School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA.
Center for Reproductive Biology, Washington State University, Pullman, Washington 99164, USA.
Genome Res. 2021 Jun;31(6):1047-1059. doi: 10.1101/gr.274373.120. Epub 2021 May 17.
Nucleosomes are a significant barrier to the repair of UV damage because they impede damage recognition by nucleotide excision repair (NER). The RSC and SWI/SNF chromatin remodelers function in cells to promote DNA access by moving or evicting nucleosomes, and both have been linked to NER in yeast. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells lacking RSC or SWI/SNF activity. Our data indicate that SWI/SNF is not generally required for NER but instead promotes repair of CPD lesions at specific yeast genes. In contrast, mutation or depletion of RSC subunits causes a general defect in NER across the yeast genome. Our data indicate that RSC is required for repair not only in nucleosomal DNA but also in neighboring linker DNA and nucleosome-free regions (NFRs). Although depletion of the RSC catalytic subunit also affects base excision repair (BER) of -methylpurine (NMP) lesions, RSC activity is less important for BER in linker DNA and NFRs. Furthermore, our data indicate that RSC plays a direct role in transcription-coupled NER (TC-NER) of transcribed DNA. These findings help to define the specific genomic and chromatin contexts in which each chromatin remodeler functions in DNA repair, and indicate that RSC plays a unique function in facilitating repair by both NER subpathways.
核小体是修复 UV 损伤的一个重要障碍,因为它们阻碍核苷酸切除修复(NER)对损伤的识别。RSC 和 SWI/SNF 染色质重塑酶在细胞中通过移动或驱逐核小体来促进 DNA 进入,并且在酵母中都与 NER 有关。在这里,我们报告了在缺乏 RSC 或 SWI/SNF 活性的酵母细胞中,紫外线诱导的环丁烷嘧啶二聚体(CPD)的全基因组修复图谱。我们的数据表明,SWI/SNF 一般不需要 NER,但它可以促进特定酵母基因中 CPD 损伤的修复。相比之下,RSC 亚基的突变或缺失会导致酵母基因组中 NER 的普遍缺陷。我们的数据表明,RSC 不仅需要修复核小体 DNA,还需要修复相邻的连接 DNA 和无核小体区域(NFR)。尽管 RSC 催化亚基的耗竭也会影响 -甲基嘌呤(NMP)损伤的碱基切除修复(BER),但 RSC 活性对链接 DNA 和 NFR 中的 BER 并不重要。此外,我们的数据表明,RSC 在转录偶联的 NER(TC-NER)中发挥直接作用。这些发现有助于确定每个染色质重塑酶在 DNA 修复中发挥作用的特定基因组和染色质环境,并表明 RSC 在促进 NER 子途径的修复方面发挥着独特的作用。