메뉴 건너뛰기




Volumn 113, Issue 32, 2016, Pages 9057-9062

Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; GENOMIC DNA; NUCLEOTIDE; PYRIMIDINE DIMER; TRANSCRIPTION FACTOR;

EID: 84982893681     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1606667113     Document Type: Article
Times cited : (121)

References (39)
  • 2
    • 56749157389 scopus 로고    scopus 로고
    • Transcription-coupled DNA repair: Two decades of progress and surprises
    • Hanawalt PC, Spivak G (2008) Transcription-coupled DNA repair: Two decades of progress and surprises. Nat Rev Mol Cell Biol 9(12):958-970.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , Issue.12 , pp. 958-970
    • Hanawalt, P.C.1    Spivak, G.2
  • 3
    • 84904642416 scopus 로고    scopus 로고
    • Understanding nucleotide excision repair and its roles in cancer and ageing
    • Marteijn JA, Lans H, Vermeulen W, Hoeijmakers JH (2014) Understanding nucleotide excision repair and its roles in cancer and ageing. Nat Rev Mol Cell Biol 15(7):465-481.
    • (2014) Nat Rev Mol Cell Biol , vol.15 , Issue.7 , pp. 465-481
    • Marteijn, J.A.1    Lans, H.2    Vermeulen, W.3    Hoeijmakers, J.H.4
  • 4
    • 74449093973 scopus 로고    scopus 로고
    • A comprehensive catalogue of somatic mutations from a human cancer genome
    • Pleasance ED, et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463(7278):191-196.
    • (2010) Nature , vol.463 , Issue.7278 , pp. 191-196
    • Pleasance, E.D.1
  • 5
    • 84880507665 scopus 로고    scopus 로고
    • Mutational heterogeneity in cancer and the search for new cancer-associated genes
    • Lawrence MS, et al. (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499(7457):214-218.
    • (2013) Nature , vol.499 , Issue.7457 , pp. 214-218
    • Lawrence, M.S.1
  • 6
    • 84892161493 scopus 로고    scopus 로고
    • Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair
    • Polak P, et al. (2014) Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair. Nat Biotechnol 32(1):71-75.
    • (2014) Nat Biotechnol , vol.32 , Issue.1 , pp. 71-75
    • Polak, P.1
  • 7
    • 84929463303 scopus 로고    scopus 로고
    • Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution
    • Hu J, Adar S, Selby CP, Lieb JD, Sancar A (2015) Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution. Genes Dev 29(9):948-960.
    • (2015) Genes Dev , vol.29 , Issue.9 , pp. 948-960
    • Hu, J.1    Adar, S.2    Selby, C.P.3    Lieb, J.D.4    Sancar, A.5
  • 8
    • 84963600093 scopus 로고    scopus 로고
    • Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis
    • Adar S, Hu J, Lieb JD, Sancar A (2016) Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis. Proc Natl Acad Sci USA 113(15): E2124-E2133.
    • (2016) Proc Natl Acad Sci USA , vol.113 , Issue.15 , pp. E2124-E2133
    • Adar, S.1    Hu, J.2    Lieb, J.D.3    Sancar, A.4
  • 9
    • 84964403759 scopus 로고    scopus 로고
    • Nucleotide excision repair is impaired by binding of transcription factors to DNA
    • Sabarinathan R, Mularoni L, Deu-Pons J, Gonzalez-Perez A, López-Bigas N (2016) Nucleotide excision repair is impaired by binding of transcription factors to DNA. Nature 532(7598):264-267.
    • (2016) Nature , vol.532 , Issue.7598 , pp. 264-267
    • Sabarinathan, R.1    Mularoni, L.2    Deu-Pons, J.3    Gonzalez-Perez, A.4    López-Bigas, N.5
  • 10
    • 84964345447 scopus 로고    scopus 로고
    • Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes
    • Perera D, et al. (2016) Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes. Nature 532(7598):259-263.
    • (2016) Nature , vol.532 , Issue.7598 , pp. 259-263
    • Perera, D.1
  • 11
    • 0005001210 scopus 로고
    • UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases
    • Gale JM, Nissen KA, Smerdon MJ (1987) UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases. Proc Natl Acad Sci USA 84(19):6644-6648.
    • (1987) Proc Natl Acad Sci USA , vol.84 , Issue.19 , pp. 6644-6648
    • Gale, J.M.1    Nissen, K.A.2    Smerdon, M.J.3
  • 12
    • 0021190168 scopus 로고
    • Use of light for footprinting DNA in vivo
    • Becker MM, Wang JC (1984) Use of light for footprinting DNA in vivo. Nature 309(5970):682-687.
    • (1984) Nature , vol.309 , Issue.5970 , pp. 682-687
    • Becker, M.M.1    Wang, J.C.2
  • 13
    • 0030815234 scopus 로고    scopus 로고
    • Strand-specific modulation of UV photoproducts in 5S rDNA by TFIIIA binding and their effect on TFIIIA complex formation
    • Liu X, Conconi A, Smerdon MJ (1997) Strand-specific modulation of UV photoproducts in 5S rDNA by TFIIIA binding and their effect on TFIIIA complex formation. Biochemistry 36(44):13710-13717.
    • (1997) Biochemistry , vol.36 , Issue.44 , pp. 13710-13717
    • Liu, X.1    Conconi, A.2    Smerdon, M.J.3
  • 14
    • 0034711722 scopus 로고    scopus 로고
    • Ultraviolet damage and nucleosome folding of the 5S ribosomal RNA gene
    • Liu X, Mann DB, Suquet C, Springer DL, Smerdon MJ (2000) Ultraviolet damage and nucleosome folding of the 5S ribosomal RNA gene. Biochemistry 39(3):557-566.
    • (2000) Biochemistry , vol.39 , Issue.3 , pp. 557-566
    • Liu, X.1    Mann, D.B.2    Suquet, C.3    Springer, D.L.4    Smerdon, M.J.5
  • 15
    • 79551497695 scopus 로고    scopus 로고
    • A novel method for the genome-wide high resolution analysis of DNA damage
    • Teng Y, et al. (2011) A novel method for the genome-wide high resolution analysis of DNA damage. Nucleic Acids Res 39(2):e10.
    • (2011) Nucleic Acids Res , vol.39 , Issue.2 , pp. e10
    • Teng, Y.1
  • 16
    • 84929495561 scopus 로고    scopus 로고
    • 3D-DIP-Chip: A microarray-based method to measure genomic DNA damage
    • Powell JR, et al. (2015) 3D-DIP-Chip: A microarray-based method to measure genomic DNA damage. Sci Rep 5:7975.
    • (2015) Sci Rep , vol.5 , pp. 7975
    • Powell, J.R.1
  • 17
    • 84961971182 scopus 로고    scopus 로고
    • Genomic approaches to DNA repair and mutagenesis
    • Wyrick JJ, Roberts SA (2015) Genomic approaches to DNA repair and mutagenesis. DNA Repair (Amst) 36:146-155.
    • (2015) DNA Repair (Amst) , vol.36 , pp. 146-155
    • Wyrick, J.J.1    Roberts, S.A.2
  • 18
    • 84907207991 scopus 로고    scopus 로고
    • High resolution mapping of modified DNA nucleobases using excision repair enzymes
    • Bryan DS, Ransom M, Adane B, York K, Hesselberth JR (2014) High resolution mapping of modified DNA nucleobases using excision repair enzymes. Genome Res 24(9): 1534-1542.
    • (2014) Genome Res , vol.24 , Issue.9 , pp. 1534-1542
    • Bryan, D.S.1    Ransom, M.2    Adane, B.3    York, K.4    Hesselberth, J.R.5
  • 19
    • 84940497269 scopus 로고    scopus 로고
    • Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq
    • Ding J, Taylor MS, Jackson AP, Reijns MA (2015) Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq. Nat Protoc 10(9):1433-1444.
    • (2015) Nat Protoc , vol.10 , Issue.9 , pp. 1433-1444
    • Ding, J.1    Taylor, M.S.2    Jackson, A.P.3    Reijns, M.A.4
  • 20
    • 0032567081 scopus 로고    scopus 로고
    • Dissecting the regulatory circuitry of a eukaryotic genome
    • Holstege FC, et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95(5):717-728.
    • (1998) Cell , vol.95 , Issue.5 , pp. 717-728
    • Holstege, F.C.1
  • 21
    • 84862979650 scopus 로고    scopus 로고
    • A map of nucleosome positions in yeast at base-pair resolution
    • Brogaard K, Xi L, Wang JP, Widom J (2012) A map of nucleosome positions in yeast at base-pair resolution. Nature 486(7404):496-501.
    • (2012) Nature , vol.486 , Issue.7404 , pp. 496-501
    • Brogaard, K.1    Xi, L.2    Wang, J.P.3    Widom, J.4
  • 22
    • 84925743476 scopus 로고    scopus 로고
    • Nucleosome structure and function
    • McGinty RK, Tan S (2015) Nucleosome structure and function. Chem Rev 115(6): 2255-2273.
    • (2015) Chem Rev , vol.115 , Issue.6 , pp. 2255-2273
    • McGinty, R.K.1    Tan, S.2
  • 23
    • 84895072244 scopus 로고    scopus 로고
    • High-resolution mapping of transcription factor binding sites on native chromatin
    • Kasinathan S, Orsi GA, Zentner GE, Ahmad K, Henikoff S (2014) High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods 11(2): 203-209.
    • (2014) Nat Methods , vol.11 , Issue.2 , pp. 203-209
    • Kasinathan, S.1    Orsi, G.A.2    Zentner, G.E.3    Ahmad, K.4    Henikoff, S.5
  • 24
    • 0028206277 scopus 로고
    • Contacts of the ABF1 protein of Saccharomyces cerevisiae with a DNA binding site at MATa
    • McBroom LD, Sadowski PD (1994) Contacts of the ABF1 protein of Saccharomyces cerevisiae with a DNA binding site at MATa. J Biol Chem 269(23):16455-16460.
    • (1994) J Biol Chem , vol.269 , Issue.23 , pp. 16455-16460
    • McBroom, L.D.1    Sadowski, P.D.2
  • 25
    • 84893293856 scopus 로고    scopus 로고
    • High-resolution characterization of CPD hotspot formation in human fibroblasts
    • Zavala AG, Morris RT, Wyrick JJ, Smerdon MJ (2014) High-resolution characterization of CPD hotspot formation in human fibroblasts. Nucleic Acids Res 42(2):893-905.
    • (2014) Nucleic Acids Res , vol.42 , Issue.2 , pp. 893-905
    • Zavala, A.G.1    Morris, R.T.2    Wyrick, J.J.3    Smerdon, M.J.4
  • 26
    • 0026577472 scopus 로고
    • Effects of DNA looping on pyrimidine dimer formation
    • Pehrson JR, Cohen LH (1992) Effects of DNA looping on pyrimidine dimer formation. Nucleic Acids Res 20(6):1321-1324.
    • (1992) Nucleic Acids Res , vol.20 , Issue.6 , pp. 1321-1324
    • Pehrson, J.R.1    Cohen, L.H.2
  • 27
    • 0032601589 scopus 로고    scopus 로고
    • Modulation of DNA damage and DNA repair in chromatin
    • Smerdon MJ, Conconi A (1999) Modulation of DNA damage and DNA repair in chromatin. Prog Nucleic Acid Res Mol Biol 62:227-255.
    • (1999) Prog Nucleic Acid Res Mol Biol , vol.62 , pp. 227-255
    • Smerdon, M.J.1    Conconi, A.2
  • 28
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs R, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461(7268):1248-1253.
    • (2009) Nature , vol.461 , Issue.7268 , pp. 1248-1253
    • Rohs, R.1
  • 29
    • 28844474197 scopus 로고    scopus 로고
    • Accommodation and repair of a UV photoproduct in DNA at different rotational settings on the nucleosome surface
    • Svedruzic ZM, Wang C, Kosmoski JV, Smerdon MJ (2005) Accommodation and repair of a UV photoproduct in DNA at different rotational settings on the nucleosome surface. J Biol Chem 280(48):40051-40057.
    • (2005) J Biol Chem , vol.280 , Issue.48 , pp. 40051-40057
    • Svedruzic, Z.M.1    Wang, C.2    Kosmoski, J.V.3    Smerdon, M.J.4
  • 30
    • 34147162118 scopus 로고    scopus 로고
    • ATP-dependent chromatin remodeling factors and DNA damage repair
    • Osley MA, Tsukuda T, Nickoloff JA (2007) ATP-dependent chromatin remodeling factors and DNA damage repair. Mutat Res 618(1-2):65-80.
    • (2007) Mutat Res , vol.618 , Issue.1-2 , pp. 65-80
    • Osley, M.A.1    Tsukuda, T.2    Nickoloff, J.A.3
  • 31
    • 84962032647 scopus 로고    scopus 로고
    • Histone modification and chromatin remodeling during NER
    • Waters R, van Eijk P, Reed S (2015) Histone modification and chromatin remodeling during NER. DNA Repair (Amst) 36:105-113.
    • (2015) DNA Repair (Amst) , vol.36 , pp. 105-113
    • Waters, R.1    Van Eijk, P.2    Reed, S.3
  • 32
    • 0026566518 scopus 로고
    • Binding of transcription factors creates hot spots for UV photoproducts in vivo
    • Pfeifer GP, Drouin R, Riggs AD, Holmquist GP (1992) Binding of transcription factors creates hot spots for UV photoproducts in vivo. Mol Cell Biol 12(4):1798-1804.
    • (1992) Mol Cell Biol , vol.12 , Issue.4 , pp. 1798-1804
    • Pfeifer, G.P.1    Drouin, R.2    Riggs, A.D.3    Holmquist, G.P.4
  • 33
    • 78651271733 scopus 로고    scopus 로고
    • Integrative genomics viewer
    • Robinson JT, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24-26.
    • (2011) Nat Biotechnol , vol.29 , Issue.1 , pp. 24-26
    • Robinson, J.T.1
  • 35
    • 0024452308 scopus 로고
    • Structure-function studies of the T4 endonuclease V repair enzyme
    • Dodson ML, Lloyd RS (1989) Structure-function studies of the T4 endonuclease V repair enzyme. Mutat Res 218(2):49-65.
    • (1989) Mutat Res , vol.218 , Issue.2 , pp. 49-65
    • Dodson, M.L.1    Lloyd, R.S.2
  • 36
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357-359.
    • (2012) Nat Methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 37
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/Map format and SAMtools
    • 1000 Genome Project Data Processing Subgroup
    • Li H, et al.; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078-2079.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1
  • 38
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM (2010) BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841-842.
    • (2010) Bioinformatics , vol.26 , Issue.6 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 39
    • 75349098018 scopus 로고    scopus 로고
    • A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
    • Jiang C, Pugh BF (2009) A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol 10(10):R109.
    • (2009) Genome Biol , vol.10 , Issue.10 , pp. R109
    • Jiang, C.1    Pugh, B.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.