Sequence and chromatin features guide DNA double-strand break resection initiation

DNA double-strand breaks (DSBs) are cytotoxic genome lesions that must be accurately and efficiently re-paired to ensure genome integrity. In yeast, the Mre11-Rad50-Xrs2 (MRX) complex nicks 5'-terminated DSB ends to initiate nucleolytic processing of DSBs for repair by homologous recombination. How MRX-DNA interactions support 5' strand-specific nicking and how nicking is influenced by the chromatin context have remained elusive. Using a deep sequencing-based assay, we mapped MRX nicks at single-nucleotide resolution next to multiple DSBs in the yeast genome. We observed that the DNA end-binding Ku70-Ku80 complex directed DSB-proximal nicks and that repetitive MRX cleavage extended the length of resection tracts. We identified a sequence motif and a DNA meltability profile that is preferentially nicked by MRX. Furthermore, we found that nucleosomes as well as transcription impeded MRX incisions. Our findings sug-gest that local DNA sequence and chromatin features shape the activity of this central DSB repair complex.

Automated summary

DNA double-strand breaks (DSBs) are cytotoxic genome lesions that must be accurately and efficiently repaired to maintain genome integrity. The Mre11-Rad50-Xrs2 (MRX) complex in yeast initiates nucleolytic processing of DSBs for repair by homologous recombination through 5'-terminated DSB end nicking. The study reveals that the Ku70-Ku80 complex directs DSB-proximal nicks and that repetitive MRX cleavage extends the length of resection tracts. The findings also show that local DNA sequence and chromatin features influence MRX activity.