Kose Cansu, Lindsey-Boltz Laura A, Sancar Aziz, Jiang Yuchao
Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
Department of Statistics, College of Arts and Sciences, Texas A&M University, College Station, TX 77843, USA.
bioRxiv. 2024 Mar 29:2023.10.12.562083. doi: 10.1101/2023.10.12.562083.
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 the eXcision Repair-sequencing (XR-seq) in the model organism to generate genome-wide repair maps from a wild-type strain with normal excision repair, a strain lacking TCR (), or one that only repairs by TCR (-). Analysis of the intersections between the 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.
诸如紫外线诱导产生的大体积DNA加合物，可通过核苷酸切除修复从多细胞生物体的基因组中去除，该修复过程通过两种不同机制进行：全局修复，需要DNA损伤识别因子XPC（着色性干皮病互补组C）；转录偶联修复（TCR），则不需要。当延伸的RNA聚合酶II遇到DNA损伤时，TCR启动，因此，对仅通过TCR进行修复的XPC突变体中的全基因组切除修复进行分析，提供了一个独特的机会，来绘制那些依赖于捕获RNA转录产物的方法所遗漏的转录事件，而这些方法受RNA稳定性和/或修饰（5'端加帽或3'端聚腺苷酸化）的限制。在这里，我们在模式生物中进行了切除修复测序（XR-seq），以从具有正常切除修复功能的野生型菌株、缺乏TCR的菌株（）或仅通过TCR进行修复的菌株（-）生成全基因组修复图谱。对XR-seq修复图谱与RNA映射数据集（RNA-seq、长链和短链加帽RNA-seq）之间的交叉点进行分析，揭示了以前未被识别的转录位点，并进一步加深了我们对这种重要模式生物基因组的理解。
