Cargando…

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

We present a genome-wide method to map DNA double-strand breaks (DSBs) at nucleotide resolution by direct in situ breaks labeling, enrichment on streptavidin, and next-generation sequencing (BLESS). We comprehensively validated and tested BLESS using different human and mouse cells, DSBs-inducing ag...

Descripción completa

Detalles Bibliográficos
Autores principales: Crosetto, Nicola, Mitra, Abhishek, Silva, Maria Joao, Bienko, Magda, Dojer, Norbert, Wang, Qi, Karaca, Elif, Chiarle, Roberto, Skrzypczak, Magdalena, Ginalski, Krzysztof, Pasero, Philippe, Rowicka, Maga, Dikic, Ivan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651036/
https://www.ncbi.nlm.nih.gov/pubmed/23503052
http://dx.doi.org/10.1038/nmeth.2408
_version_ 1782269151772934144
author Crosetto, Nicola
Mitra, Abhishek
Silva, Maria Joao
Bienko, Magda
Dojer, Norbert
Wang, Qi
Karaca, Elif
Chiarle, Roberto
Skrzypczak, Magdalena
Ginalski, Krzysztof
Pasero, Philippe
Rowicka, Maga
Dikic, Ivan
author_facet Crosetto, Nicola
Mitra, Abhishek
Silva, Maria Joao
Bienko, Magda
Dojer, Norbert
Wang, Qi
Karaca, Elif
Chiarle, Roberto
Skrzypczak, Magdalena
Ginalski, Krzysztof
Pasero, Philippe
Rowicka, Maga
Dikic, Ivan
author_sort Crosetto, Nicola
collection PubMed
description We present a genome-wide method to map DNA double-strand breaks (DSBs) at nucleotide resolution by direct in situ breaks labeling, enrichment on streptavidin, and next-generation sequencing (BLESS). We comprehensively validated and tested BLESS using different human and mouse cells, DSBs-inducing agents, and sequencing platforms. BLESS was able to detect telomere ends, Sce endonuclease-induced DSBs, and complex genome-wide DSBs landscapes. As a proof of principle, we characterized the genomic landscape of sensitivity to replication stress in human cells, and identified over two thousand non-uniformly 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.
format Online
Article
Text
id pubmed-3651036
institution National Center for Biotechnology Information
language English
publishDate 2013
record_format MEDLINE/PubMed
spelling pubmed-36510362013-10-01 Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing Crosetto, Nicola Mitra, Abhishek Silva, Maria Joao Bienko, Magda Dojer, Norbert Wang, Qi Karaca, Elif Chiarle, Roberto Skrzypczak, Magdalena Ginalski, Krzysztof Pasero, Philippe Rowicka, Maga Dikic, Ivan Nat Methods Article We present a genome-wide method to map DNA double-strand breaks (DSBs) at nucleotide resolution by direct in situ breaks labeling, enrichment on streptavidin, and next-generation sequencing (BLESS). We comprehensively validated and tested BLESS using different human and mouse cells, DSBs-inducing agents, and sequencing platforms. BLESS was able to detect telomere ends, Sce endonuclease-induced DSBs, and complex genome-wide DSBs landscapes. As a proof of principle, we characterized the genomic landscape of sensitivity to replication stress in human cells, and identified over two thousand non-uniformly 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. 2013-03-17 2013-04 /pmc/articles/PMC3651036/ /pubmed/23503052 http://dx.doi.org/10.1038/nmeth.2408 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Crosetto, Nicola
Mitra, Abhishek
Silva, Maria Joao
Bienko, Magda
Dojer, Norbert
Wang, Qi
Karaca, Elif
Chiarle, Roberto
Skrzypczak, Magdalena
Ginalski, Krzysztof
Pasero, Philippe
Rowicka, Maga
Dikic, Ivan
Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
title Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
title_full Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
title_fullStr Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
title_full_unstemmed Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
title_short Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
title_sort nucleotide-resolution dna double-strand breaks mapping by next-generation sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651036/
https://www.ncbi.nlm.nih.gov/pubmed/23503052
http://dx.doi.org/10.1038/nmeth.2408
work_keys_str_mv AT crosettonicola nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT mitraabhishek nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT silvamariajoao nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT bienkomagda nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT dojernorbert nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT wangqi nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT karacaelif nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT chiarleroberto nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT skrzypczakmagdalena nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT ginalskikrzysztof nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT paserophilippe nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT rowickamaga nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing
AT dikicivan nucleotideresolutiondnadoublestrandbreaksmappingbynextgenerationsequencing