DNA Repair Map Expected to Enhance Human Genome Studies

Researchers have created a map of the entire human genome that shows where repairs to DNA that has been damaged by radiation or chemical treatment are made.

Investigators at the University of North Carolina (Chapel Hill, USA) developed a technique called XR-Seq (excision repair sequencing) in order to prepare the map, which was presented in a paper published in the May 1, 2015, issue of the journal Genes & Development.

Human nucleotide excision repair generates two incisions surrounding the site of damage, creating a polymer of approximately 30 repeating units. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing.

The investigators 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 occurred exclusively on the template strand. XR-seq maps captured 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.

"Now we can say to a fellow scientist, tell us the gene you are interested in or any spot on the genome, and we will tell you how it is repaired," said senior author Dr. Aziz Sancar, professor of biochemistry and biophysics at the University of North Carolina. "Out of six billion base pairs, pick out a spot and we will tell you how it is repaired."

It is expected that 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.

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