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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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2013
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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 |
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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 |
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