The role of histone acetyltransferases Gcn5 and Esa1 in recruiting RSC and maintaining nucleosome depleted regions genome-wide in Saccharomyces cerevisiae

Chromatin remodelers are essential for the maintenance of chromatin structure and gene regulation. In this study, we examined the role of histone acetyltransferases Gcn5 and Esa1 in regulating RSC and histone occupancies and transcription genome-wide. We identify the contrasting roles of HATs in modulating RSC occupancies in promoters and ORFs. In HAT mutants, we found RSC occupancies unexpectedly accumulate in the NDRs harboring the “fragile nucleosomes (FNs)” than those with the stable -1 nucleosomes. Moreover, the accumulation was more significant in the H4 HAT Esa1 mutant than in the Gcn5 mutant. However, NDR accumulation was not observed in the cells lacking the H3 or H4 tails, suggesting that unacetylated/hypoacetylated tails are critical for the increased RSC observed in the mutants. Furthermore, we observe marked increases in histone occupancies in NDRs in the mutants genome-wide. An increase in both RSC and histones at NDRs in the HAT mutants suggests that FNs use hypoacetylated tails to recruit RSC to NDRs, and acetylation is needed for efficient histone eviction. Thus, our data implicate HATs, in addition to RSC, in maintaining NDRs. Increased histone and RSC occupancies in promoters and reduced RSC occupancies in ORFs in the HAT mutants reduce TBP and Pol II binding at promoters. Overall design: Formaldehyde crosslinked yeast cells were subjected either to MNase digestion or sonication to obtain chromatin. The input MNase, and ChIPed sonicated and MNase chroamtin was subjected to paired-end Illumina 4K sequencing.