Abstract
Here, we present two approaches to map DNA double-strand breaks (DSBs) and single-strand breaks (SSBs) in the genome of human cells. We named these methods respectively DSB-Seq and SSB-Seq. We tested the DSB and SSB-Seq in HCT1116, human colon cancer cells, and validated the results using the topoisomerase 2 (Top2)-poisoning agent etoposide (ETO). These methods are powerful tools for the direct detection of the physiological and pathological “breakome” of the DNA in human cells.
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Iacovoni JS et al (2010) High-resolution profiling of gammaH2AX around DNA double strand breaks in the mammalian genome. EMBO J 29(8):1446–1457
Blitzblau HG, Hochwagen A (2011) Genome-wide detection of meiotic DNA double-strand break hotspots using single-stranded DNA. Methods Mol Biol 745:47–63
Hu J et al (2016) Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat Protoc 11(5):853–871
Klein IA et al (2011) Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell 147(1):95–106
Chiarle R et al (2011) Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 147(1):107–119
Tsai SQ et al (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33(2):187–197
Wang XL et al (2015) Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat Biotechnol 33(2):175–178
Crosetto N et al (2013) Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods 10(4):361–365
Canela A et al (2016) DNA breaks and end resection measured genome-wide by end sequencing. Mol Cell 63(5):898–911
Aguilera A, Garcia-Muse T (2013) Causes of genome instability. Annu Rev Genet 47:1–32
Baranello L et al (2014) DNA break mapping reveals topoisomerase II activity genome-wide. Int J Mol Sci 15(7):13111–13122
Rigby PW et al (1977) Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol 113(1):237–251
Kouzine F et al (2013) Global regulation of promoter melting in naive lymphocytes. Cell 153(5):988–999
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9(4):357–359
Bardet AF et al (2012) A computational pipeline for comparative ChIP-seq analyses. Nat Protoc 7(1):45–61
Caldecott KW (2008) Single-strand break repair and genetic disease. Nat Rev Genet 9(8):619–631
Barnes DE, Lindahl T (2004) Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Annu Rev Genet 38:445–476
Sartori AA et al (2007) Human CtIP promotes DNA end resection. Nature 450(7169):509–514
Symington LS, Gautier J (2011) Double-strand break end resection and repair pathway choice. Annu Rev Genet 45:247–271
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Baranello, L. et al. (2018). Mapping DNA Breaks by Next-Generation Sequencing. In: Muzi-Falconi, M., Brown, G. (eds) Genome Instability. Methods in Molecular Biology, vol 1672. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7306-4_13
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DOI: https://doi.org/10.1007/978-1-4939-7306-4_13
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