Analyzing the In Vivo Roles of Histone Acetyltransferases GCN5 And ESA1 in RSC Recruitment and Remodeling Activity Genome-Wide in Saccharomyces Cerevisiae

Transcription is important for gene expression and is a tightly-controlled process involving multiple mechanisms of regulation, including regulation by chromatin structure. Chromatin consists of nucleosomes, which are comprised of DNA wrapped around histone proteins. Chromatin remodelers such as the Remodels the Structure of Chromatin (RSC) complex play important roles in controlling DNA accessibility to the transcriptional machinery and organizing chromatin throughout the genome. Mutations in yeast and mammalian RSC orthologs have been linked to dysregulated cell cycle progression, chromosome segregation, stress response, and developmental processes. In this study, we investigated the mechanisms by which RSC associates with chromatin on a genome-wide scale and the impact of disrupted RSC-chromatin interactions on transcription. Previous studies have suggested that nucleosome acetylation via histone acetyltransferases (HATs) may facilitate RSC binding to chromatin. To explore this, we examined the effects of removing HATs Gcn5 and Esa1 on RSC occupancy. Surprisingly, our results revealed distinct effects of HAT loss on RSC occupancy at promoters and gene bodies. In promoters, the loss of HATs increased RSC association with promoter nucleosomes, particularly in promoters containing partially-unwrapped fragile nucleosomes. Additionally, we found that HAT-mediated acetylation is crucial for maintaining nucleosome depletion at promoters. Conversely, HAT loss decreased RSC occupancy in gene bodies of highly transcribed genes. This reduction in RSC binding was dependent on histone tails, as cells lacking these tails also showed a significant loss of RSC binding to gene bodies. High-resolution mapping and analyses demonstrated that RSC-bound nucleosomes, particularly in gene bodies, were highly accessible. Consistent with these findings, loss of HAT functions resulted in widespread transcriptional changes, impacting both transcription initiation and elongation. This work provides valuable insights into how HAT-mediated histone modifications regulate RSC association with chromatin and the consequent impact on global transcription.