Strand asymmetry influences mismatch resolution during single-strand annealing

ABSTRACT Background Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. However, such biases have not yet been measured in chromatin for lack of technologies. Results Here we develop a genome-wide assay whereby the same DNA lesion is repaired in different chromatin contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated when the single strand annealing repair pathway is used. Regardless of the mismatch, we observed a 60-80% bias in the resolution in favor of one strand. The location of the lesion in the genome and the type of mismatch had little influence on the bias in this context. Instead, changing the position of the double-strand break in the reporter gave a complete reversion of the bias. Conclusion These results suggest that the processing of the double-strand break has a major influence on the repair of mismatches during single-strand annealing, irrespective of the surrounding chromatin context.