메뉴 건너뛰기




Volumn 21, Issue 11, 2011, Pages 1863-1871

Variety of genomic DNA patterns for nucleosome positioning

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; GENOMIC DNA; HISTONE; PURINE; PYRIMIDINE;

EID: 80555125013     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.116228.110     Document Type: Article
Times cited : (49)

References (48)
  • 1
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • DOI 10.1038/nature05632, PII NATURE05632
    • Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. 2007. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576. (Pubitemid 46514724)
    • (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
  • 2
    • 0033869101 scopus 로고    scopus 로고
    • A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability
    • Anselmi C, Bocchinfuso G, De Santis P, Savino M, Scipioni A. 2000. A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. Biophys J 79: 601-613. (Pubitemid 30626158)
    • (2000) Biophysical Journal , vol.79 , Issue.2 , pp. 601-613
    • Anselmi, C.1    Bocchinfuso, G.2    De Santis, P.3    Savino, M.4    Scipioni, A.5
  • 3
    • 0030575777 scopus 로고    scopus 로고
    • Naturally occurring nucleosome positioning signals in human exons and introns
    • DOI 10.1006/jmbi.1996.0592
    • Baldi P, Brunak S, Chauvin Y, Krogh A. 1996. Naturally occurring nucleosome positioning signals in human exons and introns. J Mol Biol 263: 503-510. (Pubitemid 26382069)
    • (1996) Journal of Molecular Biology , vol.263 , Issue.4 , pp. 503-510
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Krogh, A.4
  • 4
    • 0022914418 scopus 로고
    • Principles of sequence-dependent flexure of DNA
    • Calladine CR, Drew HR. 1986. Principles of sequence-dependent flexure of DNA. J Mol Biol 192: 907-918. (Pubitemid 17228140)
    • (1986) Journal of Molecular Biology , vol.192 , Issue.4 , pp. 907-918
    • Calladine, C.R.1    Drew, H.R.2
  • 5
    • 60849083224 scopus 로고    scopus 로고
    • Sequence-dependent nucleosome positioning
    • Chung HR, Vingron M. 2009. Sequence-dependent nucleosome positioning. J Mol Biol 386: 1411-1422.
    • (2009) J Mol Biol , vol.386 , pp. 1411-1422
    • Chung, H.R.1    Vingron, M.2
  • 8
    • 33947137710 scopus 로고    scopus 로고
    • Dynamics of replication-independent histone turnover in budding yeast
    • DOI 10.1126/science.1134053
    • Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. 2007. Dynamics of replication-independent histone turnover in budding yeast. Science 315: 1405-1408. (Pubitemid 46399548)
    • (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
  • 9
    • 0022230224 scopus 로고
    • DNA bending and its relation to nucleosome positioning
    • Drew HR, Travers AA. 1985. DNA bending and its relation to nucleosome positioning. J Mol Biol 186: 773-790. (Pubitemid 16087267)
    • (1985) Journal of Molecular Biology , vol.186 , Issue.4 , pp. 773-790
    • Drew, H.R.1    Travers, A.A.2
  • 10
    • 68149158205 scopus 로고    scopus 로고
    • Labile H3.3+H2A.Z nucleosomes mark 'nucleosome-free regions.'
    • Henikoff S. 2009. Labile H3.3+H2A.Z nucleosomes mark 'nucleosome-free regions.' Nat Genet 41: 865-866.
    • (2009) Nat Genet , vol.41 , pp. 865-866
    • Henikoff, S.1
  • 12
    • 0026663554 scopus 로고
    • Preferred positions of AA and TT dinucleotides in aligned nucleosome DNA sequences
    • Ioshikhes I, Bolshoy A, Trifonov EN. 1992. Preferred positions of AA and TT dinucleotides in aligned nucleosome DNA sequences. J Biomol Struct Dyn 9: 1111-1117.
    • (1992) J Biomol Struct Dyn , vol.9 , pp. 1111-1117
    • Ioshikhes, I.1    Bolshoy, A.2    Trifonov, E.N.3
  • 13
    • 0030595138 scopus 로고    scopus 로고
    • Nucleosome RNA sequence pattern revealed by multiple alignment of experimentally mapped sequences
    • DOI 10.1006/jmbi.1996.0503
    • Ioshikhes I, Bolshoy A, Derenshteyn K, Borodovsky M, Trifonov EN. 1996. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J Mol Biol 262: 129-139. (Pubitemid 26326967)
    • (1996) Journal of Molecular Biology , vol.262 , Issue.2 , pp. 129-139
    • Ioshikhes, I.1    Bolshoy, A.2    Derenshteyn, K.3    Borodovsky, M.4    Trifonov, E.N.5
  • 14
    • 33749153628 scopus 로고    scopus 로고
    • Nucleosome positions predicted through comparative genomics
    • DOI 10.1038/ng1878, PII NG1878
    • Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. 2006. Nucleosome positions predicted through comparative genomics. Nat Genet 38: 1210-1215. (Pubitemid 44470369)
    • (2006) Nature Genetics , vol.38 , Issue.10 , pp. 1210-1215
    • Ioshikhes, I.P.1    Albert, I.2    Zanton, S.J.3    Pugh, B.F.4
  • 15
    • 0029026719 scopus 로고
    • Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
    • Iyer V, Struhl K. 1995. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J 14: 2570-2579.
    • (1995) EMBO J , vol.14 , pp. 2570-2579
    • Iyer, V.1    Struhl, K.2
  • 16
    • 75349098018 scopus 로고    scopus 로고
    • A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
    • doi: 10.1186/gb-2009-10-10-r109
    • Jiang C, Pugh BF. 2009. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol 10: R109. doi: 10.1186/gb-2009-10-10-r109.
    • (2009) Genome Biol , vol.10
    • Jiang, C.1    Pugh, B.F.2
  • 17
    • 34250745886 scopus 로고    scopus 로고
    • Nucleosome stability mediated by histone variants H3.3 and H2A.Z
    • DOI 10.1101/gad.1547707
    • Jin C, Felsenfeld G. 2007. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev 21: 1519-1529. (Pubitemid 46955724)
    • (2007) Genes and Development , vol.21 , Issue.12 , pp. 1519-1529
    • Jin, C.1    Felsenfeld, G.2
  • 20
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
    • DOI 10.1006/jmbi.1997.1494
    • Lowary PT, Widom J. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 276: 19-42. (Pubitemid 28085408)
    • (1998) Journal of Molecular Biology , vol.276 , Issue.1 , pp. 19-42
    • Lowary, P.T.1    Widom, J.2
  • 24
    • 0021100990 scopus 로고
    • Nucleotide sequence-directed mapping of the nucleosomes
    • Mengeritsky G, Trifonov EN. 1983. Nucleotide sequence-directed mapping of the nucleosomes. Nucleic Acids Res 11: 3833-3851.
    • (1983) Nucleic Acids Res , vol.11 , pp. 3833-3851
    • Mengeritsky, G.1    Trifonov, E.N.2
  • 27
    • 76949093375 scopus 로고    scopus 로고
    • Nuclesome positioning: How is it established, and why does it matter?
    • Radman-Livaja M, Rando OJ. 2009. Nuclesome positioning: How is it established, and why does it matter? Dev Biol 339: 258-266.
    • (2009) Dev Biol , vol.339 , pp. 258-266
    • Radman-Livaja, M.1    Rando, O.J.2
  • 28
    • 78650937771 scopus 로고    scopus 로고
    • Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences
    • Rapoport AE, Frenkel ZM, Trifonov EN. 2011. Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. J Biomol Struct Dyn 28: 567-574.
    • (2011) J Biomol Struct Dyn , vol.28 , pp. 567-574
    • Rapoport, A.E.1    Frenkel, Z.M.2    Trifonov, E.N.3
  • 29
    • 33947514987 scopus 로고    scopus 로고
    • Sequence-directed mapping of nucleosome positions
    • Salih F, Salih B, Trifonov EN. 2007. Sequence-directed mapping of nucleosome positions. J Biomol Struct Dyn 24: 489-494.
    • (2007) J Biomol Struct Dyn , vol.24 , pp. 489-494
    • Salih, F.1    Salih, B.2    Trifonov, E.N.3
  • 30
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • DOI 10.1016/0022-2836(86)90452-3
    • Satchwell SC, Drew HR, Travers AA. 1986. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191: 659-675. (Pubitemid 17185964)
    • (1986) Journal of Molecular Biology , vol.191 , Issue.4 , pp. 659-675
    • Satchwell, S.C.1    Drew, H.R.2    Travers, A.A.3
  • 31
    • 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
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:dT) tracts: Major determinants of nucleosome organization
    • Segal E, Widom J. 2009a. Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19: 65-71.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 33
    • 68349125112 scopus 로고    scopus 로고
    • What controls nucleosome positions?
    • Segal E, Widom J. 2009b. What controls nucleosome positions? Trends Genet 25: 335-343.
    • (2009) Trends Genet , vol.25 , pp. 335-343
    • Segal, E.1    Widom, J.2
  • 35
    • 0025930248 scopus 로고
    • Nucleosome positioning: Occurrence, mechanisms, and functional consequences
    • Simpson RT. 1991. Nucleosome positioning: Occurrence, mechanisms, and functional consequences. Prog Nucleic Acid Res Mol Biol 40: 143-184.
    • (1991) Prog Nucleic Acid Res Mol Biol , vol.40 , pp. 143-184
    • Simpson, R.T.1
  • 36
    • 0026571527 scopus 로고
    • Nucleosome positioning
    • Thoma F. 1992. Nucleosome positioning. Biochim Biophys Acta 1130: 1-19.
    • (1992) Biochim Biophys Acta , vol.1130 , pp. 1-19
    • Thoma, F.1
  • 37
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • DOI 10.1101/gr.076059.108
    • Tirosh I, Barkai N. 2008. Two strategies for gene regulation by promoter nucleosomes. Genome Res 18: 1084-1091. (Pubitemid 351931159)
    • (2008) Genome Research , vol.18 , Issue.7 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 41
    • 77951969370 scopus 로고    scopus 로고
    • Nucleosome positioning by sequence, state of the art and apparent finale
    • Trifonov EN. 2010. Nucleosome positioning by sequence, state of the art and apparent finale. J Biomol Struct Dyn 27: 741-746.
    • (2010) J Biomol Struct Dyn , vol.27 , pp. 741-746
    • Trifonov, E.N.1
  • 43
    • 0024057821 scopus 로고
    • DNA sequence patterns in precisely positioned nucleosomes
    • Uberbacher EC, Harp JM, Bunick GJ. 1988. DNA sequence patterns in precisely positioned nucleosomes. J Biomol Struct Dyn 6: 105-120.
    • (1988) J Biomol Struct Dyn , vol.6 , pp. 105-120
    • Uberbacher, E.C.1    Harp, J.M.2    Bunick, G.J.3
  • 44
    • 74949110964 scopus 로고    scopus 로고
    • High-resolution nucleosome mapping reveals transcription-dependent nucleosome packaging
    • Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N. 2010. High-resolution nucleosome mapping reveals transcription-dependent nucleosome packaging. Genome Res 20: 90-100.
    • (2010) Genome Res , vol.20 , pp. 90-100
    • Weiner, A.1    Hughes, A.2    Yassour, M.3    Rando, O.J.4    Friedman, N.5
  • 45
    • 0028176808 scopus 로고
    • Nucleosome positioning and modification: Chromatin structures that potentiate transcription
    • DOI 10.1016/0968-0004(94)90148-1
    • Wolffe AP. 1994. Nucleosome positioning and modification: chromatin structures that potentiate transcription. Trends Biochem Sci 19: 240-244. (Pubitemid 24184163)
    • (1994) Trends in Biochemical Sciences , vol.19 , Issue.6 , pp. 240-244
    • Wolffe, A.P.1
  • 46
    • 22744432660 scopus 로고    scopus 로고
    • Molecular biology: Genome-scale identification of nucleosome positions in S. cerevisiae
    • DOI 10.1126/science.1112178
    • Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630. (Pubitemid 41033649)
    • (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
  • 47
    • 79956316470 scopus 로고    scopus 로고
    • A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    • Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. 2011. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332: 977-980.
    • (2011) Science , vol.332 , pp. 977-980
    • Zhang, Z.1    Wippo, C.J.2    Wal, M.3    Ward, E.4    Korber, P.5    Pugh, B.F.6
  • 48
    • 0021112366 scopus 로고
    • Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine-pyrimidine and pyrimidine-purine dimers
    • Zhurkin VB. 1983. Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine-pyrimidine and pyrimidine-purine dimers. FEBS Lett 158: 293-297.
    • (1983) FEBS Lett , vol.158 , pp. 293-297
    • Zhurkin, V.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.