DNA Breaks and End Resection Measured Genome-wide by End Sequencing

Mol Cell. 2016 Sep 1;63(5):898-911. doi: 10.1016/j.molcel.2016.06.034. Epub 2016 Jul 28.

Abstract

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.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Ataxia Telangiectasia Mutated Proteins / genetics
  • Ataxia Telangiectasia Mutated Proteins / immunology
  • B-Lymphocytes / cytology
  • B-Lymphocytes / immunology
  • Chromatin / chemistry*
  • Chromatin / immunology
  • DNA / genetics*
  • DNA / immunology
  • DNA Breaks, Double-Stranded*
  • DNA Replication
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / immunology
  • Gene Expression Regulation
  • Genome*
  • High-Throughput Nucleotide Sequencing / methods*
  • Histones / genetics
  • Histones / immunology
  • Immunoglobulin Class Switching / genetics
  • Mice
  • Precursor Cells, B-Lymphoid / cytology
  • Precursor Cells, B-Lymphoid / immunology
  • Receptors, Antigen, T-Cell, alpha-beta / genetics
  • Receptors, Antigen, T-Cell, alpha-beta / immunology
  • Recombination, Genetic
  • Thymocytes / cytology
  • Thymocytes / immunology

Substances

  • Chromatin
  • DNA-Binding Proteins
  • Histones
  • Rag2 protein, mouse
  • Receptors, Antigen, T-Cell, alpha-beta
  • DNA
  • Ataxia Telangiectasia Mutated Proteins
  • Atm protein, mouse