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New Sequencing Assay Maps Genome-Wide DNA Repair After UV Damage

NEW YORK (GenomeWeb) – Scientists from the University of North Carolina have created a new genome-wide sequencing assay to map DNA excision repair. They reported on their method, called excision repair sequencing (XR-seq) this month in Genes & Development.

"Now we can say to a fellow scientist, 'Tell us the gene you're interested in, or any spot on the genome, and we'll tell you how it is repaired,'" Aziz Sancar, co-senior author and researcher at the UNC Lineberger Comprehensive Cancer Center, said in a statement. "Out of six billion base pairs, pick out a spot and we'll tell you how it is repaired."

When UV or some other agent damages the genome, the site is cut out in a fragment of DNA, which is usually then bound by the protein TFIIH. Using an antibody to bind that enzyme, the researchers were able to isolate the fragment-protein complexes and pull them out of cells to sequence them. Mapping the fragments back onto the genome then revealed where the DNA repair took place.

XR-seq was able to produce nucleotide-level resolution of repair for two types of ultraviolet light-induced damage, cyclobutane pyrimidine dimers and (6-4) pyrimidine-pyrimidone photoproducts.

The study suggests that regulatory regions of DNA that don't encode proteins are also being repaired in the cell, Sheera Adar, a postdoc and co-first author of the paper, said. "If they're being repaired, then they're likely important. And now we can find their locations throughout the genome."

The scientists also said the assay could be used to find the specific mechanisms that allow cancer cells to repair DNA damage to survive.

In 2014, scientists from the University of Tübingen and the German Cancer Research Center in Heidelberg, Germany, reported on a qPCR method to quantify DNA damage in nuclear and mitochondrial genomes in Nucleic Acids Research.

And in December 2014, Nature Biotechnology published two studies detailing sequencing-based methods to detect double stranded breaks in DNA, including those generated by genome editing nucleases.