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Volumn 11, Issue 6, 2013, Pages

DNA structural features and architecture of promoter regions play a role in gene responsiveness of S. Cerevisiae

Author keywords

DNA structural property; gene expression variability; Promoter

Indexed keywords

FUNGAL DNA;

EID: 84891585966     PISSN: 02197200     EISSN: 17576334     Source Type: Journal    
DOI: 10.1142/S0219720013430014     Document Type: Article
Times cited : (14)

References (33)
  • 1
    • 63449105244 scopus 로고    scopus 로고
    • Intrinsic variability of gene expression encoded in nucleosome positioning sequences
    • Choi JK, Kim YJ, Intrinsic variability of gene expression encoded in nucleosome positioning sequences, Nat Genet 41(4):498-503, 2009.
    • (2009) Nat Genet , vol.41 , Issue.4 , pp. 498-503
    • Choi, J.K.1    Kim, Y.J.2
  • 2
    • 0347756647 scopus 로고    scopus 로고
    • DBTSS, DataBase of transcriptional start sites: Progress report 2004
    • (Database issue
    • Suzuki Y, Yamashita R, Sugano S, Nakai K, DBTSS, DataBase of transcriptional start sites: Progress report 2004, Nucleic Acids Res 32(Database issue):78-81, 2004.
    • (2004) Nucleic Acids Res , vol.32 , pp. 78-81
    • Suzuki, Y.1    Yamashita, R.2    Sugano, S.3    Nakai, K.4
  • 3
    • 84859243923 scopus 로고    scopus 로고
    • Promoter nucleosome organization shapes the evolution of gene expression
    • Rosin D, Hornung G, Tirosh I, Gispan A, Barkai N, Promoter nucleosome organization shapes the evolution of gene expression, PLoS Genet 8(3):e1002579, 2012.
    • (2012) PLoS Genet , vol.8 , Issue.3
    • Rosin, D.1    Hornung, G.2    Tirosh, I.3    Gispan, A.4    Barkai, N.5
  • 5
    • 20344396385 scopus 로고    scopus 로고
    • Structural properties of promoters: Similarities and di® erences between prokaryotes and eukaryotes
    • Kanhere A, Bansal M, Structural properties of promoters: Similarities and di® erences between prokaryotes and eukaryotes, Nucleic Acids Res 33(10):3165-3175, 2005.
    • (2005) Nucleic Acids Res , vol.33 , Issue.10 , pp. 3165-3175
    • Kanhere, A.1    Bansal, M.2
  • 6
    • 0032575756 scopus 로고    scopus 로고
    • DNA structure in human RNA polymerase II promoters
    • Pedersen AG, Baldi P, Chauvin Y, Brunak S, DNA structure in human RNA polymerase II promoters, J Mol Biol 281(4):663-673, 1998.
    • (1998) J Mol Biol , vol.281 , Issue.4 , pp. 663-673
    • Pedersen, A.G.1    Baldi, P.2    Chauvin, Y.3    Brunak, S.4
  • 8
    • 13444288385 scopus 로고    scopus 로고
    • DNA supercoiling-A global transcriptional regulator for enterobacterial growth?
    • Travers A, Muskhelishvili G, DNA supercoiling-a global transcriptional regulator for enterobacterial growth? Nat Rev Microbiol 3(2):157-169, 2005.
    • (2005) Nat Rev Microbiol , vol.3 , Issue.2 , pp. 157-169
    • Travers, A.1    Muskhelishvili, G.2
  • 9
    • 84880207699 scopus 로고    scopus 로고
    • The genomewide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli
    • Du X, Wojtowicz D, Bowers AA, Levens D, Benham CJ, Przytycka TM, The genomewide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli, Nucleic Acids Res 41(12):5965-5977, 2013.
    • (2013) Nucleic Acids Res , vol.41 , Issue.12 , pp. 5965-5977
    • Du, X.1    Wojtowicz, D.2    Bowers, A.A.3    Levens, D.4    Benham, C.J.5    Przytycka, T.M.6
  • 11
    • 39049168212 scopus 로고    scopus 로고
    • Generic eukaryotic core promoter prediction using structural features of DNA
    • Abeel T, Saeys Y, Bonnet E, Rouze P, van de Peer Y, Generic eukaryotic core promoter prediction using structural features of DNA, Genome Res 18(2):310-323, 2008.
    • (2008) Genome Res , vol.18 , Issue.2 , pp. 310-323
    • Abeel, T.1    Saeys, Y.2    Bonnet, E.3    Rouze, P.4    Van De Peer, Y.5
  • 12
    • 79951736762 scopus 로고    scopus 로고
    • High-quality annotation of promoter regions for 913 bacterial genomes
    • Rangannan V, Bansal M, High-quality annotation of promoter regions for 913 bacterial genomes, Bioinformatics 26(24):3043-3050, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.24 , pp. 3043-3050
    • Rangannan, V.1    Bansal, M.2
  • 13
    • 84876991257 scopus 로고    scopus 로고
    • Promoter sequence determines the relationship between expression level and noise
    • Carey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E, Promoter sequence determines the relationship between expression level and noise, PLoS Biol 11(4):e1001528, 2013.
    • (2013) PLoS Biol , vol.11 , Issue.4
    • Carey, L.B.1    Van Dijk, D.2    Sloot, P.M.3    Kaandorp, J.A.4    Segal, E.5
  • 15
    • 84878869936 scopus 로고    scopus 로고
    • Sequence features of yeast and human core promoters that are predictive of maximal promoter activity
    • Lubliner S, Keren L, Segal E, Sequence features of yeast and human core promoters that are predictive of maximal promoter activity, Nucleic Acids Res 41(11):5569-5581, 2013.
    • (2013) Nucleic Acids Res , vol.41 , Issue.11 , pp. 5569-5581
    • Lubliner, S.1    Keren, L.2    Segal, E.3
  • 17
    • 1542328960 scopus 로고    scopus 로고
    • Identīcation and distinct regulation of yeast TATA box-containing genes
    • Basehoar AD, Zanton SJ, Pugh BF, Identīcation and distinct regulation of yeast TATA box-containing genes, Cell 116(5):699-709, 2004.
    • (2004) Cell , vol.116 , Issue.5 , pp. 699-709
    • Basehoar, A.D.1    Zanton, S.J.2    Pugh, B.F.3
  • 18
    • 78649708844 scopus 로고    scopus 로고
    • Con°ict between noise and plasticity in yeast
    • Lehner B, Con°ict between noise and plasticity in yeast, PLoS Genet 6(11):e1001185, 2010.
    • (2010) PLoS Genet , vol.6 , Issue.11
    • Lehner, B.1
  • 19
    • 79952756695 scopus 로고    scopus 로고
    • Gene clustering pattern promoter architecture, and gene expression stability in eukaryotic genomes
    • Woo YH, Li WH, Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes, Proc Natl Acad Sci USA 108(8):3306-3311, 2011.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.8 , pp. 3306-3311
    • Woo, Y.H.1    Li, W.H.2
  • 20
    • 74549187509 scopus 로고    scopus 로고
    • Promoter architecture and the evolvability of gene expression
    • Tirosh I, Barkai N, Verstrepen KJ, Promoter architecture and the evolvability of gene expression, J Biol 8(11):95, 2009.
    • (2009) J Biol , vol.8 , Issue.11 , pp. 95
    • Tirosh, I.1    Barkai, N.2    Verstrepen, K.J.3
  • 22
    • 33745583768 scopus 로고    scopus 로고
    • A genetic signature of interspecies variations in gene expression
    • Tirosh I, Weinberger A, Carmi M, Barkai N, A genetic signature of interspecies variations in gene expression, Nat Genet 38(7):830-834, 2006.
    • (2006) Nat Genet , vol.38 , Issue.7 , pp. 830-834
    • Tirosh, I.1    Weinberger, A.2    Carmi, M.3    Barkai, N.4
  • 24
    • 38649094557 scopus 로고    scopus 로고
    • Epigenetic regulation and the variability of gene expression
    • Choi JK, Kim YJ, Epigenetic regulation and the variability of gene expression, Nat Genet 40(2):141-147, 2008.
    • (2008) Nat Genet , vol.40 , Issue.2 , pp. 141-147
    • Choi, J.K.1    Kim, Y.J.2
  • 25
    • 34250785284 scopus 로고    scopus 로고
    • Genetic properties in°uencing the evolvability of gene expression
    • Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL, Genetic properties in°uencing the evolvability of gene expression, Science 317(5834):118-121, 2007.
    • (2007) Science , vol.317 , Issue.5834 , pp. 118-121
    • Landry, C.R.1    Lemos, B.2    Rifkin, S.A.3    Dickinson, W.J.4    Hartl, D.L.5
  • 26
    • 0037572260 scopus 로고    scopus 로고
    • Population genetic variation in genome-wide gene expression
    • Townsend J, Cavalieri D, Hartl D, Population genetic variation in genome-wide gene expression, Mol Biol Evol 20(6):955-963, 2003.
    • (2003) Mol Biol Evol , vol.20 , Issue.6 , pp. 955-963
    • Townsend, J.1    Cavalieri, D.2    Hartl, D.3
  • 28
    • 0032539693 scopus 로고    scopus 로고
    • A unīed view of polymer dumbbell, and oligonucleotide DNA nearestneighbor thermodynamics
    • SantaLucia J, A unīed view of polymer, dumbbell, and oligonucleotide DNA nearestneighbor thermodynamics, Proc Natl Acad Sci USA 95(4):1460-1465, 1998.
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.4 , pp. 1460-1465
    • Santalucia, J.1
  • 29
    • 0029039118 scopus 로고
    • Sequence-dependent bending propensity of DNA as revealed by DNase I: Parameters for trinucleotides
    • Brukner I, Sanchez R, Suck D, Pongor S, Sequence-dependent bending propensity of DNA as revealed by DNase I: Parameters for trinucleotides, EMBO J 14(8):1812-1818, 1995.
    • (1995) EMBO J , vol.14 , Issue.8 , pp. 1812-1818
    • Brukner, I.1    Sanchez, R.2    Suck, D.3    Pongor, S.4
  • 30
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell SC, Drew HR, Travers AA, Sequence periodicities in chicken nucleosome core DNA, J Mol Biol 191(4):659-675, 1986.
    • (1986) J Mol Biol , vol.191 , Issue.4 , pp. 659-675
    • Satchwell, S.C.1    Drew, H.R.2    Travers, A.A.3
  • 31
    • 0024057971 scopus 로고
    • A general procedure for generation of curved DNA molecules
    • Bhattacharya D, Bansal M, A general procedure for generation of curved DNA molecules, J Biomol Struct Dyn 6(1):93-104, 1988.
    • (1988) J Biomol Struct Dyn , vol.6 , Issue.1 , pp. 93-104
    • Bhattacharya, D.1    Bansal, M.2
  • 32
    • 0026089491 scopus 로고
    • Curved DNA without A-A: Experimental estimation of all 16 DNA wedge angles
    • Bolshoy A, McNamara P, Harrington RE, Trifonov EN, Curved DNA without A-A: Experimental estimation of all 16 DNA wedge angles, Proc Natl Acad Sci USA 88 (6):2312-2316, 1991.
    • (1991) Proc Natl Acad Sci USA , vol.88 , Issue.6 , pp. 2312-2316
    • Bolshoy, A.1    McNamara, P.2    Harrington, R.E.3    Trifonov, E.N.4
  • 33
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • Tirosh I, Barkai N, Two strategies for gene regulation by promoter nucleosomes, Genome Res 18(7):1084-1091, 2008.
    • (2008) Genome Res , vol.18 , Issue.7 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.