Rice specific Histone H4 Variant forecasts a stress dependent epigenetic program by virtue of distinct nucleosome properties [RNA-Seq]

Probing the rice genome for novel histone coding genes revealed a genera specific, histone H4 variant with several variations in N-terminal tail sequence motifs, expressing in a tissue-specific manner. Genetic perturbation of the H4 variant in rice led to defects in growth and fertility. Probing the chromatin binding sites of the H4 variant with a custom antibody revealed its binding at specific genes and its knockout led to mis-expression of stress-associated genes. Stress-challenged plants showed loss of the H4 variant and re-distribution of other H4 linked histone marks. In vitro reconstituted rice nucleosomes with H4 variant histones displayed atypical properties in terms of stability, intra-nucleosome binding and structure, when compared to the canonical nucleosomes. Overall design: We performed RNA seq analyses to look at the expression of the genes in WT , h4v knockout (h4v), overexpression (OE) of H4 variant (OE_H4V), H4 canonical (OE_H4C) and chimeric H4 (OE_H4CHMR) in seedlings and leaves. Seedlings were also administered salt stress to evaluate the gene expression changes upon salt stress in WT and h4v knockout plants. These are performed in biological duplicates and plants grown uniformly were used for the analyses.