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 not only RSC binds to nucleosomes in coding sequences (CDSs) but also remodels them to promote transcription. RSC MNase ChIP-seq data revealed that RSC-protected fragments were very heterogenous (~80 bp to 180 bp) compared to the sharper profile displayed by the MNase inputs (140 bp to 160 bp), supporting the idea that RSC activity promotes accessibility of nucleosomal DNA. Importantly, RSC binding to +1 nucleosomes and CDSs, but not with -1 nucleosomes, strongly correlated with Pol II occupancies suggesting that the RSC enrichment in CDSs is important for efficient transcription. This is further supported by a similar heterogenous distribution of Pol II-protected fragments. As such, the genes harboring high-levels of RSC in their CDSs were the most strongly affected by ablating RSC function. Altogether, this study provides a mechanism by which RSC-mediated remodeling aids in RNA Pol II traversal though coding sequence nucleosomes in vivo.染色质结构重塑复合物RSC（Remodels the Structure of Chromatin）是一类保守的ATP依赖型染色质重塑复合物，可调控诸多生物学过程，其中包括RNA聚合酶II（Pol II）介导的转录。本研究发现，RSC不仅可结合编码序列（CDSs）中的核小体，还可对其进行重塑以促进转录。RSC的微球菌核酸酶染色质免疫共沉淀测序（MNase ChIP-seq）数据显示，相较于微球菌核酸酶输入样本呈现的140 bp至160 bp的尖锐分布特征，RSC保护的DNA片段异质性极强，长度范围约为80 bp至180 bp，这一结果佐证了RSC活性可提升核小体DNA可及性的观点。值得注意的是，RSC与+1核小体及编码序列的结合，而非-1核小体，与RNA聚合酶II的占据水平呈显著正相关，这表明编码序列中RSC的富集对于高效转录具有重要意义。这一结论进一步得到了RNA聚合酶II保护片段具有相似异质性分布的佐证。据此，那些在编码序列中高丰度富集RSC的基因，其转录过程受敲除RSC功能的影响最为显著。综上，本研究揭示了一种机制：RSC介导的染色质重塑可在体内辅助RNA聚合酶II穿越编码序列中的核小体。