Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.
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.
Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA;
Jinchuan
J
Hu
Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
Sheera
S
Adar
Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA;
Christopher P
CP
Selby
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA aziz_sancar@med.unc.edu jdlieb@uchicago.edu.
Jason D
JD
Lieb
Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA; aziz_sancar@med.unc.edu jdlieb@uchicago.edu.
Aziz
A
Sancar
D002460:Cell Line; D004249:DNA Damage / Q000528:radiation effects*; D004260:DNA Repair / Q000235:genetics*; D004742:Enhancer Elements, Genetic / Q000235:genetics; D055106:Genome-Wide Association Study; D006801:Humans; D009711:Nucleotides / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011740:Pyrimidine Dimers / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics; D014466:Ultraviolet Rays
D009711:Nucleotides; D011740:Pyrimidine Dimers; C058406:pyrimidine-pyrimidone dimer
UV damage; divergent transcription; enhancer; genome-wide; nucleotide excision repair; transcription-coupled repair