Nucleotide-resolution DNA Double-strand Break Mapping by Next-generation Sequencing

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2013 Mar 19

PMID 23503052

Citations 235

Authors

Nicola Crosetto

Abhishek Mitra

Maria Joao Silva

Magda Bienko

Norbert Dojer

Qi Wang

Elif Karaca

Roberto Chiarle

Magdalena Skrzypczak

Krzysztof Ginalski

Philippe Pasero

Maga Rowicka

Ivan Dikic

Affiliations

Soon will be listed here.

Abstract

We present a genome-wide approach to map DNA double-strand breaks (DSBs) at nucleotide resolution by a method we termed BLESS (direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing). We validated and tested BLESS using human and mouse cells and different DSBs-inducing agents and sequencing platforms. BLESS was able to detect telomere ends, Sce endonuclease-induced DSBs and complex genome-wide DSB landscapes. As a proof of principle, we characterized the genomic landscape of sensitivity to replication stress in human cells, and we identified >2,000 nonuniformly distributed aphidicolin-sensitive regions (ASRs) overrepresented in genes and enriched in satellite repeats. ASRs were also enriched in regions rearranged in human cancers, with many cancer-associated genes exhibiting high sensitivity to replication stress. Our method is suitable for genome-wide mapping of DSBs in various cells and experimental conditions, with a specificity and resolution unachievable by current techniques.

Citing Articles

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