DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [ChIP-Seq]

DNA methylation and histone modifications cooperate to shape the epigenetic landscape for transcription regulation, but their orchestration is not fully understood due to the lack of met1 drm1 drm2 cmt2 cmt3 mutants (mddcc), in which total DNA methylation were eliminated. This is the first time to generate mddcc that allow us to elucidate the roles of DNA methylation in the upheaval of histone modification landscape, transposon activity and gene expression. We found that DNA methylation elimination-triggered genome-wide transcriptional reprogramming is largely orchestrated by the redistribution and conversion of histone modifications. We also distinguished the contribution of CG and non-CG methylation to the histone modification landscape. Furthermore, we reveal histone modifications can serve as an independent regulatory system despite the influence of DNA methylation. Taken together, we provide comprehensive insights into the roles of DNA methylation in shaping epigenomic landscape for genome transcription, which deep understanding of epigenomic regulation. Overall design: Here, we generated genome-wide profiling of six histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach in wild-type (Col-0), ddcc (drm1 drm2 cmt2 cmt3), met1, and mddcc (met1 drm1 drm2 cmt2 cmt3). By integrating DNA methylation, and transcriptome datasets, we revealed the roles of DNA methylation in histone modification landscape and transcriptional regulation.