ORCID Profile
0000-0002-4689-8747
Current Organisation
UNSW Sydney
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Genetics | Developmental Genetics (incl. Sex Determination) | Genomics | Gene Expression | Genome Structure | Molecular Evolution | Epigenetics (incl. Genome Methylation and Epigenomics) | Evolution of Developmental Systems | Gene Expression (incl. Microarray and other genome-wide approaches) | Genome Structure and Regulation |
Expanding Knowledge in the Biological Sciences | Biological sciences | Effects of Climate Change and Variability on Australia (excl. Social Impacts) | Expanding Knowledge in the Environmental Sciences | Expanding Knowledge in the Agricultural and Veterinary Sciences | Expanding Knowledge in the Medical and Health Sciences
Publisher: Springer Science and Business Media LLC
Date: 08-11-2008
DOI: 10.1007/S10577-008-1266-Y
Abstract: Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two chromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and 'neo-X' regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.
Publisher: Springer Netherlands
Date: 2010
Publisher: Public Library of Science (PLoS)
Date: 25-04-2011
Publisher: Springer Science and Business Media LLC
Date: 06-06-2019
Publisher: Springer Netherlands
Date: 2010
Publisher: Cold Spring Harbor Laboratory
Date: 23-11-2019
DOI: 10.1101/851949
Abstract: Brain derived neurotrophic factor (BDNF) is critical for the extinction of drug-seeking. Expression of the Bdnf gene is highly regulated via interactions with non-coding RNA, which themselves are altered following drug exposure. Here we investigate whether a novel long non-coding RNA antisense to Bdnf prevents extinction of drug-seeking. METHODS: Strand-specific RNA sequencing identified a novel long non-coding RNA antisense to exon IV of the Bdnf gene in the ventromedial prefrontal cortex of 8 adult male rats. We then assessed asBdnf-IV expression using strand-specific reverse transcription and quantitative polymerase chain reaction following acquisition, extinction or abstinence from intravenous nicotine self-administration (N = 116). A functional role of the asBdnf-IV in extinction of nicotine-seeking was established by infusing gapmer oligonucleotides into the infralimbic cortex prior to extinction and testing for the effect of these infusions on reinstatement and reacquisition of nicotine-seeking (N = 36). RNA sequencing identified the presence of a novel long non-coding RNA antisense to exon IV of the Bdnf gene ( asBdnf-IV ). Expression of asBdnf-IV was elevated following intravenous nicotine self-administration but not experimenter-administered nicotine. Elevated asBdnf-IV persisted across abstinence and to a greater extent following extinction training, suggesting an interaction between abstinence and extinction learning. In support of this, knockdown of the asBdnf-IV across extinction, but not abstinence, significantly attenuated nicotine-primed reinstatement of nicotine-seeking. asBdnf-IV accumulates in the infralimbic cortex across self-administration training, interferes with the inhibitory learning that underpins extinction of drug-seeking, and predisposes animals to drug relapse.
Publisher: Elsevier BV
Date: 06-2022
Publisher: Springer Science and Business Media LLC
Date: 06-2005
DOI: 10.1007/S10577-005-0978-5
Abstract: Mammalian sex chromosomes evolved from an ancient autosomal pair. Mapping of human X- and Y-borne genes in distantly related mammals and non-mammalian vertebrates has proved valuable to help deduce the evolution of this unique part of the genome. The platypus, a monotreme mammal distantly related to eutherians and marsupials, has an extraordinary sex chromosome system comprising five X and five Y chromosomes that form a translocation chain at male meiosis. The largest X chromosome (X1), which lies at one end of the chain, has considerable homology to the human X. Using comparative mapping and the emerging chicken database, we demonstrate that part of the therian X chromosome, previously thought to be conserved across all mammals, was lost from the platypus X1 to an autosome. This region included genes flanking the XIST locus, and also genes with Y-linked homologues that are important to male reproduction in therians. Since these genes lie on the X in marsupials and eutherians, and also on the homologous region of chicken chromosome 4, this represents a loss from the monotreme X rather than an additional evolutionary stratum of the human X.
Publisher: CSIRO Publishing
Date: 2009
DOI: 10.1071/RD09250
Abstract: In vertebrates, a highly conserved pathway of genetic events controls male and female development, to the extent that many genes involved in human sex determination are also involved in fish sex determination. Surprisingly, the master switch to this pathway, which intuitively could be considered the most critical step, is inconsistent between vertebrate taxa. Interspersed in the vertebrate tree there are species that determine sex by environmental cues such as the temperature at which eggs are incubated, and then there are genetic sex-determination systems, with male heterogametic species (XY systems) and female heterogametic species (ZW systems), some of which have heteromorphic, and others homomorphic, sex chromosomes. This plasticity of sex-determining switches in vertebrates has made tracking the events of sex chromosome evolution in amniotes a daunting task, but comparative gene mapping is beginning to reveal some striking similarities across even distant taxa. In particular, the recent completion of the platypus genome sequence has completely changed our understanding of when the therian mammal X and Y chromosomes first arose (they are up to 150 million years younger than previously thought) and has also revealed the unexpected insight that sex determination of the amniote ancestor might have been controlled by a bird-like ZW system.
Publisher: Springer Science and Business Media LLC
Date: 12-2009
DOI: 10.1007/S10577-009-9102-6
Abstract: Reptiles show a erse array of sex chromosomal systems but, remarkably, the Z sex chromosomes of chicken are homologous to the ZW sex chromosomes of a species of gecko, Gekko hokouensis, suggesting an ancient but common origin. This is in contrast to the ZW sex chromosomes of snakes and a species of soft-shelled turtle, Pelodiscus sinensis, which are nonhomologous to those of chicken or each other and appear to have been independently derived. In this paper, we determine what homology, if any, the sex chromosomes of the Australian dragon lizard Pogona vitticeps shares with those of snake and chicken by mapping the dragon homologs of five snake Z chromosome genes (WAC, KLF6, TAX1BP1, RAB5A, and CTNNB1) and five chicken Z chromosome genes (ATP5A1, GHR, DMRT1, CHD1, and APTX) to chromosomes in the dragon. The dragon homologs of snake and chicken sex chromosome genes map to chromosomes 6 and chromosome 2, respectively, in the dragon and that DMRT1, the bird sex-determining gene, is not located on the sex chromosomes of P. vitticeps. Indeed, our data show that the dragon homolog to the chicken Z chromosome is likely to be wholly contained within chromosome 2 in P. vitticeps, which suggests that the sex-determining factor in P. vitticeps is not the sex-determining gene of chicken. Homology between chicken Z chromosome and G. hokouensis ZW chromosome pairs has been interpreted as retention of ancient ZW sex chromosomes in which case the nonhomologous sex chromosomes of snake and dragons would be independently derived. Our data add another case of independently derived sex chromosomes in a squamate reptile, which makes retention of ancient sex chromosome homology in the squamates less plausible. Alternatively, the conservation between the bird Z chromosome and the G. hokouensis ZW chromosomes pairs is coincidental, may be an ex le of convergent evolution, its status as the Z chromosome having been independently derived in birds and G. hokouensis.
Publisher: Cold Spring Harbor Laboratory
Date: 13-05-2009
Abstract: Comparative gene mapping of human X-borne genes in marsupials defined an ancient conserved region and a recently added region of the eutherian X, and the separate evolutionary origins of these regions was confirmed by their locations on chicken chromosomes 4p and 1q, respectively. However, two groups of genes, from the pericentric region of the short arm of the human X (at Xp11) and a large group of genes from human Xq28, were thought to be part of a third evolutionary block, being located in a single region in fish, but mapping to chicken chromosomes other than 4p and 1q. We tested this hypothesis by comparative mapping of genes in these regions. Our gene mapping results show that human Xp11 genes are located on the marsupial X chromosome and platypus chromosome 6, indicating that the Xp11 region was part of original therian X chromosome. We investigated the evolutionary origin of genes from human Xp11 and Xq28, finding that chicken paralogs of human Xp11 and Xq28 genes had been misidentified as orthologs, and their true orthologs are represented in the chicken EST database, but not in the current chicken genome assembly. This completely undermines the evidence supporting a separate evolutionary origin for this region of the human X chromosome, and we conclude, instead, that it was part of the ancient autosome, which became the conserved region of the therian X chromosome 166 million years ago.
Publisher: Springer Science and Business Media LLC
Date: 29-07-2004
DOI: 10.1007/S00412-004-0301-9
Abstract: Long interspersed nuclear elements (LINEs) comprise about 21% of the human genome (of which L1 is most abundant) and are preferentially accumulated in AT-rich regions, as well as the X and Y chromosomes. Most knowledge of L1 distribution in mammals is restricted to human and mouse. Here we report the first investigation of L1 distribution in the genomes of a wide variety of eutherian mammals, including species in the two basal clades, Afrotheria and Xenarthra. Our results show L1 accumulation on the X of all eutherian mammals, an observation consistent with an ancestral involvement of these elements in the X-inactivation process (the Lyon repeat hypothesis). Surprisingly, conspicuous accumulation of L1 in AT-rich regions of the genome was not observed in any species outside of Euarchontoglires (represented by human, mouse and rabbit). Although several features were common to most species investigated, our comprehensive survey shows that the patterns observed in human and mouse are, in many aspects, far from typical for all mammals. We discuss these findings with reference to models that have previously been proposed to explain the AT distribution bias of L1 in human and mouse, and how this relates to the evolution of these elements in other eutherian genomes.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 02-06-2017
Abstract: Alternative splicing in chromatin-modifying genes is associated with temperature-dependent sex in ergent reptile lineages.
Publisher: Springer Science and Business Media LLC
Date: 20-10-2020
DOI: 10.1038/S41598-020-73706-9
Abstract: Hibernation is a physiological state employed by many animals that are exposed to limited food and adverse winter conditions. Controlling tissue-specific and organism wide changes in metabolism and cellular function requires precise regulation of gene expression, including by microRNAs (miRNAs). Here we profile miRNA expression in the central bearded dragon ( Pogona vitticeps ) using small RNA sequencing of brain, heart, and skeletal muscle from in iduals in late hibernation and four days post-arousal. A total of 1295 miRNAs were identified in the central bearded dragon genome 664 of which were novel to central bearded dragon. We identified differentially expressed miRNAs (DEmiRs) in all tissues and correlated mRNA expression with known and predicted target mRNAs. Functional analysis of DEmiR targets revealed an enrichment of differentially expressed mRNA targets involved in metabolic processes. However, we failed to reveal biologically relevant tissue-specific processes subjected to miRNA-mediated regulation in heart and skeletal muscle. In brain, neuroprotective pathways were identified as potential targets regulated by miRNAs. Our data suggests that miRNAs are necessary for modulating the shift in cellular metabolism during hibernation and regulating neuroprotection in the brain. This study is the first of its kind in a hibernating reptile and provides key insight into this ephemeral phenotype.
Publisher: Cold Spring Harbor Laboratory
Date: 07-07-2021
DOI: 10.1101/2021.07.06.451394
Abstract: Microchromosomes, once considered unimportant shreds of the chicken genome, are gene rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds, and share synteny with single small chromosomes of the chordate hioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time surprisingly de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently multiple rearrangements fueled the extraordinary karyotypic ersity of therian mammals. Thus microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles, that are atypical. Genomes of birds and reptiles, but not mammals, consist of a few large chromosomes and many tiny microchromosomes. Once considered unimportant shreds of the genome, microchromosomes are gene rich and highly conserved among bird and reptiles, and share homology with one or more of the tiny chromosomes of an invertebrate that erged from the vertebrate lineage 684 million years ago. Microchromosomes interact strongly and crowd together at the centre of cells, suggesting functional coherence. Many microchromosomes have been lost independently in turtles, snakes and lizards as they have fused with each other, or with larger chromosomes. In mammals they have completely disappeared, yet some chromosomes of the basal platypus line up with several microchromosomes, suggesting that they are the building blocks of the atypically variable chromosomes of mammals.
Publisher: Springer Science and Business Media LLC
Date: 27-02-2013
Abstract: There is growing recognition that horizontal DNA transfer, a process known to be common in prokaryotes, is also a significant source of genomic variation in eukaryotes. Horizontal transfer of transposable elements (HTT) may be especially prevalent in eukaryotes given the inherent mobility, widespread occurrence, and prolific abundance of these elements in many eukaryotic genomes. Here, we provide evidence for a new case of HTT of the transposon family OposCharlie1 (OC1) in the Tasmanian devil, Sarcophilus harrisii. Bioinformatic analyses of OC1 sequences in the Tasmanian devil genome suggest that this transposon infiltrated the common ancestor of the Dasyuridae family ~17 million years ago. This estimate is corroborated by a PCR-based screen for the presence/absence of this family in Tasmanian devils and closely-related species. This case of HTT is the first to be reported in dasyurids. It brings the number of animal lineages independently invaded by OC1 to 12, and adds a fourth continent to the pandemic-like pattern of invasion of this transposon. In the context of these data, we discuss the evolutionary history of this transposon family and its potential impact on the ersification of marsupials.
Publisher: Springer Science and Business Media LLC
Date: 17-10-2023
Publisher: Springer Science and Business Media LLC
Date: 12-2014
Publisher: Springer Science and Business Media LLC
Date: 29-03-2015
DOI: 10.1007/S10048-015-0445-1
Abstract: Pervasive transcription of the genome produces a erse array of functional non-coding RNAs (ncRNAs). One particular class of ncRNAs, long intervening non-coding RNAs (lincRNAs) are thought to play a role in regulating gene expression and may be a major contributor to organism and tissue complexity. The human brain with its heterogeneous cellular make-up is a rich source of lincRNAs however, the functions of the majority of lincRNAs are unknown. Recently, by completing RNA sequencing (RNA-Seq) of the human frontal cortex, we identified linc00320 as being highly expressed in the white matter compared to grey matter in multiple system atrophy (MSA) brain. Here, we further investigate the expression patterns of linc00320 and conclude that it is involved in specific brain regions rather than having involvement in the MSA disease process. We also show that the full-length linc00320 is only expressed in human brain tissue and not in other primates, suggesting that it may be involved in improved functional connectivity for higher human brain cognition.
Publisher: Springer Science and Business Media LLC
Date: 30-09-2009
DOI: 10.1007/S10577-009-9079-1
Abstract: All therian mammals (eutherians and marsupials) have an XX female/XY male sex chromosome system or some variant of it. The X and Y evolved from a homologous pair of autosomes over the 166 million years since therian mammals erged from monotremes. Comparing the sex chromosomes of eutherians and marsupials defined an ancient X conserved region that is shared between species of these mammalian clades. However, the eutherian X (and the Y) was augmented by a recent addition (XAR) that is autosomal in marsupials. XAR is part of the X in primates, rodents, and artiodactyls (which belong to the eutherian clade Boreoeutheria), but it is uncertain whether XAR is part of the X chromosome in more distantly related eutherian mammals. Here we report on the gene content and order on the X of the elephant (Loxodonta africana)-a representative of Afrotheria, a basal endemic clade of African mammals-and compare these findings to those of other documented eutherian species. A total of 17 genes were mapped to the elephant X chromosome. Our results support the hypothesis that the eutherian X and Y chromosomes were augmented by the addition of autosomal material prior to eutherian radiation. Not only does the elephant X bear the same suite of genes as other eutherian X chromosomes, but gene order appears to have been maintained across 105 million years of evolution, perhaps reflecting strong constraints posed by the eutherian X inactivation system.
Publisher: Springer Science and Business Media LLC
Date: 02-07-2018
Publisher: Public Library of Science (PLoS)
Date: 17-01-2007
Publisher: Proceedings of the National Academy of Sciences
Date: 11-2021
Abstract: Genomes of birds and reptiles, but not mammals, consist of a few large chromosomes and many tiny microchromosomes. Microchromosomes are gene-rich and highly conserved among birds and reptiles and share homology with one or more of the tiny chromosomes of an invertebrate that erged from the vertebrate lineage 684 Ma. Microchromosomes interact strongly and crowd together at the center of cells, suggesting functional coherence. Many microchromosomes have been lost independently in turtles, snakes, and lizards as they have fused with each other or with larger chromosomes. In mammals they have completely disappeared, yet some chromosomes of the basal platypus line up with several microchromosomes, suggesting that they are the building blocks of the atypically variable chromosomes of mammals.
Publisher: Springer Science and Business Media LLC
Date: 05-2006
DOI: 10.1007/S10709-005-2483-3
Abstract: Genomic stress resulting from the interspecific hybridization of marsupials has been shown to lead to hypomethylation and transposable element over- lification. Here we investigated both methylation status and transposable element (LINE-1) activity in an F1 hybrid between the black (Diceros bicornis) and white rhinoceros (Ceratotherium simum). Our data show that in this instance the hybrid genome was not characterised by gross hypomethylation and LINE-1 over- lification thus extending previous investigations on eutherian mammals. These findings underscore observations that wide-scale genomic instability involving hypomethylation and mobile element release may be marsupial specific phenomena within Mammalia.
Publisher: Public Library of Science (PLoS)
Date: 18-07-2013
Publisher: Oxford University Press (OUP)
Date: 28-09-2015
Publisher: Springer Science and Business Media LLC
Date: 12-2007
DOI: 10.1007/S10577-007-1185-3
Abstract: In eutherian ('placental') mammals, sex is determined by the presence or absence of the Y chromosome-borne gene SRY, which triggers testis determination. Marsupials also have a Y-borne SRY gene, implying that this mechanism is ancestral to therians, the SRY gene having erged from its X-borne homologue SOX3 at least 180 million years ago. The rare exceptions have clearly lost and replaced the SRY mechanism recently. Other vertebrate classes have a variety of sex-determining mechanisms, but none shares the therian SRY-driven XX female:XY male system. In monotreme mammals (platypus and echidna), which branched from the therian lineage 210 million years ago, no orthologue of SRY has been found. In this study we show that its partner SOX3 is autosomal in platypus and echidna, mapping among human X chromosome orthologues to platypus chromosome 6, and to the homologous chromosome 16 in echidna. The autosomal localization of SOX3 in monotreme mammals, as well as non-mammal vertebrates, implies that SRY is absent in Prototheria and evolved later in the therian lineage 210-180 million years ago. Sex determination in platypus and echidna must therefore depend on another male-determining gene(s) on the Y chromosomes, or on the different dosage of a gene(s) on the X chromosomes.
Publisher: Springer Science and Business Media LLC
Date: 12-2007
DOI: 10.1007/S10577-007-1187-1
Abstract: The genomes of the egg-laying platypus and echidna are of particular interest because monotremes are the most basal mammal group. The chromosomal distribution of an ancient family of short interspersed repeats (SINEs), the core-SINEs, was investigated to better understand monotreme genome organization and evolution. Previous studies have identified the core-SINE as the predominant SINE in the platypus genome, and in this study we quantified, characterized and localized subfamilies. Dot blot analysis suggested that a very large fraction (32% of the platypus and 16% of the echidna genome) is composed of Mon core-SINEs. Core-SINE-specific primers were used to lify PCR products from platypus and echidna genomic DNA. Sequence analysis suggests a common consensus sequence Mon 1-B, shared by platypus and echidna, as well as platypus-specific Mon 1-C and echidna specific Mon 1-D consensus sequences. FISH mapping of the Mon core-SINE products to platypus metaphase spreads demonstrates that the Mon-1C subfamily is responsible for the striking Mon core-SINE accumulation in the distal regions of the six large autosomal pairs and the largest X chromosome. This unusual distribution highlights the dichotomy between the seven large chromosome pairs and the 19 smaller pairs in the monotreme karyotype, which has some similarity to the macro- and micro-chromosomes of birds and reptiles, and suggests that accumulation of repetitive sequences may have enlarged small chromosomes in an ancestral vertebrate. In the forthcoming sequence of the platypus genome there are still large gaps, and the extensive Mon core-SINE accumulation on the distal regions of the six large autosomal pairs may provide one explanation for this missing sequence.
Publisher: Cold Spring Harbor Laboratory
Date: 07-05-2008
DOI: 10.1101/GR.7101908
Abstract: In therian mammals (placentals and marsupials), sex is determined by an XX female: XY male system, in which a gene ( SRY ) on the Y affects male determination. There is no equivalent in other amniotes, although some taxa (notably birds and snakes) have differentiated sex chromosomes. Birds have a ZW female: ZZ male system with no homology with mammal sex chromosomes, in which dosage of a Z-borne gene (possibly DMRT1 ) affects male determination. As the most basal mammal group, the egg-laying monotremes are ideal for determining how the therian XY system evolved. The platypus has an extraordinary sex chromosome complex, in which five X and five Y chromosomes pair in a translocation chain of alternating X and Y chromosomes. We used physical mapping to identify genes on the pairing regions between adjacent X and Y chromosomes. Most significantly, comparative mapping shows that, contrary to earlier reports, there is no homology between the platypus and therian X chromosomes. Orthologs of genes in the conserved region of the human X (including SOX3 , the gene from which SRY evolved) all map to platypus chromosome 6, which therefore represents the ancestral autosome from which the therian X and Y pair derived. Rather, the platypus X chromosomes have substantial homology with the bird Z chromosome (including DMRT1 ) and to segments syntenic with this region in the human genome. Thus, platypus sex chromosomes have strong homology with bird, but not to therian sex chromosomes, implying that the therian X and Y chromosomes (and the SRY gene) evolved from an autosomal pair after the ergence of monotremes only 166 million years ago. Therefore, the therian X and Y are more than 145 million years younger than previously thought.
Publisher: Springer Science and Business Media LLC
Date: 05-2008
DOI: 10.1038/NATURE06936
Publisher: MDPI AG
Date: 05-2018
DOI: 10.3390/GENES9050230
Publisher: Cold Spring Harbor Laboratory
Date: 16-05-2019
Abstract: The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analog of eutherian Xist . Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity. However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist , these repeat domains are known to be critical for function. Using k -mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of nonlinear sequence similarity. Xist Repeats B, C, and D were most similar to each other and to Rsx Repeat 1, whereas Xist Repeats A and E were most similar to each other and to Rsx Repeats 2, 3, and 4. Similarities at the level of k -mers corresponded to domain-specific enrichment of protein-binding motifs. Within in idual domains, protein-binding motifs were often enriched to extreme levels. Our data support the hypothesis that Xist and Rsx encode similar functions through different spatial arrangements of functionally analogous protein-binding domains. We propose that the two clusters of repeat domains in Xist and Rsx function in part to cooperatively recruit PRC1 and PRC2 to chromatin. The physical manner in which these domains engage with protein cofactors may be just as critical to the function of the domains as the protein cofactors themselves. The general approaches we outline in this report should prove useful in the study of any set of RNAs.
Publisher: S. Karger AG
Date: 2003
DOI: 10.1159/000076317
Publisher: Springer Science and Business Media LLC
Date: 05-2007
DOI: 10.1038/NATURE05805
Abstract: We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to ersification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the ergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
Publisher: Springer Science and Business Media LLC
Date: 20-12-2007
DOI: 10.1007/S00412-007-0140-6
Abstract: We describe the outcome of a comprehensive cytogenetic survey of the common mole-rat, Cryptomys hottentotus, based on G and C banding, fluorescence in situ hybridisation and the analysis of meiotic chromosomes using immunostaining of proteins involved in the formation of synaptonemal complex (SCP1 and SCP3). We identified the presence of a Y-autosome translocation that is responsible for a fixed diploid number difference between males (2n = 53) and females (2n = 54), a character that likely defines the C. hottentotus lineage. Immunostaining, combined with C banding of spermatocytes, revealed a linearised sex trivalent with X(1) at one end and X(2) at the other, with evidence of reduced recombination between Y and X(2) that seems to be heterochromatin dependant in the C. hottentotus lineage. We suggest that this could depict the likely initial step in the differentiation of a true neo-X, and that this may mimic an early stage in the mammalian meiotic chain formation, an evolutionary process that has been taken to an extreme in a monotreme mammal, the platypus.
Publisher: Elsevier BV
Date: 12-2008
DOI: 10.1016/J.GENE.2008.08.013
Abstract: SINEs retrotranspose using their partner LINE's enzymatic machinery. It has recently been proposed that AfroSINEs ending with GGTTT 3' tandem repeats were mobilized by RTE elements ending with CAA 3' tandem repeats in the Afrotherian genome. Using sequences from the elephant genome, we show that AfroSINEs derive from RTE ending with GGTTT-like 3' tandem repeats, a subgroup of RTE1_LA that only reached low copy number, and confirm that they were most likely mobilized by RTE ending with CAA(n) tandem repeats (RTE1_LA-CAA(n)). This partnership is supported by sequence similarity between two regions of the elements, overlap in the timing of their activity, common features of their target site consensus that are not shared by other members of the RTE family, and their high copy number. Detailed analyses of pre-insertion loci reveal that like many other apurinic/apyrimidinic endonuclease encoding elements, RTE1_LA-CAA(n) shows loose target site specificity. In addition, the RTE1_LA-CAA(n) target site consensus shares several structural and primary sequence features with that of LINE1, suggesting that these two elements share close functional similarity in the target primed reverse transcription (TPRT) reaction. Interestingly, although globally similar, the target site consensus of AfroSINE(Anc) and RTE1_LA-CAA(n) differ in several aspects. These differences, not observed among all SINE/LINE pairs so far examined, are most likely due to the fact that AfroSINEs and RTE1_LA-CAA(n) are terminated by a different tandem repeat motif. We propose that these differences reflect constraints imposed by base pairing interactions between the mRNA 3' terminal tandem repeats and the target DNA at the onset of TPRT. So in addition to the endonuclease nicking preference, the mRNA of these elements appears to play an important role in integration site choice through a passive, post-nicking, selective process.
Publisher: Wiley
Date: 15-09-2017
Publisher: Humana Press
Date: 2008
DOI: 10.1007/978-1-59745-581-7_14
Abstract: Long-interspersed nuclear element-1 (LINE-1) is a non-terminal repeat transposon that constitutes a major component of the mammalian genome. LINE-1 has a dynamic evolutionary history characterized by the rise, fall, and replacement of subfamilies. The distribution of LINE-1 elements can be viewed from a chromosomal perspective using fluorescence in-situ hybridization (FISH), as well as at the sequence level. We have designed LINE-1 primers from regions conserved among mouse, rat, rabbit, and human L1, which were able to lify part of ORF2 from all eutherian (placental) mammals tested thus far. The product generated can be used as a FISH painting probe to examine the genomic distribution of L1 in different species. It can also be cloned and sequenced for phylogenetic analysis. Although FISH patterns resulting from LINE-1 chromosome painting and bioinformatic analyses have shown that this element accumulates in AT-rich regions of the genomes of mouse and human, our PCR lified LINE-1 probe suggests that this is not a universal phenomenon, and that the patterns displayed in laurasiatherian, afrotherian and xenarthran species are less prominent. The "banding" like distribution of LINE-1 observed in human and mouse, therefore, appears to reflect aspects of genome architecture unique to Euarchontoglires (Supraprimates), the superordinal clade to which they belong. By sequencing the cloned licons used for FISH experiments and supplementing these with L1 sequences obtained from public databases, analysis by parsimony, distance-based, maximum likelihood, and "hierarchical Bayesian" or "marginal likelihood" methods provides a powerful adjunct to the FISH data. Using this approach, relatively intact LINE-1 from most placental orders tend to reflect accepted eutherian evolutionary relationships. This suggests that there were often only closely related copies active near branch points in the tree, that inactive copies tended to become extinct quite readily, and that for many orders recently active copies belong to a single lineage of this LINE.
Publisher: Springer Science and Business Media LLC
Date: 08-2011
DOI: 10.1007/S10577-011-9227-2
Abstract: The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus using chromosome banding, cross-species painting (Zoo-fluorescent in situ hybridization or FISH) and BAC-FISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for ex le, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BAC-mapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology.
Publisher: Humana Press
Date: 2008
DOI: 10.1007/978-1-59745-581-7_15
Abstract: Comparative molecular cytogenetics provides a powerful tool for deciphering the evolutionary history of vertebrate sex chromosomes. We have adapted cell culture and molecular cytogenetic techniques to study the sex chromosomes of many exotic mammals, birds, and reptiles. Here we describe differential chromosome banding and staining techniques that distinguish sex chromosomes in species with no morphologically distinct XY or ZW chromosome pairs. We describe a method to isolate, identify, and map genomic BAC clones from the Y chromosome, and we also identify strategies for isolating candidate sex chromosome genes.
Publisher: Wiley
Date: 10-08-2015
Publisher: Public Library of Science (PLoS)
Date: 14-09-2015
Publisher: Wiley
Date: 14-03-2008
Publisher: Frontiers Media SA
Date: 12-10-2022
DOI: 10.3389/FCELL.2022.1009776
Abstract: During meiotic prophase I, tightly regulated processes take place, from pairing and synapsis of homologous chromosomes to recombination, which are essential for the generation of genetically variable haploid gametes. These processes have canonical meiotic features conserved across different phylogenetic groups. However, the dynamics of meiotic prophase I in non-mammalian vertebrates are poorly known. Here, we compare four species from Sauropsida to understand the regulation of meiotic prophase I in reptiles: the Australian central bearded dragon ( Pogona vitticeps ), two geckos ( Paroedura picta and Coleonyx variegatus ) and the painted turtle ( Chrysemys picta ). We first performed a histological characterization of the spermatogenesis process in both the bearded dragon and the painted turtle. We then analyzed prophase I dynamics, including chromosome pairing, synapsis and the formation of double strand breaks (DSBs). We show that meiosis progression is highly conserved in reptiles with telomeres clustering forming the bouquet , which we propose promotes homologous pairing and synapsis, along with facilitating the early pairing of micro-chromosomes during prophase I (i.e., early zygotene). Moreover, we detected low levels of meiotic DSB formation in all taxa. Our results provide new insights into reptile meiosis.
Publisher: Oxford University Press (OUP)
Date: 17-11-2017
Abstract: DNA methylation plays a key role in maintaining transcriptional silence on the inactive X chromosome of eutherian mammals. Beyond eutherians, there are limited genome wide data on DNA methylation from other vertebrates. Previous studies of X borne genes in various marsupial models revealed no differential DNA methylation of promoters between the sexes, leading to the conclusion that CpG methylation plays no role in marsupial X-inactivation. Using reduced representation bisulfite sequencing, we generated male and female CpG methylation profiles in four representative vertebrates (mouse, gray short-tailed opossum, platypus, and chicken). A variety of DNA methylation patterns were observed. Platypus and chicken displayed no large-scale differential DNA methylation between the sexes on the autosomes or the sex chromosomes. As expected, a metagene analysis revealed hypermethylation at transcription start sites (TSS) of genes subject to X-inactivation in female mice. This contrasted with the opossum, in which metagene analysis did not detect differential DNA methylation between the sexes at TSSs of genes subject to X-inactivation. However, regions flanking TSSs of these genes were hypomethylated. Our data are the first to demonstrate that, for genes subject to X-inactivation in both eutherian and marsupial mammals, there is a consistent difference between DNA methylation levels at TSSs and immediate flanking regions, which we propose has a silencing effect in both groups.
Publisher: S. Karger AG
Date: 2002
DOI: 10.1159/000068539
Abstract: Group B SOX genes, the closest relatives to the sex-determining gene SRY, are thought to have evolved from a single ancestral SOX B by a series of duplications and translocations. The two SOX B genes SOX2 and SOX14 co-localize to chromosome 3q in humans. SOX2 and SOX14 homologues were cloned and characterized in the platypus, a monotreme mammal distantly related to man. The two genes were found to co-localize to chromosome 1q in this species. Proximity of the two related genes has therefore been conserved for 170 Myr, since humans and platypus erged. The sequence similarity and conserved synteny of these group B genes provide clues to their origin. A simple model of SOX group B gene evolution is proposed.
Publisher: Wiley
Date: 18-12-2023
Abstract: The molecular mechanism of temperature‐dependent sex determination (TSD) is a long‐standing mystery. How is the thermal signal sensed, captured and transduced to regulate key sex genes? Although there is compelling evidence for pathways via which cells capture the temperature signal, there is no known mechanism by which cells transduce those thermal signals to affect gene expression. Here we propose a novel hypothesis we call 3D‐TSD (the three dimensions of thermolabile sex determination). We postulate that the genome has capacity to remodel in response to temperature by changing 3D chromatin conformation, perhaps via temperature‐sensitive transcriptional condensates. This could rewire enhancer–promoter interactions to alter the expression of key sex‐determining genes. This hypothesis can accommodate monogenic or multigenic thermolabile sex‐determining systems, and could be combined with upstream thermal sensing and transduction to the epigenome to commit gonadal fate.
Publisher: MDPI AG
Date: 10-11-2021
DOI: 10.3390/NCRNA7040072
Abstract: Currently there are nine known ex les of transmissible cancers in nature. They have been observed in domestic dog, Tasmanian devil, and six bivalve species. These tumours can overcome host immune defences and spread to other members of the same species. Non-coding RNAs (ncRNAs) are known to play roles in tumorigenesis and immune system evasion. Despite their potential importance in transmissible cancers, there have been no studies on ncRNA function in this context to date. Here, we present possible applications of the CRISPR/Cas system to study the RNA biology of transmissible cancers. Specifically, we explore how ncRNAs may play a role in the immortality and immune evasion ability of these tumours.
Publisher: Springer Science and Business Media LLC
Date: 2010
Publisher: Public Library of Science (PLoS)
Date: 07-02-2022
DOI: 10.1371/JOURNAL.PGEN.1010040
Abstract: During meiotic prophase I, homologous chromosomes pair, synapse and recombine in a tightly regulated process that ensures the generation of genetically variable haploid gametes. Although the mechanisms underlying meiotic cell ision have been well studied in model species, our understanding of the dynamics of meiotic prophase I in non-traditional model mammals remains in its infancy. Here, we reveal key meiotic features in previously uncharacterised marsupial species (the tammar wallaby and the fat-tailed dunnart), plus the fat-tailed mouse opossum, with a focus on sex chromosome pairing strategies, recombination and meiotic telomere homeostasis. We uncovered differences between phylogroups with important functional and evolutionary implications. First, sex chromosomes, which lack a pseudo-autosomal region in marsupials, had species specific pairing and silencing strategies, with implications for sex chromosome evolution. Second, we detected two waves of γH2AX accumulation during prophase I. The first wave was accompanied by low γH2AX levels on autosomes, which correlated with the low recombination rates that distinguish marsupials from eutherian mammals. In the second wave, γH2AX was restricted to sex chromosomes in all three species, which correlated with transcription from the X in tammar wallaby. This suggests non-canonical functions of γH2AX on meiotic sex chromosomes. Finally, we uncover evidence for telomere elongation in primary spermatocytes of the fat-tailed dunnart, a unique strategy within mammals. Our results provide new insights into meiotic progression and telomere homeostasis in marsupials, highlighting the importance of capturing the ersity of meiotic strategies within mammals.
Publisher: S. Karger AG
Date: 2001
DOI: 10.1159/000056872
Abstract: Mapping of human X-borne genes in distantly related mammals has defined a conserved region shared by the X chromosome in all three extant mammalian groups, plus a region that was recently added to the eutherian X but is still autosomal in marsupials and monotremes. Using comparative mapping of human Y-borne genes, we now directly show that the eutherian Y is also composed of a conserved and an added region which contains most of the ubiquitously expressed Y-borne genes. Little of the ancient conserved region remains, and the human Y chromosome is largely derived from the added region.
Publisher: Springer US
Date: 2021
Publisher: Springer Science and Business Media LLC
Date: 27-09-2011
Publisher: Springer Science and Business Media LLC
Date: 10-01-2015
Publisher: Oxford University Press (OUP)
Date: 16-06-2020
DOI: 10.1093/ICB/ICAA082
Abstract: The developmental environment can exert powerful effects on animal phenotype. Recently, epigenetic modifications have emerged as one mechanism that can modulate developmentally plastic responses to environmental variability. For ex le, the DNA methylation profile at promoters of hormone receptor genes can affect their expression and patterns of hormone release. Across taxonomic groups, epigenetic alterations have been linked to changes in glucocorticoid (GC) physiology. GCs are metabolic hormones that influence growth, development, transitions between life-history stages, and thus fitness. To date, relatively few studies have examined epigenetic effects on phenotypic traits in wild animals, especially in hibians. Here, we examined the effects of exposure to predation threat (alarm cues) and experimentally manipulated DNA methylation on corticosterone (CORT) levels in tadpoles and metamorphs of the invasive cane toad (Rhinella marina). We included offspring of toads s led from populations across the species’ Australian range. In these animals, exposure to chemical cues from injured conspecifics induces shifts in developmental trajectories, putatively as an adaptive response that lessens vulnerability to predation. We exposed tadpoles to these alarm cues, and measured changes in DNA methylation and CORT levels, both of which are mechanisms that have been implicated in the control of phenotypically plastic responses in tadpoles. To test the idea that DNA methylation drives shifts in GC physiology, we also experimentally manipulated methylation levels with the drug zebularine. We found differentially methylated regions (DMRs) between control tadpoles and their full-siblings exposed to alarm cues, zebularine, or both treatments. However, the effects of these manipulations on methylation patterns were weaker than clutch (e.g., genetic, maternal, etc.) effects. CORT levels were higher in larval cane toads exposed to alarm cues and zebularine. We found little evidence of changes in DNA methylation across the GC receptor gene (NR3C1) promoter region in response to alarm cue or zebularine exposure. In both alarm cue and zebularine-exposed in iduals, we found differentially methylated DNA in the suppressor of cytokine signaling 3 gene (SOCS3), which may be involved in predator avoidance behavior. In total, our data reveal that alarm cues have significant impacts on tadpole physiology, but show only weak links between DNA methylation and CORT levels. We also identify genes containing DMRs in tadpoles exposed to alarm cues and zebularine, particularly in range-edge populations, that warrant further investigation.
Publisher: Springer Science and Business Media LLC
Date: 23-04-2014
DOI: 10.1038/NATURE13151
Abstract: Y chromosomes underlie sex determination in mammals, but their repeat-rich nature has h ered sequencing and associated evolutionary studies. Here we trace Y evolution across 15 representative mammals on the basis of high-throughput genome and transcriptome sequencing. We uncover three independent sex chromosome originations in mammals and birds (the outgroup). The original placental and marsupial (therian) Y, containing the sex-determining gene SRY, emerged in the therian ancestor approximately 180 million years ago, in parallel with the first of five monotreme Y chromosomes, carrying the probable sex-determining gene AMH. The avian W chromosome arose approximately 140 million years ago in the bird ancestor. The small Y/W gene repertoires, enriched in regulatory functions, were rapidly defined following stratification (recombination arrest) and erosion events and have remained considerably stable. Despite expression decreases in therians, Y/W genes show notable conservation of proto-sex chromosome expression patterns, although various Y genes evolved testis-specificities through differential regulatory decay. Thus, although some genes evolved novel functions through spatial/temporal expression shifts, most Y genes probably endured, at least initially, because of dosage constraints.
Publisher: Elsevier BV
Date: 10-2020
Publisher: S. Karger AG
Date: 2002
DOI: 10.1159/000071058
Publisher: Springer Science and Business Media LLC
Date: 16-11-2011
DOI: 10.1038/HDY.2011.106
Publisher: Cold Spring Harbor Laboratory
Date: 29-11-2011
Abstract: We report here the isolation and sequencing of 10 Y-specific tammar wallaby ( Macropus eugenii ) BAC clones, revealing five hitherto undescribed tammar wallaby Y genes (in addition to the five genes already described) and several pseudogenes. Some genes on the wallaby Y display testis-specific expression, but most have low widespread expression. All have partners on the tammar X, along with homologs on the human X. Nonsynonymous and synonymous substitution ratios for nine of the tammar XY gene pairs indicate that they are each under purifying selection. All 10 were also identified as being on the Y in Tasmanian devil ( Sarcophilus harrisii a distantly related Australian marsupial) however, seven have been lost from the human Y. Maximum likelihood phylogenetic analyses of the wallaby YX genes, with respective homologs from other vertebrate representatives, revealed that three marsupial Y genes ( HCFC1X/Y, MECP2X/Y , and HUWE1X/Y ) were members of the ancestral therian pseudoautosomal region (PAR) at the time of the marsupial/eutherian split three XY pairs ( SOX3/SRY, RBMX/Y , and ATRX/Y ) were isolated from each other before the marsupial/eutherian split, and the remaining three ( RPL10X/Y, PHF6X/Y , and UBA1/UBE1Y ) have a more complex evolutionary history. Thus, the small marsupial Y chromosome is surprisingly rich in ancient genes that are retained in at least Australian marsupials and evolved from testis–brain expressed genes on the X.
Publisher: S. Karger AG
Date: 2022
DOI: 10.1159/000529376
Publisher: Elsevier BV
Date: 06-2007
DOI: 10.1016/J.SEMCDB.2007.02.007
Abstract: Sex determination in vertebrates is accomplished through a highly conserved genetic pathway. But surprisingly, the downstream events may be activated by a variety of triggers, including sex determining genes and environmental cues. Amongst species with genetic sex determination, the sex determining gene is anything but conserved, and the chromosomes that bear this master switch subscribe to special rules of evolution and function. In mammals, with a few notable exceptions, female are homogametic (XX) and males have a single X and a small, heterochromatic and gene poor Y that bears a male dominant sex determining gene SRY. The bird sex chromosome system is the converse in that females are the heterogametic sex (ZW) and males the homogametic sex (ZZ). There is no SRY in birds, and the dosage-sensitive Z-borne DMRT1 gene is a credible candidate sex determining gene. Different sex determining switches seem therefore to have evolved independently in different lineages, although the complex sex chromosomes of the platypus offer us tantalizing clues that the mammal XY system may have evolved directly from an ancient reptile ZW system. In this review we will discuss the organization and evolution of the sex chromosomes across a broad range of mammals, and speculate on how the Y chromosome, and SRY, evolved.
Publisher: Springer Science and Business Media LLC
Date: 12-2004
DOI: 10.1007/S10577-005-5265-Y
Abstract: Transposable elements (TEs) sometimes induce karyotypic changes following recombination, breakage and rearrangement. We used FISH and Southern blot analyses to investigate the amount and distribution of LINE-1 retrotransposons in rodents (genus Taterillus, Muridae, Gerbillinae) that have recently undergone an important genome repatterning. Our results were interpreted in a known phylogenetic framework and clearly showed that LINE-1 elements were greatly lified and non-randomly distributed in the most rearranged karyotypes. A comparison between FISH and conventional banding patterns provided evidence that LINE-1 insertion sites and chromosome breakpoints were not strongly correlated, thus suggesting that LINE-1 lification subsequently accompanied Taterillus chromosome evolution. Similar patterns are observed in some cases of genomic stresses (hybrid genomes, cancer and DNA-damaged cells) and usually associated with DNA hypomethylation. We propose that intensively repatterned genomes face transient stress phases during which some epigenetic features, such as DNA methylation, are relaxed, thus allowing TE lification.
Publisher: Springer Science and Business Media LLC
Date: 22-04-2022
DOI: 10.1038/S41437-022-00532-2
Abstract: Sex-linked inheritance is a stark exception to Mendel’s Laws of Heredity. Here we discuss how the evolution of heteromorphic sex chromosomes (mainly the Y) has been shaped by the intricacies of the meiotic programme. We propose that persistence of Y chromosomes in distantly related mammalian phylogroups can be explained in the context of pseudoautosomal region (PAR) size, meiotic pairing strategies, and the presence of Y-borne executioner genes that regulate meiotic sex chromosome inactivation. We hypothesise that variation in PAR size can be an important driver for the evolution of recombination frequencies genome wide, imposing constraints on Y fate. If small PAR size compromises XY segregation during male meiosis, the stress of producing aneuploid gametes could drive function away from the Y (i.e., a fragile Y). The Y chromosome can avoid fragility either by acquiring an achiasmatic meiotic XY pairing strategy to reduce aneuploid gamete production, or gain meiotic executioner protection (a persistent Y). Persistent Ys will then be under strong pressure to maintain high recombination rates in the PAR (and subsequently genome wide), as improper segregation has fatal consequences for germ cells. In the event that executioner protection is lost, the Y chromosome can be maintained in the population by either PAR rejuvenation (extension by addition of autosome material) or gaining achiasmatic meiotic pairing, the alternative is Y loss. Under this dynamic cyclic evolutionary scenario, understanding the meiotic programme in vertebrate and invertebrate species will be crucial to further understand the plasticity of the rise and fall of heteromorphic sex chromosomes.
Publisher: Elsevier BV
Date: 12-2022
Publisher: S. Karger AG
Date: 2009
DOI: 10.1159/000207522
Abstract: Marsupials, which erged from eutherian mammals 150 million years ago (MYA), occupy a phylogenetic position that is very valuable in genome comparisons of mammal and other vertebrate species. Within the marsupials, the Australian and American clades (represented by the tammar wallaby i Macropus eugenii, /i and the opossum i Monodelphis domestica /i ) erged about 70 MYA. G-banding and chromosome painting suggest that tammar wallaby chromosome 6q has homology to opossum chromosome 7q. We tested this conservation by physically mapping the tammar wallaby orthologs of opossum chromosome 7q genes. We isolated 28 tammar wallaby BAC clones that contained orthologs of 16 opossum chromosome 7q genes. We used fluorescence in situ hybridization (FISH) to show that they all mapped specifically to the tammar wallaby chromosome 6q in nearly the same order as their orthologs on opossum chromosome 7q. Thus this chromosome arm is genetically, as well as cytologically, conserved over the 55–80 million years that separate kangaroos and the opossum.
Publisher: Springer Science and Business Media LLC
Date: 12-2022
Publisher: Georg Thieme Verlag KG
Date: 08-2015
Abstract: In females, X chromosome inactivation (XCI) ensures transcriptional silencing of one of the two Xs (either in a random or imprinted fashion) in somatic cells. Comparing this silencing between species has offered insight into different mechanisms of X inactivation, providing clues into the evolution of this epigenetic process in mammals. Long-noncoding RNAs have emerged as a common theme in XCI of therian mammals (eutherian and marsupial). Eutherian X inactivation is regulated by the noncoding RNA product of XIST, within a cis-acting master control region called the X inactivation center (XIC). Marsupials XCI is XIST independent. Instead, XCI is controlled by the long-noncoding RNA Rsx, which appears to be a functional analog of the eutherian XIST gene, insofar that its transcript coats the inactive X and represses activity of genes in cis. In this review we discuss XCI in eutherians, and contrast imprinted X inactivation in mouse and marsupials. We provide particular focus on the evolution of genomic elements that confer the unique epigenetic features that characterize the inactive X chromosome.
Publisher: Springer Science and Business Media LLC
Date: 12-2004
DOI: 10.1007/S10577-005-5376-5
Abstract: In eutherians, the sex-reversing ATRX gene on the X has no homologue on the Y chromosome. However, testis-specific and ubiquitously expressed X-borne genes have been identified in Australian marsupials. We studied nucleotide sequence and chromosomal location of ATRX homologues in two American marsupials, the opossums Didelphis virginiana and Monodelphis domestica. A PCR fragment of M. domestica ATRX was used to probe Southern blots and to screen male genomic libraries. Southern analysis demonstrated ATRX homologues on both X and Y in D. virginiana, and two clones were isolated which hybridized to a single position on the Y chromosome in male-derived cells but to multiple sites of the X in female cells. In M. domestica, there was a single clone that mapped to the X but not to the Y, suggesting that it represents the M. domestica ATRX. However a male-specific band was detected in Southern blots probed with the D. virginiana ATRY and with a mouse ATRX clone, which implies that the Y copy in M. domestica has erged further from other ATRX homologues. Thus there appears to be a Y-borne copy of ATRY in American, as well as Australian marsupials, although it has erged in sequence, as have other Y genes that are testis-specific in both eutherian and marsupial lineages.
Publisher: Springer Science and Business Media LLC
Date: 27-10-2022
DOI: 10.1038/S41467-022-34138-3
Abstract: The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis -regulatory elements during hypoxic response and UV protection.
Publisher: Springer Science and Business Media LLC
Date: 26-06-2008
DOI: 10.1007/S00018-008-8109-Z
Abstract: Therian mammals (marsupials and placentals) have an XX female: XY male sex chromosome system, which is homologous to autosomes in other vertebrates. The testis-determining gene, SRY, is conserved on the Y throughout therians, but is absent in other vertebrates, suggesting that the mammal system evolved about 310 million years ago (MYA). However, recent work on the basal monotreme mammals has completely changed our conception of how and when this change occurred. Platypus and echidna lack SRY, and the therian X and Y are represented by autosomes, implying that SRY evolved in therians after their ergence from monotremes only 166 MYA. Clues to the ancestral mechanism usurped by SRY in therians are provided by the monotremes, whose sex chromosomes are homologous to the ZW of birds. This suggests that the therian X and Y, and the SRY gene, evolved from an ancient bird-like sex chromosome system which predates the ergence of mammals and reptiles 310 MYA.
Start Date: 06-2009
End Date: 05-2014
Amount: $560,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2018
End Date: 12-2021
Amount: $432,108.00
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2021
End Date: 05-2024
Amount: $812,340.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2010
End Date: 12-2013
Amount: $315,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2022
End Date: 12-2025
Amount: $1,257,021.00
Funder: Australian Research Council
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