Dataset Information

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

ABSTRACT: The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

SUBMITTER: Kawakatsu T

PROVIDER: S-EPMC5172462 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Kawakatsu Taiji T Huang Shao-Shan Carol SC Jupe Florian F Sasaki Eriko E Schmitz Robert J RJ Urich Mark A MA Castanon Rosa R Nery Joseph R JR Barragan Cesar C He Yupeng Y Chen Huaming H Dubin Manu M Lee Cheng-Ruei CR Wang Congmao C Bemm Felix F Becker Claude C O'Neil Ryan R O'Malley Ronan C RC Quarless Danjuma X DX Schork Nicholas J NJ Weigel Detlef D Nordborg Magnus M Ecker Joseph R JR

Cell 20160701 2

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation le ...[more]

PMID: 27419873

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Project description:BackgroundSeed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination.ResultsWe present an integrated analysis of high-resolution RNA sequencing, small RNA sequencing and MethylC sequencing over ten developmental time points in Arabidopsis thaliana seeds, finding extensive transcriptomic and epigenomic transformations associated with seed germination. We identify previously unannotated loci from which messenger RNAs are expressed transiently during germination and find widespread alternative splicing and divergent isoform abundance of genes involved in RNA processing and splicing. We generate the first dynamic transcription factor network model of germination, identifying known and novel regulatory factors. Expression of both microRNA and short interfering RNA loci changes significantly during germination, particularly between the seed and the post-germinative seedling. These are associated with changes in gene expression and large-scale demethylation observed towards the end of germination, as the epigenome transitions from an embryo-like to a vegetative seedling state.ConclusionsThis study reveals the complex dynamics and interactions of the transcriptome and epigenome during seed germination, including the extensive remodelling of the seed DNA methylome from an embryo-like to vegetative-like state during the seed-to-seedling transition. Data are available for exploration in a user-friendly browser at https://jbrowse.latrobe.edu.au/germination_epigenome .

Dataset Information

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Publications

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Similar Datasets

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