DNA breaks and end resection measured genome-wide by end sequencing

Molecular Cell Cover - Vol. 63, No. 5, September 1, 2016

About the Cover

The cover depicts a ribbon of DNA portrayed as a city skyline. The central gap in the landscape localizes to the precise site of the DNA break. The features surrounding the break denote the processing of DNA-end structures (end-resection) emanating from the break location. Cover artwork by Ethan Tyler, NIH.


DNA double-strand breaks (DSBs) arise during physiological transcription, DNA replication, and antigen receptor diversification. Mistargeting or misprocessing of DSBs can result in pathological structural variation and mutation. Here we describe a sensitive method (END-seq) to monitor DNA end resection and DSBs genome-wide at base-pair resolution in vivo. We utilized END-seq to determine the frequency and spectrum of restriction-enzyme-, zinc-finger-nuclease-, and RAG-induced DSBs. Beyond sequence preference, chromatin features dictate the repertoire of these genome-modifying enzymes. END-seq can detect at least one DSB per cell among 10,000 cells not harboring DSBs, and we estimate that up to one out of 60 cells contains off-target RAG cleavage. In addition to site-specific cleavage, we detect DSBs distributed over extended regions during immunoglobulin class-switch recombination. Thus, END-seq provides a snapshot of DNA ends genome-wide, which can be utilized for understanding genome-editing specificities and the influence of chromatin on DSB pathway choice.

Laboratory of Genome Integrity

DNA breaks and end resection measured genome-wide by end sequencing. Canela A, Sridharan S, Sciascia N, Tubbs A, Meltzer P, Sleckman BP, and Nussenzweig A . Mol Cell. 2016 Sep 1;63(5):898-911.

Published Date: 
September, 2016