메뉴 건너뛰기




Volumn 2, Issue 2, 2011, Pages 71-77

Promoter architectures in the yeast ribosomal expression program

Author keywords

Rap1; Ribosomal protein; Ribosome biogenesis; RNA polymerase II; SnoRNA; Tbf1; Telomeres

Indexed keywords

FORKHEAD TRANSCRIPTION FACTOR; RIBI PROTEIN; RIBOSOME PROTEIN; SMALL NUCLEOLAR RIBONUCLEOPROTEIN; TATA BINDING PROTEIN; THREONINE TRANSFER RNA LIGASE; UNCLASSIFIED DRUG;

EID: 79952474518     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.2.2.14486     Document Type: Article
Times cited : (26)

References (49)
  • 1
    • 5444237797 scopus 로고    scopus 로고
    • What better measure than ribo-some synthesis?
    • Rudra D, Warner JR. What better measure than ribo-some synthesis? Genes Dev 2004; 18:2431-2436.
    • (2004) Genes Dev , vol.18 , pp. 2431-2436
    • Rudra, D.1    Warner, J.R.2
  • 2
    • 0032929162 scopus 로고    scopus 로고
    • DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences
    • Lascaris RF, Mager WH, Planta RJ. DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences. Bioinformatics 1999; 15:267-77.
    • (1999) Bioinformatics , vol.15 , pp. 267-277
    • Lascaris, R.F.1    Mager, W.H.2    Planta, R.J.3
  • 4
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • Lieb JD, Liu X, Botstein D, Brown PO. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 2001; 28:327-334.
    • (2001) Nat Genet , vol.28 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 5
    • 77953287639 scopus 로고    scopus 로고
    • Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast
    • Zhang J, Vingron M, Roepcke S. Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast. BMC Res Notes 2008; 1:109.
    • (2008) BMC Res Notes , vol.1 , pp. 109
    • Zhang, J.1    Vingron, M.2    Roepcke, S.3
  • 6
    • 11144231369 scopus 로고    scopus 로고
    • The transcription fac- tor Ifh1 is a key regulator of yeast ribosomal protein genes
    • Wade JT, Hall DB, Struhl K. The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 2004; 432:1054-1058.
    • (2004) Nature , vol.432 , pp. 1054-1058
    • Wade, J.T.1    Hall, D.B.2    Struhl, K.3
  • 7
    • 11144244771 scopus 로고    scopus 로고
    • Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1
    • Schawalder SB, Kabani M, Howald I, Choudhury U, Werner M, Shore D. Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature 2004; 432:1058-1061.
    • (2004) Nature , vol.432 , pp. 1058-1061
    • Schawalder, S.B.1    Kabani, M.2    Howald, I.3    Choudhury, U.4    Werner, M.5    Shore, D.6
  • 8
    • 0036304346 scopus 로고    scopus 로고
    • In vivo topography of Rap1p-DNA complex at Saccharomyces cerevisiae TEF2 UAS(RPG) during transcriptional regulation
    • De Sanctis V, La Terra S, Bianchi A, Shore D, Burderi L, Di Mauro E, et al. In vivo topography of Rap1p-DNA complex at Saccharomyces cerevisiae TEF2 UAS(RPG) during transcriptional regulation. J Mol Biol 2002; 318:333-349.
    • (2002) J Mol Biol , vol.318 , pp. 333-349
    • de Sanctis, V.1    la Terra, S.2    Bianchi, A.3    Shore, D.4    Burderi, L.5    di Mauro, E.6
  • 9
    • 5144229125 scopus 로고    scopus 로고
    • Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression
    • Marion RM, Regev A, Segal E, Barash Y, Koller D, Friedman N, et al. Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci USA 2004; 101:14315-14322.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 14315-14322
    • Marion, R.M.1    Regev, A.2    Segal, E.3    Barash, Y.4    Koller, D.5    Friedman, N.6
  • 10
    • 5444256434 scopus 로고    scopus 로고
    • A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size
    • Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 2004; 18:2491-2505.
    • (2004) Genes Dev , vol.18 , pp. 2491-2505
    • Jorgensen, P.1    Rupes, I.2    Sharom, J.R.3    Schneper, L.4    Broach, J.R.5    Tyers, M.6
  • 11
    • 14844282303 scopus 로고    scopus 로고
    • Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins
    • Rudra D, Zhao Y, Warner JR. Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J 2005; 24:533-542.
    • (2005) EMBO J , vol.24 , pp. 533-542
    • Rudra, D.1    Zhao, Y.2    Warner, J.R.3
  • 12
    • 70350731108 scopus 로고    scopus 로고
    • Distinguishing direct versus indirect transcription factor-DNA interactions
    • Gordan R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 2009; 19:2090-2100.
    • (2009) Genome Res , vol.19 , pp. 2090-2100
    • Gordan, R.1    Hartemink, A.J.2    Bulyk, M.L.3
  • 13
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:DT) tracts: Major determinants of nucleosome organization
    • Segal E, Widom J. Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 2009; 19:65-71.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 15
    • 23244467882 scopus 로고    scopus 로고
    • Rewiring of the yeast transcriptional network through the evolution of motif usage
    • Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, Berman J, et al. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 2005; 309:938-940.
    • (2005) Science , vol.309 , pp. 938-940
    • Ihmels, J.1    Bergmann, S.2    Gerami-Nejad, M.3    Yanai, I.4    McClellan, M.5    Berman, J.6
  • 17
    • 1542328960 scopus 로고    scopus 로고
    • Identification and distinct regulation of yeast TATA box-containing genes
    • Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast TATA box-containing genes. Cell 2004; 116:699-709.
    • (2004) Cell , vol.116 , pp. 699-709
    • Basehoar, A.D.1    Zanton, S.J.2    Pugh, B.F.3
  • 18
    • 78651343432 scopus 로고    scopus 로고
    • Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae
    • Sugihara F, Kasahara K, Kokubo T Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae. Nucleic Acids Res 2010; 39:59-75.
    • (2010) Nucleic Acids Res , vol.39 , pp. 59-75
    • Sugihara, F.1    Kasahara, K.2    Kokubo, T.3
  • 19
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • Beer MA, Tavazoie S. Predicting gene expression from sequence. Cell 2004; 117:185-98.
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 20
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000; 296:1205-1214.
    • (2000) J Mol Biol , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 21
    • 33645744221 scopus 로고    scopus 로고
    • The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes
    • Wade CH, Umbarger MA, McAlear MA. The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes. Yeast 2006; 23:293-306.
    • (2006) Yeast , vol.23 , pp. 293-306
    • Wade, C.H.1    Umbarger, M.A.2    McAlear, M.A.3
  • 22
    • 52349095482 scopus 로고    scopus 로고
    • Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression
    • Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ. Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. PLoS ONE 2008; 3:3112.
    • (2008) PLoS ONE , vol.3 , pp. 3112
    • Boorsma, A.1    Lu, X.J.2    Zakrzewska, A.3    Klis, F.M.4    Bussemaker, H.J.5
  • 23
    • 57749121616 scopus 로고    scopus 로고
    • A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
    • Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 2008; 32:878-887.
    • (2008) Mol Cell , vol.32 , pp. 878-887
    • Badis, G.1    Chan, E.T.2    van Bakel, H.3    Pena-Castillo, L.4    Tillo, D.5    Tsui, K.6
  • 24
    • 63849315606 scopus 로고    scopus 로고
    • High-resolution DNA-binding specificity analysis of yeast transcription factors
    • Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 2009; 19:556-566.
    • (2009) Genome Res , vol.19 , pp. 556-566
    • Zhu, C.1    Byers, K.J.2    McCord, R.P.3    Shi, Z.4    Berger, M.F.5    Newburger, D.E.6
  • 25
    • 70549086622 scopus 로고    scopus 로고
    • Growth control and ribosome biogenesis
    • Lempiainen H, Shore D. Growth control and ribosome biogenesis. Curr Opin Cell Biol 2009; 21:855-863.
    • (2009) Curr Opin Cell Biol , vol.21 , pp. 855-863
    • Lempiainen, H.1    Shore, D.2
  • 26
    • 34548838840 scopus 로고    scopus 로고
    • Stb3 binds to ribosomal RNA processing element motifs that control transcriptional responses to growth in Saccharomyces cerevisiae
    • Liko D, Slattery MG, Heideman W Stb3 binds to ribosomal RNA processing element motifs that control transcriptional responses to growth in Saccharomyces cerevisiae. J Biol Chem 2007; 282:26623-26628.
    • (2007) J Biol Chem , vol.282 , pp. 26623-26628
    • Liko, D.1    Slattery, M.G.2    Heideman, W.3
  • 27
    • 73949150346 scopus 로고    scopus 로고
    • Protein kinase A and TORC1 activate genes for ribosomal biogenesis by inactivating repressors encoded by Dot6 and its homolog Tod6
    • Lippman SI, Broach JR. Protein kinase A and TORC1 activate genes for ribosomal biogenesis by inactivating repressors encoded by Dot6 and its homolog Tod6. Proc Natl Acad Sci USA 2009; 106:19928-19933.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 19928-19933
    • Lippman, S.I.1    Broach, J.R.2
  • 28
    • 78349264244 scopus 로고    scopus 로고
    • Stb3 plays a role in the glucose-induced transition from quiescence to growth in Saccharomyces cerevisiae
    • Liko D, Conway MK, Grunwald DS, Heideman W Stb3 plays a role in the glucose-induced transition from quiescence to growth in Saccharomyces cerevisiae. Genetics 2010; 185:797-810.
    • (2010) Genetics , vol.185 , pp. 797-810
    • Liko, D.1    Conway, M.K.2    Grunwald, D.S.3    Heideman, W.4
  • 29
    • 77952562645 scopus 로고    scopus 로고
    • The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae
    • Preti M, Ribeyre C, Pascali C, Bosio MC, Cortelazzi B, Rougemont J, et al. The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae. Mol Cell 2010; 38:614-620.
    • (2010) Mol Cell , vol.38 , pp. 614-620
    • Preti, M.1    Ribeyre, C.2    Pascali, C.3    Bosio, M.C.4    Cortelazzi, B.5    Rougemont, J.6
  • 30
    • 77950553742 scopus 로고    scopus 로고
    • Evolutionary tinkering with conserved components of a transcriptional regulatory network
    • Lavoie H, Hogues H, Mallick J, Sellam A, Nantel A, Whiteway M. Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol 2010; 8:100-329.
    • (2010) PLoS Biol , vol.8 , pp. 100-329
    • Lavoie, H.1    Hogues, H.2    Mallick, J.3    Sellam, A.4    Nantel, A.5    Whiteway, M.6
  • 32
    • 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 2008; 18:1084-1091.
    • (2008) Genome Res , vol.18 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 33
    • 0037440656 scopus 로고    scopus 로고
    • Rap1p and other transcriptional regulators can function in defining distinct domains of gene expression
    • Yu Q, Qiu R, Foland TB, Griesen D, Galloway CS, Chiu YH, et al. Rap1p and other transcriptional regulators can function in defining distinct domains of gene expression. Nucleic Acids Res 2003; 31:1224-1233.
    • (2003) Nucleic Acids Res , vol.31 , pp. 1224-1233
    • Yu, Q.1    Qiu, R.2    Foland, T.B.3    Griesen, D.4    Galloway, C.S.5    Chiu, Y.H.6
  • 34
    • 63449135035 scopus 로고    scopus 로고
    • Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
    • Field Y, Fondufe-Mittendorf Y, Moore IK, Mieczkowski P, Kaplan N, Lubling Y, et al. Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet 2009; 41:438-445.
    • (2009) Nat Genet , vol.41 , pp. 438-445
    • Field, Y.1    Fondufe-Mittendorf, Y.2    Moore, I.K.3    Mieczkowski, P.4    Kaplan, N.5    Lubling, Y.6
  • 35
    • 77953711351 scopus 로고    scopus 로고
    • TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation
    • Papai G, Tripathi MK, Ruhlmann C, Layer JH, Weil PA, Schultz P. TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation. Nature 2010; 465:956-960.
    • (2010) Nature , vol.465 , pp. 956-960
    • Papai, G.1    Tripathi, M.K.2    Ruhlmann, C.3    Layer, J.H.4    Weil, P.A.5    Schultz, P.6
  • 36
    • 48249151081 scopus 로고    scopus 로고
    • Genome-wide expression profiling, in vivo DNA binding analysis and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration and sporulation in yeast
    • Schlecht U, Erb I, Demougin P, Robine N, Borde V, Nimwegen E, et al. Genome-wide expression profiling, in vivo DNA binding analysis and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration and sporulation in yeast. Mol Biol Cell 2008; 19:2193-2207.
    • (2008) Mol Biol Cell , vol.19 , pp. 2193-2207
    • Schlecht, U.1    Erb, I.2    Demougin, P.3    Robine, N.4    Borde, V.5    Nimwegen, E.6
  • 38
    • 11144273952 scopus 로고    scopus 로고
    • TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1
    • Martin DE, Soulard A, Hall MN. TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 2004; 119:969-979.
    • (2004) Cell , vol.119 , pp. 969-979
    • Martin, D.E.1    Soulard, A.2    Hall, M.N.3
  • 39
    • 78649507129 scopus 로고    scopus 로고
    • A complete set of nascent transcription rates for yeast genes
    • Pelechano V, Chavez S, Perez-Ortin JE. A complete set of nascent transcription rates for yeast genes. PLoS One 2010; 5:15442.
    • (2010) PLoS One , vol.5 , pp. 15442
    • Pelechano, V.1    Chavez, S.2    Perez-Ortin, J.E.3
  • 41
    • 36048959205 scopus 로고    scopus 로고
    • Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription
    • Berger AB, Decourty L, Badis G, Nehrbass U, Jacquier A, Gadal O. Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription. Mol Cell Biol 2007; 27:8015-8026.
    • (2007) Mol Cell Biol , vol.27 , pp. 8015-8026
    • Berger, A.B.1    Decourty, L.2    Badis, G.3    Nehrbass, U.4    Jacquier, A.5    Gadal, O.6
  • 42
    • 67649933366 scopus 로고    scopus 로고
    • Eukaryotic snoR-NAs: A paradigm for gene expression flexibility
    • Dieci G, Preti M, Montanini B. Eukaryotic snoR-NAs: A paradigm for gene expression flexibility. Genomics 2009; 94:83-88.
    • (2009) Genomics , vol.94 , pp. 83-88
    • Dieci, G.1    Preti, M.2    Montanini, B.3
  • 44
    • 18844374522 scopus 로고    scopus 로고
    • Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
    • Tanay A, Regev A, Shamir R. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci USA 2005; 102:7203-7208.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7203-7208
    • Tanay, A.1    Regev, A.2    Shamir, R.3
  • 45
    • 40649126603 scopus 로고    scopus 로고
    • Transcription factor substitution during the evolution of fungal ribosome regulation
    • Hogues H, Lavoie H, Sellam A, Mangos M, Roemer T, Purisima E, et al. Transcription factor substitution during the evolution of fungal ribosome regulation. Mol Cell 2008; 29:552-562.
    • (2008) Mol Cell , vol.29 , pp. 552-562
    • Hogues, H.1    Lavoie, H.2    Sellam, A.3    Mangos, M.4    Roemer, T.5    Purisima, E.6
  • 47
    • 78649919213 scopus 로고    scopus 로고
    • Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays
    • Sellam A, Hogues H, Askew C, Tebbji F, van Het Hoog M, Lavoie H, et al. Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays. Genome Biol 2010; 11:71.
    • (2010) Genome Biol , vol.11 , pp. 71
    • Sellam, A.1    Hogues, H.2    Askew, C.3    Tebbji, F.4    van Het Hoog, M.5    Lavoie, H.6
  • 48
    • 0033522443 scopus 로고    scopus 로고
    • Cohabitation of insulators and silencing elements in yeast subtelomeric regions
    • Fourel G, Revardel E, Koering CE, Gilson E. Cohabitation of insulators and silencing elements in yeast subtelomeric regions. EMBO J 1999; 18:2522-2537
    • (1999) EMBO J , vol.18 , pp. 2522-2537
    • Fourel, G.1    Revardel, E.2    Koering, C.E.3    Gilson, E.4
  • 49
    • 77955176031 scopus 로고    scopus 로고
    • Mammalian Rap1 widens its impact
    • Crabbe L, Karlseder J. Mammalian Rap1 widens its impact. Nat Cell Biol 2010; 12:733-735.
    • (2010) Nat Cell Biol , vol.12 , pp. 733-735
    • Crabbe, L.1    Karlseder, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.