Impact of dynamics of H2A variants on transcription

Gene expression in multicellular eukaryotes is regulated by histones, proteins that directly associate with DNA. Among the five families of histones, the H2A family contains variants that specifically occupy either expressed genes, repressed genes, or transposons. The regulatory mechanisms that control their specific patterns of deposition of H2A variants remains largely unknown. We have identified that the chromatin remodeler DDM1 is responsible for the deposition of the variant H2A.W on transposons in flowering plants. This chromatin remodeler and its ortholog in mammals were identified twenty years ago for their impact on transposon silencing and DNA methylation but their mechanism of action had remained unclear. This proposal will use a new genomic approach to determine whether the deposition of H2A.W by DDM1 is directly responsible for transposon silencing. We will use a combination of genetic and biochemical approaches to identify regulatory partners of DDM1. As histones and their associated chromatin remodelers in animals evolved in parallel with those in plants, this research will impact our understanding of chromatin dynamics in all eukaryotes.

Transposons are a major threat to genome integrity, and DNA methylation systems have a central role in preventing their mobilization. DNA methylation takes place in the context of the nucleosome, the fundamental unit of chromatin that wraps 147 base pairs (bp) of DNA around an octamer comprising a central tetramer of two histone H3-H4 dimers flanked by two histone H2A-H2B dimers. The deposition of DNA methylation and of specific H2A variants depend on the activity of DHL chromatin remodellers that perform a variety of processes on nucleosomes, including assembling, spacing, sliding, and evicting nucleosomes to make DNA more or less accessible. The plant DHL remodeller DDM1 deposits H2A.W to silence transposons. The purpose of this proposal was to identify the mechanisms of action of DDM1 and H2A.W in silencing the transcription of transposons. We collaborated to the discovery of the structure of DDM1 complexed with H2A.W. We have demonstrated that H2A.W acts in synergy with H3K9methylation to silence transposons and this largely independently from DNA methylation. We have also identified a cofactor of DDM1 and showed that it is subjected to evolutionary selection to change the epigenome to adapt natural plant populations to distinct life-styles. So our results expands the field of transposon silencing and put these new mechanisms in perspective of evolution and adaptation.