Biernat, E. | Search bioRxiv

bioRxiv2022

The role of histone acetyltransferases Gcn5 and Esa1 in recruiting the RSC complex 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 (HATs) Gcn5 and Esa1 in regulating RSC and histone occupancies and their effects on transcription genome-wide. We identified contrasting roles of HATs in modulating RSC occupancies in promoters and ORFs. In HAT mutants, RSC accumulated in nucleosome depleted regions (NDRs) with "fragile nucleosomes (FNs)" more than those with stable -1 nucleosomes. Moreover, the accumulation was more significant in the Esa1 mutant than in the Gcn5 mutant. However, RSC NDR accumulation was not observed in cells lacking H3 or H4 tails. Furthermore, we observed marked increases in histone occupancies in NDRs in the HAT mutants genome-wide. Overall, these data suggest that FNs use hypoacetylated tails to recruit RSC to NDRs, and subsequent acetylation of the tails promote histone eviction. In contrast to the promoters, RSC occupancies were significantly reduced in transcribed ORFs in the HAT mutants. Additionally, the HAT mutants showed reduced TBP and Pol II binding at promoters. Thus, our data implicate HATs and RSC in maintaining NDRs, regulating chromatin structure, and promoting transcription.

genomics↗

bioRxiv2020

The RSC complex remodels nucleosomes in transcribed coding sequences and promotes transcription in Saccharomyces cerevisiae

RSC (Remodels the Structure of Chromatin) is a conserved ATP-dependent chromatin remodeling complex that regulates many biological processes, including transcription by RNA polymerase II (Pol II). We report that RSC contributes to generation of accessible nucleosomes in transcribed coding sequences (CDSs). RSC MNase ChIP-seq data revealed that RSC-bound nucleosome fragments were very heterogenous (~80 bp to 180 bp) compared to a sharper profile displayed by the MNase inputs (140 bp to 160 bp), supporting the idea that RSC promotes accessibility of nucleosomal DNA. Notably, RSC binding to +1 nucleosomes and CDSs, but not with -1 nucleosomes, strongly correlated with Pol II occupancies, suggesting that RSC enrichment in CDSs is linked to transcription. We also observed that Pol II associates with nucleosomes throughout transcribed CDSs, and similar to RSC, Pol II-protected fragments were highly heterogenous, consistent with the idea that Pol II interacts with remodeled nucleosome in CDSs. This idea is supported by the observation that the genes harboring high-levels of RSC in their CDSs were the most strongly affected by ablating RSC function. We also find that rapid nuclear depletion of Sth1 decreases nucleosome accessibility and results in accumulation of Pol II in highly transcribed CDSs. This is consistent with a slower clearance of elongating Pol II in cells with reduced RSC function, and is distinct from the effect of RSC depletion on PIC assembly. Altogether, our data provide evidence in support of the role of RSC in promoting Pol II elongation, in addition to its role in regulating transcription initiation.

genomics↗