ArticleNature protocols2014
Quantifying DNA double-strand breaks induced by site-specific endonucleases in living cells by ligation-mediated purification.
Article in Nature protocols, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 34 citations in OpenAlex.
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- Article
- qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing.Nature communications · 2019Article
- Local activation of mammalian separase in interphase promotes double-strand break repair and prevents oncogenic transformation.The EMBO journal · 2018Article
- Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair.Nature communications · 2018Article
- Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations.Nature communications · 2018Article
- Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders.Nature · 2018Article
- A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks.Nature communications · 2017Article
- Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes.Nature structural & molecular biology · 2017Article
- Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53.Scientific reports · 2017Article
- WRN regulates pathway choice between classical and alternative non-homologous end joining.Nature communications · 2016Article
- Non-redundant Functions of ATM and DNA-PKcs in Response to DNA Double-Strand Breaks.Cell reports · 2015Article
- Target specificity of the CRISPR-Cas9 system.Quantitative biology (Beijing, China) · 2014Article
- Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks.Nature structural & molecular biology · 2014Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in our understanding of the management and repair of DNA double-strand breaks (DSBs) rely on the study of targeted DSBs that have been induced in living cells by the controlled activity of site-specific endonucleases, usually recombinant restriction enzymes. Here we describe a protocol for quantifying these endonuclease-induced DSBs; this quantification is essential to an interpretation of how DSBs are managed and repaired. A biotinylated double-stranded oligonucleotide is ligated to enzyme-cleaved genomic DNA, allowing the purification of the cleaved DNA on streptavidin beads. The extent of cleavage is then quantified either by quantitative PCR (qPCR) at a given site or at multiple sites by genome-wide techniques (e.g., microarrays or high-throughput sequencing). This technique, named ligation-mediated purification, can be performed in 2 d. It is more accurate and sensitive than existing alternative methods, and it is compatible with genome-wide analysis. It allows the amount of endonuclease-mediated breaks to be precisely compared between two conditions or across the genome, thereby giving insight into the influence of a given factor or of various chromatin contexts on local repair parameters.
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