Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America.
Department of Statistics, College of Arts and Sciences, Texas A&M University, College Station, Texas, United States of America.
PLoS Genet. 2024 Jul 19;20(7):e1011365. doi: 10.1371/journal.pgen.1011365. eCollection 2024 Jul.
Bulky DNA adducts such as those induced by ultraviolet light are removed from the genomes of multicellular organisms by nucleotide excision repair, which occurs through two distinct mechanisms, global repair, requiring the DNA damage recognition-factor XPC (xeroderma pigmentosum complementation group C), and transcription-coupled repair (TCR), which does not. TCR is initiated when elongating RNA polymerase II encounters DNA damage, and thus analysis of genome-wide excision repair in XPC-mutants only repairing by TCR provides a unique opportunity to map transcription events missed by methods dependent on capturing RNA transcription products and thus limited by their stability and/or modifications (5'-capping or 3'-polyadenylation). Here, we have performed eXcision Repair-sequencing (XR-seq) in the model organism Caenorhabditis elegans to generate genome-wide repair maps in a wild-type strain with normal excision repair, a strain lacking TCR (csb-1), and a strain that only repairs by TCR (xpc-1). Analysis of the intersections between the xpc-1 XR-seq repair maps with RNA-mapping datasets (RNA-seq, long- and short-capped RNA-seq) reveal previously unrecognized sites of transcription and further enhance our understanding of the genome of this important model organism.
大体积 DNA 加合物，如紫外线诱导的加合物，可通过核苷酸切除修复从多细胞生物的基因组中去除，该修复通过两种不同的机制发生，即全局修复，需要 DNA 损伤识别因子 XPC（着色性干皮病互补组 C），和转录偶联修复（TCR），不需要。当延伸的 RNA 聚合酶 II 遇到 DNA 损伤时，TCR 就会启动，因此，在 XPC 突变体中仅通过 TCR 进行全基因组切除修复的分析，为绘制转录事件提供了独特的机会，这些转录事件会被依赖于捕获 RNA 转录产物的方法所遗漏，因此受到其稳定性和/或修饰（5' - 加帽或 3' - 多聚腺苷酸化）的限制。在这里，我们在模式生物秀丽隐杆线虫中进行了切除修复测序（XR-seq），以在具有正常切除修复的野生型菌株、缺乏 TCR（csb-1）的菌株和仅通过 TCR 修复的菌株（xpc-1）中生成全基因组修复图谱。xpc-1 XR-seq 修复图谱与 RNA 图谱数据集（RNA-seq、长和短加帽 RNA-seq）之间的交点分析揭示了以前未被识别的转录位点，并进一步增强了我们对这一重要模式生物基因组的理解。
