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Volumn 6, Issue , 2016, Pages

Nucleosome architecture throughout the cell cycle

Author keywords

[No Author keywords available]

Indexed keywords

CELL CYCLE; CELL CYCLE G1 PHASE; CELL CYCLE G2 PHASE; CELL CYCLE M PHASE; CELL CYCLE S PHASE; CHOREOGRAPHY; DNA REPLICATION ORIGIN; DNA TRANSCRIPTION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REARRANGEMENT; GENETIC TRANSCRIPTION; GENOME; NUCLEOSOME; PLASTICITY; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; BIOSYNTHESIS; DNA REPLICATION; GENETICS; METABOLISM; PHYSIOLOGY;

EID: 84955585450     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep19729     Document Type: Article
Times cited : (28)

References (74)
  • 1
    • 0033529565 scopus 로고    scopus 로고
    • Twenty-five years of the nucleosome, review fundamental particle of the eukaryote chromosome
    • Kornberg, R. D. & Lorch, Y. Twenty-five years of the nucleosome, review fundamental particle of the eukaryote chromosome. Cell 98, 285-294 (1999).
    • (1999) Cell , vol.98 , pp. 285-294
    • Kornberg, R.D.1    Lorch, Y.2
  • 2
    • 0242407193 scopus 로고    scopus 로고
    • Phylogenomics of the nucleosome
    • Malik, H. S. & Henikoff, S. Phylogenomics of the nucleosome. Nat. Struct. Biol. 10, 882-91 (2003).
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 882-891
    • Malik, H.S.1    Henikoff, S.2
  • 3
    • 0026599021 scopus 로고
    • Chromatin as an essential part of the transcriptional mechanim
    • Felsenfeld, G. Chromatin as an essential part of the transcriptional mechanim. Nature 355, 219-224 (1992).
    • (1992) Nature , vol.355 , pp. 219-224
    • Felsenfeld, G.1
  • 4
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: Advances through genomics
    • Jiang, C. & Pugh, B. F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10, 161-72 (2009).
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 161-172
    • Jiang, C.1    Pugh, B.F.2
  • 5
    • 0842324785 scopus 로고    scopus 로고
    • The nucleosome: From genomic organization to genomic regulation
    • Khorasanizadeh, S. The nucleosome: from genomic organization to genomic regulation. Cell 116, 259-272 (2004).
    • (2004) Cell , vol.116 , pp. 259-272
    • Khorasanizadeh, S.1
  • 6
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genomewide
    • Lee, C.-K., Shibata, Y., Rao, B., Strahl, B. D. & Lieb, J. D. Evidence for nucleosome depletion at active regulatory regions genomewide. Nat. Genet. 36, 900-905 (2004).
    • (2004) Nat. Genet. , vol.36 , pp. 900-905
    • Lee, C.-K.1    Shibata, Y.2    Rao, B.3    Strahl, B.D.4    Lieb, J.D.5
  • 7
    • 33747500567 scopus 로고    scopus 로고
    • A genomic code for nucleosome positioning
    • Segal, E. et al. A genomic code for nucleosome positioning. Nature 442, 772-8 (2006).
    • (2006) Nature , vol.442 , pp. 772-778
    • Segal, E.1
  • 8
    • 34748826166 scopus 로고    scopus 로고
    • A high-resolution atlas of nucleosome occupancy in yeast
    • Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet. 39, 1235-44 (2007).
    • (2007) Nat. Genet. , vol.39 , pp. 1235-1244
    • Lee, W.1
  • 9
    • 62649085538 scopus 로고    scopus 로고
    • The DNA-encoded nucleosome organization of a eukaryotic genome
    • Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458, 362-6 (2009).
    • (2009) Nature , vol.458 , pp. 362-366
    • Kaplan, N.1
  • 10
    • 80054693934 scopus 로고    scopus 로고
    • Genome-wide 're'-modeling of nucleosome positions
    • Sadeh, R. & Allis, C. D. Genome-wide 're'-modeling of nucleosome positions. Cell 147, 263-6 (2011).
    • (2011) Cell , vol.147 , pp. 263-266
    • Sadeh, R.1    Allis, C.D.2
  • 11
    • 78651477233 scopus 로고    scopus 로고
    • High-resolution genome-wide mapping of the primary structure of chromatin
    • Zhang, Z. & Pugh, B. F. High-resolution genome-wide mapping of the primary structure of chromatin. Cell 144, 175-86 (2011).
    • (2011) Cell , vol.144 , pp. 175-186
    • Zhang, Z.1    Pugh, B.F.2
  • 12
    • 80053539409 scopus 로고    scopus 로고
    • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    • Song, L. et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21, 1757-1767 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1757-1767
    • Song, L.1
  • 13
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • Albert, I. et al. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446, 572-6 (2007).
    • (2007) Nature , vol.446 , pp. 572-576
    • Albert, I.1
  • 14
    • 80053471251 scopus 로고    scopus 로고
    • Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast
    • Deniz, Ö. et al. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics 12, 489 (2011).
    • (2011) BMC Genomics , vol.12 , pp. 489
    • Deniz, Ö.1
  • 15
    • 79956316470 scopus 로고    scopus 로고
    • A Packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    • Zhang, Z. et al. A Packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science (80). 332, 977-980 (2011).
    • (2011) Science (80) , vol.332 , pp. 977-980
    • Zhang, Z.1
  • 16
    • 77950962157 scopus 로고    scopus 로고
    • Conserved nucleosome positioning defines replication origins
    • Eaton, M. L., Galani, K., Kang, S., Bell, S. P. & MacAlpine, D. M. Conserved nucleosome positioning defines replication origins. Genes Dev. 24, 748-53 (2010).
    • (2010) Genes Dev. , vol.24 , pp. 748-753
    • Eaton, M.L.1    Galani, K.2    Kang, S.3    Bell, S.P.4    MacAlpine, D.M.5
  • 17
    • 84899881366 scopus 로고    scopus 로고
    • Fuzziness and noise in nucleosomal architecture
    • Flores, O., Deniz, O., Soler-Lopez, M. & Orozco, M. Fuzziness and noise in nucleosomal architecture. Nucleic Acids Res. 42(8), 4934-46 (2014). doi: 10.1093/nar/gku165.
    • (2014) Nucleic Acids Res. , vol.42 , Issue.8 , pp. 4934-4946
    • Flores, O.1    Deniz, O.2    Soler-Lopez, M.3    Orozco, M.4
  • 18
    • 0024438911 scopus 로고
    • Nucleosomes inhibit both transcriptional initiation and elongation by RNA polymerase III in vitro
    • Morse, R. H. Nucleosomes inhibit both transcriptional initiation and elongation by RNA polymerase III in vitro. EMBO J. 8, 2343-51 (1989).
    • (1989) EMBO J , vol.8 , pp. 2343-2351
    • Morse, R.H.1
  • 19
    • 0027477501 scopus 로고
    • Multiple functions of nucleosomes and regulatory factors in transcription
    • Workman, J. L. & Buchman, A. R. Multiple functions of nucleosomes and regulatory factors in transcription. Trends Biochem. Sci. 18, 90-5 (1993).
    • (1993) Trends Biochem. Sci. , vol.18 , pp. 90-95
    • Workman, J.L.1    Buchman, A.R.2
  • 20
    • 46449112319 scopus 로고    scopus 로고
    • A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    • Mavrich, T. N. et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 18, 1073-83 (2008).
    • (2008) Genome Res. , vol.18 , pp. 1073-1083
    • Mavrich, T.N.1
  • 21
    • 65249164132 scopus 로고    scopus 로고
    • Mechanisms that specify promoter nucleosome location and identity
    • Hartley, P. D. & Madhani, H. D. Mechanisms that specify promoter nucleosome location and identity. Cell 137, 445-458 (2009).
    • (2009) Cell , vol.137 , pp. 445-458
    • Hartley, P.D.1    Madhani, H.D.2
  • 22
    • 80054081798 scopus 로고    scopus 로고
    • Genomic and chromatin signals underlying transcription start-site selection
    • Valen, E. & Sandelin, A. Genomic and chromatin signals underlying transcription start-site selection. Trends Genet. 27, 475-485 (2011).
    • (2011) Trends Genet. , vol.27 , pp. 475-485
    • Valen, E.1    Sandelin, A.2
  • 23
    • 81055155906 scopus 로고    scopus 로고
    • Nucleosomes and the accessibility problem
    • Wang, X., Bai, L., Bryant, G. O. & Ptashne, M. Nucleosomes and the accessibility problem. Trends Genet. 27, 487-492 (2011).
    • (2011) Trends Genet. , vol.27 , pp. 487-492
    • Wang, X.1    Bai, L.2    Bryant, G.O.3    Ptashne, M.4
  • 24
    • 84875196326 scopus 로고    scopus 로고
    • Determinants of nucleosome positioning
    • Struhl, K. & Segal, E. Determinants of nucleosome positioning. Nat. Struct. Mol. Biol. 20, 267-73 (2013).
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 267-273
    • Struhl, K.1    Segal, E.2
  • 25
    • 0033604609 scopus 로고    scopus 로고
    • Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast
    • Wyrick, J. J. et al. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418-421 (1999).
    • (1999) Nature , vol.402 , pp. 418-421
    • Wyrick, J.J.1
  • 26
    • 77957852519 scopus 로고    scopus 로고
    • Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription
    • Yadon, A. N. et al. Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription. Mol. Cell. Biol. 30, 5110-5122 (2010).
    • (2010) Mol. Cell. Biol. , vol.30 , pp. 5110-5122
    • Yadon, A.N.1
  • 28
    • 79959803077 scopus 로고    scopus 로고
    • Patterns and mechanisms of ancestral histone protein inheritance in budding yeast
    • Radman-Livaja, M. et al. Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol. 9, e1001075 (2011).
    • (2011) PLoS Biol. , vol.9
    • Radman-Livaja, M.1
  • 30
    • 0025067370 scopus 로고
    • Nucleosome positioning can affect the function of a cis-acting DNA element in vivo
    • Simpson, R. T. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature 343, 387-9 (1990).
    • (1990) Nature , vol.343 , pp. 387-389
    • Simpson, R.T.1
  • 31
    • 84884698163 scopus 로고    scopus 로고
    • A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast
    • Hoggard, T., Shor, E., Müller, C. A., Nieduszynski, C. A. & Fox, C. A. A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast. PLoS Genet. 9, e1003798 (2013).
    • (2013) PLoS Genet. , vol.9
    • Hoggard, T.1    Shor, E.2    Müller, C.A.3    Nieduszynski, C.A.4    Fox, C.A.5
  • 32
    • 84857271408 scopus 로고    scopus 로고
    • Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
    • Dabney, J. & Meyer, M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52, 87-94 (2012).
    • (2012) Biotechniques , vol.52 , pp. 87-94
    • Dabney, J.1    Meyer, M.2
  • 33
    • 0035104474 scopus 로고    scopus 로고
    • Nucleosomes positioned by ORC facilitate the initiation of DNA replication
    • Lipford, J. R. & Bell, S. P. Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol. Cell 7, 21-30 (2001).
    • (2001) Mol. Cell , vol.7 , pp. 21-30
    • Lipford, J.R.1    Bell, S.P.2
  • 34
    • 84873405188 scopus 로고    scopus 로고
    • Chromatin-dependent and -independent regulation of DNA replication origin activation in budding yeast
    • Lõoke, M., Kristjuhan, K., Värv, S. & Kristjuhan, A. Chromatin-dependent and -independent regulation of DNA replication origin activation in budding yeast. EMBO Rep. 14, 191-8 (2013).
    • (2013) EMBO Rep. , vol.14 , pp. 191-198
    • Lõoke, M.1    Kristjuhan, K.2    Värv, S.3    Kristjuhan, A.4
  • 35
    • 63449105244 scopus 로고    scopus 로고
    • Intrinsic variability of gene expression encoded in nucleosome positioning sequences
    • Choi, J. K. & Kim, Y.-J. Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat. Genet. 41, 498-503 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 498-503
    • Choi, J.K.1    Kim, Y.-J.2
  • 36
    • 74549187509 scopus 로고    scopus 로고
    • Promoter architecture and the evolvability of gene expression
    • Tirosh, I., Barkai, N. & Verstrepen, K. J. Promoter architecture and the evolvability of gene expression. J. Biol. 8, 95 (2009).
    • (2009) J. Biol. , vol.8 , pp. 95
    • Tirosh, I.1    Barkai, N.2    Verstrepen, K.J.3
  • 37
    • 77349100416 scopus 로고    scopus 로고
    • New insights into two distinct nucleosome distributions: Comparison of cross-platform positioning datasets in the yeast genome
    • Feng, J. et al. New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome. BMC Genomics 11, 33 (2010).
    • (2010) BMC Genomics , vol.11 , pp. 33
    • Feng, J.1
  • 38
    • 76349103252 scopus 로고    scopus 로고
    • Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae
    • Lantermann, A. B. et al. Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat. Struct. Mol. Biol. 17, 251-7 (2010).
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 251-257
    • Lantermann, A.B.1
  • 39
    • 84855306788 scopus 로고    scopus 로고
    • A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast
    • Zaugg, J. B. & Luscombe, N. M. A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast. Genome Res. 22(1), 84-94 (2011).
    • (2011) Genome Res. , vol.22 , Issue.1 , pp. 84-94
    • Zaugg, J.B.1    Luscombe, N.M.2
  • 40
    • 84867371116 scopus 로고    scopus 로고
    • A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern
    • Hughes, A. L., Jin, Y., Rando, O. J. & Struhl, K. A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern. Mol. Cell 48(1), 5-15 (2012).
    • (2012) Mol. Cell , vol.48 , Issue.1 , pp. 5-15
    • Hughes, A.L.1    Jin, Y.2    Rando, O.J.3    Struhl, K.4
  • 41
    • 79959557189 scopus 로고    scopus 로고
    • Determinants of nucleosome organization in primary human cells
    • Valouev, A. et al. Determinants of nucleosome organization in primary human cells. Nature 474, 516-520 (2011).
    • (2011) Nature , vol.474 , pp. 516-520
    • Valouev, A.1
  • 42
    • 84869014491 scopus 로고    scopus 로고
    • Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling
    • Nadal-Ribelles, M. et al. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol. 13, R106 (2012).
    • (2012) Genome Biol. , vol.13 , pp. R106
    • Nadal-Ribelles, M.1
  • 43
    • 29444455715 scopus 로고    scopus 로고
    • Cell-cycle control of gene expression in budding and fission yeast
    • Bähler, J. Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet. 39, 69-94 (2005).
    • (2005) Annu. Rev. Genet. , vol.39 , pp. 69-94
    • Bähler, J.1
  • 44
    • 33749406106 scopus 로고    scopus 로고
    • Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters
    • Hogan, G. J., Lee, C. K. & Lieb, J. D. Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet. 2, e158 (2006).
    • (2006) PLoS Genet. , vol.2 , pp. e158
    • Hogan, G.J.1    Lee, C.K.2    Lieb, J.D.3
  • 45
    • 0026607331 scopus 로고
    • ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex
    • Bell, S. P. & Stillman, B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357, 128-34 (1992).
    • (1992) Nature , vol.357 , pp. 128-134
    • Bell, S.P.1    Stillman, B.2
  • 46
    • 84902596852 scopus 로고    scopus 로고
    • Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity
    • Small, E. C., Xi, L., Wang, J.-P., Widom, J. & Licht, J. D. Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity. Proc. Natl. Acad. Sci. USA 111, E2462-71 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. E2462-E2471
    • Small, E.C.1    Xi, L.2    Wang, J.-P.3    Widom, J.4    Licht, J.D.5
  • 48
    • 79955559703 scopus 로고    scopus 로고
    • Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation
    • Xi, Y., Yao, J., Chen, R., Li, W. & He, X. Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation. Genome Res. 21, 718-24 (2011).
    • (2011) Genome Res. , vol.21 , pp. 718-724
    • Xi, Y.1    Yao, J.2    Chen, R.3    Li, W.4    He, X.5
  • 49
    • 74949110964 scopus 로고    scopus 로고
    • High-resolution nucleosome mapping reveals transcriptiondependent promoter packaging
    • Weiner, A., Hughes, A., Yassour, M., Rando, O. J. & Friedman, N. High-resolution nucleosome mapping reveals transcriptiondependent promoter packaging. Genome Res. 20, 90-100 (2010).
    • (2010) Genome Res. , vol.20 , pp. 90-100
    • Weiner, A.1    Hughes, A.2    Yassour, M.3    Rando, O.J.4    Friedman, N.5
  • 50
    • 67650711140 scopus 로고    scopus 로고
    • Genome-wide views of chromatin structure
    • Rando, O. J. & Chang, H. Y. Genome-wide views of chromatin structure. Annu. Rev. Biochem. 78, 245-71 (2009).
    • (2009) Annu. Rev. Biochem. , vol.78 , pp. 245-271
    • Rando, O.J.1    Chang, H.Y.2
  • 51
    • 1542328960 scopus 로고    scopus 로고
    • Identification and distinct regulation of yeast TATA box-containing genes
    • Basehoar, A. D., Zanton, S. J. & Pugh, B. F. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709 (2004).
    • (2004) Cell , vol.116 , pp. 699-709
    • Basehoar, A.D.1    Zanton, S.J.2    Pugh, B.F.3
  • 52
    • 84858165145 scopus 로고    scopus 로고
    • Genome-wide structure and organization of eukaryotic pre-initiation complexes
    • Rhee, H. S. & Pugh, B. F. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483, 295-301 (2012).
    • (2012) Nature , vol.483 , pp. 295-301
    • Rhee, H.S.1    Pugh, B.F.2
  • 53
    • 33745790132 scopus 로고    scopus 로고
    • Chromatin remodelling: The industrial revolution of DNA around histones
    • Saha, A., Wittmeyer, J. & Cairns, B. R. Chromatin remodelling: the industrial revolution of DNA around histones. Nat. Rev. Mol. Cell Biol. 7, 437-47 (2006).
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 437-447
    • Saha, A.1    Wittmeyer, J.2    Cairns, B.R.3
  • 54
    • 73049098277 scopus 로고    scopus 로고
    • Predicting nucleosome positions on the DNA: Combining intrinsic sequence preferences and remodeler activities
    • Teif, V. B. & Rippe, K. Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Res. 37, 5641-55 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5641-5655
    • Teif, V.B.1    Rippe, K.2
  • 55
    • 84862643713 scopus 로고    scopus 로고
    • Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers
    • Yen, K., Vinayachandran, V., Batta, K., Koerber, R. T. & Pugh, B. F. Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers. Cell 149, 1461-1473 (2012).
    • (2012) Cell , vol.149 , pp. 1461-1473
    • Yen, K.1    Vinayachandran, V.2    Batta, K.3    Koerber, R.T.4    Pugh, B.F.5
  • 56
    • 0028799428 scopus 로고
    • Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae
    • Althoefer, H., Schleiffer, A., Wassmann, K., Nordheim, A. & Ammerer, G. Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 15, 5917-28 (1995).
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 5917-5928
    • Althoefer, H.1    Schleiffer, A.2    Wassmann, K.3    Nordheim, A.4    Ammerer, G.5
  • 58
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 59
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
    • (2004) Genome Biol. , vol.5 , pp. R80
    • Gentleman, R.C.1
  • 60
    • 79960434317 scopus 로고    scopus 로고
    • NucleR: A package for non-parametric nucleosome positioning
    • Flores, O. & Orozco, M. nucleR: a package for non-parametric nucleosome positioning. Bioinformatics 27, 2149-2150 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2149-2150
    • Flores, O.1    Orozco, M.2
  • 61
    • 0036668464 scopus 로고    scopus 로고
    • Mapping of early firing origins on a replication profile of budding yeast
    • Yabuki, N., Terashima, H. & Kitada, K. Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7, 781-9 (2002).
    • (2002) Genes Cells , vol.7 , pp. 781-789
    • Yabuki, N.1    Terashima, H.2    Kitada, K.3
  • 62
    • 33846689706 scopus 로고    scopus 로고
    • Using GOstats to test gene lists for GO term association
    • Falcon, S. & Gentleman, R. Using GOstats to test gene lists for GO term association. Bioinformatics 23, 257-8 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 257-258
    • Falcon, S.1    Gentleman, R.2
  • 63
    • 79960610118 scopus 로고    scopus 로고
    • REVIGO summarizes and visualizes long lists of gene ontology terms
    • Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6, e21800 (2011).
    • (2011) PLoS One , vol.6
    • Supek, F.1    Bošnjak, M.2    Škunca, N.3    Šmuc, T.4
  • 64
    • 42449095007 scopus 로고    scopus 로고
    • Towards a molecular dynamics consensus view of B-DNA flexibility
    • Pérez, A., Lankas, F., Luque, F. J. & Orozco, M. Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res. 36, 2379-94 (2008).
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2379-2394
    • Pérez, A.1    Lankas, F.2    Luque, F.J.3    Orozco, M.4
  • 65
    • 0242290881 scopus 로고    scopus 로고
    • DNA basepair step deformability inferred from molecular dynamics simulations
    • Lankas, F., Sponer, J., Langowski, J. & Cheatham, T. E. DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J. 85, 2872-83 (2003).
    • (2003) Biophys. J. , vol.85 , pp. 2872-2883
    • Lankas, F.1    Sponer, J.2    Langowski, J.3    Cheatham, T.E.4
  • 66
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251-60 (1997).
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mäder, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 68
    • 0033664380 scopus 로고    scopus 로고
    • Crystal structure of a nucleosome core particle containing the variant histone H2A.Z
    • Suto, R. K., Clarkson, M. J., Tremethick, D. J. & Luger, K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat. Struct. Biol. 7, 1121-4 (2000).
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 1121-1124
    • Suto, R.K.1    Clarkson, M.J.2    Tremethick, D.J.3    Luger, K.4
  • 69
    • 0037436337 scopus 로고    scopus 로고
    • Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands
    • Suto, R. K. et al. Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. J. Mol. Biol. 326, 371-80 (2003).
    • (2003) J. Mol. Biol. , vol.326 , pp. 371-380
    • Suto, R.K.1
  • 70
    • 77957252758 scopus 로고    scopus 로고
    • Crystal Structures of Nucleosome Core Particles Containing the '601' Strong Positioning Sequence
    • Vasudevan, D., Chua, E. Y. D. & Davey, C. A. Crystal Structures of Nucleosome Core Particles Containing the '601' Strong Positioning Sequence. J. Mol. Biol. 403, 1-10 (2010).
    • (2010) J. Mol. Biol. , vol.403 , pp. 1-10
    • Vasudevan, D.1    Chua, E.Y.D.2    Davey, C.A.3
  • 71
    • 1542320757 scopus 로고    scopus 로고
    • Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions
    • Muthurajan, U. M. et al. Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J. 23, 260-71 (2004).
    • (2004) EMBO J. , vol.23 , pp. 260-271
    • Muthurajan, U.M.1
  • 72
    • 34147191973 scopus 로고    scopus 로고
    • DNA stretching and extreme kinking in the nucleosome core
    • Ong, M. S., Richmond, T. J. & Davey, C. A. DNA stretching and extreme kinking in the nucleosome core. J. Mol. Biol. 368, 1067-74 (2007).
    • (2007) J. Mol. Biol. , vol.368 , pp. 1067-1074
    • Ong, M.S.1    Richmond, T.J.2    Davey, C.A.3
  • 73
    • 33746793264 scopus 로고    scopus 로고
    • Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure
    • Bao, Y., White, C. L. & Luger, K. Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure. J. Mol. Biol. 361, 617-24 (2006).
    • (2006) J. Mol. Biol. , vol.361 , pp. 617-624
    • Bao, Y.1    White, C.L.2    Luger, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.