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

Jinchuan Hu, Sheera Adar, Christopher P. Selby, Jason D. Lieb, Aziz Sancar*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

189 Scopus citations

Abstract

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.

Original languageAmerican English
Pages (from-to)948-960
Number of pages13
JournalGenes and Development
Volume29
Issue number9
DOIs
StatePublished - 1 May 2015

Bibliographical note

Publisher Copyright:
© 2015 Hu et al.

Keywords

  • Divergent transcription
  • Genome-wide
  • Nucleotide excision repair
  • Transcription-coupled repair
  • UV damage

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