메뉴 건너뛰기




Volumn 5, Issue 4, 2015, Pages

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

Author keywords

Genome evolution; Nucleosomes; Protein composition

Indexed keywords

SACCHAROMYCETALES;

EID: 84934966303     PISSN: None     EISSN: 20462441     Source Type: Journal    
DOI: 10.1098/rsob.140218     Document Type: Article
Times cited : (10)

References (46)
  • 1
    • 84875149194 scopus 로고    scopus 로고
    • Regulation of nucleosome dynamics by histone modifications
    • Zentner GE, Henikoff S. 2013 Regulation of nucleosome dynamics by histone modifications. Nat. Struct. Mol. Biol. 20, 259-266. (doi:10.1038/nsmb. 2470)
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 259-266
    • Zentner, G.E.1    Henikoff, S.2
  • 2
    • 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. (doi:10.1126/science.1200508)
    • (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
  • 4
    • 84868679486 scopus 로고    scopus 로고
    • Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription
    • Hennig BP, Bendrin K, Zhou Y, Fischer T. 2012 Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription. EMBO Rep. 13, 997-1003. (doi:10.1038/embor.2012.146)
    • (2012) EMBO Rep. , vol.13 , pp. 997-1003
    • Hennig, B.P.1    Bendrin, K.2    Zhou, Y.3    Fischer, T.4
  • 5
    • 84870510245 scopus 로고    scopus 로고
    • CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S
    • Pointner J et al. 2012 CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J. 31, 4388-4403. (doi:10.1038/emboj.2012.289)
    • (2012) Pombe. EMBO J. , vol.31 , pp. 4388-4403
    • Pointner, J.1
  • 6
    • 84870575288 scopus 로고    scopus 로고
    • Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin
    • Shim YS, Choi Y, Kang K, Cho K, Oh S, Lee J, Grewal SIS, Lee D. 2012 Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin. EMBO J. 31, 4375-4387. (doi:10.1038/emboj.2012.267)
    • (2012) EMBO J. , vol.31 , pp. 4375-4387
    • Shim, Y.S.1    Choi, Y.2    Kang, K.3    Cho, K.4    Oh, S.5    Lee, J.6    Grewal, S.I.S.7    Lee, D.8
  • 7
    • 77952245290 scopus 로고    scopus 로고
    • Divergence of nucleosome positioning between two closely related yeast species: Genetic basis and functional consequences
    • Tirosh I, Sigal N, Barkai N. 2010 Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol. Syst. Biol. 6, 365. (doi:10.1038/msb.2010.20)
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 365
    • Tirosh, I.1    Sigal, N.2    Barkai, N.3
  • 8
    • 0023777538 scopus 로고
    • Statistical distributions of nucleosomes: Nonrandom locations by a stochastic mechanism
    • Kornberg RD, Stryer L. 1988 Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res. 16, 6677-6690. (doi:10.1093/nar/16.14.6677)
    • (1988) Nucleic Acids Res. , vol.16 , pp. 6677-6690
    • Kornberg, R.D.1    Stryer, L.2
  • 9
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 1997 Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251-260. (doi:10.1038/38444)
    • (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
  • 10
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • Richmond TJ, Davey CA. 2003 The structure of DNA in the nucleosome core. Nature 423, 145-150. (doi:10.1038/nature01595)
    • (2003) Nature , vol.423 , pp. 145-150
    • Richmond, T.J.1    Davey, C.A.2
  • 11
    • 0039837085 scopus 로고    scopus 로고
    • Sequence motifs and free energies of selected natural and nonnatural nucleosome positioning DNA sequences
    • Thåström A, Lowary PT, Widlund HR, Cao H, Kubista M, Widom J. 1999 Sequence motifs and free energies of selected natural and nonnatural nucleosome positioning DNA sequences. J. Mol. Biol. 288, 213-229. (doi:10.1006/jmbi. 1999.2686)
    • (1999) J. Mol. Biol. , vol.288 , pp. 213-229
    • Thåström, A.1    Lowary, P.T.2    Widlund, H.R.3    Cao, H.4    Kubista, M.5    Widom, J.6
  • 12
    • 0001415964 scopus 로고
    • The pitch of chromatin DNA is reflected in its nucleotide sequence
    • Trifonov EN, Sussman JL. 1980 The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl Acad. Sci. USA 77, 3816-3820. (doi:10.1073/pnas.77.7.3816)
    • (1980) Proc. Natl Acad. Sci. USA , vol.77 , pp. 3816-3820
    • Trifonov, E.N.1    Sussman, J.L.2
  • 13
    • 0030595138 scopus 로고    scopus 로고
    • Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences
    • 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. (doi:10.1006/jmbi.1996.0503)
    • (1996) J. Mol. Biol. , vol.262 , pp. 129-139
    • Ioshikhes, I.1    Bolshoy, A.2    Derenshteyn, K.3    Borodovsky, M.4    Trifonov, E.N.5
  • 15
    • 33749153628 scopus 로고    scopus 로고
    • Nucleosome positions predicted through comparative genomics
    • Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. 2006 Nucleosome positions predicted through comparative genomics. Nat. Genet. 38, 1210-1215. (doi:10.1038/ng1878)
    • (2006) Nat. Genet. , vol.38 , pp. 1210-1215
    • Ioshikhes, I.P.1    Albert, I.2    Zanton, S.J.3    Pugh, B.F.4
  • 16
    • 80555125013 scopus 로고    scopus 로고
    • Variety of genomic DNA patterns for nucleosome positioning
    • Ioshikhes I, Hosid S, Pugh BF. 2011 Variety of genomic DNA patterns for nucleosome positioning. Genome Res. 21, 1863-1871. (doi:10.1101/gr. 116228.110)
    • (2011) Genome Res. , vol.21 , pp. 1863-1871
    • Ioshikhes, I.1    Hosid, S.2    Pugh, B.F.3
  • 17
    • 79957929301 scopus 로고    scopus 로고
    • Stable and dynamic nucleosome states during a meiotic developmental process
    • Zhang L, Ma H, Pugh BF. 2011 Stable and dynamic nucleosome states during a meiotic developmental process. Genome Res. 21, 875-884. (doi:10.1101/gr.117465.110)
    • (2011) Genome Res. , vol.21 , pp. 875-884
    • Zhang, L.1    Ma, H.2    Pugh, B.F.3
  • 18
    • 84887900495 scopus 로고    scopus 로고
    • Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe
    • Soriano I, Quintales L, Antequera F. 2013 Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe. BMC Genomics 14, 813. (doi:10.1186/1471-2164-14-813)
    • (2013) BMC Genomics , vol.14 , pp. 813
    • Soriano, I.1    Quintales, L.2    Antequera, F.3
  • 21
    • 83255187902 scopus 로고    scopus 로고
    • Evolution of nucleosome occupancy: Conservation of global properties and divergence of gene-specific patterns
    • Tsui K, Dubuis S, Gebbia M, Morse RH, Barkai N, Tirosh I, Nislow C. 2011 Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns. Mol. Cell. Biol. 31, 4348-4355. (doi:10.1128/MCB.05276-11)
    • (2011) Mol. Cell. Biol. , vol.31 , pp. 4348-4355
    • Tsui, K.1    Dubuis, S.2    Gebbia, M.3    Morse, R.H.4    Barkai, N.5    Tirosh, I.6    Nislow, C.7
  • 22
    • 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, Rando OJ. 2011 Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res. 21, 1851-1862. (doi:10.1101/gr. 122267.111)
    • (2011) Genome Res. , vol.21 , pp. 1851-1862
    • Tsankov, A.1    Yanagisawa, Y.2    Rhind, N.3    Regev, A.4    Rando, O.J.5
  • 23
    • 84855351444 scopus 로고    scopus 로고
    • Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast
    • De Castro E, Soriano I, Marín L, Serrano R, Quintales L, Antequera F. 2012 Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast. EMBO J. 31, 124-137. (doi:10.1038/emboj.2011.350)
    • (2012) EMBO J. , vol.31 , pp. 124-137
    • De Castro, E.1    Soriano, I.2    Marín, L.3    Serrano, R.4    Quintales, L.5    Antequera, F.6
  • 24
    • 76349103252 scopus 로고    scopus 로고
    • Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae
    • Lantermann AB, Straub T, Strålfors A, Yuan G-C, Ekwall K, 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. (doi:10.1038/nsmb.1741)
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 251-257
    • Lantermann, A.B.1    Straub, T.2    Strålfors, A.3    Yuan, G.-C.4    Ekwall, K.5    Korber, P.6
  • 25
    • 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 SL. 2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. (doi:10.1186/gb-2009-10-3-r25)
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 26
    • 0003833285 scopus 로고
    • Philadelphia, PA: Society for Industrial and Applied Mathematics
    • Daubechies I. 1992 Ten lectures on wavelets. Philadelphia, PA: Society for Industrial and Applied Mathematics.
    • (1992) Ten Lectures on Wavelets
    • Daubechies, I.1
  • 27
    • 84929952110 scopus 로고    scopus 로고
    • Comparative analysis of methods for genome-wide nucleosome cartography
    • In press
    • Quintales L, Vázquez E, Antequera F. In press. Comparative analysis of methods for genome-wide nucleosome cartography. Brief. Bioinform. (doi:10. 1093/bib/bbu037)
    • Brief. Bioinform
    • Quintales, L.1    Vázquez, E.2    Antequera, F.3
  • 28
    • 79956319465 scopus 로고    scopus 로고
    • Comparative functional genomics of the fission yeasts
    • Rhind N et al. 2011 Comparative functional genomics of the fission yeasts. Science 332, 930-936. (doi:10.1126/science.1203357)
    • (2011) Science , vol.332 , pp. 930-936
    • Rhind, N.1
  • 29
    • 0034577919 scopus 로고    scopus 로고
    • Where does fission yeast sit on the tree of life?
    • Sipiczki M. 2000 Where does fission yeast sit on the tree of life? Genome Biol. 1, reviews1011. (doi:10. 1186/gb-2000-1-2-reviews1011)
    • (2000) Genome Biol. , vol.1
    • Sipiczki, M.1
  • 30
    • 84929961336 scopus 로고    scopus 로고
    • Nucleosome positioning in yeasts: Methods, maps, and mechanisms
    • In press
    • Lieleg C, Krietenstein N, Walker M, Korber P. In press. Nucleosome positioning in yeasts: methods, maps, and mechanisms. Chromosoma. (doi:10.1007/s00412-014-0501-x)
    • Chromosoma
    • Lieleg, C.1    Krietenstein, N.2    Walker, M.3    Korber, P.4
  • 31
    • 33646190728 scopus 로고    scopus 로고
    • Periodicity of SNP distribution around transcription start sites
    • Higasa K, Hayashi K. 2006 Periodicity of SNP distribution around transcription start sites. BMC Genomics 7, 66. (doi:10.1186/1471-2164-7-66)
    • (2006) BMC Genomics , vol.7 , pp. 66
    • Higasa, K.1    Hayashi, K.2
  • 32
    • 56049115800 scopus 로고    scopus 로고
    • A novel DNA sequence periodicity decodes nucleosome positioning
    • Chen K, Meng Q, Ma L, Liu Q, Tang P, Chiu C, Hu S, Yu J. 2008 A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res. 36, 6228-6236. (doi:10.1093/nar/gkn626)
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6228-6236
    • Chen, K.1    Meng, Q.2    Ma, L.3    Liu, Q.4    Tang, P.5    Chiu, C.6    Hu, S.7    Yu, J.8
  • 33
    • 56649089682 scopus 로고    scopus 로고
    • Evolutionary footprints of nucleosome positions in yeast
    • Washietl S, Machné R, Goldman N. 2008 Evolutionary footprints of nucleosome positions in yeast. Trends Genet. 24, 583-587. (doi:10.1016/j. tig.2008.09.003)
    • (2008) Trends Genet , vol.24 , pp. 583-587
    • Washietl, S.1    Machné, R.2    Goldman, N.3
  • 34
    • 75149135277 scopus 로고    scopus 로고
    • G + C content dominates intrinsic nucleosome occupancy
    • Tillo D, Hughes TR. 2009 G + C content dominates intrinsic nucleosome occupancy. BMC Bioinform. 10, 442. (doi:10.1186/1471-2105-10-442)
    • (2009) BMC Bioinform. , vol.10 , pp. 442
    • Tillo, D.1    Hughes, T.R.2
  • 35
    • 58449116917 scopus 로고    scopus 로고
    • Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
    • Sasaki S et al. 2009 Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323, 401-404. (doi:10.1126/science.1163183)
    • (2009) Science , vol.323 , pp. 401-404
    • Sasaki, S.1
  • 37
    • 76949093375 scopus 로고    scopus 로고
    • Nucleosome positioning: How is it established, and why does it matter?
    • Radman-Livaja M, Rando OJ. 2010 Nucleosome positioning: how is it established, and why does it matter? Dev. Biol. 339, 258-266. (doi:10.1016/j. ydbio.2009.06.012)
    • (2010) Dev. Biol. , vol.339 , pp. 258-266
    • Radman-Livaja, M.1    Rando, O.J.2
  • 39
    • 80555156662 scopus 로고    scopus 로고
    • Widespread signatures of recent selection linked to nucleosome positioning in the human lineage
    • Prendergast JGD, Semple C A M. 2011 Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Res. 21, 1777-1787. (doi:10.1101/gr.122275.111)
    • (2011) Genome Res. , vol.21 , pp. 1777-1787
    • Prendergast, J.G.D.1    Semple, C.A.M.2
  • 40
    • 57149100569 scopus 로고    scopus 로고
    • The impact of the nucleosome code on protein-coding sequence evolution in yeast
    • Warnecke T, Batada NN, Hurst LD. 2008 The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet. 4, e1000250. (doi:10.1371/journal.pgen. 1000250)
    • (2008) PLoS Genet. , vol.4 , pp. e1000250
    • Warnecke, T.1    Batada, N.N.2    Hurst, L.D.3
  • 42
    • 0026513573 scopus 로고
    • Species specific protein-DNA interactions may determine the chromatin units of genes in S. Cerevisiae and in S. Pombe
    • Bernardi F, Zatchej M, Thoma F. 1992 Species specific protein-DNA interactions may determine the chromatin units of genes in S. cerevisiae and in S. pombe. EMBO J. 11, 1177-1185.
    • (1992) EMBO J. , vol.11 , pp. 1177-1185
    • Bernardi, F.1    Zatchej, M.2    Thoma, F.3
  • 43
    • 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 AL, Jin Y, Rando OJ, 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. (doi:10.1016/j.molcel. 2012.07.003)
    • (2012) Mol. Cell , vol.48 , pp. 5-15
    • Hughes, A.L.1    Jin, Y.2    Rando, O.J.3    Struhl, K.4
  • 45
    • 20444403749 scopus 로고    scopus 로고
    • Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast
    • Sekinger EA, Moqtaderi Z, Struhl K. 2005 Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell 18, 735-748. (doi:10.1016/j.molcel.2005.05.003)
    • (2005) Mol. Cell , vol.18 , pp. 735-748
    • Sekinger, E.A.1    Moqtaderi, Z.2    Struhl, K.3
  • 46
    • 79958038927 scopus 로고    scopus 로고
    • Working the kinks out of nucleosomal DNA
    • Olson WK, Zhurkin VB. 2011 Working the kinks out of nucleosomal DNA. Curr. Opin. Struct. Biol. 21, 348-357. (doi:10.1016/j.sbi.2011.03.006)
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 348-357
    • Olson, W.K.1    Zhurkin, V.B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.