메뉴 건너뛰기




Volumn 22, Issue 12, 2012, Pages 2497-2506

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA; TRANSCRIPTION FACTOR CTCF;

EID: 84870552401     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.143008.112     Document Type: Article
Times cited : (334)

References (38)
  • 1
    • 83255192190 scopus 로고    scopus 로고
    • Dynamic nucleosome depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells
    • Andreu-Vieyra C, Lai J, Berman BP, Frenkel B, Jia L, Jones PA, Coetzee GA. 2011. Dynamic nucleosome depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells. Mol Cell Biol 31: 4648-4662.
    • (2011) Mol Cell Biol , vol.31 , pp. 4648-4662
    • Andreu-Vieyra, C.1    Lai, J.2    Berman, B.P.3    Frenkel, B.4    Jia, L.5    Jones, P.A.6    Coetzee, G.A.7
  • 2
    • 34249026300 scopus 로고    scopus 로고
    • High-Resolution Profiling of Histone Methylations in the Human Genome
    • DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
    • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. 2007.High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837. (Pubitemid 46802390)
    • (2007) Cell , vol.129 , Issue.4 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.-Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 5
    • 70449723345 scopus 로고    scopus 로고
    • Analysis of individual remodeled nucleosomes reveals decreased histone-DNA contacts created by hSWI/SNF
    • Bouazoune K, Miranda TB, Jones PA, Kingston RE. 2009. Analysis of individual remodeled nucleosomes reveals decreased histone-DNA contacts created by hSWI/SNF. Nucleic Acids Res 37: 5279-5294.
    • (2009) Nucleic Acids Res , vol.37 , pp. 5279-5294
    • Bouazoune, K.1    Miranda, T.B.2    Jones, P.A.3    Kingston, R.E.4
  • 8
    • 60149095014 scopus 로고    scopus 로고
    • Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    • Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. 2009. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19: 24-32.
    • (2009) Genome Res , vol.19 , pp. 24-32
    • Cuddapah, S.1    Jothi, R.2    Schones, D.E.3    Roh, T.Y.4    Cui, K.5    Zhao, K.6
  • 9
    • 33749403746 scopus 로고    scopus 로고
    • Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting
    • doi: 10.1371/journal.pgen.0020160
    • Gal-Yam EN, Jeong S, Tanay A, Egger G, Lee AS, Jones PA. 2006. Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. PLoS Genet 2: e160. doi: 10.1371/journal.pgen.0020160.
    • (2006) PLoS Genet , vol.2
    • Gal-Yam, E.N.1    Jeong, S.2    Tanay, A.3    Egger, G.4    Lee, A.S.5    Jones, P.A.6
  • 10
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    • DOI 10.1101/gr.5533506
    • Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. 2007. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17: 877-885. (Pubitemid 46919722)
    • (2007) Genome Research , vol.17 , Issue.6 , pp. 877-885
    • Giresi, P.G.1    Kim, J.2    McDaniell, R.M.3    Iyer, V.R.4    Lieb, J.D.5
  • 13
    • 1642408613 scopus 로고    scopus 로고
    • Mapping chromatin structure in vivo using DNA methyltransferases
    • DOI 10.1016/j.ymeth.2003.10.025, PII S1046202303002962
    • Jessen WJ, Dhasarathy A, Hoose SA, Carvin CD, Risinger AL, Kladde MP. 2004. Mapping chromatin structure in vivo using DNA methyltransferases. Methods 33: 68-80. (Pubitemid 38369093)
    • (2004) Methods , vol.33 , Issue.1 , pp. 68-80
    • Jessen, W.J.1    Dhasarathy, A.2    Hoose, S.A.3    Carvin, C.D.4    Risinger, A.L.5    Kladde, M.P.6
  • 14
    • 33644794061 scopus 로고    scopus 로고
    • Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters
    • DOI 10.1038/nsmb1062, PII N1062
    • Jessen WJ, Hoose SA, Kilgore JA, Kladde MP. 2006. Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nat Struct Mol Biol 13: 256-263. (Pubitemid 43348512)
    • (2006) Nature Structural and Molecular Biology , vol.13 , Issue.3 , pp. 256-263
    • Jessen, W.J.1    Hoose, S.A.2    Kilgore, J.A.3    Kladde, M.P.4
  • 15
    • 77956931047 scopus 로고    scopus 로고
    • H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes
    • Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA. 2010. H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell 39: 901-911.
    • (2010) Mol Cell , vol.39 , pp. 901-911
    • Kelly, T.K.1    Miranda, T.B.2    Liang, G.3    Berman, B.P.4    Lin, J.C.5    Tanay, A.6    Jones, P.A.7
  • 16
    • 33847049022 scopus 로고    scopus 로고
    • Single-molecule and population probing of chromatin structure using DNA methyltransferases
    • Kilgore JA, Hoose SA, Gustafson TL, Porter W, Kladde MP. 2007. Single-molecule and population probing of chromatin structure using DNA methyltransferases. Methods 41: 320-332.
    • (2007) Methods , vol.41 , pp. 320-332
    • Kilgore, J.A.1    Hoose, S.A.2    Gustafson, T.L.3    Porter, W.4    Kladde, M.P.5
  • 17
  • 18
    • 84856498057 scopus 로고    scopus 로고
    • DNA methylome analysis using short bisulfite sequencing data
    • Krueger F, Kreck B, Franke A, Andrews SR. 2012. DNA methylome analysis using short bisulfite sequencing data. Nat Methods 9: 145-151.
    • (2012) Nat Methods , vol.9 , pp. 145-151
    • Krueger, F.1    Kreck, B.2    Franke, A.3    Andrews, S.R.4
  • 20
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 21
    • 35748936148 scopus 로고    scopus 로고
    • Role of Nucleosomal Occupancy in the Epigenetic Silencing of the MLH1 CpG Island
    • DOI 10.1016/j.ccr.2007.10.014, PII S1535610807002991
    • Lin JC, Jeong S, Liang G, Takai D, Fatemi M, Tsai YC, Egger G, Gal-Yam EN, Jones PA. 2007. Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell 12: 432-444. (Pubitemid 350046405)
    • (2007) Cancer Cell , vol.12 , Issue.5 , pp. 432-444
    • Lin, J.C.1    Jeong, S.2    Liang, G.3    Takai, D.4    Fatemi, M.5    Tsai, Y.C.6    Egger, G.7    Gal-Yam, E.N.8    Jones, P.A.9
  • 23
    • 84863565553 scopus 로고    scopus 로고
    • Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data
    • doi: 10.1186/gb-2012-13-7-r61
    • Liu Y, Siegmund KD, Laird PW, Berman BP. 2012. Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol 13: R61. doi: 10.1186/gb-2012-13-7-r61.
    • (2012) Genome Biol , vol.13
    • Liu, Y.1    Siegmund, K.D.2    Laird, P.W.3    Berman, B.P.4
  • 25
  • 27
    • 78651336469 scopus 로고    scopus 로고
    • MethylViewer: Computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects
    • doi: 10.1093/nar/gkq716
    • Pardo CE, Carr IM, Hoffman CJ, Darst RP, Markham AF, Bonthron DT, Kladde MP. 2010. MethylViewer: Computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects. Nucleic Acids Res 39: e5. doi: 10.1093/nar/gkq716.
    • (2010) Nucleic Acids Res , vol.39
    • Pardo, C.E.1    Carr, I.M.2    Hoffman, C.J.3    Darst, R.P.4    Markham, A.F.5    Bonthron, D.T.6    Kladde, M.P.7
  • 29
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic Regulation of Nucleosome Positioning in the Human Genome
    • DOI 10.1016/j.cell.2008.02.022, PII S0092867408002705
    • Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898. (Pubitemid 351312809)
    • (2008) Cell , vol.132 , Issue.5 , pp. 887-898
    • Schones, D.E.1    Cui, K.2    Cuddapah, S.3    Roh, T.-Y.4    Barski, A.5    Wang, Z.6    Wei, G.7    Zhao, K.8
  • 32
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
    • doi: 10.1093/bib/bbs017
    • Thorvaldsdottir H, Robinson JT, Mesirov JP. 2012. Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform doi: 10.1093/bib/bbs017.
    • (2012) Brief Bioinform
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 33
    • 79959653996 scopus 로고    scopus 로고
    • SWI/SNF nucleosome remodellers and cancer
    • Wilson BG, Roberts CW. 2011. SWI/SNF nucleosome remodellers and cancer. Nat Rev Cancer 11: 481-492.
    • (2011) Nat Rev Cancer , vol.11 , pp. 481-492
    • Wilson, B.G.1    Roberts, C.W.2
  • 34
    • 77952414230 scopus 로고    scopus 로고
    • Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer
    • doi: 10.1371/journal.pgen.1000917
    • Wolff EM, Byun HM, Han HF, Sharma S, NicholsPW, Siegmund KD, Yang AS, Jones PA, Liang G. 2010. Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet 6: e1000917. doi: 10.1371/journal.pgen.1000917.
    • (2010) PLoS Genet , vol.6
    • Wolff, E.M.1    Byun, H.M.2    Han, H.F.3    Sharma, S.4    Nichols, P.W.5    Siegmund, K.D.6    Yang, A.S.7    Jones, P.A.8    Liang, G.9
  • 35
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: Whole genome bisulfite sequence MAPping program
    • doi: 10.1186/1471-2105-10-232
    • Xi Y, Li W. 2009. BSMAP: Whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10: 232. doi: 10.1186/1471-2105-10-232.
    • (2009) BMC Bioinformatics , vol.10 , pp. 232
    • Xi, Y.1    Li, W.2
  • 37
    • 0032169570 scopus 로고    scopus 로고
    • Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC
    • Xu M, Kladde MP, Van Etten JL, Simpson RT. 1998. Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC. Nucleic Acids Res 26: 3961-3966. (Pubitemid 28401347)
    • (1998) Nucleic Acids Research , vol.26 , Issue.17 , pp. 3961-3966
    • Xu, M.1    Kladde, M.P.2    Van Etten, J.L.3    Simpson, R.T.4
  • 38
    • 80052284848 scopus 로고    scopus 로고
    • OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes
    • You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang G, Jones PA. 2011. OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes. Proc Natl Acad Sci 108: 14497-14502.
    • (2011) Proc Natl Acad Sci , vol.108 , pp. 14497-14502
    • You, J.S.1    Kelly, T.K.2    De Carvalho, D.D.3    Taberlay, P.C.4    Liang, G.5    Jones, P.A.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.