메뉴 건너뛰기




Volumn 7, Issue , 2016, Pages

The topography of mutational processes in breast cancer genomes

(33)  Morganella, Sandro a   Alexandrov, Ludmil B b,c,d   Glodzik, Dominik b   Zou, Xueqing b   Davies, Helen b   Staaf, Johan e   Sieuwerts, Anieta M f   Brinkman, Arie B g   Martin, Sancha b   Ramakrishna, Manasa b   Butler, Adam b   Kim, Hyung Yong h   Borg, Åke e   Sotiriou, Christos i   Futreal, P Andrew a,j   Campbell, Peter J b   Span, Paul N k   Van Laere, Steven l,m   Lakhani, Sunil R n,o   Eyfjord, Jorunn E p   more..


Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; PROTEIN APOBEC; UNCLASSIFIED DRUG; APOLIPOPROTEIN B; CHROMATIN;

EID: 84965121461     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms11383     Document Type: Article
Times cited : (217)

References (55)
  • 1
    • 83255189766 scopus 로고    scopus 로고
    • DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes
    • De, S. & Michor, F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat. Biotechnol. 29, 1103-1108 (2011).
    • (2011) Nat. Biotechnol , vol.29 , pp. 1103-1108
    • De, S.1    Michor, F.2
  • 2
    • 84873390533 scopus 로고    scopus 로고
    • Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
    • Drier, Y. et al. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res. 23, 228-235 (2013).
    • (2013) Genome Res. , vol.23 , pp. 228-235
    • Drier, Y.1
  • 3
    • 84870955253 scopus 로고    scopus 로고
    • Differential relationship of DNA replication timing to different forms of human mutation and variation
    • Koren, A. et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am. J. Hum. Genet. 91, 1033-1040 (2012).
    • (2012) Am. J. Hum. Genet. , vol.91 , pp. 1033-1040
    • Koren, A.1
  • 4
    • 84865777820 scopus 로고    scopus 로고
    • Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
    • Kundaje, A. et al. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 22, 1735-1747 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1735-1747
    • Kundaje, A.1
  • 5
    • 84874585488 scopus 로고    scopus 로고
    • DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes
    • Liu, L., De, S. & Michor, F. DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nat. Commun. 4, 1502 (2013).
    • (2013) Nat. Commun. , vol.4 , pp. 1502
    • Liu, L.1    De, S.2    Michor, F.3
  • 6
    • 84925615834 scopus 로고    scopus 로고
    • Differential DNA mismatch repair underlies mutation rate variation across the human genome
    • Supek, F. & Lehner, B. Differential DNA mismatch repair underlies mutation rate variation across the human genome. Nature 521, 81-84 (2015).
    • (2015) Nature , vol.521 , pp. 81-84
    • Supek, F.1    Lehner, B.2
  • 7
    • 84866067741 scopus 로고    scopus 로고
    • DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes
    • Woo, Y. H. & Li, W. H. DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nat. Commun. 3, 1004 (2012).
    • (2012) Nat. Commun. , vol.3 , pp. 1004
    • Woo, Y.H.1    Li, W.H.2
  • 8
    • 63449141981 scopus 로고    scopus 로고
    • Human mutation rate associated with DNA replication timing
    • Stamatoyannopoulos, J. A. et al. Human mutation rate associated with DNA replication timing. Nat. Genet. 41, 393-395 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 393-395
    • Stamatoyannopoulos, J.A.1
  • 9
    • 84865248380 scopus 로고    scopus 로고
    • Chromatin organization is a major influence on regional mutation rates in human cancer cells
    • Schuster-Bockler, B. & Lehner, B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488, 504-507 (2012).
    • (2012) Nature , vol.488 , pp. 504-507
    • Schuster-Bockler, B.1    Lehner, B.2
  • 10
    • 84923358817 scopus 로고    scopus 로고
    • Cell-of-origin chromatin organization shapes the mutational landscape of cancer
    • Polak, P. et al. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518, 360-364 (2015).
    • (2015) Nature , vol.518 , pp. 360-364
    • Polak, P.1
  • 11
    • 84861541343 scopus 로고    scopus 로고
    • Mutational processes molding the genomes of 21 breast cancers
    • Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979-993 (2012).
    • (2012) Cell , vol.149 , pp. 979-993
    • Nik-Zainal, S.1
  • 12
    • 84861550476 scopus 로고    scopus 로고
    • The life history of 21 breast cancers
    • Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994-1007 (2012).
    • (2012) Cell , vol.149 , pp. 994-1007
    • Nik-Zainal, S.1
  • 13
    • 84906303775 scopus 로고    scopus 로고
    • Mechanisms underlying mutational signatures in human cancers
    • Helleday, T., Eshtad, S. & Nik-Zainal, S. Mechanisms underlying mutational signatures in human cancers. Nat. Rev. Genet. 15, 585-598 (2014).
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 585-598
    • Helleday, T.1    Eshtad, S.2    Nik-Zainal, S.3
  • 14
    • 84882837534 scopus 로고    scopus 로고
    • Signatures of mutational processes in human cancer
    • Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
    • (2013) Nature , vol.500 , pp. 415-421
    • Alexandrov, L.B.1
  • 15
    • 84973594792 scopus 로고    scopus 로고
    • Landscape of somatic mutations in 560 breast cancer whole-genome sequences
    • Nik-Zainal, S. et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature http://dx.doi.org/10.1038/nature17676 (2016).
    • (2016) Nature
    • Nik-Zainal, S.1
  • 16
    • 84860510016 scopus 로고    scopus 로고
    • Mammalian mismatch repair: Error-free or error-prone?
    • Pena-Diaz, J. & Jiricny, J. Mammalian mismatch repair: error-free or error-prone? Trends Biochem. Sci. 37, 206-214 (2012).
    • (2012) Trends Biochem. Sci. , vol.37 , pp. 206-214
    • Pena-Diaz, J.1    Jiricny, J.2
  • 17
  • 20
    • 84965109911 scopus 로고    scopus 로고
    • ENCODE. https://http://www.encodeproject.org (2012).
    • (2012)
  • 21
    • 74049163810 scopus 로고    scopus 로고
    • Decreased replication origin activity in temporal transition regions
    • Guan, Z. et al. Decreased replication origin activity in temporal transition regions. J. Cell Biol. 187, 623-635 (2009).
    • (2009) J. Cell Biol. , vol.187 , pp. 623-635
    • Guan, Z.1
  • 22
    • 84855272663 scopus 로고    scopus 로고
    • Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome
    • Guilbaud, G. et al. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput. Biol. 7, e1002322 (2011).
    • (2011) PLoS Comput. Biol. , vol.7
    • Guilbaud, G.1
  • 23
    • 84965111648 scopus 로고    scopus 로고
    • Signatures, C. M. http://cancer.sanger.ac.uk/cosmic/signatures (2015).
    • (2015) Signatures C.M.
  • 24
    • 50349093233 scopus 로고    scopus 로고
    • The AID/APOBEC family of nucleic acid mutators
    • Conticello, S. G. The AID/APOBEC family of nucleic acid mutators. Genome Biol. 9, 229 (2008).
    • (2008) Genome Biol. , vol.9 , pp. 229
    • Conticello, S.G.1
  • 25
    • 0036863733 scopus 로고    scopus 로고
    • RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators
    • Harris, R. S., Petersen-Mahrt, S. K. & Neuberger, M. S. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 10, 1247-1253 (2002).
    • (2002) Mol. Cell , vol.10 , pp. 1247-1253
    • Harris, R.S.1    Petersen-Mahrt, S.K.2    Neuberger, M.S.3
  • 26
    • 84878677763 scopus 로고    scopus 로고
    • NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity
    • Byeon, I. J. et al. NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity. Nat. Commun. 4, 1890 (2013).
    • (2013) Nat. Commun. , vol.4 , pp. 1890
    • Byeon, I.J.1
  • 27
    • 84880231858 scopus 로고    scopus 로고
    • APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure
    • Holtz, C. M., Sadler, H. A. & Mansky, L. M. APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure. Nucleic Acids Res. 41, 6139-6148 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. 6139-6148
    • Holtz, C.M.1    Sadler, H.A.2    Mansky, L.M.3
  • 28
    • 84899645475 scopus 로고    scopus 로고
    • Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer
    • Nik-Zainal, S. et al. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nat. Genet. 46, 487-491 (2014).
    • (2014) Nat. Genet. , vol.46 , pp. 487-491
    • Nik-Zainal, S.1
  • 29
    • 62349131315 scopus 로고    scopus 로고
    • DNA repair in mammalian cells : Nucleotide excision repair: Variations on versatility
    • Nouspikel, T. DNA repair in mammalian cells : Nucleotide excision repair: variations on versatility. Cell. Mol. Life Sci. 66, 994-1009 (2009).
    • (2009) Cell. Mol. Life Sci. , vol.66 , pp. 994-1009
    • Nouspikel, T.1
  • 30
    • 74449093973 scopus 로고    scopus 로고
    • A comprehensive catalogue of somatic mutations from a human cancer genome
    • Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196 (2010).
    • (2010) Nature , vol.463 , pp. 191-196
    • Pleasance, E.D.1
  • 31
    • 56749157389 scopus 로고    scopus 로고
    • Transcription-coupled DNA repair: Two decades of progress and surprises
    • Hanawalt, P. C. & Spivak, G. Transcription-coupled DNA repair: two decades of progress and surprises. Nature Rev. Mol. Cell Biol. 9, 958-970 (2008).
    • (2008) Nature Rev. Mol. Cell Biol. , vol.9 , pp. 958-970
    • Hanawalt, P.C.1    Spivak, G.2
  • 33
    • 33748990904 scopus 로고    scopus 로고
    • Transcription arrest at an abasic site in the transcribed strand of template DNA
    • Tornaletti, S., Maeda, L. S. & Hanawalt, P. C. Transcription arrest at an abasic site in the transcribed strand of template DNA. Chem. Res. Toxicol. 19, 1215-1220 (2006).
    • (2006) Chem. Res. Toxicol. , vol.19 , pp. 1215-1220
    • Tornaletti, S.1    Maeda, L.S.2    Hanawalt, P.C.3
  • 35
    • 58449116917 scopus 로고    scopus 로고
    • Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
    • Sasaki, S. et al. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323, 401-404 (2009).
    • (2009) Science , vol.323 , pp. 401-404
    • Sasaki, S.1
  • 36
    • 84857131972 scopus 로고    scopus 로고
    • Interplay between mismatch repair and chromatin assembly
    • Schopf, B. et al. Interplay between mismatch repair and chromatin assembly. Proc. Natl Acad. Sci. USA 109, 1895-1900 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 1895-1900
    • Schopf, B.1
  • 37
    • 84923948943 scopus 로고    scopus 로고
    • Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition
    • Lujan, S. A. et al. Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. Genome Res. 24, 1751-1764 (2014).
    • (2014) Genome Res. , vol.24 , pp. 1751-1764
    • Lujan, S.A.1
  • 38
    • 0036012782 scopus 로고    scopus 로고
    • The "A" rule revisited: Polymerases as determinants of mutational specificity
    • Strauss, B. S. The "A" rule revisited: polymerases as determinants of mutational specificity. DNA Repair 1, 125-135 (2002).
    • (2002) DNA Repair , vol.1 , pp. 125-135
    • Strauss, B.S.1
  • 39
    • 77955841149 scopus 로고    scopus 로고
    • Collaboration and competition between DNA double-strand break repair pathways
    • Kass, E. M. & Jasin, M. Collaboration and competition between DNA double-strand break repair pathways. FEBS Lett. 584, 3703-3708 (2010).
    • (2010) FEBS Lett. , vol.584 , pp. 3703-3708
    • Kass, E.M.1    Jasin, M.2
  • 40
    • 84923090502 scopus 로고    scopus 로고
    • Mammalian polymerase theta promotes alternative NHEJ and suppresses recombination
    • Mateos-Gomez, P. A. et al. Mammalian polymerase theta promotes alternative NHEJ and suppresses recombination. Nature 518, 254-257 (2015).
    • (2015) Nature , vol.518 , pp. 254-257
    • Mateos-Gomez, P.A.1
  • 41
    • 84923082911 scopus 로고    scopus 로고
    • Homologous-recombination-deficient tumours are dependent on Poltheta-mediated repair
    • Ceccaldi, R. et al. Homologous-recombination-deficient tumours are dependent on Poltheta-mediated repair. Nature 518, 258-262 (2015).
    • (2015) Nature , vol.518 , pp. 258-262
    • Ceccaldi, R.1
  • 42
    • 84892743776 scopus 로고    scopus 로고
    • Break-induced replication repair of damaged forks induces genomic duplications in human cells
    • Costantino, L. et al. Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science 343, 88-91 (2014).
    • (2014) Science , vol.343 , pp. 88-91
    • Costantino, L.1
  • 43
    • 25444517122 scopus 로고    scopus 로고
    • Good timing in the cell cycle for precise DNA repair by BRCA1
    • Durant, S. T. & Nickoloff, J. A. Good timing in the cell cycle for precise DNA repair by BRCA1. Cell Cycle 4, 1216-1222 (2005).
    • (2005) Cell Cycle , vol.4 , pp. 1216-1222
    • Durant, S.T.1    Nickoloff, J.A.2
  • 44
    • 39449096135 scopus 로고    scopus 로고
    • Genome instability: A mechanistic view of its causes and consequences
    • Aguilera, A. & Gomez-Gonzalez, B. Genome instability: a mechanistic view of its causes and consequences. Nat. Rev. Genet. 9, 204-217 (2008).
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 204-217
    • Aguilera, A.1    Gomez-Gonzalez, B.2
  • 45
    • 84887402750 scopus 로고    scopus 로고
    • Replication stress-induced genome instability: The dark side of replication maintenance by homologous recombination
    • Carr, A. M. & Lambert, S. Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination. J. Mol. Biol. 425, 4733-4744 (2013).
    • (2013) J. Mol. Biol. , vol.425 , pp. 4733-4744
    • Carr, A.M.1    Lambert, S.2
  • 46
    • 0037388452 scopus 로고    scopus 로고
    • Rev1 is essential for DNA damage tolerance and non-templated immunoglobulin gene mutation in a vertebrate cell line
    • Simpson, L. J. & Sale, J. E. Rev1 is essential for DNA damage tolerance and non-templated immunoglobulin gene mutation in a vertebrate cell line. EMBO J. 22, 1654-1664 (2003).
    • (2003) EMBO J , vol.22 , pp. 1654-1664
    • Simpson, L.J.1    Sale, J.E.2
  • 48
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
  • 49
    • 84923920881 scopus 로고    scopus 로고
    • The spatial and temporal organization of origin firing during the S-phase of fission yeast
    • Kaykov, A. & Nurse, P. The spatial and temporal organization of origin firing during the S-phase of fission yeast. Genome Res. 25, 391-401 (2015).
    • (2015) Genome Res. , vol.25 , pp. 391-401
    • Kaykov, A.1    Nurse, P.2
  • 50
    • 0035812742 scopus 로고    scopus 로고
    • Making sense of eukaryotic DNA replication origins
    • Gilbert, D. M. Making sense of eukaryotic DNA replication origins. Science 294, 96-100 (2001).
    • (2001) Science , vol.294 , pp. 96-100
    • Gilbert, D.M.1
  • 51
    • 33751520767 scopus 로고    scopus 로고
    • DNA replication timing: Random thoughts about origin firing
    • Rhind, N. DNA replication timing: random thoughts about origin firing. Nat. Cell Biol. 8, 1313-1316 (2006).
    • (2006) Nat. Cell Biol. , vol.8 , pp. 1313-1316
    • Rhind, N.1
  • 52
    • 1842733112 scopus 로고    scopus 로고
    • RNase-sensitive DNA modification(s) initiates S. pombe mating-type switching
    • Vengrova, S. & Dalgaard, J. Z. RNase-sensitive DNA modification(s) initiates S. pombe mating-type switching. Genes Dev. 18, 794-804 (2004).
    • (2004) Genes Dev. , vol.18 , pp. 794-804
    • Vengrova, S.1    Dalgaard, J.Z.2
  • 53
    • 0034654537 scopus 로고    scopus 로고
    • Fission yeast switches mating type by a replication-recombination coupled process
    • Arcangioli, B. & de Lahondes, R. Fission yeast switches mating type by a replication-recombination coupled process. EMBO J. 19, 1389-1396 (2000).
    • (2000) EMBO J , vol.19 , pp. 1389-1396
    • Arcangioli, B.1    De Lahondes, R.2
  • 54
    • 84955559498 scopus 로고    scopus 로고
    • Molecular combing of single DNA molecules on the 10 megabase scale
    • Kaykov, A., Taillefumier, T., Bensimon, A. & Nurse, P. Molecular combing of single DNA molecules on the 10 megabase scale. Sci. Rep. 6, 19636 (2016).
    • (2016) Sci. Rep. , vol.6
    • Kaykov, A.1    Taillefumier, T.2    Bensimon, A.3    Nurse, P.4
  • 55
    • 84870674869 scopus 로고    scopus 로고
    • Controls of nucleosome positioning in the human genome
    • Gaffney, D. J. et al. Controls of nucleosome positioning in the human genome. PLoS Genet. 8, e1003036 (2012).
    • (2012) PLoS Genet. , vol.8
    • Gaffney, D.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.