Covalent DNA–protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs and how cells respond when RNA polymerases stall at DPCs is unknown. Here we find that DPC formation arrests transcription and induces ubiquitylation and degradation of RNA polymerase II. Using genetic screens and a method for the genome-wide mapping of DNA–protein adducts, DPC sequencing, we discover that Cockayne syndrome (CS) proteins CSB and CSA provide resistance to DPC-inducing agents by promoting DPC repair in actively transcribed genes. Consequently, CSB- or CSA-deficient cells fail to efficiently restart transcription after induction of DPCs. In contrast, nucleotide excision repair factors that act downstream of CSB and CSA at ultraviolet light-induced DNA lesions are dispensable. Our study describes a transcription-coupled DPC repair pathway and suggests that defects in this pathway may contribute to the unique neurological features of CS.

共价 DNA-蛋白质交联 (DPC) 是有毒的 DNA 损伤，会阻止复制并需要通过多种途径进行修复。转录阻断是否会导致 DPC 的毒性以及当 RNA 聚合酶在 DPC 上停滞时细胞如何反应尚不清楚。在这里，我们发现 DPC 的形成会阻止转录并诱导 RNA 聚合酶 II 的泛素化和降解。使用遗传筛选和 DNA-蛋白质加合物全基因组作图方法以及 DPC 测序，我们发现科凯恩综合征 (CS) 蛋白 CSB 和 CSA 通过促进活跃转录基因中的 DPC 修复来提供对 DPC 诱导剂的抗性。因此，CSB 或 CSA 缺陷的细胞在诱导 DPC 后无法有效地重新启动转录。相比之下，在紫外线诱导的 DNA 损伤中作用于 CSB 和 CSA 下游的核苷酸切除修复因子是可有可无的。我们的研究描述了转录偶联的 DPC 修复途径，并表明该途径的缺陷可能导致 CS 独特的神经学特征。