Rice specific Histone H4 Variant forecasts a stress dependent epigenetic program by virtue of distinct nucleosome properties [ChIP-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. We performed ChIP seq analyses to look at the binding sites of histone H4 variant in WT , h4v knockout (h4vko), overexpression of H4 variant (H4VOE) seedlings. Seedlings were also administered salt stress to evaluate the binding site differences upon salt stress. These are performed in biological replicates and plants grown uniformly were used for the analyses. For histone H4 variant, custom generated antibody was used while for other histone marks like canonical H4 and H4K5Ac, commercially available antibodies were used.