ChIP-seq for Histone variants and Histone modifictaions in WT and ddm1(-/-)  in 1st generation Leaves.
How histone intrinsic sequence variation or regulatory modifications regulate nucleosome interactions with transcription remain unclear. To clarify this question, we examined how histone variants and histone modifications assemble in the Arabidopsis thaliana genome, identifying a limited number of chromatin states that divide euchromatin and heterochromatin in biologically significant subdomains. We showed that histone variants were as significant as histone modifications to determine the composition of chromatin states. The loss of function of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) prevented the exchange between the histone variants H2A.Z and H2A.W over transposons resulting in their enrichment in chromatin states found only on proteins coding genes in the wild type. Hence, the dynamics of histone H2A variants exchange impacted the definition and distribution of chromatin states. We propose that dynamics of histone variants control the organization of histone modifications into chromatin states to achieve landmarks that signify the ability for transcription. Chromatin immunoprecipitation sequencing (ChIP-seq) for histone H2A variants and histone modifications in Col0 and ddm1(-/-) . Overall design: ChIP-seq for Histone Variant and histone modifications WT and ddm1(-/-) was performed with 2 or more biological replicates each.