메뉴 건너뛰기




Volumn 16, Issue 8, 2006, Pages 962-972

Extensive low-affinity transcriptional interactions in the yeast genome

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 33746691336     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5113606     Document Type: Article
Times cited : (192)

References (44)
  • 2
    • 1442306129 scopus 로고    scopus 로고
    • Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli
    • Brown, C.T. and Callan Jr., C.G. 2004. Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli. Proc. Natl. Acad. Sci. 101: 2404-2409.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 2404-2409
    • Brown, C.T.1    Callan Jr., C.G.2
  • 3
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker, H.J., Li, H., and Siggia, E.D. 2001. Regulatory element detection using correlation with expression. Nat. Genet. 27: 167-171.
    • (2001) Nat. Genet. , vol.27 , pp. 167-171
    • Bussemaker, H.J.1    Li, H.2    Siggia, E.D.3
  • 4
    • 10744226888 scopus 로고    scopus 로고
    • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    • Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J., et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1    Bekiranov, S.2    Ng, H.H.3    Kapranov, P.4    Sekinger, E.A.5    Kampa, D.6    Piccolboni, A.7    Sementchenko, V.8    Cheng, J.9    Williams, A.J.10
  • 6
    • 0027200714 scopus 로고
    • The DAL82 protein of Saccharomyces cerevisiae binds to the DAL upstream induction sequence (UIS)
    • Dorrington, R.A. and Cooper, T.G. 1993. The DAL82 protein of Saccharomyces cerevisiae binds to the DAL upstream induction sequence (UIS). Nucleic Acids Res. 21: 3777-3784.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 3777-3784
    • Dorrington, R.A.1    Cooper, T.G.2
  • 7
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • Elowitz, M.B., Levine, A.J., Siggia, E.D., and Swain, P.S. 2002. Stochastic gene expression in a single cell. Science 297: 1183-1186.
    • (2002) Science , vol.297 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 8
    • 0037126028 scopus 로고    scopus 로고
    • Physical constraints and functional characteristics of transcription factor-DNA interaction
    • Gerland, U., Moroz, J.D., and Hwa, T. 2002. Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc. Natl. Acad. Sci. 99: 12015-12020.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 12015-12020
    • Gerland, U.1    Moroz, J.D.2    Hwa, T.3
  • 9
    • 34548087820 scopus 로고    scopus 로고
    • Explicit equilibrium modeling of transcription-factor binding and gene regulation
    • Granek, J.A. and Clarke, N.D. 2005. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol. 6: R87.
    • (2005) Genome Biol. , vol.6
    • Granek, J.A.1    Clarke, N.D.2
  • 12
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., and Brown, P.O. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3    Botstein, D.4    Snyder, M.5    Brown, P.O.6
  • 13
    • 0031027203 scopus 로고    scopus 로고
    • A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus. Mol
    • Jia, Y., Rothermel, B., Thornton, J., and Butow, R.A. 1997. A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus. Mol. Cell. Biol. 17: 1110-1117.
    • (1997) Cell. Biol. , vol.17 , pp. 1110-1117
    • Jia, Y.1    Rothermel, B.2    Thornton, J.3    Butow, R.A.4
  • 14
    • 0343924289 scopus 로고    scopus 로고
    • Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters
    • Kadosh, D. and Struhl, K. 1997. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89: 365-371.
    • (1997) Cell , vol.89 , pp. 365-371
    • Kadosh, D.1    Struhl, K.2
  • 15
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 16
    • 0035912781 scopus 로고    scopus 로고
    • Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors
    • Kuruvilla, F.G., Shamji, A.F., and Schreiber, S.L. 2001. Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors. Proc. Natl. Acad. Sci. 98: 7283-7288.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 7283-7288
    • Kuruvilla, F.G.1    Shamji, A.F.2    Schreiber, S.L.3
  • 18
    • 0038492517 scopus 로고    scopus 로고
    • A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
    • Li, Z., Van Calcar, S., Qu, C., Cavenee, W.K., Zhang, M.Q., and Ren, B. 2003. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc. Natl. Acad. Sci. 100: 8164-8169.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 8164-8169
    • Li, Z.1    Van Calcar, S.2    Qu, C.3    Cavenee, W.K.4    Zhang, M.Q.5    Ren, B.6
  • 19
    • 0036396542 scopus 로고    scopus 로고
    • Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities
    • Liu, X. and Clarke, N.D. 2002. Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities. J. Mol. Biol. 323: 1-8.
    • (2002) J. Mol. Biol. , vol.323 , pp. 1-8
    • Liu, X.1    Clarke, N.D.2
  • 20
    • 0030868697 scopus 로고    scopus 로고
    • Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family
    • Mai, B. and Breeden, L. 1997. Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family. Mol. Cell. Biol. 17: 6491-6501.
    • (1997) Mol. Cell. Biol. , vol.17 , pp. 6491-6501
    • Mai, B.1    Breeden, L.2
  • 21
    • 0035023140 scopus 로고    scopus 로고
    • Xbp1-mediated repression of CLB gene expression contributes to the modifications of yeast cell morphology and cell cycle seen during nitrogen-limited growth
    • Miled, C., Mann, C., and Faye, G. 2001. Xbp1-mediated repression of CLB gene expression contributes to the modifications of yeast cell morphology and cell cycle seen during nitrogen-limited growth. Mol. Cell. Biol. 21: 3714-3724.
    • (2001) Mol. Cell. Biol. , vol.21 , pp. 3714-3724
    • Miled, C.1    Mann, C.2    Faye, G.3
  • 22
    • 0642368358 scopus 로고    scopus 로고
    • Position specific variation in the rate of evolution in transcription factor binding sites
    • Moses, A.M., Chiang, D.Y., Kellis, M., Lander, E.S., and Eisen, M.B. 2003. Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol. Biol. 3: 19.
    • (2003) BMC Evol. Biol. , vol.3 , pp. 19
    • Moses, A.M.1    Chiang, D.Y.2    Kellis, M.3    Lander, E.S.4    Eisen, M.B.5
  • 23
    • 27644482258 scopus 로고    scopus 로고
    • Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies
    • Mustonen, V. and Lassig, M. 2005. Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies. Proc. Natl. Acad. Sci. 102: 15936-15941.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 15936-15941
    • Mustonen, V.1    Lassig, M.2
  • 24
    • 14844307159 scopus 로고    scopus 로고
    • Inferring quantitative models of regulatory networks from expression data
    • Nachman, I., Regev, A., and Friedman, N. 2004. Inferring quantitative models of regulatory networks from expression data. Bioinformatics (Suppl 1) 20: I248-I256.
    • (2004) Bioinformatics (Suppl 1) , vol.20
    • Nachman, I.1    Regev, A.2    Friedman, N.3
  • 26
    • 0842285841 scopus 로고    scopus 로고
    • Summing up the noise in gene networks
    • Paulsson, J. 2004. Summing up the noise in gene networks. Nature 427: 415-418.
    • (2004) Nature , vol.427 , pp. 415-418
    • Paulsson, J.1
  • 27
    • 2942576308 scopus 로고    scopus 로고
    • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
    • Rajewsky, N., Vergassola, M., Gaul, U., and Siggia, E.D. 2002. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3: 30.
    • (2002) BMC Bioinformatics , vol.3 , pp. 30
    • Rajewsky, N.1    Vergassola, M.2    Gaul, U.3    Siggia, E.D.4
  • 28
    • 25444468618 scopus 로고    scopus 로고
    • Noise in gene expression: Origins, consequences, and control
    • Raser, J.M. and O'Shea, E.K. 2005. Noise in gene expression: Origins, consequences, and control. Science 309: 2010-2013.
    • (2005) Science , vol.309 , pp. 2010-2013
    • Raser, J.M.1    O'Shea, E.K.2
  • 29
    • 1042288539 scopus 로고    scopus 로고
    • Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors
    • Ren, B. and Dynlacht, B.D. 2004. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol. 376: 304-315.
    • (2004) Methods Enzymol. , vol.376 , pp. 304-315
    • Ren, B.1    Dynlacht, B.D.2
  • 32
    • 0036678794 scopus 로고    scopus 로고
    • Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
    • Ronen, M., Rosenberg, R., Shraiman, B.I., and Alon, U. 2002. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. 99: 10555-10560.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 10555-10560
    • Ronen, M.1    Rosenberg, R.2    Shraiman, B.I.3    Alon, U.4
  • 33
    • 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
  • 34
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
    • Siepel, A. and Haussler, D. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21: 468-488.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 468-488
    • Siepel, A.1    Haussler, D.2
  • 37
    • 0000133199 scopus 로고
    • Identifying protein-binding sites from unaligned DNA fragments
    • Stormo, G.D. and Hartzell III, G.W. 1989. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. 86: 1183-1187.
    • (1989) Proc. Natl. Acad. Sci. , vol.86 , pp. 1183-1187
    • Stormo, G.D.1    Hartzell III, G.W.2
  • 39
    • 3142550629 scopus 로고    scopus 로고
    • Multilevel modeling and inference of transcription regulation
    • Tanay, A. and Shamir, R. 2004. Multilevel modeling and inference of transcription regulation. J. Comput. Biol. 11: 357-375.
    • (2004) J. Comput. Biol. , vol.11 , pp. 357-375
    • Tanay, A.1    Shamir, R.2
  • 40
    • 2442691539 scopus 로고    scopus 로고
    • A global view of the selection forces in the evolution of yeast cis-regulation
    • Tanay, A., Gat-Viks, I., and Shamir, R. 2004a. A global view of the selection forces in the evolution of yeast cis-regulation. Genome Res. 14: 829-834.
    • (2004) Genome Res. , vol.14 , pp. 829-834
    • Tanay, A.1    Gat-Viks, I.2    Shamir, R.3
  • 41
    • 1542357674 scopus 로고    scopus 로고
    • Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genome-wide data
    • Tanay, A., Sharan, R., Kupiec, M., and Shamir, R. 2004b. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genome-wide data. Proc. Natl. Acad. Sci. 101: 2981-2986.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 2981-2986
    • Tanay, A.1    Sharan, R.2    Kupiec, M.3    Shamir, R.4
  • 42
    • 18844374522 scopus 로고    scopus 로고
    • Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
    • Tanay, A., Regev, A., and Shamir, R. 2005. Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast. Proc. Natl. Acad. Sci. 102: 7203-7208.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 7203-7208
    • Tanay, A.1    Regev, A.2    Shamir, R.3
  • 43
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.