메뉴 건너뛰기




Volumn 42, Issue 8, 2014, Pages 4934-4946

Fuzziness and noise in nucleosomal architecture

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; MICROCOCCAL NUCLEASE; NUCLEOSOMAL DNA; UNCLASSIFIED DRUG;

EID: 84899881366     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku165     Document Type: Article
Times cited : (23)

References (64)
  • 1
    • 0033529565 scopus 로고    scopus 로고
    • Twenty-five years of the nucleosome, review fundamental particle of the eukaryote chromosome
    • Kornberg, R.D. and Lorch, Y. (1999) Twenty-five years of the nucleosome, review fundamental particle of the eukaryote chromosome. Cell, 98, 285-294.
    • (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. and Henikoff, S. (2003) Phylogenomics of the nucleosome. Nat. Struct. Biol., 10, 882-891.
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 882-891
    • Malik, H.S.1    Henikoff, S.2
  • 3
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. and Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature, 389, 251-260.
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 6
    • 0027477501 scopus 로고
    • Multiple functions of nucleosomes and regulatory factors in transcription
    • Workman, J.L. and Buchman, A.R. (1993) Multiple functions of nucleosomes and regulatory factors in transcription. Trends Biochem. Sci., 18, 90-95.
    • (1993) Trends Biochem. Sci. , vol.18 , pp. 90-95
    • Workman, J.L.1    Buchman, A.R.2
  • 7
    • 75349098018 scopus 로고    scopus 로고
    • A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
    • Jiang, C. and Pugh, B.F. (2009) A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol., 10, R109.
    • (2009) Genome Biol. , vol.10
    • Jiang, C.1    Pugh, B.F.2
  • 9
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genome-wide
    • Lee, C.-K., Shibata, Y., Rao, B., Strahl, B.D. and Lieb, J.D. (2004) Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet., 36, 900-905.
    • (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
  • 11
    • 80054693934 scopus 로고    scopus 로고
    • Genome-wide ''re''-modeling of nucleosome positions
    • Sadeh, R. and Allis, C.D. (2011) Genome-wide ''re''-modeling of nucleosome positions. Cell, 147, 263-266.
    • (2011) Cell , vol.147 , pp. 263-266
    • Sadeh, R.1    Allis, C.D.2
  • 13
    • 79957929301 scopus 로고    scopus 로고
    • Stable and dynamic nucleosome states during a meiotic developmental process
    • Zhang, L., Ma, H. and Pugh, B.F. (2011) Stable and dynamic nucleosome states during a meiotic developmental process. Genome Res., 21, 875-884.
    • (2011) Genome Res. , vol.21 , pp. 875-884
    • Zhang, L.1    Ma, H.2    Pugh, B.F.3
  • 14
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • Albert, I., Mavrich, T.N., Tomsho, L.P., Qi, J., Zanton, S.J., Schuster, S.C. and Pugh, B.F. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature, 446, 572-576.
    • (2007) Nature , vol.446 , 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
  • 15
    • 80053471251 scopus 로고    scopus 로고
    • Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast
    • Deniz, O., Flores, O., Battistini, F., Perez, A., Soler-Lopez, M. and Orozco, M. (2011) Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics, 12, 489.
    • (2011) BMC Genomics , vol.12 , pp. 489
    • Deniz, O.1    Flores, O.2    Battistini, F.3    Perez, A.4    Soler-Lopez, M.5    Orozco, M.6
  • 16
    • 79851485916 scopus 로고    scopus 로고
    • Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level
    • Rach, E.A., Winter, D.R., Benjamin, A.M., Corcoran, D.L., Ni, T., Zhu, J. and Ohler, U. (2011) Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet., 7, e1001274.
    • (2011) PLoS Genet. , vol.7
    • Rach, E.A.1    Winter, D.R.2    Benjamin, A.M.3    Corcoran, D.L.4    Ni, T.5    Zhu, J.6    Ohler, U.7
  • 18
    • 79956316470 scopus 로고    scopus 로고
    • A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    • Zhang, Z., Wippo, C.J., Wal, M., Ward, E., Korber, P. and Pugh, B.F. (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
  • 19
    • 81055155906 scopus 로고    scopus 로고
    • Nucleosomes and the accessibility problem
    • Wang, X., Bai, L., Bryant, G.O. and Ptashne, M. (2011) Nucleosomes and the accessibility problem. Trends Genet., 27, 487-492.
    • (2011) Trends Genet. , vol.27 , pp. 487-492
    • Wang, X.1    Bai, L.2    Bryant, G.O.3    Ptashne, M.4
  • 20
    • 0019879337 scopus 로고
    • The location of nucleosomes in chromatin: Specific or statistical?
    • Kornberg, R. (1981) The location of nucleosomes in chromatin: specific or statistical? Nature, 292, 579-580.
    • (1981) Nature , vol.292 , pp. 579-580
    • Kornberg, R.1
  • 25
    • 76349103252 scopus 로고    scopus 로고
    • Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae
    • Lantermann, A.B., Straub, T., Stralfors, A., Yuan, G.-C., Ekwall, K. and Korber, P. (2010) Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat. Struct. Mol. Biol., 17, 251-257.
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 251-257
    • Lantermann, A.B.1    Straub, T.2    Stralfors, A.3    Yuan, G.-C.4    Ekwall, K.5    Korber, P.6
  • 26
    • 80555125013 scopus 로고    scopus 로고
    • Variety of genomic DNA patterns for nucleosome positioning
    • Ioshikhes, I., Hosid, S. and Pugh, F. (2011) Variety of genomic DNA patterns for nucleosome positioning. Genome Res., 21, 1863-1871.
    • (2011) Genome Res. , vol.21 , pp. 1863-1871
    • Ioshikhes, I.1    Hosid, S.2    Pugh, F.3
  • 27
    • 79955465450 scopus 로고    scopus 로고
    • Predicting Nucleosome Positioning in Genomes: Physical and Bioinformatic Approaches
    • Scipioni, A. and De Santis, P. (2011) Predicting Nucleosome Positioning in Genomes: Physical and Bioinformatic Approaches. Biophys. Chem., 155, 53-64.
    • (2011) Biophys. Chem. , vol.155 , pp. 53-64
    • Scipioni, A.1    De Santis, P.2
  • 28
    • 79952183494 scopus 로고    scopus 로고
    • Cracking the chromatin code: Precise rule of nucleosome positioning
    • Trifonov, E.N. (2011) Cracking the chromatin code: Precise rule of nucleosome positioning. Phys. Life Rev., 8, 39-50.
    • (2011) Phys. Life Rev. , vol.8 , pp. 39-50
    • Trifonov, E.N.1
  • 30
    • 79959557189 scopus 로고    scopus 로고
    • Determinants of nucleosome organization in primary human cells
    • Valouev, A., Johnson, S.M., Boyd, S.D., Smith, C.L., Fire, A.Z. and Sidow, A. (2011) Determinants of nucleosome organization in primary human cells. Nature, 474, 516-520.
    • (2011) Nature , vol.474 , pp. 516-520
    • Valouev, A.1    Johnson, S.M.2    Boyd, S.D.3    Smith, C.L.4    Fire, A.Z.5    Sidow, A.6
  • 31
    • 84862643713 scopus 로고    scopus 로고
    • Genome-wide nucleosome specificity and directionality of chromatin remodelers
    • Yen, K., Vinayachandran, V., Batta, K., Koerber, R.T. and Pugh, B.F. (2012) Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell, 149, 1461-1473.
    • (2012) Cell , vol.149 , pp. 1461-1473
    • Yen, K.1    Vinayachandran, V.2    Batta, K.3    Koerber, R.T.4    Pugh, B.F.5
  • 32
    • 84875196326 scopus 로고    scopus 로고
    • Determinants of nucleosome positioning
    • Struhl, K. and Segal, E. (2013) Determinants of nucleosome positioning. Nat. Struct. Mol. Biol., 20, 267-273.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 267-273
    • Struhl, K.1    Segal, E.2
  • 33
    • 80555156654 scopus 로고    scopus 로고
    • Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
    • Tsankov, A., Yanagisawa, Y., Rhind, N., Regev, A. and Rando, O.J. (2011) Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res., 21, 1851-1862.
    • (2011) Genome Res. , vol.21 , pp. 1851-1862
    • Tsankov, A.1    Yanagisawa, Y.2    Rhind, N.3    Regev, A.4    Rando, O.J.5
  • 35
    • 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. and Struhl, K. (2012) A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol. Cell, 48, 5-15.
    • (2012) Mol. Cell , vol.48 , pp. 5-15
    • Hughes, A.L.1    Jin, Y.2    Rando, O.J.3    Struhl, K.4
  • 36
    • 68349125112 scopus 로고    scopus 로고
    • What controls nucleosome positions?
    • Segal, E. and Widom, J. (2009) What controls nucleosome positions? Trends Genet., 25, 335-343.
    • (2009) Trends Genet. , vol.25 , pp. 335-343
    • Segal, E.1    Widom, J.2
  • 38
    • 84875873326 scopus 로고    scopus 로고
    • Toward a unified physical model of nucleosome patterns flanking transcription start sites
    • Mobius, W., Osberg, B., Tsankov, A.M., Rando, O.J. and Gerland, U. (2013) Toward a unified physical model of nucleosome patterns flanking transcription start sites. Proc. Natl Acad. Sci. USA, 110, 5719-5724.
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 5719-5724
    • Mobius, W.1    Osberg, B.2    Tsankov, A.M.3    Rando, O.J.4    Gerland, U.5
  • 39
    • 84855306788 scopus 로고    scopus 로고
    • A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast
    • Zaugg, J.B. and Luscombe, N.M. (2011) A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast. Genome Res., 22, 84-94.
    • (2011) Genome Res. , vol.22 , pp. 84-94
    • Zaugg, J.B.1    Luscombe, N.M.2
  • 40
    • 79955610452 scopus 로고    scopus 로고
    • Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome
    • Vavouri, T. and Lehner, B. (2011) Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome. PLoS Genet., Apr; 7, e1002036.
    • (2011) PLoS Genet., Apr; , Issue.7
    • Vavouri, T.1    Lehner, B.2
  • 41
    • 77953305748 scopus 로고    scopus 로고
    • A structural perspective on the where, how, why, and what of nucleosome positioning
    • Arya, G., Maitra, A. and Grigoryev, S.A. (2010) A structural perspective on the where, how, why, and what of nucleosome positioning. J. Biomol. Struct. Dyn., 27, 803-820.
    • (2010) J. Biomol. Struct. Dyn. , vol.27 , pp. 803-820
    • Arya, G.1    Maitra, A.2    Grigoryev, S.A.3
  • 43
    • 84861368045 scopus 로고    scopus 로고
    • Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators
    • Huebert, D.J., Kuan, P.-F., Keles, S. and Gasch, A.P. (2012) Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol. Cell. Biol., 32, 1645-1653.
    • (2012) Mol. Cell. Biol. , vol.32 , pp. 1645-1653
    • Huebert, D.J.1    Kuan, P.-F.2    Keles, S.3    Gasch, A.P.4
  • 44
    • 77957883572 scopus 로고    scopus 로고
    • Gene regulation by nucleosome positioning
    • Bai, L. and Morozov, A.V. (2010) Gene regulation by nucleosome positioning. Trends Genet., 26, 476-483.
    • (2010) Trends Genet. , vol.26 , pp. 476-483
    • Bai, L.1    Morozov, A.V.2
  • 45
    • 68249131547 scopus 로고    scopus 로고
    • A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions
    • Article 29
    • Kuan, P.F., Huebert, D., Gasch, A. and Keles, S. (2009) A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions. Stat. Appl. Genet. Mol. Biol., 8:Article 29.
    • (2009) Stat. Appl. Genet. Mol. Biol. , vol.8
    • Kuan, P.F.1    Huebert, D.2    Gasch, A.3    Keles, S.4
  • 46
    • 77955045449 scopus 로고    scopus 로고
    • The role of nucleosome positioning in the evolution of gene regulation
    • Tsankov, A.M., Thompson, D.A., Socha, A., Regev, A. and Rando, O.J. (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol., 8, e1000414.
    • (2010) PLoS Biol. , vol.8
    • Tsankov, A.M.1    Thompson, D.A.2    Socha, A.3    Regev, A.4    Rando, O.J.5
  • 47
    • 84883369935 scopus 로고    scopus 로고
    • Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers
    • Ozonov, E.A. and van Nimwegen, E. (2013) Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Comput. Biol., 9, e1003181.
    • (2013) PLoS Comput. Biol. , vol.9
    • Ozonov, E.A.1    Van Nimwegen, E.2
  • 48
    • 77958537326 scopus 로고    scopus 로고
    • Weakly positioned nucleosomes enhance the transcriptional competency of chromatin
    • Belch, Y., Yang, J., Liu, Y., Malkaram, S.A., Liu, R., Riethoven, J.J. and Ladunga, I. (2010) Weakly positioned nucleosomes enhance the transcriptional competency of chromatin. PLoS One 24, 5, e12984.
    • (2010) PLoS One , vol.24 , Issue.5
    • Belch, Y.1    Yang, J.2    Liu, Y.3    Malkaram, S.A.4    Liu, R.5    Riethoven, J.J.6    Ladunga, I.7
  • 49
    • 78649708844 scopus 로고    scopus 로고
    • Conflict between noise and plasticity in yeast
    • Lehner, B. (2010) Conflict between noise and plasticity in yeast. PLoS Genet., 6, e1001185.
    • (2010) PLoS Genet. , vol.6
    • Lehner, B.1
  • 50
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 52
    • 79960434317 scopus 로고    scopus 로고
    • NucleR: A package for non-parametric nucleosome positioning
    • Flores, O. and Orozco, M. (2011) nucleR: a package for non-parametric nucleosome positioning. Bioinformatics, 27, 2149-2150.
    • (2011) Bioinformatics , vol.27 , pp. 2149-2150
    • Flores, O.1    Orozco, M.2
  • 53
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson, W.K. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci., 95, 11163-11168.
    • (1998) Proc. Natl Acad. Sci. , vol.95 , pp. 11163-11168
    • Olson, W.K.1
  • 54
    • 0242290881 scopus 로고    scopus 로고
    • DNA basepair step deformability inferred from molecular dynamics simulations
    • Lankas, F., Sponer, J., Langowski, J. and Cheatham, T.E. (2003) DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J., 85, 2872-2883.
    • (2003) Biophys. J. , vol.85 , pp. 2872-2883
    • Lankas, F.1    Sponer, J.2    Langowski, J.3    Cheatham, T.E.4
  • 56
    • 42449095007 scopus 로고    scopus 로고
    • Towards a molecular dynamics consensus view of B-DNA flexibility
    • Perez, A., Lankas, F., Luque, F.J. and Orozco, M. (2008) Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res., 36, 2379-2394.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2379-2394
    • Perez, A.1    Lankas, F.2    Luque, F.J.3    Orozco, M.4
  • 57
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
    • Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A. and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 60
    • 84888223867 scopus 로고    scopus 로고
    • Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations
    • Portella, G., Battistini, F. and Orozco, M. (2013) Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations. PLoS Comput. Biol., Nov; 9, e1003354.
    • (2013) PLoS Comput. Biol., Nov; , Issue.9
    • Portella, G.1    Battistini, F.2    Orozco, M.3
  • 61
    • 75549089771 scopus 로고    scopus 로고
    • Cyclebase.org: Version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
    • Gauthier, N.P., Jensen, L.J., Wernersson, R., Brunak, S. and Jensen, T.S. (2010) Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Res., 38, D699-D702.
    • (2010) Nucleic Acids Res. , vol.38
    • Gauthier, N.P.1    Jensen, L.J.2    Wernersson, R.3    Brunak, S.4    Jensen, T.S.5
  • 62
    • 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. and Meyer, M. (2012) 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) Biotechniques , vol.52 , pp. 87-94
    • Dabney, J.1    Meyer, M.2
  • 63
    • 0031587289 scopus 로고    scopus 로고
    • Characterization of nucleosome core particles containing histone proteins made in bacteria
    • Luger, K., Rechsteiner, T.J., Flaus, A.J., Waye, M.M. and Richmond, T.J. (1997) Characterization of nucleosome core particles containing histone proteins made in bacteria. J. Mol. Biol., 272, 301-311.
    • (1997) J. Mol. Biol. , vol.272 , pp. 301-311
    • Luger, K.1    Rechsteiner, T.J.2    Flaus, A.J.3    Waye, M.M.4    Richmond, T.J.5
  • 64
    • 33644625997 scopus 로고    scopus 로고
    • Dynamic nucleosomes
    • Luger, K. (2006) Dynamic nucleosomes. Chromosome Res., 14, 5-16.
    • (2006) Chromosome Res. , vol.14 , pp. 5-16
    • Luger, K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.