Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE43858 | GEO | 2013/03/05
SECONDARY ACCESSION(S): PRJNA187928
REPOSITORIES: GEO
Similar Datasets
Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. Here, we report population-wide DNA sequencing of genomes, transcriptomes, and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are unlinked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified 2,372 methylQTL, which revealed the first population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically reactivated during male gametogenesis, which facilitates their silencing across generations. RNA-seq from naturally-occurring Arabidopsis accessions
2013-03-05 | E-GEOD-43858 | biostudies-arrayexpress
Project description:Like protein coding genes, loci that produce microRNAs (miRNAs) are generally considered to be under purifying selection, consistent with miRNA polymorphisms being able to cause disease. Nevertheless, it has been hypothesized that variation in miRNA genes may contribute to phenotypic diversity. Here we demonstrate that a naturally occurring polymorphism in the MIR164A gene interacts epistatically with an unlinked locus to affect leaf shape and shoot architecture in Arabidopsis thaliana. A single-base pair substitution in the miRNA complementary sequence alters the stability of the miRNA:miRNA* duplex. It thereby interferes with processing of the precursor and greatly reduces miRNA accumulation. We demonstrate that this is not a rare exception, but that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA processability due to cis mutations is a common contributor to phenotypic variation in plants. sRNA sequencing transgenic A. thaliana
2012-10-31 | E-GEOD-32927 | biostudies-arrayexpress
Project description:Like protein coding genes, loci that produce microRNAs (miRNAs) are generally considered to be under purifying selection, consistent with miRNA polymorphisms being able to cause disease. Nevertheless, it has been hypothesized that variation in miRNA genes may contribute to phenotypic diversity. Here we demonstrate that a naturally occurring polymorphism in the MIR164A gene interacts epistatically with an unlinked locus to affect leaf shape and shoot architecture in Arabidopsis thaliana. A single-base pair substitution in the miRNA complementary sequence alters the stability of the miRNA:miRNA* duplex. It thereby interferes with processing of the precursor and greatly reduces miRNA accumulation. We demonstrate that this is not a rare exception, but that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA processability due to cis mutations is a common contributor to phenotypic variation in plants.
2012-10-31 | GSE32927 | GEO
Project description:Genetic variation is regarded as a prerequisite for evolution. Theoretical models suggest epigenetic information inherited independently of DNA sequence can also enable evolution. However, whether epigenetic inheritance mediates phenotypic evolution in natural populations is unknown. Here we show that natural epigenetic DNA methylation variation in gene bodies regulates genes expression, and thereby influences the natural variation of complex traits in Arabidopsis thaliana. Notably, the effects of methylation variation on phenotypic diversity and gene expression variance are comparable with those of DNA sequence polymorphism. We also identify methylation epialleles in numerous genes associated with environmental conditions in native habitats, suggesting that intragenic methylation facilitates adaptation to fluctuating environments. Our results demonstrate that methylation variation fundamentally shapes phenotypic diversity in natural populations and provides an epigenetic basis for adaptive Darwinian evolution independent of genetic polymorphism.
2022-06-30 | GSE183785 | GEO
Project description:Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. However, genes that are located in non-syntenic genomic positions relative to species related closely to maize exhibit higher levels of DNA methylation independent of expression state. A comparison of the DNA methylation levels in two different inbred genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions. The regions of differential methylation in B73 and Mo17 often occur in intergenic regions but some of these regions are located within or near genes. There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes. A comparison of the genotype and epigenotype in a panel of near-isogenic lines reveals evidence for epigenetic variation that is conditioned by linked regions as well as examples of epigenetic variation that is conditioned by unlinked genomic regions. Our many examples of epigenetic variation, including some without tightly linked genetic variation, have implications for plant breeding and for natural selection.
2011-11-21 | GSE29099 | GEO
Project description:Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. However, genes that are located in non-syntenic genomic positions relative to species related closely to maize exhibit higher levels of DNA methylation independent of expression state. A comparison of the DNA methylation levels in two different inbred genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions. The regions of differential methylation in B73 and Mo17 often occur in intergenic regions but some of these regions are located within or near genes. There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes. A comparison of the genotype and epigenotype in a panel of near-isogenic lines reveals evidence for epigenetic variation that is conditioned by linked regions as well as examples of epigenetic variation that is conditioned by unlinked genomic regions. Our many examples of epigenetic variation, including some without tightly linked genetic variation, have implications for plant breeding and for natural selection. Methylation profiles in seedling tissue of the maize inbred lines B73 and Mo17. Each genotype was compared for three biological replications using a gene-focused custom 2.1M NimbleGen array.
2011-11-21 | E-GEOD-29099 | biostudies-arrayexpress
Project description:The contribution of epigenetic variation to phenotypic variation is unclear. Imprinted genes, because of their strong association with epigenetic modifications, represent an opportunity for the discovery of such phenomena. In mammals and flowering plants, a subset of genes are expressed from only one parental allele in a process called gene imprinting. Imprinting is associated with differential DNA methylation and chromatin modifications between parental alleles. In flowering plants imprinting occurs in endosperm seed tissue. Proper endosperm development is essential for the production of viable seeds. We previously showed that in Arabidopsis thaliana intraspecific imprinting variation is correlated with naturally occurring DNA methylation polymorphisms. Here, we investigated the mechanisms and function of allele-specific imprinting of the class IV homeodomain-Leucine zipper (HD-ZIP) transcription factor HDG3. In imprinted strains, HDG3 is expressed primarily from the methylated paternally inherited allele. We manipulated the methylation state of endogenous HDG3 in a non-imprinted strain and demonstrated that methylation of a proximal transposable element is sufficient to promote HDG3 expression and imprinting. Gain of HDG3 imprinting was associated with earlier endosperm cellularization. These results indicate that epigenetic variation alone is sufficient to explain imprinting variation and show that epialleles can underlie variation in seed development phenotypes.
2018-10-29 | GSE118371 | GEO
Project description:In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. Selected populations exerted significant differences in flowering time and the number of branches and fruits, differences that were maintained over two to three generations in the absence of selection. We identified 4,629 and 5,158 differentially methylated cytosines which were overrepresented in genes that regulate flowering time, epigenetic processes, development and morphogenesis. Differentially methylated genes were enriched in differentially expressed genes. Thus, epigenetic variation is subject to selection and may play an important role in the adaptive response of populations in rapidly changing natural environments. Genomic DNA was extracted from whole-plant above-ground tissue of individual 25-day-old plants with the Qiagen DNeasy kit (Qiagen). DNA from two randomly chosen CVL39 individuals from ancestral (A3) lines and from 7 selected (S3) lines that had experienced 5 generations of selection in the three replicated dynamic landscapes (2xD1, 3xD5,2xD6) was sequenced (paired-end, 100 bp) using the Illumina Highseq 2000 Instrument. Single nucleotide polymorphisms and TE insertions were mapped with respect to the recombinant reference genome and compared between selected and ancestral lines.
2014-09-01 | E-GEOD-47490 | biostudies-arrayexpress
Project description:DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell type specific patterns of DNA methylation, especially in the CHH sequence context. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized to date. It is hypermethylated within transposable elements, accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24 nt small RNAs. Absence of the nucleosome remodeler DECREASED DNA METHYLATION 1, required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing excess 24 nt small RNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types. RNA-seq from six cell populations covering the major cell types of the Arabidopsis root meristem.
2016-03-31 | E-GEOD-79709 | biostudies-arrayexpress
Project description:DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell type specific patterns of DNA methylation, especially in the CHH sequence context. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized to date. It is hypermethylated within transposable elements, accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24 nt small RNAs. Absence of the nucleosome remodeler DECREASED DNA METHYLATION 1, required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing excess 24 nt small RNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types. MethylC-seq from six cell populations covering the major cell types of the Arabidopsis root meristem.
2016-03-31 | E-GEOD-79708 | biostudies-arrayexpress