independent pathways in response to these different signals, bound by the same cyclic nucleotide monophosphate-binding pocket.

Orthologous microRNA genes are located in cancer-associated genomic regions in human and mouse.

Publisher: Public Library of Science (PLoS)

Date: 07-11-2007

DOI: 10.1371/JOURNAL.PONE.0001133

The eukaryotic genome as an RNA machine

Publisher: American Association for the Advancement of Science (AAAS)

Date: 28-03-2008

DOI: 10.1126/SCIENCE.1155472

Abstract: The past few years have revealed that the genomes of all studied eukaryotes are almost entirely transcribed, generating an enormous number of non–protein-coding RNAs (ncRNAs). In parallel, it is increasingly evident that many of these RNAs have regulatory functions. Here, we highlight recent advances that illustrate the ersity of ncRNA control of genome dynamics, cell biology, and developmental programming.

RNA driving the epigenetic bus

Publisher: Wiley

Date: 02-2012

DOI: 10.1038/EMBOJ.2011.479

Integrative analysis of 111 reference human epigenomes

Publisher: Springer Science and Business Media LLC

Date: 18-02-2015

DOI: 10.1038/NATURE14248

Publisher: Springer Science and Business Media LLC

Date: 2003

DOI: 10.1186/GB-2003-5-1-P2

RNA editing, DNA recoding and the evolution of human cognition.

Publisher: Elsevier BV

Date: 05-2008

DOI: 10.1016/J.TINS.2008.02.003

Abstract: RNA editing appears to be the major mechanism by which environmental signals overwrite encoded genetic information to modify gene function and regulation, particularly in the brain. We suggest that the predominance of Alu elements in the human genome is the result of their evolutionary co-adaptation as a modular substrate for RNA editing, driven by selection for higher-order cognitive function. We show that RNA editing alters transcripts from loci encoding proteins involved in neural cell identity, maturation and function, as well as in DNA repair, implying a role for RNA editing not only in neural transmission and network plasticity but also in brain development, and suggesting that communication of productive changes back to the genome might constitute the molecular basis of long-term memory and higher-order cognition.

The conservation of dinucleotide microsatellites among mammalian genomes allows the use of heterologous PCR primer pairs in closely related species.

Publisher: Elsevier BV

Date: 07-1991

DOI: 10.1016/0888-7543(91)90448-N

Fimbriae of Bacteroides nodosus: protein engineering of the structural subunit for the production of an exogenous peptide.

Publisher: Oxford University Press (OUP)

Date: 1989

DOI: 10.1093/PROTEIN/2.5.365

Fimbrial biogenesis genes of Pseudomonas aeruginosa: pilW and pilX increase the similarity of type 4 fimbriae to the GSP protein-secretion systems and pilY1 encodes a gonococcal PilC homologue.

Publisher: Wiley

Date: 10-1996

DOI: 10.1111/J.1365-2958.1996.TB02665.X

Prioritising the application of genomic medicine

Publisher: Springer Science and Business Media LLC

Date: 21-11-2017

DOI: 10.1038/S41525-017-0037-0

Abstract: The clinical translation of genomic sequencing is h ered by the limited information available to guide investment into those areas where genomics is well placed to deliver improved health and economic outcomes. To date, genomic medicine has achieved its greatest successes through applications to diseases that have a high genotype–phenotype correlation and high penetrance, with a near certainty that the in idual will develop the condition in the presence of the genotype. It has been anticipated that genomics will play an important role in promoting population health by targeting at-risk in iduals and reducing the incidence of highly prevalent, costly, complex diseases, with potential applications across screening, prevention, and treatment decisions. However, where primary or secondary prevention requires behavioural changes, there is currently very little evidence to support reduction in disease incidence. A better understanding of the relationship between genomic variation and complex diseases will be necessary before effective genomic risk identification and management of the risk of complex diseases in healthy in iduals can be carried out in clinical practice. Our recommended approach is that priority for genomic testing should focus on diseases where there is strong genotype–phenotype correlation, high or certain penetrance, the effects of the disease are serious and near-term, there is the potential for prevention and/or treatment, and the net costs incurred are acceptable for the health gains achieved.

PilS and PilR, a two-component transcriptional regulatory system controlling expression of type 4 fimbriae in Pseudomonas aeruginosa.

Publisher: Wiley

Date: 03-1993

DOI: 10.1111/J.1365-2958.1993.TB01158.X

Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data

Publisher: Cold Spring Harbor Laboratory

Date: 05-2012

DOI: 10.1101/GR.130237.111

Abstract: Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand in its major groove. This sequence-specific process offers a potent mechanism for targeting genomic loci of interest that is of great value for biotechnological and gene-therapeutic applications. It is likely that nature has leveraged this addressing system for gene regulation, because computational studies have uncovered an abundance of putative triplex target sites in various genomes, with enrichment particularly in gene promoters. However, to draw a more complete picture of the in vivo role of triplexes, not only the putative targets but also the sequences acting as the third strand and their capability to pair with the predicted target sites need to be studied. Here we present Triplexator, the first computational framework that integrates all aspects of triplex formation, and showcase its potential by discussing research ex les for which the different aspects of triplex formation are important. We find that chromatin-associated RNAs have a significantly higher fraction of sequence features able to form triplexes than expected at random, suggesting their involvement in gene regulation. We furthermore identify hundreds of human genes that contain sequence features in their promoter predicted to be able to form a triplex with a target within the same promoter, suggesting the involvement of triplexes in feedback-based gene regulation. With focus on biotechnological applications, we screen mammalian genomes for high-affinity triplex target sites that can be used to target genomic loci specifically and find that triplex formation offers a resolution of ∼1300 nt.

Characterization of pilQ, a new gene required for the biogenesis of type 4 fimbriae in Pseudomonas aeruginosa.

Publisher: Wiley

Date: 08-1993

DOI: 10.1111/J.1365-2958.1993.TB01744.X

MicroRNA regulation of neural plasticity and memory

Publisher: Elsevier BV

Date: 07-2011

DOI: 10.1016/J.NLM.2011.04.004

Abstract: MicroRNAs (miRNAs) are a class of endogenous, small non-coding RNAs that mediate post-transcriptional gene silencing by complementary binding to the 3'untranslated region of target mRNAs. The transient and localized expression of these small RNAs in dendrites, their capacity to respond in an activity-dependent manner, and the observation that a single miRNA can simultaneously regulate many genes, make brain-specific miRNAs ideal candidates for the fine-tuning of gene expression associated with neural plasticity and memory formation. Here we provide an overview of the current literature, which supports the proposal that non-coding RNA-mediated regulation of gene function represents an important, yet underappreciated, layer of epigenetic control that contributes to learning and memory in the adult brain.

Conservation of the regulatory subunit for the Clp ATP-dependent protease in prokaryotes and eukaryotes.

Publisher: Proceedings of the National Academy of Sciences

Date: 05-1990

DOI: 10.1073/PNAS.87.9.3513

Abstract: Bacteria, tomatoes, and trypanosomes all contain genes for a large protein with extensive homology to the regulatory subunit, ClpA, of the ATP-dependent protease of Escherichia coli, Clp. All members of the family have between 756 and 926 amino acids and contain two large regions, of 233 and 192 amino acids, each containing consensus sequences for nucleotide binding. Within these regions there is at least 85% similarity between the most distant members of the family. The high degree of similarity among the ClpA-like proteins suggests that Clp-like proteases are likely to be important participants in energy-dependent proteolysis in prokaryotic and eukaryotic cells.

Has evolution learnt how to learn?

Publisher: EMBO

Date: 07-2009

DOI: 10.1038/EMBOR.2009.135

RNA out of the mist

Publisher: Elsevier BV

Date: 03-2023

DOI: 10.1016/J.TIG.2022.11.001

Charting the unknown epitranscriptome

Publisher: Springer Science and Business Media LLC

Date: 10-05-2017

DOI: 10.1038/NRM.2017.49

Abstract: RNA modifications can alter RNA structure-function relationships and various cellular processes. However, the genomic distribution and biological roles of most RNA modifications remain uncharacterized. Here, we propose using phage display antibody technology and direct sequencing through nanopores to facilitate systematic interrogation of the distribution, location and dynamics of RNA modifications.

Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function

Publisher: Elsevier BV

Date: 2006

DOI: 10.1016/J.TIG.2005.10.003

Abstract: The mammalian transcriptome contains many non-protein-coding RNAs (ncRNAs), but most of these are of unclear significance and lack strong sequence conservation, prompting suggestions that they might be non-functional. However, certain long functional ncRNAs such as Air and Xist are also poorly conserved. In this article, we systematically analyzed the conservation of several groups of functional ncRNAs, including miRNAs, snoRNAs and longer ncRNAs whose function has been either documented or confidently predicted. As expected, miRNAs and snoRNAs were highly conserved. By contrast, the longer functional non-micro, non-sno ncRNAs were much less conserved with many displaying rapid sequence evolution. Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function.

Sequencing and expression of the aroA gene from Dichelobacter nodosus.

Publisher: Elsevier BV

Date: 07-1994

DOI: 10.1016/0378-1119(94)90329-8

Long-term gene expression profile dynamics following cecal ligation and puncture in the rat

Publisher: Elsevier BV

Date: 11-2012

DOI: 10.1016/J.JSS.2012.03.052

Abstract: Despite the fact that the treatment options for septic patients have been significantly improved, the pathophysiologic changes caused by various septic cases have not been well understood. One commonly observed clinical phenomenon is the onset of a polymicrobial infection caused by bacteria that originate in the intestine but enter the peritoneum via translocation from the gut. This triggers a systemic inflammatory response via the innate immune system, which needs to be well characterized. Cecal ligation and puncture (CLP) is considered to be the gold-standard animal model by establishing infection with mixed bacterial flora and necrotic tissue to induce an inflammatory response. The aim of this study is to analyze the long-term gene expression dynamics in the rats subject to CLP in order to characterize the impact of sepsis upon liver function over an 8-d time period. Rats received CLP or its control, sham CLP (SCLP), and then they were sacrificed at 9 am on days 0 (no treatment), 1, 2, 5, and 8 post injury to collect liver s les for microarray analysis. Differentially expressed probe sets in CLP versus SCLP (q value <0.001 and P value <0.001) were combined to form one single matrix, which was then clustered using the approach of "consensus clustering" to identify subsets of transcripts with coherent expression patterns. Finally, the gene expression patterns of the clusters were further transformed into principal components, which account for 65% of the total data. Three major clusters were obtained. The first cluster, which is mainly related to genes of anti-inflammatory response and antioxidative properties, is suppressed early in the CLP condition and later upregulated compared to the SCLP condition. Cluster 2 represents pro-inflammatory responses and signaling, along with amino acid metabolism. Cluster 3 is also associated with pro-inflammatory response. The genes of toll-like receptor signaling and hypermetabolism were identified in this cluster as well. Clusters 2 and 3 are both suppressed in the long-term response following CLP. Clusters 1 and 2 acting in concert return to the time 0 baseline in both groups, indicating resolution of both the anti-inflammatory and pro-inflammatory response however, the SCLP response in cluster 3 shows persistent downregulation. Characterization of long-term hepatic responses to injury is critical to understanding the dynamics of transcriptional changes following the induction of the inflammatory response, and to monitoring its effective resolution. These results showed that each condition has unique dynamics that indicate fundamental differences in the response. Furthermore, the gene ontologies suggest a link to oxidative stress over the long term that may be able to be explored for clinical treatments.

Expression of distinct RNAs from 3′ untranslated regions

Publisher: Oxford University Press (OUP)

Date: 12-11-2010

DOI: 10.1093/NAR/GKQ1158

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Publisher: Cold Spring Harbor Laboratory

Date: 02-11-2010

DOI: 10.1101/GR.112128.110

Abstract: The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5′ capping. Here, we show that post-transcriptional cleavage of RNA contributes to the ersification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage- and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome.

Identification of a gene, pilV, required for type 4 fimbrial biogenesis in Pseudomonas aeruginosa, whose product possesses a pre-pilin-like leader sequence.

Publisher: Wiley

Date: 05-1995

DOI: 10.1111/J.1365-2958.1995.TB02413.X

Dynamic isomiR regulation in Drosophila development.

Publisher: Cold Spring Harbor Laboratory

Date: 30-08-2010

DOI: 10.1261/RNA.2379610

Abstract: Several recent reports have demonstrated that microRNAs (miRNAs) can exhibit heterogeneous ends and post-transcriptional nontemplate 3′ end additions of uridines or adenosines. Using two small RNA deep-sequencing data sets, we show here that these miRNA isoforms (isomiRs) are differentially expressed across Drosophila melanogaster development and tissues. Specifically, we demonstrate that: (1) nontemplate nucleotide additions of adenosines to miRNA 3′ ends are highly abundant in early development (2) a subset of miRNAs with nontemplate 3′ Us are expressed in adult tissues and (3) the size of at least eight “mature” (unmodified) miRNAs varies in a life-cycle or tissue-specific manner. These results suggest that subtle variability in isomiR expression, which is widely thought to be the result of inexact Dicer processing, is regulated and biologically meaningful. Indeed, a subset of the miRNAs enriched for 3′ adenosine additions during early embryonic development, including miR-282 and miR-312, show enrichment for target sites in developmental genes that are expressed during late embryogenesis, suggesting that nontemplate additions increase miRNA stability or strengthen miRNA:target interactions. This work suggests that isomiR expression is an important aspect of miRNA biology, which warrants further investigation.

Non-coding RNAs in the nervous system

Publisher: Wiley

Date: 24-08-2006

DOI: 10.1113/JPHYSIOL.2006.113191

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data.

Publisher: Springer Science and Business Media LLC

Date: 02-2010

DOI: 10.1186/1471-2164-11-77

Abstract: The increasing interest in small non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs) and recent advances in sequencing technology have yielded large numbers of short (18-32 nt) RNA sequences from different organisms, some of which are derived from small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs). We observed that these short ncRNAs frequently cover the entire length of annotated snoRNAs or tRNAs, which suggests that other loci specifying similar ncRNAs can be identified by clusters of short RNA sequences. We combined publicly available datasets of tens of millions of short RNA sequence tags from Drosophila melanogaster , and mapped them to the Drosophila genome. Approximately 6 million perfectly mapping sequence tags were then assembled into 521,302 tag-contigs (TCs) based on tag overlap. Most transposon-derived sequences, exons and annotated miRNAs, tRNAs and snoRNAs are detected by TCs, which show distinct patterns of length and tag-depth for different categories. The typical length and tag-depth of snoRNA-derived TCs was used to predict 7 previously unrecognized box H/ACA and 26 box C/D snoRNA candidates. We also identified one snRNA candidate and 86 loci with a high number of tags that are yet to be annotated, 7 of which have a particular 18mer motif and are located in introns of genes involved in development. A subset of new snoRNA candidates and putative ncRNA candidates was verified by Northern blot. In this study, we have introduced a new approach to identify new members of known classes of ncRNAs based on the features of TCs corresponding to known ncRNAs. A large number of the identified TCs are yet to be examined experimentally suggesting that many more novel ncRNAs remain to be discovered.

Intergenic disease-associated regions are abundant in novel transcripts

Publisher: Springer Science and Business Media LLC

Date: 12-2017

DOI: 10.1186/S13059-017-1363-3

Extragenic suppressor mutations that restore twitching motility to fimL mutants of Pseudomonas aeruginosa are associated with elevated intracellular cyclic AMP levels

Publisher: Wiley

Date: 28-11-2012

DOI: 10.1002/MBO3.49

NRED: A database of long noncoding RNA expression

Publisher: Oxford University Press (OUP)

Date: 10-2009

DOI: 10.1093/NAR/GKN617

SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer.

Publisher: Cold Spring Harbor Laboratory

Date: 04-2011

DOI: 10.1261/RNA.2528811

Abstract: Long noncoding RNAs (lncRNAs) are increasingly recognized to play major regulatory roles in development and disease. To identify novel regulators in breast biology, we identified differentially regulated lncRNAs during mouse mammary development. Among the highest and most differentially expressed was a transcript ( Zfas1 ) antisense to the 5′ end of the protein-coding gene Znfx1 . In vivo, Zfas1 RNA is localized within the ducts and alveoli of the mammary gland. Zfas1 intronically hosts three previously undescribed C/D box snoRNAs (SNORDs): Snord12 , Snord12b , and Snord12c . In contrast to the general assumption that noncoding SNORD-host transcripts function only as vehicles to generate snoRNAs, knockdown of Zfas1 in a mammary epithelial cell line resulted in increased cellular proliferation and differentiation, while not substantially altering the levels of the SNORDs. In support of an independent function, we also found that Zfas1 is extremely stable, with a half-life h. Expression analysis of the SNORDs revealed these were expressed at different levels, likely a result of distinct structures conferring differential stability. While there is relatively low primary sequence conservation between Zfas1 and its syntenic human ortholog ZFAS1 , their predicted secondary structures have similar features. Like Zfas1 , ZFAS1 is highly expressed in the mammary gland and is down-regulated in breast tumors compared to normal tissue. We propose a functional role for Zfas1/ ZFAS1 in the regulation of alveolar development and epithelial cell differentiation in the mammary gland, which, together with its dysregulation in human breast cancer, suggests ZFAS1 as a putative tumor suppressor gene.

Stoichiometry based steady-state hepatic flux analysis: computational and experimental aspects.

Publisher: MDPI AG

Date: 14-03-2012

DOI: 10.3390/METABO2010268

The Human Mitochondrial Transcriptome

Publisher: Elsevier BV

Date: 08-2011

DOI: 10.1016/J.CELL.2011.06.051

Garvan Institute Of Medical Research

Location: Australia

View Organisation

University Of New South Wales

Location: Australia

View Organisation

Discovery Projects - Grant ID: DP0346653

Start Date: 2003

End Date: 12-2005

Amount: $225,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP120100729

Start Date: 2012

End Date: 03-2015

Amount: $500,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0667246

Start Date: 2006

End Date: 12-2008

Amount: $455,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0988851

Start Date: 2009

End Date: 09-2012

Amount: $600,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0343598

Start Date: 2003

End Date: 12-2007

Amount: $195,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP210103233

Start Date: 06-2021

End Date: 12-2024

Amount: $649,910.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0348038

Start Date: 2003

End Date: 08-2006

Amount: $240,000.00

Funder: Australian Research Council

ARC Centres Of Excellence - Grant ID: CE0348205

Start Date: 2003

End Date: 12-2010

Amount: $5,271,140.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0775726

Start Date: 02-2007

End Date: 02-2008

Amount: $306,270.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0988754

Start Date: 2009

End Date: 12-2011

Amount: $460,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP120103828

Start Date: 2012

End Date: 06-2016

Amount: $480,000.00

Funder: Australian Research Council

Special Research Initiatives - Grant ID: SR0354861

Start Date: 03-2004

End Date: 10-2004

Amount: $15,000.00

Funder: Australian Research Council

Federation Fellowships - Grant ID: FF0561986

Start Date: 12-2005

End Date: 12-2010

Amount: $1,551,625.00

Funder: Australian Research Council

Special Research Initiatives - Grant ID: SR0354610

Start Date: 12-2003

End Date: 12-2004

Amount: $10,000.00

Funder: Australian Research Council