Distinct development-associated roles of rice histonevariant H2A.X in suppressing deposition of activeH3K4me3 marks and in restricting H2A.W incorporation

Histone variant H2A.X is a well-conserved histone that plays crucial roles in mediating DNA damage response across eukaryotes. Although H2A.X expresses even without any stress, and decorates gene bodies of actively expressed genes, it is not known if H2A.X has functions beyond DNA damage repair. Using genetic, high throughput genomics and molecular approaches, we identified a previously unappreciated role of H2A.X in regulating development-associated genes. Using custom-made antibodies specific to H2A.X variant, we show that it suppressed the deposition of active H3K4me3 marks over gene bodies and Transposable elements (TE)s, specifically regulating several root development, photosynthesis, and pigmentation-related genes as seen by the impairment of these processes in h2a.x ko (knockout) plants. H2A.X also suppressed global deposition of repressive mark H3K9me2 by restricting activity of H2A variant H2A.W. In agreement with this, there was a genome-wide re-localization of H2A.W to TEs and a few genes in h2a.x ko plants. H2A.X overexpressing plants exhibited stress phenotypes including increased anthocyanin levels, mimicking the transcriptome of DNA damaged wildtype plants. The transcriptome of kd lines of FACT complex, a known chaperone of H2A.X, was largely similar to that of h2a.x ko, suggesting that the development-associated functions of FACT are at least partially due to H2A.X. These results suggest a key role of H2A.X in regulating the competing histone marks and this function might be conserved across plants. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/707635v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1b2fe74org.highwire.dtl.DTLVardef@5fa3c8org.highwire.dtl.DTLVardef@f9b741org.highwire.dtl.DTLVardef@6e1101_HPS_FORMAT_FIGEXP M_FIG C_FIG