GSE116643
H2A.W is essential for silencing of whole genome heterochromatin in Arabidopsis
Heterochromatin of flowering plants is occupied by histone variant H2A.W and marked by DNA and H3K9 methylation. The relative impact of these heterochromatic features on activity of Transposable Elements (TEs) remains largely unknown. We obtained mutants deficient for H2A.W and key components controlling each of the key heterochromatic pathway in Arabidopsis and observed that knock out of individual pathway does not affect in a major manner TEs activity. However, when we combine the loss of H2A.W with any of the other heterochromatin controller we observe synergistic effects on heterochromatin compaction as well TEs activity. H2A.W appears to control expression of all TEs while each other heterochromatin controller target distinct subsets of TEs. We also observe an impact of linker histone H1. We propose that H2A.W acts together with several components of heterochromatin to prevents activity of distinct sets of TEs activity and chromatin architecture. Synergistic action with H2A.W is more prominent specifically in pathways controlled by the plant specific DNA chromomethyltransferases, CMT2 and CMT3. Overall design: To study the role of H2A.W in the regulation of whole genome heterochromatin in Arabidopsis, we used high-throughput RNA-Seq and BS-seq approaches to investigate key mutants and double mutants potentially involved in RdDM pathways and chromatin structures.  The samples include WT, and mutants of h2aw, h1 double, h2aw/h1 quadruple, kyp6, h2aw/kyp6, nrpd2a, h2aw/nrpd2a, drm2-2-55103, h2aw_drm2-2-55105, cmt2-3, h2aw/cmt2-3