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Volumn 35, Issue 1, 2007, Pages 193-202

Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; PROTEIN ABF1; RAP1 PROTEIN; UNCLASSIFIED DRUG;

EID: 33846694307     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1059     Document Type: Article
Times cited : (59)

References (44)
  • 1
    • 0033981095 scopus 로고    scopus 로고
    • RAP, RAP, open up! new wrinkles for RAP1 in yeast
    • Morse,R.H. (2000) RAP, RAP, open up! new wrinkles for RAP1 in yeast. Trends Genet., 16, 51-53.
    • (2000) Trends Genet. , vol.16 , pp. 51-53
    • Morse, R.H.1
  • 2
    • 0036135629 scopus 로고    scopus 로고
    • Identification of a multifunctional domain in autonomously replicating sequence-binding factor 1 required for transcriptional activation, DNA replication, and gene silencing
    • Miyake,T., Loch,C.M. and Li,R. (2002) Identification of a multifunctional domain in autonomously replicating sequence-binding factor 1 required for transcriptional activation, DNA replication, and gene silencing. Mol. Cell. Biol., 22, 505-516.
    • (2002) Mol. Cell. Biol. , vol.22 , pp. 505-516
    • Miyake, T.1    Loch, C.M.2    Li, R.3
  • 3
    • 0028130685 scopus 로고
    • RAP1: A protean regulator in yeast
    • Shore,D. (1994) RAP1: A protean regulator in yeast. Trends Genet., 10, 408-412.
    • (1994) Trends Genet. , vol.10 , pp. 408-412
    • Shore, D.1
  • 5
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • Lieb,J.D., Liu,X., Botstein,D. and Brown,P.O.(2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nature Genet., 28, 327-334.
    • (2001) Nature Genet. , vol.28 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 8
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe,N.M., Babu,M.M., Yu,H., Snyder,M., Teichmann,S.A. and Gerstein,M. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 9
    • 4744375319 scopus 로고    scopus 로고
    • Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae
    • Yarragudi,A., Miyake,T., Li,R. and Morse,R.H. (2004) Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae. Mol. Cell. Biol., 24, 9152-9164.
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 9152-9164
    • Yarragudi, A.1    Miyake, T.2    Li, R.3    Morse, R.H.4
  • 10
    • 0032584594 scopus 로고    scopus 로고
    • Genetic tests of the role of Abf1p in driving transcription of the yeast TATA box binding protein-encoding gene, SPT15
    • Schroeder,S.C. and Weil,P.A. (1998) Genetic tests of the role of Abf1p in driving transcription of the yeast TATA box binding protein-encoding gene, SPT15. J. Biol. Chem., 273, 19884-19891.
    • (1998) J. Biol. Chem. , vol.273 , pp. 19884-19891
    • Schroeder, S.C.1    Weil, P.A.2
  • 11
    • 0025938044 scopus 로고
    • DMSO-enhanced whole cell yeast transformation
    • [published erratum appears in Nucleic Acids Res 1991 Dec 11; 19(23):6688]
    • Hill,J., Donald,K.A., Griffiths,D.E. and Donald,G. (1991) DMSO-enhanced whole cell yeast transformation [published erratum appears in Nucleic Acids Res 1991 Dec 11; 19(23):6688]. Nucleic Acids Res., 19, 5791.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 5791
    • Hill, J.1    Donald, K.A.2    Griffiths, D.E.3    Donald, G.4
  • 13
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Roy. Statist. Soc. B, 57, 289-300.
    • (1995) J. Roy. Statist. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 14
    • 0041620271 scopus 로고    scopus 로고
    • Regulatory sequence analysis tools
    • van Helden,J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res., 31, 3593-3596.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3593-3596
    • van Helden, J.1
  • 15
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 16
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 18
    • 0025809264 scopus 로고
    • RAP1 protein activates and silences transcription of mating-type genes in yeast
    • Kurtz,S. and Shore,D. (1991) RAP1 protein activates and silences transcription of mating-type genes in yeast. Genes Dev., 5, 616-628.
    • (1991) Genes Dev. , vol.5 , pp. 616-628
    • Kurtz, S.1    Shore, D.2
  • 19
    • 0026557754 scopus 로고
    • Role of multifunctional autonomously replicating sequence binding factor 1 in the initiation of DNA replication and transcriptional control in Saccharomyces cerevisiae
    • Rhode,P.R., Elsasser,S. and Campbell,J.L. (1992) Role of multifunctional autonomously replicating sequence binding factor 1 in the initiation of DNA replication and transcriptional control in Saccharomyces cerevisiae. Mol. Cell. Biol., 12, 1064-1077.
    • (1992) Mol. Cell. Biol. , vol.12 , pp. 1064-1077
    • Rhode, P.R.1    Elsasser, S.2    Campbell, J.L.3
  • 22
    • 23144463134 scopus 로고    scopus 로고
    • T-profiler: Scoring the activity of predefined groups of genes using gene expression data
    • Boorsma,A., Foat,B.C., Vis,D., Klis,F. and Bussemaker,H.J. (2005) T-profiler: Scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res., 33, W592-W595.
    • (2005) Nucleic Acids Res. , vol.33
    • Boorsma, A.1    Foat, B.C.2    Vis, D.3    Klis, F.4    Bussemaker, H.J.5
  • 24
    • 0033229970 scopus 로고    scopus 로고
    • The economics of ribosome biosynthesis in yeast
    • Warner,J.R. (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci., 24, 437-440.
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 437-440
    • Warner, J.R.1
  • 25
    • 14844282303 scopus 로고    scopus 로고
    • Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins
    • Rudra,D., Zhao,Y. and Warner,J.R. (2005) Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J., 24, 533-542.
    • (2005) EMBO J. , vol.24 , pp. 533-542
    • Rudra, D.1    Zhao, Y.2    Warner, J.R.3
  • 26
    • 11144244771 scopus 로고    scopus 로고
    • Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1
    • Schawalder,S.B., Kabani,M., Howald,I., Choudhury,U., Werner,M. and Shore,D. (2004) Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature, 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
  • 27
    • 11144231369 scopus 로고    scopus 로고
    • The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes
    • Wade,J.T., Hall,D.B. and Struhl,K. (2004) The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature, 432, 1054-1058.
    • (2004) Nature , vol.432 , pp. 1054-1058
    • Wade, J.T.1    Hall, D.B.2    Struhl, K.3
  • 28
    • 0025898596 scopus 로고
    • RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene
    • Devlin,C., Tice-Baldwin,K., Shore,D. and Arndt,K.T. (1991) RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol. Cell. Biol., 11, 3642-3651.
    • (1991) Mol. Cell. Biol. , vol.11 , pp. 3642-3651
    • Devlin, C.1    Tice-Baldwin, K.2    Shore, D.3    Arndt, K.T.4
  • 29
    • 0027189756 scopus 로고
    • GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain
    • Tornow,J., Zeng,X., Gao,W. and Santangelo,G.M. (1993) GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain. EMBO J., 12, 2431-2437.
    • (1993) EMBO J. , vol.12 , pp. 2431-2437
    • Tornow, J.1    Zeng, X.2    Gao, W.3    Santangelo, G.M.4
  • 31
    • 3042526849 scopus 로고    scopus 로고
    • Calculating the statistical significance of physical clusters of co-regulated genes in the genome: The role of chromatin in domain-wide gene regulation
    • Chang,C.F., Wai,K.M. and Patterton,H.G. (2004) Calculating the statistical significance of physical clusters of co-regulated genes in the genome: The role of chromatin in domain-wide gene regulation. Nucleic Acids Res., 32, 1798-1807.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1798-1807
    • Chang, C.F.1    Wai, K.M.2    Patterton, H.G.3
  • 32
    • 0030990291 scopus 로고    scopus 로고
    • Molecular model for telomeric heterochromatin in yeast
    • Grunstein,M. (1997) Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell. Biol., 9, 383-387.
    • (1997) Curr. Opin. Cell. Biol. , vol.9 , pp. 383-387
    • Grunstein, M.1
  • 33
    • 0033522444 scopus 로고    scopus 로고
    • Limitations of silencing at native yeast telomeres
    • Pryde,F.E. and Louis,E.J. (1999) Limitations of silencing at native yeast telomeres. EMBO J., 18, 2538-2550.
    • (1999) EMBO J. , vol.18 , pp. 2538-2550
    • Pryde, F.E.1    Louis, E.J.2
  • 35
    • 23644431878 scopus 로고    scopus 로고
    • In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae
    • Beinoraviciute-Kellner,R., Lipps,G. and Krauss,G. (2005) In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS Lett., 579, 4535-4540.
    • (2005) FEBS Lett. , vol.579 , pp. 4535-4540
    • Beinoraviciute-Kellner, R.1    Lipps, G.2    Krauss, G.3
  • 36
    • 4544297212 scopus 로고    scopus 로고
    • Genome-wide analysis of ARS (autonomously replicating sequence) binding factor 1 (Abf1p)-mediated transcriptional regulation in Saccharomyces cerevisiae
    • Miyake,T., Reese,J., Loch,C.M., Auble,D.T. and Li,R. (2004) Genome-wide analysis of ARS (autonomously replicating sequence) binding factor 1 (Abf1p)-mediated transcriptional regulation in Saccharomyces cerevisiae. J. Biol. Chem., 279, 34865-34872.
    • (2004) J. Biol. Chem. , vol.279 , pp. 34865-34872
    • Miyake, T.1    Reese, J.2    Loch, C.M.3    Auble, D.T.4    Li, R.5
  • 37
    • 3543020250 scopus 로고    scopus 로고
    • Biochemical and genetic characterization of the dominant positive element driving transcription of the yeast TBP-encoding gene, SPT15
    • Schroeder,S.C. and Weil,P.A. (1998) Biochemical and genetic characterization of the dominant positive element driving transcription of the yeast TBP-encoding gene, SPT15. Nucleic Acids Res., 26, 4186-4195.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4186-4195
    • Schroeder, S.C.1    Weil, P.A.2
  • 38
    • 0034653847 scopus 로고    scopus 로고
    • Different roles for Abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene
    • Lascaris,R.F., Groot,E., Hoen,P.B., Mager,W.H. and Planta,R.J. (2000) Different roles for Abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res., 28, 1390-1396.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1390-1396
    • Lascaris, R.F.1    Groot, E.2    Hoen, P.B.3    Mager, W.H.4    Planta, R.J.5
  • 39
    • 0026659968 scopus 로고
    • Global regulation of mitochondrial biogenesis in Saccharomyces cerevisiae: ABF1 and CPF1 play opposite roles in regulating expression of the QCR8 gene, which encodes subunit VIII of the mitochondrial ubiquinol-cytochrome c oxidoreductase
    • de Winde,J.H. and Grivell,L.A. (1992) Global regulation of mitochondrial biogenesis in Saccharomyces cerevisiae: ABF1 and CPF1 play opposite roles in regulating expression of the QCR8 gene, which encodes subunit VIII of the mitochondrial ubiquinol-cytochrome c oxidoreductase. Mol. Cell. Biol., 12, 2872-2883.
    • (1992) Mol. Cell. Biol. , vol.12 , pp. 2872-2883
    • de Winde, J.H.1    Grivell, L.A.2
  • 40
    • 0025272212 scopus 로고
    • The ABF1 factor is the transcriptional activator of the L2 ribosomal protein genes in Saccharomyces cerevisiae
    • Della Seta,F., Ciafre,S.A., Marck,C., Santoro,B., Presutti,C., Sentenac,A. and Bozzoni,I. (1990) The ABF1 factor is the transcriptional activator of the L2 ribosomal protein genes in Saccharomyces cerevisiae. Mol. Cell. Biol., 10, 2437-2441.
    • (1990) Mol. Cell. Biol. , vol.10 , pp. 2437-2441
    • Della Seta, F.1    Ciafre, S.A.2    Marck, C.3    Santoro, B.4    Presutti, C.5    Sentenac, A.6    Bozzoni, I.7
  • 41
    • 0030001055 scopus 로고    scopus 로고
    • Activation mechanism of the multifunctional transcription factor repressor-activator protein 1 (Rap1p)
    • Drazinic,C.M., Smerage,J.B., Lopez,M.C. and Baker,H.V. (1996) Activation mechanism of the multifunctional transcription factor repressor-activator protein 1 (Rap1p). Mol. Cell. Biol., 16, 3187-3196.
    • (1996) Mol. Cell. Biol. , vol.16 , pp. 3187-3196
    • Drazinic, C.M.1    Smerage, J.B.2    Lopez, M.C.3    Baker, H.V.4
  • 43
    • 33746691336 scopus 로고    scopus 로고
    • Extensive low-affinity transcriptional interactions in the yeast genome
    • Tanay,A. (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res., 16, 962-972.
    • (2006) Genome Res. , vol.16 , pp. 962-972
    • Tanay, A.1
  • 44
    • 24744455483 scopus 로고    scopus 로고
    • Epigenome programming by Polycomb and Trithorax proteins
    • Cernilogar,F.M. and Orlando,V. (2005) Epigenome programming by Polycomb and Trithorax proteins. Biochem. Cell. Biol., 83, 322-331.
    • (2005) Biochem. Cell. Biol. , vol.83 , pp. 322-331
    • Cernilogar, F.M.1    Orlando, V.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.