Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic inheritance mediates phenotypic evolution in natural populations

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE183785 | GEO | 2022/06/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

Project description:Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences. MethylC-seq of Arabidopsis thaliana

2015-05-13 | E-GEOD-64463 | biostudies-arrayexpress

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

2015-05-13 | GSE64463 | GEO

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)

2013-03-05 | E-GEOD-43857 | biostudies-arrayexpress

Epigenomic and genome structural diversity in a worldwide collection of Arabidopsis thaliana

Project description:Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. Physical genome maps for nine of the most diverse accessions revealed how transposable elements and other structural variations shaped the epigenome to allow rapid adaptation to environmental changes, with strong emphasis on disease resistance. Analysis of the cistromes and epicistromes in these accessions revealed a significant association between both methylation and nucleotide variation and the conservation of transcription factor binding sites. The Arabidopsis thaliana 1001 Epigenomes Project now provides a comprehensive resource to help further understand how epigenetic variation contributes to both molecular and phenotypes in natural populations of the most widely studied reference plant.

2016-07-14 | GSE80744 | GEO

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)

2013-03-05 | GSE43857 | GEO

Natural selection on cis and trans regulation in yeasts

Project description:Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans activating factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we investigate the global patterns of gene expression evolution in Saccharomyces cerivisiae. We report statistical methods useful in quantifying cis and trans regulation using next generation sequencing data. Using these methods, measured genome-wide allele-specific expression by deep sequencing to investigate the genetic architecture of gene regulatory variation between two strains of Saccharomyces cerevisiae. We find that expression polymorphism in yeast is common for both cis and trans regulation, though trans variation is more common. Our detailed analyses of the effects of functional constraint on expression variation as indicated by measures such as protein connectivity, gene essentiality, and the ratio of nonsynonymous substitutions to synonymous substitutions clearly reveal that both classes of variation are under purifying selection, but trans variation is more sensitive to selective constraint. Comparing interspecific expression divergence between S. cerevisiae and S. paradoxus to our intraspecific variation suggests that natural selection strongly influences the patterns of variation we observe. Further analyses revealed that cis divergence is more frequently mediated by positive Darwinian selection than trans divergence, which is compatible with neutral evolution. Study the gene expression patterns in two strains of yeast (BY and RM)

2010-04-02 | E-GEOD-20749 | biostudies-arrayexpress

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)

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

Natural selection on cis and trans regulation in yeasts

2010-04-02 | GSE20749 | GEO

Intra-species variation of H3K14ac in S. cerevisiae

Project description:Quantitative variation of epigenetic marks, such as histone modifications, can modify gene expression and eventually contribute to inter-individual phenotypic variation. Our goal is to investigate natural inter-individual variation of the epigenome in a quantitative manner. To probe the degree of natural epigenomic diversity in S. cerevisiae, we compared two unrelated wild strains using replicated Mnase-seq and ChIP-seq profiling at mononucleosomal resolution for H3K14 acetylation.

2015-07-22 | E-MTAB-2671 | biostudies-arrayexpress

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)

2013-03-05 | GSE43858 | GEO