Conservation of chromatin states and their association with transcription in land plants

The complexity of varied modifications of chromatin composition is reduced to archetypal combinations called chromatin states that broadly define the local potential for transcription. The degree of conservation of chromatin states has not been established amongst plants, and how they interact with transcription factors is unknown. We have identified and characterized chromatin states in the flowering plant Arabidopsis thaliana and the bryophyte Marchantia polymorpha, showing a large degree of functional conservation over more than 450 million years of land plant evolution. We analyzed the interplay between transcription factors and chromatin states to understand their influence on gene regulation. Combining binding sites with activity of transcription factors, we have shown their preferential association with specific chromatin states in both species. These associations define three main groups of transcription factors that bind in the promoter 5' of the transcription start site, at the +1 nucleosome or inside the gene body downstream of the transcription start site. These groups broadly associate with distinct functions, such as house-keeping genes, putative pioneer factors, development, and response to the environment, suggesting co-evolution of the chromatin regulatory mechanisms with transcription factors. Overall design: ChIP-seq for histone H2A variants: H2A.Z, H2A.X.1, H2A.X.2, H2A.M.2 performed in 14 days old thalie of Marchantia polymorpha (wt-Tak1). ChIP-seq for histone modifications H3K27me3, H2AKUb, H3K4me3, H3K27me1, and H3K9me1 in wild type and Mpez1,Mpknox2 double mutant of of Marchantia polymorpha.