Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Abstract

SUMMARY 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 reveals 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.

TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death inArabidopsis

“…Consistent with this interpretation, public methylation data indicate that the ∼830 bp section immediately upstream of RBA1 is methylated to a lower extent in Ag-0 than in Col-0 ( Fig. S2G) (26). This region contains the 725-bp promoter used to drive our native promoter RBA1 construct and thus is sufficient for function.…”

Mapping genome-wide transcription-factor binding sites using DAP-seq

“…DAP-seq is particularly attractive for species where generation of transgenic lines for ChIP-seq is lengthy, costly, or technically challenging. DAP-seq can also be modified to study the effects of various perturbations such as nucleotide variation in DNA-binding domains (genetic variants) or TF binding variation due to DNA methylation (epigenomic variants) 24 . Furthermore, as the assay is in vitro, additional components or protein interaction partners can easily be added to assess their impact on DNA binding without interference from unknown factors.…”

Genetic and epigenetic variation of transposable elements in Arabidopsis

“…The study of natural Arabidopsis accessions has revealed insights into genetic and epigenetic TE polymorphisms, and variation in TE copy number and sequence [19,33–35]. Furthermore, the identification of novel TE insertion sites, compared to the Col-0 reference, in hundreds of natural accessions has identified COPIA and MuDR elements as the most active TEs in the recent history of the species [19].…”

“…Since their divergence, any two Arabidopsis accessions are predicted to have between 200 and 300 new TE insertions, and the flowering time regulator FLC and various NLR immunity genes were identified to be prone to TE insertion and haplotype maintenance [19]. Arabidopsis accessions show significant variation in DNA methylation, which includes a geographical component [35–37]. TE epigenetic variation may be influenced by genetic control by trans acting factors, due to genetic variation in cis within the element or due to epiallelic variation in cis [19,35,36].…”