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Volumn 11, Issue 5, 2016, Pages 853-871

Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing

Author keywords

[No Author keywords available]

Indexed keywords

SINGLE STRANDED DNA; DEOXYRIBONUCLEASE;

EID: 84962784449     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2016.043     Document Type: Article
Times cited : (194)

References (46)
  • 1
    • 77950955761 scopus 로고    scopus 로고
    • Origin of chromosomal translocations in lymphoid cancer
    • Nussenzweig, A., Nussenzweig, M.C. Origin of chromosomal translocations in lymphoid cancer. Cell 141, 27-38 (2010).
    • (2010) Cell , vol.141 , pp. 27-38
    • Nussenzweig, A.1    Nussenzweig, M.C.2
  • 2
    • 84873320525 scopus 로고    scopus 로고
    • Mechanisms of programmed DNA lesions and genomic instability in the immune system
    • Alt, F.W., Zhang, Y., Meng, F.-L., Guo, C., Schwer, B. Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell 152, 417-429 (2013).
    • (2013) Cell , vol.152 , pp. 417-429
    • Alt, F.W.1    Zhang, Y.2    Meng, F.-L.3    Guo, C.4    Schwer, B.5
  • 4
    • 84867386682 scopus 로고    scopus 로고
    • Classical and alternative end-joining pathways for repair of lymphocyte-specific and general DNA double-strand breaks
    • Boboila, C., Alt, F.W., Schwer, B. Classical and alternative end-joining pathways for repair of lymphocyte-specific and general DNA double-strand breaks. Adv. Immunol. 116, 1-49 (2012).
    • (2012) Adv. Immunol. , vol.116 , pp. 1-49
    • Boboila, C.1    Alt, F.W.2    Schwer, B.3
  • 5
    • 80755187806 scopus 로고    scopus 로고
    • Double-strand break end resection and repair pathway choice
    • Symington, L.S., Gautier, J. Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 45, 247-271 (2011).
    • (2011) Annu. Rev. Genet. , vol.45 , pp. 247-271
    • Symington, L.S.1    Gautier, J.2
  • 6
    • 84923275611 scopus 로고    scopus 로고
    • Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
    • Frock, R.L. et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat. Biotechnol. 33, 179-186 (2015).
    • (2015) Nat. Biotechnol. , vol.33 , pp. 179-186
    • Frock, R.L.1
  • 7
    • 84958157371 scopus 로고    scopus 로고
    • Long neural genes harbor recurrent DNA break clusters in neural stem/progenitor cells
    • Wei, P.C. et al. Long neural genes harbor recurrent DNA break clusters in neural stem/progenitor cells. Cell 164, 644-655.
    • Cell , vol.164 , pp. 644-655
    • Wei, P.C.1
  • 8
    • 84919903836 scopus 로고    scopus 로고
    • Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability
    • Meng, F.-L. et al. Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability. Cell 159, 1538-1548 (2014).
    • (2014) Cell , vol.159 , pp. 1538-1548
    • Meng, F.-L.1
  • 9
    • 84946200292 scopus 로고    scopus 로고
    • Chromosomal loop domains direct the recombination of antigen receptor genes
    • Hu, J. et al. Chromosomal loop domains direct the recombination of antigen receptor genes. Cell 163, 947-959 (2015).
    • (2015) Cell , vol.163 , pp. 947-959
    • Hu, J.1
  • 10
    • 84940942139 scopus 로고    scopus 로고
    • Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching
    • Dong, J. et al. Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching. Nature 525, 134-139 (2015).
    • (2015) Nature , vol.525 , pp. 134-139
    • Dong, J.1
  • 11
    • 80053558376 scopus 로고    scopus 로고
    • Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells
    • Chiarle, R. et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 147, 107-119 (2011).
    • (2011) Cell , vol.147 , pp. 107-119
    • Chiarle, R.1
  • 12
    • 84894302814 scopus 로고    scopus 로고
    • IgH class switching exploits a general property of two DNA breaks to be joined in cis over long chromosomal distances
    • Gostissa, M. et al. IgH class switching exploits a general property of two DNA breaks to be joined in cis over long chromosomal distances. Proc. Natl. Acad. Sci. USA 111, 2644-2649 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 2644-2649
    • Gostissa, M.1
  • 13
    • 84862778059 scopus 로고    scopus 로고
    • Spatial organization of the mouse genome and its role in recurrent chromosomal translocations
    • Zhang, Y. et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148, 908-921 (2012).
    • (2012) Cell , vol.148 , pp. 908-921
    • Zhang, Y.1
  • 14
    • 39149115111 scopus 로고    scopus 로고
    • An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome
    • OMalley, R.C., Alonso, J.M., Kim, C.J., Leisse, T.J., Ecker, J.R. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. Nat. Protoc. 2, 2910-2917 (2007).
    • (2007) Nat. Protoc. , vol.2 , pp. 2910-2917
    • Omalley, R.C.1    Alonso, J.M.2    Kim, C.J.3    Leisse, T.J.4    Ecker, J.R.5
  • 15
    • 33745351130 scopus 로고    scopus 로고
    • Amplification of complex gene libraries by emulsion PCR
    • Williams, R. et al. Amplification of complex gene libraries by emulsion PCR. Nat. Methods 3, 545-550 (2006).
    • (2006) Nat. Methods , vol.3 , pp. 545-550
    • Williams, R.1
  • 16
    • 36749052217 scopus 로고    scopus 로고
    • High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR)
    • Schmidt, M. et al. High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR). Nat. Methods 4, 1051-1057 (2007).
    • (2007) Nat. Methods , vol.4 , pp. 1051-1057
    • Schmidt, M.1
  • 17
    • 77955220225 scopus 로고    scopus 로고
    • Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing
    • Paruzynski, A. et al. Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. Nat. Protoc. 5, 1379-1395 (2010).
    • (2010) Nat. Protoc. , vol.5 , pp. 1379-1395
    • Paruzynski, A.1
  • 18
    • 84876004639 scopus 로고    scopus 로고
    • Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method
    • Zhou, Z.-X. et al. Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method. Genome Res. 23, 705-715 (2013).
    • (2013) Genome Res. , vol.23 , pp. 705-715
    • Zhou, Z.-X.1
  • 19
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 20
    • 84867316247 scopus 로고    scopus 로고
    • YAHA: Fast and flexible long-read alignment with optimal breakpoint detection
    • Faust, G.G., Hall, I.M. YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics 28, 2417-2424 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 2417-2424
    • Faust, G.G.1    Hall, I.M.2
  • 21
    • 84958205734 scopus 로고    scopus 로고
    • Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells
    • Schwer, B. et al. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Proc. Natl. Acad. Sci. USA 113, 2258-2263 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.113 , pp. 2258-2263
    • Schwer, B.1
  • 22
    • 0030032063 scopus 로고    scopus 로고
    • Hybrid restriction enzymes: Zinc finger fusions to Fok i cleavage domain
    • Kim, Y.G., Cha, J., Chandrasegaran, S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl Acad. Sci. USA 93, 1156-1160 (1996).
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 1156-1160
    • Kim, Y.G.1    Cha, J.2    Chandrasegaran, S.3
  • 23
    • 84865070369 scopus 로고    scopus 로고
    • A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
    • Jinek, M. et al. A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
    • (2012) Science , vol.337 , pp. 816-821
    • Jinek, M.1
  • 24
    • 84873734105 scopus 로고    scopus 로고
    • RNA-guided human genome engineering via Cas9
    • Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826 (2013).
    • (2013) Science , vol.339 , pp. 823-826
    • Mali, P.1
  • 25
    • 84873729095 scopus 로고    scopus 로고
    • Multiplex genome engineering using CRISPR/Cas systems
    • Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
    • (2013) Science , vol.339 , pp. 819-823
    • Cong, L.1
  • 26
    • 84898778301 scopus 로고    scopus 로고
    • A guide to genome engineering with programmable nucleases
    • Kim, H., Kim, J.-S. A guide to genome engineering with programmable nucleases. Nat. Rev. Genet. 15, 321-334 (2014).
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 321-334
    • Kim, H.1    Kim, J.-S.2
  • 27
    • 84923266604 scopus 로고    scopus 로고
    • GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
    • Tsai, S.Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187-197 (2014).
    • (2014) Nat. Biotechnol. , vol.33 , pp. 187-197
    • Tsai, S.Q.1
  • 28
    • 84923221641 scopus 로고    scopus 로고
    • Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors
    • Wang, X. et al. Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat. Biotechnol. 33, 175-178 (2015).
    • (2015) Nat. Biotechnol. , vol.33 , pp. 175-178
    • Wang, X.1
  • 29
    • 84975678715 scopus 로고    scopus 로고
    • Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system
    • Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163, 759-771 (2015).
    • (2015) Cell , vol.163 , pp. 759-771
    • Zetsche, B.1
  • 30
    • 84904294782 scopus 로고    scopus 로고
    • Developmental propagation of V(D) J recombination-associated DNA breaks and translocations in mature B cells via dicentric chromosomes
    • Hu, J., Tepsuporn, S., Meyers, R.M., Gostissa, M., Alt, F.W. Developmental propagation of V(D)J recombination-associated DNA breaks and translocations in mature B cells via dicentric chromosomes. Proc. Natl. Acad. Sci. USA 111, 10269-10274 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 10269-10274
    • Hu, J.1    Tepsuporn, S.2    Meyers, R.M.3    Gostissa, M.4    Alt, F.W.5
  • 31
    • 77149176004 scopus 로고    scopus 로고
    • Alternative end-joining catalyzes class switch recombination in the absence of both Ku70 and DNA ligase 4
    • Boboila, C. et al. Alternative end-joining catalyzes class switch recombination in the absence of both Ku70 and DNA ligase 4. J. Exp. Med. 207, 417-427 (2010).
    • (2010) J. Exp. Med. , vol.207 , pp. 417-427
    • Boboila, C.1
  • 32
    • 84939167512 scopus 로고    scopus 로고
    • RAG represents a widespread threat to the lymphocyte genome
    • Teng, G. et al. RAG represents a widespread threat to the lymphocyte genome. Cell 162, 751-765 (2015).
    • (2015) Cell , vol.162 , pp. 751-765
    • Teng, G.1
  • 33
    • 80053502216 scopus 로고    scopus 로고
    • Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes
    • Klein, I.A. et al. Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell 147, 95-106 (2011).
    • (2011) Cell , vol.147 , pp. 95-106
    • Klein, I.A.1
  • 34
    • 84873310832 scopus 로고    scopus 로고
    • Identification of early replicating fragile sites that contribute to genome instability
    • Barlow, J.H. et al. Identification of early replicating fragile sites that contribute to genome instability. Cell 152, 620-632 (2013).
    • (2013) Cell , vol.152 , pp. 620-632
    • Barlow, J.H.1
  • 35
    • 84940748541 scopus 로고    scopus 로고
    • Nbs1 ChIP-seq identifies off-target DNA double-strand breaks induced by AID in activated splenic B cells
    • Khair, L., Baker, R.E., Linehan, E.K., Schrader, C.E., Stavnezer, J. Nbs1 ChIP-seq identifies off-target DNA double-strand breaks induced by AID in activated splenic B cells. PLoS Genet. 11, e1005438 (2015).
    • (2015) PLoS Genet. , vol.11 , pp. e1005438
    • Khair, L.1    Baker, R.E.2    Linehan, E.K.3    Schrader, C.E.4    Stavnezer, J.5
  • 36
    • 84905020953 scopus 로고    scopus 로고
    • DNA break mapping reveals topoisomerase II activity genome-wide
    • Baranello, L. et al. DNA break mapping reveals topoisomerase II activity genome-wide. Int. J. Mol. Sci. 15, 13111-13122 (2014).
    • (2014) Int. J. Mol. Sci. , vol.15 , pp. 13111-13122
    • Baranello, L.1
  • 37
    • 84875754465 scopus 로고    scopus 로고
    • Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing
    • Crosetto, N. et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat. Methods 10, 361-365 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 361-365
    • Crosetto, N.1
  • 38
    • 84927514894 scopus 로고    scopus 로고
    • In vivo genome editing using Staphylococcus aureus Cas9
    • Ran, F.A. et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520, 186-191 (2015).
    • (2015) Nature , vol.520 , pp. 186-191
    • Ran, F.A.1
  • 39
    • 67651162117 scopus 로고    scopus 로고
    • Cellular responses to DNA double-strand breaks after low-dose-irradiation
    • Asaithamby, A., Chen, D.J. Cellular responses to DNA double-strand breaks after low-dose-irradiation. Nucleic Acids Res. 37, 3912-3923 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3912-3923
    • Asaithamby, A.1    Chen, D.J.2
  • 40
    • 84881255212 scopus 로고    scopus 로고
    • Spatial dynamics of chromosome translocations in living cells
    • Roukos, V. et al. Spatial dynamics of chromosome translocations in living cells. Science 341, 660-664 (2013).
    • (2013) Science , vol.341 , pp. 660-664
    • Roukos, V.1
  • 41
    • 0032052803 scopus 로고    scopus 로고
    • Stimulation and suppression of PCR-mediated recombination
    • Judo, M.S., Wedel, A.B., Wilson, C. Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Res. 26, 1819-1825 (1998).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1819-1825
    • Judo, M.S.1    Wedel, A.B.2    Wilson, C.3
  • 42
    • 17444446261 scopus 로고    scopus 로고
    • Improved full-length cDNA production based on RNA tagging by T4 DNA ligase
    • Clepet, C. Improved full-length cDNA production based on RNA tagging by T4 DNA ligase. Nucleic Acids Res. 32, 6e-6 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6e-6
    • Clepet, C.1
  • 43
    • 84887010498 scopus 로고    scopus 로고
    • Genome engineering using the CRISPR-Cas9 system
    • Ran, F.A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281-2308 (2013).
    • (2013) Nat. Protoc. , vol.8 , pp. 2281-2308
    • Ran, F.A.1
  • 44
    • 84923846574 scopus 로고    scopus 로고
    • Digenome-seq: Genome-wide profiling of CRISPR-Cas9 off-target effects in human cells
    • Kim, D. et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat. Methods 12, 237-243 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 237-243
    • Kim, D.1
  • 45
    • 80052766645 scopus 로고    scopus 로고
    • An unbiased genome-wide analysis of zinc-finger nuclease specificity
    • Gabriel, R. et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol. 29, 816-823 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 816-823
    • Gabriel, R.1
  • 46
    • 84904010334 scopus 로고    scopus 로고
    • Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing
    • Veres, A. et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 15, 27-30 (2014).
    • (2014) Cell Stem Cell , vol.15 , pp. 27-30
    • Veres, A.1


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