Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

被引：343

作者：

Crosetto, Nicola ^{[1
,2
]}

Mitra, Abhishek ^{[3
]}

Silva, Maria Joao ^{[4
]}

Bienko, Magda ^{[1
,2
]}

Dojer, Norbert ^{[3
]}

Wang, Qi ^{[5
,6
]}

Karaca, Elif ^{[5
,6
]}

Chiarle, Roberto ^{[5
,6
,7
]}

Skrzypczak, Magdalena ^{[8
]}

Ginalski, Krzysztof ^{[8
]}

Pasero, Philippe ^{[4
]}

Rowicka, Maga ^{[3
,9
,10
]}

Dikic, Ivan ^{[1
,2
]}

机构：

[1] Goethe Univ Frankfurt, Sch Med, Inst Biochem 2, D-60054 Frankfurt, Germany

[2] Goethe Univ Frankfurt, Sch Med, Buchmann Inst Mol Life Sci, D-60054 Frankfurt, Germany

[3] Univ Texas Med Branch Galveston UTMB, Inst Translat Sci, Galveston, TX USA

[4] CNRS, IGH, Unite Propre Rech 1142, Montpellier, France

[5] Childrens Hosp, Dept Pathol, Boston, MA 02115 USA

[6] Harvard Univ, Sch Med, Boston, MA USA

[7] Univ Turin, Dept Mol Biotechnol & Hlth Sci, Turin, Italy

[8] Univ Warsaw, Ctr New Technol, Lab Bioinformat & Syst Biol, Warsaw, Poland

[9] UTMB, Dept Biochem & Mol Biol, Galveston, TX USA

[10] UTMB, Sealy Ctr Mol Med, Galveston, TX USA

来源：

NATURE METHODS | 2013年 / 10卷 / 04期

基金：

欧洲研究理事会;

关键词：

CLASS SWITCH RECOMBINATION; HUMAN CANCER GENES; H2AX PHOSPHORYLATION; GENOMIC INSTABILITY; DAMAGE RESPONSE; FRAGILE SITES; REPLICATION; GAMMA-H2AX; CHROMOSOME; CELLS;

D O I：

10.1038/nmeth.2408

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：361 / +

页数：8

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