Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

• Published in: Genes & development Vol. 29; no. 9; pp. 948 - 960
• Main Authors: Hu, Jinchuan, Adar, Sheera, Selby, Christopher P, Lieb, Jason D, Sancar, Aziz
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.05.2015
• Subjects: Cell Line; DNA Damage - radiation effects; DNA Repair - genetics; Enhancer Elements, Genetic - genetics; Genome-Wide Association Study; Humans; Nucleotides - genetics; Promoter Regions, Genetic - genetics; Pyrimidine Dimers - genetics; Research Paper; Transcription, Genetic - genetics; Ultraviolet Rays; enhancer; genome-wide; UV damage; nucleotide excision repair; divergent transcription; transcription-coupled repair
• ISSN: 0890-9369; 1549-5477
• DOI: 10.1101/gad.261271.115

We developed a method for genome-wide mapping of DNA excision repair named XR-seq (excision repair sequencing). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating an ∼30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells: cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts [(6-4)PPs]. In wild-type cells, CPD repair was highly associated with transcription, specifically with the template strand. Experiments in cells defective in either transcription-coupled excision repair or general excision repair isolated the contribution of each pathway to the overall repair pattern and showed that transcription-coupled repair of both photoproducts occurs exclusively on the template strand. XR-seq maps capture transcription-coupled repair at sites of divergent gene promoters and bidirectional enhancer RNA (eRNA) production at enhancers. XR-seq data also uncovered the repair characteristics and novel sequence preferences of CPDs and (6-4)PPs. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells.