ORCID Profile
0000-0003-3923-9740
Current Organisation
CSIRO Black Mountain Laboratories
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Publisher: Oxford University Press (OUP)
Date: 02-2019
DOI: 10.1104/PP.18.01205
Abstract: Hybrids are used extensively in agriculture due to their superior performance in seed yield and plant growth, yet the molecular mechanisms underpinning hybrid performance are not well understood. Recent evidence has suggested that a decrease in basal defense response gene expression regulated by reduced levels of salicylic acid (SA) may be important for vigor in certain hybrid combinations. Decreasing levels of SA in the Arabidopsis (Arabidopsis thaliana) accession C24 through the introduction of the SA catabolic enzyme salicylate1 hydroxylase (NahG) increases plant size, phenocopying the large-sized C24/Landsberg erecta (Ler) F1 hybrids. C24♀ × Ler♂ F1 hybrids and C24 NahG lines shared differentially expressed genes and pathways associated with plant defense and leaf senescence including decreased expression of SA biosynthetic genes and SA response genes. The expression of TL1 BINDING TRANSCRIPTION FACTOR1, a key regulator in resource allocation between growth and defense, was decreased in both the F1 hybrid and the C24 NahG lines, which may promote growth. Both C24 NahG lines and the F1 hybrids showed decreased expression of the key senescence-associated transcription factors WRKY53, NAC-CONTAINING PROTEIN29, and ORESARA1 with a delayed onset of senescence compared to C24 plants. The delay in senescence resulted in an extension of the photosynthetic period in the leaves of F1 hybrids compared to the parental lines, potentially allowing each leaf to contribute more resources toward growth.
Publisher: Proceedings of the National Academy of Sciences
Date: 17-10-2016
Abstract: We show that the changes in DNA methylation that occur in F1 hybrids of Arabidopsis are mostly dependent on the presence of 24-nt siRNAs at the locus. The methylation change at a locus results in the two alleles becoming similar to each other in methylation pattern. The methylation changes occur through the processes of trans-chromosomal methylation and trans-chromosomal demethylation. These altered methylation states can be inherited in the F2 generation and can be associated with changes in levels of gene activity, which may contribute to the phenotypic heterogeneity in the F2.
Publisher: Proceedings of the National Academy of Sciences
Date: 02-11-2015
Abstract: Hybrids are extensively used in agriculture to deliver increases in crop yields, yet the molecular basis of their superior performance (heterosis) is not well understood. We report that some Arabidopsis F1 hybrids show changes to salicylic acid- and auxin-regulated defense and stress response gene expression. These changes could be important for generating the greater growth of some hybrids given the antagonistic relationship between plant growth and defense responses. Hybrids showing different levels of heterosis have changes in the salicylic acid- and auxin-regulated pathways that correlate with differences in the enhanced leaf growth. The larger leaves, and thus greater capacity for energy production, support the increased growth vigor and seed yields of the hybrids.
Publisher: Proceedings of the National Academy of Sciences
Date: 25-01-2011
Abstract: Intraspecific hybrids between the Arabidopsis thaliana accessions C24 and Landsberg erecta have strong heterosis. The reciprocal hybrids show a decreased level of 24-nt small RNA (sRNA) relative to the parents with the decrease greatest for those loci where the parents had markedly different 24-nt sRNA levels. The genomic regions with reduced 24-nt sRNA levels were largely associated with genes and their flanking regions indicating a potential effect on gene expression. We identified several ex les of genes with altered 24-nt sRNA levels that showed correlated changes in DNA methylation and expression levels. We suggest that such epigenetically generated differences in gene activity may contribute to hybrid vigor and that the epigenetic ersity between ecotypes provides increased allelic (epi-allelic) variability that could contribute to heterosis.
Publisher: Oxford University Press (OUP)
Date: 25-09-2005
DOI: 10.1093/NAR/GKI874
Publisher: Springer Science and Business Media LLC
Date: 13-06-2004
DOI: 10.1038/NSMB786
Publisher: Springer Science and Business Media LLC
Date: 2008
Abstract: RNA interference (RNAi) is a powerful tool for the functional analysis of essential genes in the mammalian genome. Here, we present a simple ecdysone-based inducible RNAi approach that allows high induction and adjustable control of short hairpin RNA (shRNA) expression for silencing gene expression in a wide range of mammalian cells. This protocol describes the following: the design and cloning of inducible shRNA testing and validation of gene knockdown and methodology for establishing stable cell lines. This step-by-step protocol offers a quick and cost-effective approach for addressing the function of genes essential for cell cycle regulation and development and can be completed in less than 6 weeks.
Publisher: Proceedings of the National Academy of Sciences
Date: 21-01-2014
Abstract: Hybridization of two epigenetically distinct Arabidopsis accessions is associated with an altered methylome in the F1 hybrid brought about by the processes of Trans Chromosomal Methylation and deMethylation. In the loci studied, the altered F1 cytosine methylation ( m C) patterns are inherited to the F2. These observations of trans- m C events are reminiscent of paramutation described in maize and may be common in hybridization events. In one locus, the altered m C states are associated with changed mRNA levels in the F1 hybrid and F2 plants. These events may contribute to F1 hybrid vigor and to the phenotypic heterogeneity and loss of vigor in the F2 through segregation of genetic and epigenetic determinants.
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: Wiley
Date: 17-09-2016
DOI: 10.1111/TPJ.13285
Abstract: Hybrid vigour (heterosis) has been used for decades in crop industries, especially in the production of maize and rice. Hybrid varieties usually exceed their parents in plant biomass and seed yield. But the molecular basis of hybrid vigour is not fully understood. In this project, we studied heterosis at early stages of seedling development in Arabidopsis hybrids derived from crossing Ler and C24 accessions. We found that early heterosis is associated with non-additive gene expression that resulted from earlier changes in gene expression in the hybrids relative to the parents. The non-additively expressed genes are involved in metabolic pathways, including photosynthesis, critical for plant growth. The early increased expression levels of genes involved in energy production in hybrids is associated with heterosis in the young seedlings that could be essential for biomass heterosis at later developmental stages of the plant.
Publisher: Proceedings of the National Academy of Sciences
Date: 09-01-2007
Abstract: Mammalian centromere function depends upon a specialized chromatin organization where distinct domains of CENP-A and dimethyl K4 histone H3, forming centric chromatin, are uniquely positioned on or near the surface of the chromosome. These distinct domains are embedded in pericentric heterochromatin (characterized by H3 methylated at K9). The mechanisms that underpin this complex spatial organization are unknown. Here, we identify the essential histone variant H2A.Z as a new structural component of the centromere. Along linear chromatin fibers H2A.Z is distributed nonuniformly throughout heterochromatin, and centric chromatin where regions of nucleosomes containing H2A.Z and dimethylated K4 H3 are interspersed between subdomains of CENP-A. At metaphase, using the inactive X chromosome centromere as a model, complex folding of this fiber produces spatially positioned domains where H2A.Z/dimethylated K4 H3 chromatin juxtaposes one side of CENP-A chromatin, whereas a region of H2A/trimethyl K9 H3 borders the other side. A second region of H2A.Z is found, with trimethyl K9 H3 at the inner centromere. We therefore propose that H2A.Z plays an integral role in organizing centromere structure.
Publisher: Springer Science and Business Media LLC
Date: 2001
Abstract: Chromosome arrangements have been studied in metaphase and interphase somatic cells and in sperm of many animal species, but there are conflicting data and it is still not clear whether chromosomes are arranged randomly or non-randomly. We used chromosome painting to reveal the positions of chromosomes in marsupial sperm. Marsupials are ideally suited for these studies because they have only a few large chromosomes. Here, we show that chromosomes occupy fixed positions in the immature and mature sperm of Sminthopsis crassicaudata. We suggest that the non-random arrangement of chromosomes in marsupial sperm may be important in establishing chromosome arrangement and patterns of gene activity within the developing embryo.
Publisher: Springer Science and Business Media LLC
Date: 2003
Abstract: We used chromosome painting to show directly that chromosomes occupy fixed positions in the nuclei of mammal but not chicken sperm. We found that the positions of homologous chromosomes are conserved in sperm of two marsupial species that erged 50-60 million years ago. We also discovered that the X chromosome lies in the region that makes first contact with the egg in marsupial and monotreme mammals, as well as eutherians, and suggest that this position may be related to its propensity for inactivation, and its high rate of loss from ICSI embryos. We propose that nuclear architecture in sperm is important for spatial chromatin differentiation and normal development of the fertilized egg, and evolved along with mammal-specific regulatory systems such as X inactivation and genomic imprinting.
Publisher: Proceedings of the National Academy of Sciences
Date: 17-08-2015
Abstract: Hybrids have an important role in many crops used for global food production. The increased production levels of biomass and grain are restricted to the first-generation hybrid. We report stabilization of hybrid vigor traits in pure breeding hybrid mimic lines. Comparison of the patterns of their gene activity with those of the F1 hybrids has identified metabolic pathways associated with the generation of the hybrid vigor phenotype. The hybrid mimics are homozygous for long chromosomal segments showing that heterozygosity is not required for the production of the heterotic phenotype. Interactions between the two parental genomes and epigenomes contribute to the vigor of the Arabidopsis hybrids and are likely to be the basis of hybrid vigor in other plant species.
Publisher: Informa UK Limited
Date: 18-08-2012
DOI: 10.4161/EPI.20820
Publisher: Elsevier BV
Date: 04-2020
DOI: 10.1016/J.JEP.2019.112526
Abstract: Hedyotis diffusa Willd. (H) and Scutellaria barbata D.Don (S) are ancient anti-cancer Chinese herb medicines. When combined, known as HS, it is one of the most commonly prescribed Chinese Medicines for cancer patients today in China. The prevention of disease progression is a dominant concern for the growing number of men with prostate cancer. The purpose of this work is to evaluate the action and mode of action of Chinese Medicine recipe HS in inhibiting prostate cancer progression in preclinical models. Effects of HS were analyzed in prostate cancer cell lines by evaluating proliferation, cell cycle profile, DNA damage and key regulators responsible for G HS treatment was observed to reduce DNA content and accumulated prostate cancer cells at the G HS acts by impeding the G
Publisher: Informa UK Limited
Date: 07-2006
DOI: 10.1128/MCB.00519-06
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.TIG.2013.07.004
Abstract: Hybrid vigour, or heterosis, refers to the increased yield and biomass of hybrid offspring relative to the parents. Although this has been exploited in plants for agriculture and horticulture, the molecular and cellular mechanisms underlying hybrid vigour are largely unknown. Genetic analyses show that there are a large number of quantitative trait loci (QTLs) that contribute to the heterotic phenotype, indicating that it is a complex phenomenon. Gene expression in hybrids is regulated by the interactions of the two parental epigenetic systems and the underlying genomes. Increasing understanding of the interplay of small RNA (sRNA) molecules, DNA methylation, and histone marks provides new opportunities to define the basis of hybrid vigour and to understand why F1 heterosis is not passed on to subsequent generations. We discuss recent findings that suggest the existence of several pathways that alter DNA methylation patterns, which may lead to transcriptional changes resulting in the heterotic phenotype.
Publisher: Oxford University Press (OUP)
Date: 29-07-2014
Abstract: Heterosis is important for agriculture however, little is known about the mechanisms driving hybrid vigor. Ultimately, heterosis depends on the interactions of specific alleles and epialleles provided by the parents, which is why hybrids can exhibit different levels of heterosis, even within the same species. We characterize the development of several intraspecific Arabidopsis (Arabidopsis thaliana) F1 hybrids that show different levels of heterosis at maturity. We identify several phases of heterosis beginning during embryogenesis and culminating in a final phase of vegetative maturity and seed production. During each phase, the hybrids show different levels and patterns of growth, despite the close relatedness of the parents. For instance, during the vegetative phases, the hybrids develop larger leaves than the parents to varied extents, and they do so by exploiting increases in cell size and cell numbers in different ratios. Consistent with this finding, we observed changes in the expression of genes known to regulate leaf size in developing rosettes of the hybrids, with the patterns of altered expression differing between combinations. The data show that heterosis is dependent on changes in development throughout the growth cycle of the hybrid, with the traits of mature vegetative biomass and reproductive yield as cumulative outcomes of heterosis at different levels, tissues, and times of development.
Publisher: Elsevier BV
Date: 08-2011
DOI: 10.1016/J.BBAGRM.2011.03.006
Abstract: In this review we have analysed two major biological systems involving epigenetic control of gene activity. In the first system we demonstrate the interplay between genetic and epigenetic controls over the transcriptional activity of FLC, a major repressor of flowering in Arabidopsis. FLC is down-regulated by low temperature treatment (vernalisation) releasing the repressor effect on flowering. We discuss the mechanisms of the reduced transcription and the memory of the vernalisation treatment through vegetative development. We also discuss the resetting of the repressed activity level of the FLC gene, following vernalisation, to the default high activity level and show it occurs during both male and female gametogenesis but with different timing in each. In the second part of the review discussed the complex multigenic system which is responsible for the patterns of gene activity which bring about hybrid vigour in crosses between genetically similar but epigenetically distinct parents. The epigenetic systems that we have identified as contributing to the heterotic phenotype are the 24nt siRNAs and their effects on RNA dependent DNA methylation (RdDM) at the target loci leading to changed expression levels. We conclude that it is likely that epigenetic controls are involved in expression systems in many aspects of plant development and plant function.
Publisher: Springer Science and Business Media LLC
Date: 2009
DOI: 10.1007/S10577-009-9020-7
Abstract: The inactivation of one of the two X chromosomes in female placental mammals represents a remarkable ex le of epigenetic silencing. X inactivation occurs also in marsupial mammals, but is phenotypically different, being incomplete, tissue-specific and paternal. Paternal X inactivation occurs also in the extraembryonic cells of rodents, suggesting that imprinted X inactivation represents a simpler ancestral mechanism. This evolved into a complex and random process in placental mammals under the control of the XIST gene, involving notably variant and modified histones. Molecular mechanisms of X inactivation in marsupials are poorly known, but occur in the absence of an XIST homologue. We analysed the specific pattern of histone modifications using immunofluorescence on metaphasic chromosomes of a model kangaroo, the tammar wallaby. We found that all active marks are excluded from the inactive X in marsupials, as in placental mammals, so this represents a common feature of X inactivation throughout mammals. However, we were unable to demonstrate the accumulation of inactive histone marks, suggesting some fundamental differences in the molecular mechanism of X inactivation between marsupial and placental mammals. A better understanding of the epigenetic mechanisms underlying X inactivation in marsupials will provide important insights into the evolution of this complex process.
No related grants have been discovered for Ian Greaves.