메뉴 건너뛰기




Volumn 11, Issue 1, 2010, Pages

New insights into two distinct nucleosome distributions: Comparison of cross-platform positioning datasets in the yeast genome

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMATIN STRUCTURE; COMPARATIVE STUDY; CONTROLLED STUDY; FUNGAL GENETICS; FUNGAL GENOME; GENE ACTIVATION; GENE CONTROL; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOSOME; PROMOTER REGION; REPRODUCIBILITY; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; BIOLOGY; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; SACCHAROMYCES CEREVISIAE;

EID: 77349100416     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-33     Document Type: Article
Times cited : (12)

References (41)
  • 1
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S. cerevisiae
    • 10.1126/science.1112178, 15961632
    • Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005, 309(5734):626-630. 10.1126/science.1112178, 15961632.
    • (2005) Science , vol.309 , Issue.5734 , pp. 626-630
    • Yuan, G.C.1    Liu, Y.J.2    Dion, M.F.3    Slack, M.D.4    Wu, L.F.5    Altschuler, S.J.6    Rando, O.J.7
  • 2
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • 10.1038/nature05632, 17392789
    • Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 2007, 446(7135):572-576. 10.1038/nature05632, 17392789.
    • (2007) Nature , vol.446 , Issue.7135 , pp. 572-576
    • Albert, I.1    Mavrich, T.N.2    Tomsho, L.P.3    Qi, J.4    Zanton, S.J.5    Schuster, S.C.6    Pugh, B.F.7
  • 3
    • 34748826166 scopus 로고    scopus 로고
    • A high-resolution atlas of nucleosome occupancy in yeast
    • 10.1038/ng2117, 17873876
    • Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 2007, 39(10):1235-1244. 10.1038/ng2117, 17873876.
    • (2007) Nat Genet , vol.39 , Issue.10 , pp. 1235-1244
    • Lee, W.1    Tillo, D.2    Bray, N.3    Morse, R.H.4    Davis, R.W.5    Hughes, T.R.6    Nislow, C.7
  • 4
    • 37249077649 scopus 로고    scopus 로고
    • Chromatin remodelling at promoters suppresses antisense transcription
    • 10.1038/nature06391, 18075583
    • Whitehouse I, Rando OJ, Delrow J, Tsukiyama T. Chromatin remodelling at promoters suppresses antisense transcription. Nature 2007, 450(7172):1031-1035. 10.1038/nature06391, 18075583.
    • (2007) Nature , vol.450 , Issue.7172 , pp. 1031-1035
    • Whitehouse, I.1    Rando, O.J.2    Delrow, J.3    Tsukiyama, T.4
  • 5
    • 46449112319 scopus 로고    scopus 로고
    • A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    • 10.1101/gr.078261.108, 2493396, 18550805
    • Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 2008, 18(7):1073-1083. 10.1101/gr.078261.108, 2493396, 18550805.
    • (2008) Genome Res , vol.18 , Issue.7 , pp. 1073-1083
    • Mavrich, T.N.1    Ioshikhes, I.P.2    Venters, B.J.3    Jiang, C.4    Tomsho, L.P.5    Qi, J.6    Schuster, S.C.7    Albert, I.8    Pugh, B.F.9
  • 6
    • 41749091787 scopus 로고    scopus 로고
    • Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
    • 10.1371/journal.pbio.0060065, 2267817,2267817, 18351804
    • Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol 2008, 6(3):e65. 10.1371/journal.pbio.0060065, 2267817,2267817, 18351804.
    • (2008) PLoS Biol , vol.6 , Issue.3
    • Shivaswamy, S.1    Bhinge, A.2    Zhao, Y.3    Jones, S.4    Hirst, M.5    Iyer, V.R.6
  • 7
    • 33749153628 scopus 로고    scopus 로고
    • Nucleosome positions predicted through comparative genomics
    • 10.1038/ng1878, 16964265
    • Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. Nucleosome positions predicted through comparative genomics. Nat Genet 2006, 38(10):1210-1215. 10.1038/ng1878, 16964265.
    • (2006) Nat Genet , vol.38 , Issue.10 , pp. 1210-1215
    • Ioshikhes, I.P.1    Albert, I.2    Zanton, S.J.3    Pugh, B.F.4
  • 10
    • 34447643262 scopus 로고    scopus 로고
    • Nucleosome positioning determinants
    • 10.1016/j.jmb.2007.05.090, 17586522
    • Fernandez AG, Anderson JN. Nucleosome positioning determinants. J Mol Biol 2007, 371(3):649-668. 10.1016/j.jmb.2007.05.090, 17586522.
    • (2007) J Mol Biol , vol.371 , Issue.3 , pp. 649-668
    • Fernandez, A.G.1    Anderson, J.N.2
  • 11
    • 57149119464 scopus 로고    scopus 로고
    • Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    • 10.1371/journal.pcbi.1000216, 2570626, 18989395
    • Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 2008, 4(11):e1000216. 10.1371/journal.pcbi.1000216, 2570626, 18989395.
    • (2008) PLoS Comput Biol , vol.4 , Issue.11
    • Field, Y.1    Kaplan, N.2    Fondufe-Mittendorf, Y.3    Moore, I.K.4    Sharon, E.5    Lubling, Y.6    Widom, J.7    Segal, E.8
  • 13
    • 10944232800 scopus 로고    scopus 로고
    • Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
    • 10.1074/mcp.M400099-MCP200, 15326222
    • Beyer A, Hollunder J, Nasheuer HP, Wilhelm T. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics 2004, 3(11):1083-1092. 10.1074/mcp.M400099-MCP200, 15326222.
    • (2004) Mol Cell Proteomics , vol.3 , Issue.11 , pp. 1083-1092
    • Beyer, A.1    Hollunder, J.2    Nasheuer, H.P.3    Wilhelm, T.4
  • 14
    • 33847357312 scopus 로고    scopus 로고
    • A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription
    • 10.1038/ng1965, 17325681
    • Steinfeld I, Shamir R, Kupiec M. A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription. Nat Genet 2007, 39(3):303-309. 10.1038/ng1965, 17325681.
    • (2007) Nat Genet , vol.39 , Issue.3 , pp. 303-309
    • Steinfeld, I.1    Shamir, R.2    Kupiec, M.3
  • 15
    • 33947137710 scopus 로고    scopus 로고
    • Dynamics of replication-independent histone turnover in budding yeast
    • 10.1126/science.1134053, 17347438
    • Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. Dynamics of replication-independent histone turnover in budding yeast. Science 2007, 315(5817):1405-1408. 10.1126/science.1134053, 17347438.
    • (2007) Science , vol.315 , Issue.5817 , pp. 1405-1408
    • Dion, M.F.1    Kaplan, T.2    Kim, M.3    Buratowski, S.4    Friedman, N.5    Rando, O.J.6
  • 16
    • 1542328960 scopus 로고    scopus 로고
    • Identification and distinct regulation of yeast TATA box-containing genes
    • 10.1016/S0092-8674(04)00205-3, 15006352
    • Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast TATA box-containing genes. Cell 2004, 116(5):699-709. 10.1016/S0092-8674(04)00205-3, 15006352.
    • (2004) Cell , vol.116 , Issue.5 , pp. 699-709
    • Basehoar, A.D.1    Zanton, S.J.2    Pugh, B.F.3
  • 17
    • 0014421795 scopus 로고
    • The conformation dependent hydrolysis of DNA by micrococcal nuclease
    • Wingert L, Von Hippel PH. The conformation dependent hydrolysis of DNA by micrococcal nuclease. Biochim Biophys Acta 1968, 157(1):114-126.
    • (1968) Biochim Biophys Acta , vol.157 , Issue.1 , pp. 114-126
    • Wingert, L.1    Von Hippel, P.H.2
  • 18
    • 0020960593 scopus 로고
    • Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease
    • 10.1016/0092-8674(83)90303-3, 6301684
    • McGhee JD, Felsenfeld G. Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease. Cell 1983, 32(4):1205-1215. 10.1016/0092-8674(83)90303-3, 6301684.
    • (1983) Cell , vol.32 , Issue.4 , pp. 1205-1215
    • McGhee, J.D.1    Felsenfeld, G.2
  • 19
    • 0019888118 scopus 로고
    • Sequence specific cleavage of DNA by micrococcal nuclease
    • 10.1093/nar/9.12.2643, 326882, 7279658
    • Horz W, Altenburger W. Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res 1981, 9(12):2643-2658. 10.1093/nar/9.12.2643, 326882, 7279658.
    • (1981) Nucleic Acids Res , vol.9 , Issue.12 , pp. 2643-2658
    • Horz, W.1    Altenburger, W.2
  • 20
    • 29144531244 scopus 로고    scopus 로고
    • Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning
    • 10.1371/journal.pbio.0030384, 1275524,1275524, 16248679
    • Guillemette B, Bataille AR, Gevry N, Adam M, Blanchette M, Robert F, Gaudreau L. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol 2005, 3(12):e384. 10.1371/journal.pbio.0030384, 1275524,1275524, 16248679.
    • (2005) PLoS Biol , vol.3 , Issue.12
    • Guillemette, B.1    Bataille, A.R.2    Gevry, N.3    Adam, M.4    Blanchette, M.5    Robert, F.6    Gaudreau, L.7
  • 21
    • 26844511498 scopus 로고    scopus 로고
    • Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin
    • 10.1016/j.cell.2005.10.002, 2039754, 16239142
    • Raisner RM, Hartley PD, Meneghini MD, Bao MZ, Liu CL, Schreiber SL, Rando OJ, Madhani HD. Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. Cell 2005, 123(2):233-248. 10.1016/j.cell.2005.10.002, 2039754, 16239142.
    • (2005) Cell , vol.123 , Issue.2 , pp. 233-248
    • Raisner, R.M.1    Hartley, P.D.2    Meneghini, M.D.3    Bao, M.Z.4    Liu, C.L.5    Schreiber, S.L.6    Rando, O.J.7    Madhani, H.D.8
  • 22
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: advances through genomics
    • 10.1038/nrg2522, 19204718
    • Jiang C, Pugh BF. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 2009, 10(3):161-172. 10.1038/nrg2522, 19204718.
    • (2009) Nat Rev Genet , vol.10 , Issue.3 , pp. 161-172
    • Jiang, C.1    Pugh, B.F.2
  • 23
    • 33847070442 scopus 로고    scopus 로고
    • The role of chromatin during transcription
    • 10.1016/j.cell.2007.01.015, 17320508
    • Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007, 128(4):707-719. 10.1016/j.cell.2007.01.015, 17320508.
    • (2007) Cell , vol.128 , Issue.4 , pp. 707-719
    • Li, B.1    Carey, M.2    Workman, J.L.3
  • 24
    • 0033529565 scopus 로고    scopus 로고
    • Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome
    • 10.1016/S0092-8674(00)81958-3, 10458604
    • Kornberg RD, Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 1999, 98(3):285-294. 10.1016/S0092-8674(00)81958-3, 10458604.
    • (1999) Cell , vol.98 , Issue.3 , pp. 285-294
    • Kornberg, R.D.1    Lorch, Y.2
  • 25
    • 26444508841 scopus 로고    scopus 로고
    • Single-nucleosome mapping of histone modifications in S. cerevisiae
    • 10.1371/journal.pbio.0030328, 1195719,1195719, 16122352
    • Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol 2005, 3(10):e328. 10.1371/journal.pbio.0030328, 1195719,1195719, 16122352.
    • (2005) PLoS Biol , vol.3 , Issue.10
    • Liu, C.L.1    Kaplan, T.2    Kim, M.3    Buratowski, S.4    Schreiber, S.L.5    Friedman, N.6    Rando, O.J.7
  • 27
    • 33747609801 scopus 로고    scopus 로고
    • Genome-wide patterns of histone modifications in yeast
    • 10.1038/nrm1986, 16912715
    • Millar CB, Grunstein M. Genome-wide patterns of histone modifications in yeast. Nat Rev Mol Cell Biol 2006, 7(9):657-666. 10.1038/nrm1986, 16912715.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , Issue.9 , pp. 657-666
    • Millar, C.B.1    Grunstein, M.2
  • 29
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genome-wide
    • 10.1038/ng1400, 15247917
    • Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet 2004, 36(8):900-905. 10.1038/ng1400, 15247917.
    • (2004) Nat Genet , vol.36 , Issue.8 , pp. 900-905
    • Lee, C.K.1    Shibata, Y.2    Rao, B.3    Strahl, B.D.4    Lieb, J.D.5
  • 31
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • 10.1101/gr.076059.108, 2493397, 18448704
    • Tirosh I, Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res 2008, 18(7):1084-1091. 10.1101/gr.076059.108, 2493397, 18448704.
    • (2008) Genome Res , vol.18 , Issue.7 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 32
    • 33749381311 scopus 로고    scopus 로고
    • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
    • 10.1101/gr.5655606, 1665635, 17053089
    • Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res 2006, 16(12):1517-1528. 10.1101/gr.5655606, 1665635, 17053089.
    • (2006) Genome Res , vol.16 , Issue.12 , pp. 1517-1528
    • Liu, X.1    Lee, C.K.2    Granek, J.A.3    Clarke, N.D.4    Lieb, J.D.5
  • 33
    • 34250775905 scopus 로고    scopus 로고
    • The pattern and evolution of yeast promoter bendability
    • 10.1016/j.tig.2007.03.015, 17418911
    • Tirosh I, Berman J, Barkai N. The pattern and evolution of yeast promoter bendability. Trends in Genetics 2007, 23(7):318-321. 10.1016/j.tig.2007.03.015, 17418911.
    • (2007) Trends in Genetics , vol.23 , Issue.7 , pp. 318-321
    • Tirosh, I.1    Berman, J.2    Barkai, N.3
  • 34
    • 33745220278 scopus 로고    scopus 로고
    • Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
    • 10.1038/nature04785, 16699522
    • Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441(7095):840-846. 10.1038/nature04785, 16699522.
    • (2006) Nature , vol.441 , Issue.7095 , pp. 840-846
    • Newman, J.R.1    Ghaemmaghami, S.2    Ihmels, J.3    Breslow, D.K.4    Noble, M.5    DeRisi, J.L.6    Weissman, J.S.7
  • 35
    • 27944478598 scopus 로고    scopus 로고
    • Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein I
    • 10.1128/MCB.25.23.10639-10651.2005, 1291234, 16287874
    • Okuwaki M, Kato K, Shimahara H, Tate S, Nagata K. Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein I. Mol Cell Biol 2005, 25(23):10639-10651. 10.1128/MCB.25.23.10639-10651.2005, 1291234, 16287874.
    • (2005) Mol Cell Biol , vol.25 , Issue.23 , pp. 10639-10651
    • Okuwaki, M.1    Kato, K.2    Shimahara, H.3    Tate, S.4    Nagata, K.5
  • 36
    • 0033603238 scopus 로고    scopus 로고
    • ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF
    • 10.1016/S0092-8674(00)80796-5, 10399912
    • Hamiche A, Sandaltzopoulos R, Gdula DA, Wu C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 1999, 97(7):833-842. 10.1016/S0092-8674(00)80796-5, 10399912.
    • (1999) Cell , vol.97 , Issue.7 , pp. 833-842
    • Hamiche, A.1    Sandaltzopoulos, R.2    Gdula, D.A.3    Wu, C.4
  • 37
    • 0037119967 scopus 로고    scopus 로고
    • Nucleosome sliding: facts and fiction
    • 10.1093/emboj/cdf486, 126283, 12234915
    • Becker PB. Nucleosome sliding: facts and fiction. EMBO J 2002, 21(18):4749-4753. 10.1093/emboj/cdf486, 126283, 12234915.
    • (2002) EMBO J , vol.21 , Issue.18 , pp. 4749-4753
    • Becker, P.B.1
  • 39
    • 37249012276 scopus 로고    scopus 로고
    • Nucleosome destabilization in the epigenetic regulation of gene expression
    • 10.1038/nrg2206, 18059368
    • Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet 2008, 9(1):15-26. 10.1038/nrg2206, 18059368.
    • (2008) Nat Rev Genet , vol.9 , Issue.1 , pp. 15-26
    • Henikoff, S.1
  • 40
    • 15944393126 scopus 로고    scopus 로고
    • Nature of the nucleosomal barrier to RNA polymerase II
    • 10.1016/j.molcel.2005.02.027, 15808512
    • Kireeva ML, Hancock B, Cremona GH, Walter W, Studitsky VM, Kashlev M. Nature of the nucleosomal barrier to RNA polymerase II. Mol Cell 2005, 18(1):97-108. 10.1016/j.molcel.2005.02.027, 15808512.
    • (2005) Mol Cell , vol.18 , Issue.1 , pp. 97-108
    • Kireeva, M.L.1    Hancock, B.2    Cremona, G.H.3    Walter, W.4    Studitsky, V.M.5    Kashlev, M.6
  • 41
    • 20444403749 scopus 로고    scopus 로고
    • Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast
    • 10.1016/j.molcel.2005.05.003, 15949447
    • Sekinger EA, Moqtaderi Z, Struhl K. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell 2005, 18(6):735-748. 10.1016/j.molcel.2005.05.003, 15949447.
    • (2005) Mol Cell , vol.18 , Issue.6 , pp. 735-748
    • Sekinger, E.A.1    Moqtaderi, Z.2    Struhl, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.