Nucleotide-resolution DNA double-strand break 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
April 2013
Nature Methods;Apr2013, Vol. 10 Issue 4, p361
Academic Journal
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.


Related Articles

  • The Future of Mouse Genetics in Osteoporosis Research. Ackert-Bicknell, Cheryl L.; Rosen, Clifford J. // IBMS BoneKEy;Jun2009, p200 

    Focused studies examining the genetics of osteoporosis in the mouse began approximately fifteen years ago, but as these studies have progressed it has become apparent that the genetics of osteoporosis is more complicated than originally predicted. Traditional F2 inter-cross mapping in the mouse,...

  • Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells. Sequeira-Mendes, Joana; Díaz-Uriarte, Ramón; Apedaile, Anwyn; Huntley, Derek; Brockdorff, Neil; Gómez, María // PLoS Genetics;Apr2009, Vol. 5 Issue 4, p1 

    Genomic mapping of DNA replication origins (ORIs) in mammals provides a powerful means for understanding the regulatory complexity of our genome. Here we combine a genome-wide approach to identify preferential sites of DNA replication initiation at 0.4% of the mouse genome with detailed...

  • Technology: Genome-wide mapping of 5-formylcytosine. Burgess, Darren J. // Nature Reviews Genetics;Oct2012, Vol. 13 Issue 10, p675 

    The article discusses a study by researcher E. A. Raiber and colleagues which examines the genome-wide distribution of DNA demethylation of 5-formylcytosine (5fC) intermediate in the embryonic stem cells of mouse.

  • A TRF1-controlled common fragile site containing interstitial telomeric sequences. Bosco, Nazario; Lange, Titia // Chromosoma;Oct2012, Vol. 121 Issue 5, p465 

    Mouse telomeres have been suggested to resemble common fragile sites (CFS), showing disrupted TTAGGG fluorescent in situ hybridization signals after aphidicolin treatment. This 'fragile' telomere phenotype is induced by deletion of TRF1, a shelterin protein that binds telomeric DNA and promotes...

  • Of mice and men: molecular genetics of congenital heart disease. Andersen, Troels; Troelsen, Karin; Larsen, Lars // Cellular & Molecular Life Sciences;Apr2014, Vol. 71 Issue 8, p1327 

    Congenital heart disease (CHD) affects nearly 1 % of the population. It is a complex disease, which may be caused by multiple genetic and environmental factors. Studies in human genetics have led to the identification of more than 50 human genes, involved in isolated CHD or genetic syndromes,...

  • Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs. Maeda, Norihiro; Kasukawa, Takeya; Oyama, Rieko; Gough, Julian; Frith, Martin; Engström, Pär G.; Lenhard, Boris; Aturaliya, Rajith N.; Batalov, Serge; Beisel, Kirk W.; Bult, Carol J.; Fletcher, Colin F.; Forrest, Alistair R. R.; Furuno, Masaaki; Hill, David; Itoh, Masayoshi; Kanamori-Katayama, Mutsumi; Katayama, Shintaro; Katoh, Masaru; Kawashima, Tsugumi // PLoS Genetics;Apr2006, Vol. 2 Issue 4, pe62 

    The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional...

  • Genome-Scale Assessment of Age-Related DNA Methylation Changes in Mouse Spermatozoa. Kobayashi, Norio; Okae, Hiroaki; Hiura, Hitoshi; Chiba, Hatsune; Shirakata, Yoshiki; Hara, Kenshiro; Tanemura, Kentaro; Arima, Takahiro // PLoS ONE;11/23/2016, Vol. 11 Issue 11, p1 

    DNA methylation plays important roles in the production and functioning of spermatozoa. Recent studies have suggested that DNA methylation patterns in spermatozoa can change with age, but the regions susceptible to age-related methylation changes remain to be fully elucidated. In this study, we...

  • Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes. Mignone, Flavio; Anselmo, Anna; Donvito, Giacinto; Maggi, Giorgio P.; Grillo, Giorgio; Pesole, Graziano // BMC Genomics;2008, Vol. 9, Special section p1 

    Background: The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the...

  • Mouse Inbred Strain Sequence Information and Yin-Yang Crosses for Quantitative Trait Locus Fine Mapping. Shifman, Sagiv; Darvasi, Ariel // Genetics;Feb2005, Vol. 169 Issue 2, p849 

    The shared ancestry of mouse inbred strains, together with the availability of sequence and phenotype information, is a resource that can be used to map quantitative trait loci (QTL). The difficulty in using only sequence information lies in the fact that in most instances the allelic state of...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics