메뉴 건너뛰기




Volumn 439, Issue 1, 2011, Pages 15-25

Gene-specific transcription activation via long-range allosteric shape-shifting

Author keywords

Allosteric pathway; Allosteric propagation; Allostery; Enhancer; Mediator; Transcription initiation; Transcription regulation; Transcription start site

Indexed keywords

MEDIATOR COMPLEX; RNA POLYMERASE II;

EID: 80052751115     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BJ20110972     Document Type: Review
Times cited : (31)

References (127)
  • 1
    • 75149141847 scopus 로고    scopus 로고
    • Mechanisms of transcription factor selectivity
    • Pan, Y. P., Tsai, C. J., Ma, B. Y. and Nussinov, R. (2010) Mechanisms of transcription factor selectivity. Trends Genet. 26, 75-83
    • (2010) Trends Genet. , vol.26 , pp. 75-83
    • Pan, Y.P.1    Tsai, C.J.2    Ma, B.Y.3    Nussinov, R.4
  • 2
    • 68349125112 scopus 로고    scopus 로고
    • What controls nucleosome positions?
    • Segal, E. and Widom, J. (2009) What controls nucleosome positions? Trends Genet. 25, 335-343
    • (2009) Trends Genet. , vol.25 , pp. 335-343
    • Segal, E.1    Widom, J.2
  • 6
    • 70350782360 scopus 로고    scopus 로고
    • How do transcription factors select specific binding sites in the genome?
    • Pan, Y. P., Tsai, C. J., Ma, B. Y. and Nussinov, R. (2009) How do transcription factors select specific binding sites in the genome? Nat. Struct. Mol. Biol. 16, 1118-1120
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 1118-1120
    • Pan, Y.P.1    Tsai, C.J.2    Ma, B.Y.3    Nussinov, R.4
  • 7
    • 77949853850 scopus 로고    scopus 로고
    • Why does binding of proteins to DNA or proteins to proteins not necessarily spell function?
    • Ma, B. Y., Tsai, C. J., Pan, Y. P. and Nussinov, R. (2010) Why does binding of proteins to DNA or proteins to proteins not necessarily spell function? ACS Chem. Biol. 5, 265-272
    • (2010) ACS Chem. Biol. , vol.5 , pp. 265-272
    • Ma, B.Y.1    Tsai, C.J.2    Pan, Y.P.3    Nussinov, R.4
  • 10
    • 65249167505 scopus 로고    scopus 로고
    • DNA binding site sequence directs glucocorticoid receptor structure and activity
    • Meijsing, S. H., Pufall, M. A., So, A. Y., Bates, D. L., Chen, L. and Yamamoto, K. R. (2009) DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324, 407-410
    • (2009) Science , vol.324 , pp. 407-410
    • Meijsing, S.H.1    Pufall, M.A.2    So, A.Y.3    Bates, D.L.4    Chen, L.5    Yamamoto, K.R.6
  • 11
    • 68049144731 scopus 로고    scopus 로고
    • Allosteric effects govern nuclear receptor action: DNA appears as a player
    • Gronemeyer, H. and Bourguet, W. (2009) Allosteric effects govern nuclear receptor action: DNA appears as a player. Sci. Signal 2, pe34
    • (2009) Sci. Signal , vol.2
    • Gronemeyer, H.1    Bourguet, W.2
  • 13
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser, J. S., Clarkson, M. W., Degnan, S. C., Erion, R., Kern, D. and Alber, T. (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462, 669-673
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1    Clarkson, M.W.2    Degnan, S.C.3    Erion, R.4    Kern, D.5    Alber, T.6
  • 14
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai, C. J., Kumar, S., Ma, B. Y. and Nussinov, R. (1999) Folding funnels, binding funnels, and protein function. Protein Sci. 8, 1181-1190
    • (1999) Protein Sci. , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.Y.3    Nussinov, R.4
  • 16
    • 70349745516 scopus 로고    scopus 로고
    • Mediator complex association with constitutively transcribed genes in yeast
    • Ansari, S. A., He, Q. Y. and Morse, R. H. (2009) Mediator complex association with constitutively transcribed genes in yeast. Proc. Natl. Acad. Sci. U.S.A. 106, 16734-16739
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 16734-16739
    • Ansari, S.A.1    He, Q.Y.2    Morse, R.H.3
  • 17
    • 18844451820 scopus 로고    scopus 로고
    • Mediator and the mechanism of transcriptional activation
    • Kornberg, R. D. (2005) Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci. 30, 235-239
    • (2005) Trends Biochem. Sci. , vol.30 , pp. 235-239
    • Kornberg, R.D.1
  • 18
    • 2342524114 scopus 로고    scopus 로고
    • Regulatory diversity among metazoan co-activator complexes
    • Taatjes, D. J., Marr, M. T. and Tjian, R. (2004) Regulatory diversity among metazoan co-activator complexes. Nat. Rev. Mol. Cell Biol. 5, 403-410
    • (2004) Nat. Rev. Mol. Cell Biol. , vol.5 , pp. 403-410
    • Taatjes, D.J.1    Marr, M.T.2    Tjian, R.3
  • 19
    • 33644852483 scopus 로고    scopus 로고
    • Mediator as a general transcription factor
    • Takagi, Y. and Kornberg, R. D. (2006) Mediator as a general transcription factor. J. Biol. Chem. 281, 80-89
    • (2006) J. Biol. Chem. , vol.281 , pp. 80-89
    • Takagi, Y.1    Kornberg, R.D.2
  • 20
    • 68149157248 scopus 로고    scopus 로고
    • The origin of allosteric functional modulation: Multiple pre-existing pathways
    • del Sol, A., Tsai, C. J., Ma, B. Y. and Nussinov, R. (2009) The origin of allosteric functional modulation: multiple pre-existing pathways. Structure 17, 1042-1050
    • (2009) Structure , vol.17 , pp. 1042-1050
    • Del Sol, A.1    Tsai, C.J.2    Ma, B.Y.3    Nussinov, R.4
  • 21
    • 70450191983 scopus 로고    scopus 로고
    • Dynamic activation of an allosteric regulatory protein
    • Tzeng, S. R. and Kalodimos, C. G. (2009) Dynamic activation of an allosteric regulatory protein. Nature 462, 368-372
    • (2009) Nature , vol.462 , pp. 368-372
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 22
    • 41149104308 scopus 로고    scopus 로고
    • Allostery: Absence of a change in shape does not imply that allostery is not at play
    • Tsai, C. J., del Sol, A. and Nussinov, R. (2008) Allostery: absence of a change in shape does not imply that allostery is not at play. J. Mol. Biol. 378, 1-11
    • (2008) J. Mol. Biol. , vol.378 , pp. 1-11
    • Tsai, C.J.1    Del Sol, A.2    Nussinov, R.3
  • 26
    • 77950643587 scopus 로고    scopus 로고
    • MED14 tethers mediator to the N-terminal fomain of peroxisome proliferator-activated receptor γ and is required for full transcriptional activity and adipogenesis
    • Grontved, L., Madsen, M. S., Boergesen, M., Roeder, R. G. and Mandrup, S. (2010) MED14 tethers mediator to the N-terminal fomain of peroxisome proliferator-activated receptor γ and is required for full transcriptional activity and adipogenesis. Mol. Cell. Biol. 30, 2155-2169
    • (2010) Mol. Cell. Biol. , vol.30 , pp. 2155-2169
    • Grontved, L.1    Madsen, M.S.2    Boergesen, M.3    Roeder, R.G.4    Mandrup, S.5
  • 28
    • 0037039776 scopus 로고    scopus 로고
    • Structure, function, and activator-induced conformations of the CRSP coactivator
    • Taatjes, D. J., Naar, A. M., Andel, F., Nogales, E. and Tjian, R. (2002) Structure, function, and activator-induced conformations of the CRSP coactivator. Science 295, 1058-1062
    • (2002) Science , vol.295 , pp. 1058-1062
    • Taatjes, D.J.1    Naar, A.M.2    Andel, F.3    Nogales, E.4    Tjian, R.5
  • 29
    • 1842839787 scopus 로고    scopus 로고
    • RNA polymerase II structure, and organization of the preinitiation complex
    • Asturias, F. J. (2004) RNA polymerase II structure, and organization of the preinitiation complex. Curr. Opin. Struct. Biol. 14, 121-129
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 121-129
    • Asturias, F.J.1
  • 30
    • 0036671095 scopus 로고    scopus 로고
    • Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction
    • Davis, J. A., Takagi, Y., Kornberg, R. D. and Asturias, F. J. (2002) Structure of the yeast RNA polymerase II holoenzyme: mediator conformation and polymerase interaction. Mol. Cell 10, 409-415
    • (2002) Mol. Cell , vol.10 , pp. 409-415
    • Davis, J.A.1    Takagi, Y.2    Kornberg, R.D.3    Asturias, F.J.4
  • 31
    • 0035834772 scopus 로고    scopus 로고
    • The structural and functional organization of the yeast mediator complex
    • Kang, J. S., Kim, S. H., Hwang, M. S., Han, S. J., Lee, Y. C. and Kim, Y. J. (2001) The structural and functional organization of the yeast mediator complex. J. Biol. Chem. 276, 42003-42010
    • (2001) J. Biol. Chem. , vol.276 , pp. 42003-42010
    • Kang, J.S.1    Kim, S.H.2    Hwang, M.S.3    Han, S.J.4    Lee, Y.C.5    Kim, Y.J.6
  • 33
    • 79952803747 scopus 로고    scopus 로고
    • Direct interaction of RNA Polymerase II and Mediator required for transcription in vivo
    • Soutourina, J., Wydau, S., Ambroise, Y., Boschiero, C. and Werner, M. (2011) Direct interaction of RNA Polymerase II and Mediator required for transcription in vivo. Science 331, 1451-1454
    • (2011) Science , vol.331 , pp. 1451-1454
    • Soutourina, J.1    Wydau, S.2    Ambroise, Y.3    Boschiero, C.4    Werner, M.5
  • 34
    • 47249134314 scopus 로고    scopus 로고
    • Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex
    • Bourbon, H. M. (2008) Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Res. 36, 3993-4008
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3993-4008
    • Bourbon, H.M.1
  • 36
    • 73949115758 scopus 로고    scopus 로고
    • Med8, Med18, and Med20 subunits of the Mediator head domain are interdependent upon each other for folding and complex formation
    • Shaikhibrahim, Z., Rahaman, H., Wittung-Stafshede, P. and Bjorklund, S. (2009) Med8, Med18, and Med20 subunits of the Mediator head domain are interdependent upon each other for folding and complex formation. Proc. Natl. Acad. Sci. U.S.A. 106, 20728-20733
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 20728-20733
    • Shaikhibrahim, Z.1    Rahaman, H.2    Wittung-Stafshede, P.3    Bjorklund, S.4
  • 38
    • 24044470632 scopus 로고    scopus 로고
    • A conserved mediator hinge revealed in the structure of the MED7 center dot MED21 (Med7 • Srb7) heterodimer
    • Baumli, S., Hoeppner, S. and Cramer, P. (2005) A conserved mediator hinge revealed in the structure of the MED7 center dot MED21 (Med7 • Srb7) heterodimer. J. Biol. Chem. 280, 18171-18178
    • (2005) J. Biol. Chem. , vol.280 , pp. 18171-18178
    • Baumli, S.1    Hoeppner, S.2    Cramer, P.3
  • 39
    • 80051729454 scopus 로고    scopus 로고
    • Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization
    • Seizl, M., Larivière, L., Pfaffeneder, T., Wenzeck, L. and Cramer, P. (2011) Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization. Nucleic Acids Res. 39, 6291-6304
    • (2011) Nucleic Acids Res. , vol.39 , pp. 6291-6304
    • Seizl, M.1    Larivière, L.2    Pfaffeneder, T.3    Wenzeck, L.4    Cramer, P.5
  • 43
    • 0028303752 scopus 로고
    • Several hydrophobic amino acids in the p53 amino-terminal domain are required for transcriptional activation, binding to mdm-2 and the adenovirus 5 E1B 55-kD protein
    • Lin, J. Y., Chen, J. D., Elenbaas, B. and Levine, A. J. (1994) Several hydrophobic amino acids in the p53 amino-terminal domain are required for transcriptional activation, binding to mdm-2 and the adenovirus 5 E1B 55-kD protein. Genes Dev. 8, 1235-1246
    • (1994) Genes Dev. , vol.8 , pp. 1235-1246
    • Lin, J.Y.1    Chen, J.D.2    Elenbaas, B.3    Levine, A.J.4
  • 44
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • Tsai, C. J., Ma, B. Y. and Nussinov, R. (1999) Folding and binding cascades: shifts in energy landscapes. Proc. Natl. Acad. Sci. U.S.A. 96, 9970-9972
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 9970-9972
    • Tsai, C.J.1    Ma, B.Y.2    Nussinov, R.3
  • 45
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar, S., Ma, B. Y., Tsai, C. J., Sinha, N. and Nussinov, R. (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9, 10-19
    • (2000) Protein Sci. , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.Y.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 46
    • 60649109828 scopus 로고    scopus 로고
    • Protein allostery, signal transmission and dynamics: A classification scheme of allosteric mechanisms
    • Tsai, C. J., Del Sol, A. and Nussinov, R. (2009) Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol. Biosyst. 5, 207-216
    • (2009) Mol. Biosyst. , vol.5 , pp. 207-216
    • Tsai, C.J.1    Del Sol, A.2    Nussinov, R.3
  • 47
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr, D. D., Nussinov, R. and Wright, P. E. (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 5, 789-796
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 48
    • 0032993447 scopus 로고    scopus 로고
    • Polymer principles and protein folding
    • Dill, K. A. (1999) Polymer principles and protein folding. Protein Sci. 8, 1166-1180
    • (1999) Protein Sci. , vol.8 , pp. 1166-1180
    • Dill, K.A.1
  • 49
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder, H., Sligar, S. G. and Wolynes, P. G. (1991) The energy landscapes and motions of proteins. Science 254, 1598-1603
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 55
    • 2442681755 scopus 로고    scopus 로고
    • Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II
    • Mandal, S. S., Chu, C., Wada, T., Handa, H., Shatkin, A. J. and Reinberg, D. (2004) Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A. 101, 7572-7577
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 7572-7577
    • Mandal, S.S.1    Chu, C.2    Wada, T.3    Handa, H.4    Shatkin, A.J.5    Reinberg, D.6
  • 56
    • 77951993585 scopus 로고    scopus 로고
    • Separable functions of the fission yeast Spt5 carboxyl-terminal domain (CTD) in capping enzyme binding and transcription elongation overlap with those of the RNA Polymerase II CTD
    • Schneider, S., Pei, Y., Shuman, S. and Schwer, B. (2010) Separable functions of the fission yeast Spt5 carboxyl-terminal domain (CTD) in capping enzyme binding and transcription elongation overlap with those of the RNA Polymerase II CTD. Mol. Cell. Biol. 30, 2353-2364
    • (2010) Mol. Cell. Biol. , vol.30 , pp. 2353-2364
    • Schneider, S.1    Pei, Y.2    Shuman, S.3    Schwer, B.4
  • 57
    • 58349085943 scopus 로고    scopus 로고
    • Promoter proximal pausing on genes in metazoans
    • Gilmour, D. (2009) Promoter proximal pausing on genes in metazoans. Chromosoma 118, 1-10
    • (2009) Chromosoma , vol.118 , pp. 1-10
    • Gilmour, D.1
  • 59
    • 1442354965 scopus 로고    scopus 로고
    • The activator-recruited cofactor/Mediator coactivator subunit ARC92 is a functionally important target of the VP16 transcriptional activator
    • Yang, F. J., DeBeaumont, R., Zhou, S. and Naar, A. M. (2004) The activator-recruited cofactor/Mediator coactivator subunit ARC92 is a functionally important target of the VP16 transcriptional activator. Proc. Natl. Acad. Sci. U.S.A. 101, 2339-2344
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 2339-2344
    • Yang, F.J.1    DeBeaumont, R.2    Zhou, S.3    Naar, A.M.4
  • 60
    • 34250847654 scopus 로고    scopus 로고
    • CDK8 is a stimulus-specific positive coregulator of p53 target genes
    • Donner, A. J., Szostek, S., Hoover, J. M. and Espinosa, J. M. (2007) CDK8 is a stimulus-specific positive coregulator of p53 target genes. Mol. Cell 27, 121-133
    • (2007) Mol. Cell , vol.27 , pp. 121-133
    • Donner, A.J.1    Szostek, S.2    Hoover, J.M.3    Espinosa, J.M.4
  • 61
    • 41349094797 scopus 로고    scopus 로고
    • Transcription regulation through promoter-proximal pausing of RNA polymerase II
    • Core, L. J. and Lis, J. T. (2008) Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791-1792
    • (2008) Science , vol.319 , pp. 1791-1792
    • Core, L.J.1    Lis, J.T.2
  • 62
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. and Young, R. A. (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77-88
    • (2007) Cell , vol.130 , pp. 77-88
    • Guenther, M.G.1    Levine, S.S.2    Boyer, L.A.3    Jaenisch, R.4    Young, R.A.5
  • 67
    • 78149477660 scopus 로고    scopus 로고
    • Pausing of RNA Polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    • Gilchrist, D. A., Dos Santos, G., Fargo, D. C., Xie, B., Gao, Y. A., Li, L. P. and Adelman, K. (2010) Pausing of RNA Polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 143, 540-551
    • (2010) Cell , vol.143 , pp. 540-551
    • Gilchrist, D.A.1    Dos Santos, G.2    Fargo, D.C.3    Xie, B.4    Gao, Y.A.5    Li, L.P.6    Adelman, K.7
  • 69
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson, H. J. and Wright, P. E. (2005) Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6, 197-208
    • (2005) Nat. Rev. Mol. Cell Biol. , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 71
    • 4143107222 scopus 로고    scopus 로고
    • Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers
    • Gunasekaran, K., Tsai, C. J. and Nussinov, R. (2004) Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J. Mol. Biol. 341, 1327-1341
    • (2004) J. Mol. Biol. , vol.341 , pp. 1327-1341
    • Gunasekaran, K.1    Tsai, C.J.2    Nussinov, R.3
  • 72
    • 37749053887 scopus 로고    scopus 로고
    • Fuzzy complexes: Polymorphism and structural disorder in protein-protein interactions
    • Tompa, P. and Fuxreiter, M. (2008) Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem. Sci. 33, 2-8
    • (2008) Trends Biochem. Sci. , vol.33 , pp. 2-8
    • Tompa, P.1    Fuxreiter, M.2
  • 73
    • 38149063767 scopus 로고    scopus 로고
    • Structural disorder promotes assembly of protein complexes
    • Hegyi, H., Schad, E. and Tompa, P. (2007) Structural disorder promotes assembly of protein complexes. BMC Struct. Biol. 7, 65
    • (2007) BMC Struct. Biol. , vol.7 , pp. 65
    • Hegyi, H.1    Schad, E.2    Tompa, P.3
  • 74
    • 44949188489 scopus 로고    scopus 로고
    • MED1 phosphorylation promotes its association with Mediator: Implications for nuclear receptor signaling
    • Belakavadi, M., Pandey, P. K., Vijayvargia, R. and Fondell, J. D. (2008) MED1 phosphorylation promotes its association with Mediator: implications for nuclear receptor signaling. Mol. Cell. Biol. 28, 3932-3942
    • (2008) Mol. Cell. Biol. , vol.28 , pp. 3932-3942
    • Belakavadi, M.1    Pandey, P.K.2    Vijayvargia, R.3    Fondell, J.D.4
  • 75
  • 76
    • 33750999318 scopus 로고    scopus 로고
    • Disorder and sequence repeats in hub proteins and their implications for network evolution
    • Dosztanyi, Z., Chen, J., Dunker, A. K., Simon, I. and Tompa, P. (2006) Disorder and sequence repeats in hub proteins and their implications for network evolution. J. Proteome Res. 5, 2985-2995
    • (2006) J. Proteome Res. , vol.5 , pp. 2985-2995
    • Dosztanyi, Z.1    Chen, J.2    Dunker, A.K.3    Simon, I.4    Tompa, P.5
  • 77
    • 80052725533 scopus 로고    scopus 로고
    • Reference deleted
    • Reference deleted
  • 79
    • 77954759030 scopus 로고    scopus 로고
    • The human Mediator complex: A versatile, genome-wide regulator of transcription
    • Taatjes, D. J. (2010) The human Mediator complex: a versatile, genome-wide regulator of transcription. Trends Biochem. Sci. 35, 315-322
    • (2010) Trends Biochem. Sci. , vol.35 , pp. 315-322
    • Taatjes, D.J.1
  • 80
    • 34447522202 scopus 로고    scopus 로고
    • New problems in RNA Polymerase II transcription initiation: Matching the diversity of core promoters with a variety of promoter recognition factors
    • Muller, F., Demeny, M. A. and Tora, L. (2007) New problems in RNA Polymerase II transcription initiation: matching the diversity of core promoters with a variety of promoter recognition factors. J. Biol. Chem. 282, 14685-14689
    • (2007) J. Biol. Chem. , vol.282 , pp. 14685-14689
    • Muller, F.1    Demeny, M.A.2    Tora, L.3
  • 81
    • 77953711351 scopus 로고    scopus 로고
    • TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation
    • Papai, G., Tripathi, M. K., Ruhlmann, C., Layer, J. H., Weil, P. A. and Schultz, P. (2010) TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation. Nature 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
  • 82
    • 79953162966 scopus 로고    scopus 로고
    • New insights into the function of transcription factor TFIID from recent structural studies
    • Papai, G., Weil, P. A. and Schultz, P. (2011) New insights into the function of transcription factor TFIID from recent structural studies. Curr. Opin. Genet. Dev. 21, 219-224
    • (2011) Curr. Opin. Genet. Dev. , vol.21 , pp. 219-224
    • Papai, G.1    Weil, P.A.2    Schultz, P.3
  • 83
    • 46349085558 scopus 로고    scopus 로고
    • Discovery of novel tumor suppressor p53 response elements using information theory
    • Lyakhov, I. G., Krishnamachari, A. and Schneider, T. D. (2008) Discovery of novel tumor suppressor p53 response elements using information theory. Nucleic Acids Res. 36, 3828-3833
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3828-3833
    • Lyakhov, I.G.1    Krishnamachari, A.2    Schneider, T.D.3
  • 84
    • 67649405072 scopus 로고    scopus 로고
    • Insight into the structural basis of pro- and antiapoptotic p53 Modulation by ASPP proteins
    • Ahn, J., Byeon, I. J. L., Byeon, C. H. and Gronenborn, A. M. (2009) Insight into the structural basis of pro- and antiapoptotic p53 Modulation by ASPP proteins. J. Biol. Chem. 284, 13812-13822
    • (2009) J. Biol. Chem. , vol.284 , pp. 13812-13822
    • Ahn, J.1    Byeon, I.J.L.2    Byeon, C.H.3    Gronenborn, A.M.4
  • 85
    • 33344459086 scopus 로고    scopus 로고
    • MED14 and MED1 differentially regulate target-specific gene activation by the glucocorticoid receptor
    • Chen, W. W., Rogatsky, I. and Garabedian, M. J. (2006) MED14 and MED1 differentially regulate target-specific gene activation by the glucocorticoid receptor. Mol. Endocrinol. 20, 560-572
    • (2006) Mol. Endocrinol. , vol.20 , pp. 560-572
    • Chen, W.W.1    Rogatsky, I.2    Garabedian, M.J.3
  • 86
    • 35549006337 scopus 로고    scopus 로고
    • The mediator subunit MED1/TRAP220 is required for optimal glucocorticoid receptor-mediated transcription activation
    • Chen, W. and Roeder, R. G. (2007) The mediator subunit MED1/TRAP220 is required for optimal glucocorticoid receptor-mediated transcription activation. Nucleic Acids Res. 35, 6161-6169
    • (2007) Nucleic Acids Res. , vol.35 , pp. 6161-6169
    • Chen, W.1    Roeder, R.G.2
  • 87
    • 33745178477 scopus 로고    scopus 로고
    • A Mediator subunit, MDT-15, integrates regulation of fatty acid metabolism by NHR-49-dependent and -independent pathways in C. elegans
    • Taubert, S., Van Gilst, M. R., Hansen, M. and Yamamoto, K. R. (2006) A Mediator subunit, MDT-15, integrates regulation of fatty acid metabolism by NHR-49-dependent and -independent pathways in C. elegans. Genes Dev. 20, 1137-1149
    • (2006) Genes Dev. , vol.20 , pp. 1137-1149
    • Taubert, S.1    Van Gilst, M.R.2    Hansen, M.3    Yamamoto, K.R.4
  • 88
    • 0033105821 scopus 로고    scopus 로고
    • Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators
    • Ito, M., Yuan, C. X., Malik, S., Gu, W., Fondell, J. D., Yamamura, S., Fu, Z. Y., Zhang, X. L., Qin, J. and Roeder, R. G. (1999) Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators. Mol. Cell 3, 361-370
    • (1999) Mol. Cell , vol.3 , pp. 361-370
    • Ito, M.1    Yuan, C.X.2    Malik, S.3    Gu, W.4    Fondell, J.D.5    Yamamura, S.6    Fu, Z.Y.7    Zhang, X.L.8    Qin, J.9    Roeder, R.G.10
  • 89
    • 0034459504 scopus 로고    scopus 로고
    • In vivo requirement of activator-specific binding targets of mediator
    • Park, J. M., Kim, H. S., Han, S. J., Hwang, M. S., Lee, Y. C. and Kim, Y. J. (2000) In vivo requirement of activator-specific binding targets of mediator. Mol. Cell. Biol. 20, 8709-8719
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 8709-8719
    • Park, J.M.1    Kim, H.S.2    Han, S.J.3    Hwang, M.S.4    Lee, Y.C.5    Kim, Y.J.6
  • 90
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    • Ma, B. Y., Shatsky, M., Wolfson, H. J. and Nussinov, R. (2002) Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11, 184-197
    • (2002) Protein Sci. , vol.11 , pp. 184-197
    • Ma, B.Y.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 91
    • 70450171352 scopus 로고    scopus 로고
    • RNA polymerase II-TFIIB structure and mechanism of transcription initiation
    • Kostrewa, D., Zeller, M. E., Armache, K. J., Seizl, M., Leike, K., Thomm, M. and Cramer, P. (2009) RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462, 323-330
    • (2009) Nature , vol.462 , pp. 323-330
    • Kostrewa, D.1    Zeller, M.E.2    Armache, K.J.3    Seizl, M.4    Leike, K.5    Thomm, M.6    Cramer, P.7
  • 92
    • 74249102477 scopus 로고    scopus 로고
    • Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism
    • Liu, X., Bushnell, D. A., Wang, D., Calero, G. and Kornberg, R. D. (2010) Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 327, 206-209
    • (2010) Science , vol.327 , pp. 206-209
    • Liu, X.1    Bushnell, D.A.2    Wang, D.3    Calero, G.4    Kornberg, R.D.5
  • 93
    • 73849107519 scopus 로고    scopus 로고
    • Regulation of mRNA cap methylation
    • Cowling, V. H. (2010) Regulation of mRNA cap methylation. Biochem. J. 425, 295-302
    • (2010) Biochem. J. , vol.425 , pp. 295-302
    • Cowling, V.H.1
  • 94
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core, L. J., Waterfall, J. J. and Lis, J. T. (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 95
    • 70249104647 scopus 로고    scopus 로고
    • Defining mechanisms that regulate RNA polymerase II transcription in vivo
    • Fuda, N. J., Ardehali, M. B. and Lis, J. T. (2009) Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461, 186-192
    • (2009) Nature , vol.461 , pp. 186-192
    • Fuda, N.J.1    Ardehali, M.B.2    Lis, J.T.3
  • 96
    • 5444225805 scopus 로고    scopus 로고
    • Elongation by RNA polymerase II: The short and long of it
    • Sim, R. J., Belotserkovskaya, R. and Reinberg, D. (2004) Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18, 2437-2468
    • (2004) Genes Dev. , vol.18 , pp. 2437-2468
    • Sim, R.J.1    Belotserkovskaya, R.2    Reinberg, D.3
  • 97
    • 79953779997 scopus 로고    scopus 로고
    • Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity
    • Martinez-Rucobo, F. W., Sainsbury, S., Cheung, A. C. M. and Cramer, P. (2011) Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J. 30, 1302-1310
    • (2011) EMBO J. , vol.30 , pp. 1302-1310
    • Martinez-Rucobo, F.W.1    Sainsbury, S.2    Cheung, A.C.M.3    Cramer, P.4
  • 98
    • 33746403681 scopus 로고    scopus 로고
    • Controlling the elongation phase of transcription with p-TEFb
    • Peterlin, B. M. and Price, D. H. (2006) Controlling the elongation phase of transcription with p-TEFb. Mol. Cell 23, 297-305
    • (2006) Mol. Cell , vol.23 , pp. 297-305
    • Peterlin, B.M.1    Price, D.H.2
  • 101
    • 72149130298 scopus 로고    scopus 로고
    • Shifting players and paradigms in cell-specific transcription
    • D'Alessio, J. A., Wright, K. J. and Tjian, R. (2009) Shifting players and paradigms in cell-specific transcription. Mol. Cell 36, 924-931
    • (2009) Mol. Cell , vol.36 , pp. 924-931
    • D'Alessio, J.A.1    Wright, K.J.2    Tjian, R.3
  • 102
    • 77952354490 scopus 로고    scopus 로고
    • Seven transmembrane receptors as shapeshifting rroteins: The impact of allosteric modulation and functional selectivity on new drug discovery
    • Kenakin, T. and Miller, L. J. (2010) Seven transmembrane receptors as shapeshifting rroteins: the impact of allosteric modulation and functional selectivity on new drug discovery. Pharmacol. Rev. 62, 265-304
    • (2010) Pharmacol. Rev. , vol.62 , pp. 265-304
    • Kenakin, T.1    Miller, L.J.2
  • 103
    • 45149089670 scopus 로고    scopus 로고
    • The Med1 subunit of transcriptional mediator plays a central role in regulating CCAAT/enhancer-binding protein-β-driven transcription in response to interferon-γ
    • Li, H., Gade, P., Nallar, S. C., Raha, A., Roy, S. K., Karra, S., Reddy, J. K., Reddy, S. P. and Kalvakolanu, D. V. (2008) The Med1 subunit of transcriptional mediator plays a central role in regulating CCAAT/enhancer- binding protein-β-driven transcription in response to interferon-γ. J. Biol. Chem. 283, 13077-13086
    • (2008) J. Biol. Chem. , vol.283 , pp. 13077-13086
    • Li, H.1    Gade, P.2    Nallar, S.C.3    Raha, A.4    Roy, S.K.5    Karra, S.6    Reddy, J.K.7    Reddy, S.P.8    Kalvakolanu, D.V.9
  • 104
    • 0344413490 scopus 로고    scopus 로고
    • Coordination of p300-mediated chromatin remodeling and TRAP/mediator function through coactivator PGC-1 α
    • Wallberg, A. E., Yamamura, S., Malik, S., Spiegelman, B. M. and Roeder, R. G. (2003) Coordination of p300-mediated chromatin remodeling and TRAP/mediator function through coactivator PGC-1 α. Mol. Cell 12, 1137-1149
    • (2003) Mol. Cell , vol.12 , pp. 1137-1149
    • Wallberg, A.E.1    Yamamura, S.2    Malik, S.3    Spiegelman, B.M.4    Roeder, R.G.5
  • 105
    • 0037022631 scopus 로고    scopus 로고
    • The TRAP/mediator coactivator complex interacts directly with estrogen receptors α and β through the TRAP220 subunit and directly enhances estrogen receptor function in vitro
    • Kang, Y. K., Guermah, M., Yuan, C. X. and Roeder, R. G. (2002) The TRAP/mediator coactivator complex interacts directly with estrogen receptors α and β through the TRAP220 subunit and directly enhances estrogen receptor function in vitro. Proc. Natl. Acad. Sci. U.S.A. 99, 2642-2647
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 2642-2647
    • Kang, Y.K.1    Guermah, M.2    Yuan, C.X.3    Roeder, R.G.4
  • 106
    • 44149124228 scopus 로고    scopus 로고
    • Cracking the RNA polymerase IICTD code
    • Egloff, S. and Murphy, S. (2008) Cracking the RNA polymerase IICTD code. Trends Genet. 24, 280-288
    • (2008) Trends Genet. , vol.24 , pp. 280-288
    • Egloff, S.1    Murphy, S.2
  • 107
    • 73649143873 scopus 로고    scopus 로고
    • RNA polymerase II C-terminal heptarepeat domain ser-7 phosphorylation is established in a Mediator-dependent fashion
    • Boeing, S., Rigault, C., Heidemann, M., Eick, D. and Meisterernst, M. (2010) RNA polymerase II C-terminal heptarepeat domain ser-7 phosphorylation is established in a Mediator-dependent fashion. J. Biol. Chem. 285, 188-196
    • (2010) J. Biol. Chem. , vol.285 , pp. 188-196
    • Boeing, S.1    Rigault, C.2    Heidemann, M.3    Eick, D.4    Meisterernst, M.5
  • 108
    • 79953713243 scopus 로고    scopus 로고
    • Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly
    • Bernecky, C., Grob, P., Ebmeier, C. C., Nogales, E. and Taatjes, D. J. (2011) Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biol. 9, e1000603
    • (2011) PLoS Biol. , vol.9
    • Bernecky, C.1    Grob, P.2    Ebmeier, C.C.3    Nogales, E.4    Taatjes, D.J.5
  • 110
    • 34547812030 scopus 로고    scopus 로고
    • MED25 is distinct from TRAP220/MED1 in cooperating with CBP for retinoid receptor activation
    • Lee, H. K., Park, U. H., Kim, E. J. and Um, S. J. (2007) MED25 is distinct from TRAP220/MED1 in cooperating with CBP for retinoid receptor activation. EMBO J. 26, 3545-3557
    • (2007) EMBO J. , vol.26 , pp. 3545-3557
    • Lee, H.K.1    Park, U.H.2    Kim, E.J.3    Um, S.J.4
  • 111
    • 0036318299 scopus 로고    scopus 로고
    • TRAP/SMCC/ mediator-dependent transcriptional activation from DNA and chromatin templates by orphan nuclear receptor hepatocyte nuclear factor 4
    • Malik, S., Wallberg, A. E., Kang, Y. K. and Roeder, R. G. (2002) TRAP/SMCC/ mediator-dependent transcriptional activation from DNA and chromatin templates by orphan nuclear receptor hepatocyte nuclear factor 4. Mol. Cell. Biol. 22, 5626-5637
    • (2002) Mol. Cell. Biol. , vol.22 , pp. 5626-5637
    • Malik, S.1    Wallberg, A.E.2    Kang, Y.K.3    Roeder, R.G.4
  • 112
    • 4444333428 scopus 로고    scopus 로고
    • Structural and functional organization of TRAP220, the TRAP/Mediator subunit that is targeted by nuclear receptors
    • Malik, S., Guermah, M., Yuan, C. X., Wu, W. Z., Yamamura, S. and Roeder, R. G. (2004) Structural and functional organization of TRAP220, the TRAP/Mediator subunit that is targeted by nuclear receptors. Mol. Cell. Biol. 24, 8244-8254
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 8244-8254
    • Malik, S.1    Guermah, M.2    Yuan, C.X.3    Wu, W.Z.4    Yamamura, S.5    Roeder, R.G.6
  • 114
    • 38549087992 scopus 로고    scopus 로고
    • Alternative mechanisms by which mediator subunit MED1/TRAP220 regulates peroxisome proliferator-activated receptor γ -stimulated adipogenesis and target gene expression
    • Ge, K., Cho, Y. W., Guo, H., Hong, T. B., Guermah, M., Ito, M., Yu, H., Kalkum, M. and Roeder, R. G. (2008) Alternative mechanisms by which mediator subunit MED1/TRAP220 regulates peroxisome proliferator-activated receptor γ -stimulated adipogenesis and target gene expression. Mol. Cell. Biol. 28, 1081-1091
    • (2008) Mol. Cell. Biol. , vol.28 , pp. 1081-1091
    • Ge, K.1    Cho, Y.W.2    Guo, H.3    Hong, T.B.4    Guermah, M.5    Ito, M.6    Yu, H.7    Kalkum, M.8    Roeder, R.G.9
  • 115
    • 33744962325 scopus 로고    scopus 로고
    • Regulation of Aurora-A kinase gene expression via GABP recruitment of TRAP220/ MED1
    • Udayakumar, T. S., Belakavadi, M., Choi, K. H., Pandey, P. K. and Fondell, J. D. (2006) Regulation of Aurora-A kinase gene expression via GABP recruitment of TRAP220/ MED1. J. Biol. Chem. 281, 14691-14699
    • (2006) J. Biol. Chem. , vol.281 , pp. 14691-14699
    • Udayakumar, T.S.1    Belakavadi, M.2    Choi, K.H.3    Pandey, P.K.4    Fondell, J.D.5
  • 116
    • 0037370376 scopus 로고    scopus 로고
    • Principal role of TRAP/mediator and SWI/SNF complexes in Kaposi's sarcoma-associated herpesvirus RTA-mediated lytic reactivation
    • Gwack, Y., Baek, H. J., Nakamura, H., Lee, S. H., Meisterernst, M., Roeder, R. G. and Jung, J. U. (2003) Principal role of TRAP/mediator and SWI/SNF complexes in Kaposi's sarcoma-associated herpesvirus RTA-mediated lytic reactivation. Mol. Cell. Biol. 23, 2055-2067
    • (2003) Mol. Cell. Biol. , vol.23 , pp. 2055-2067
    • Gwack, Y.1    Baek, H.J.2    Nakamura, H.3    Lee, S.H.4    Meisterernst, M.5    Roeder, R.G.6    Jung, J.U.7
  • 117
    • 33646580781 scopus 로고    scopus 로고
    • Mediator is a transducer of Wnt/β-catenin signaling
    • Kim, S., Xu, X., Hecht, A. and Boyer, T. G. (2006) Mediator is a transducer of Wnt/β-catenin signaling. J. Biol. Chem. 281, 14066-14075
    • (2006) J. Biol. Chem. , vol.281 , pp. 14066-14075
    • Kim, S.1    Xu, X.2    Hecht, A.3    Boyer, T.G.4
  • 118
    • 33845219533 scopus 로고    scopus 로고
    • Mediator modulates Gli3-dependent sonic hedgehog signaling
    • Zhou, H. Y., Kim, S., Ishii, S. and Boyer, T. G. (2006) Mediator modulates Gli3-dependent sonic hedgehog signaling. Mol. Cell. Biol. 26, 8667-8682
    • (2006) Mol. Cell. Biol. , vol.26 , pp. 8667-8682
    • Zhou, H.Y.1    Kim, S.2    Ishii, S.3    Boyer, T.G.4
  • 119
    • 33745945633 scopus 로고    scopus 로고
    • Zebrafish Trap230/Med12 is required as a coactivator for Sox.9-dependent neural crest, cartilage and ear development
    • Rau, M. J., Fischer, S. and Neumann, C. J. (2006) Zebrafish Trap230/Med12 is required as a coactivator for Sox.9-dependent neural crest, cartilage and ear development. Dev. Biol. 296, 83-93
    • (2006) Dev. Biol. , vol.296 , pp. 83-93
    • Rau, M.J.1    Fischer, S.2    Neumann, C.J.3
  • 121
    • 3242728442 scopus 로고    scopus 로고
    • A triad of subunits from the Gal11/tail domain of Srb mediator is an in vivo target of transcriptional activator Gcn4p
    • Zhang, F., Sumibcay, L., Hinnebusch, A. G. and Swanson, M. J. (2004) A triad of subunits from the Gal11/tail domain of Srb mediator is an in vivo target of transcriptional activator Gcn4p. Mol. Cell. Biol. 24, 6871-6886
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 6871-6886
    • Zhang, F.1    Sumibcay, L.2    Hinnebusch, A.G.3    Swanson, M.J.4
  • 122
    • 0033213632 scopus 로고    scopus 로고
    • Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator
    • Natarajan, K., Jackson, B. M., Zhou, H., Winston, F. and Hinnebusch, A. G. (1999) Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator. Mol. Cell 4, 657-664
    • (1999) Mol. Cell , vol.4 , pp. 657-664
    • Natarajan, K.1    Jackson, B.M.2    Zhou, H.3    Winston, F.4    Hinnebusch, A.G.5
  • 123
    • 4444349833 scopus 로고    scopus 로고
    • Selective coactivator interactions in gene activation by SREBP-1a and -1c
    • Toth, J. I., Datta, S., Athanikar, J. N., Freedman, L. P. and Osborne, T. F. (2004) Selective coactivator interactions in gene activation by SREBP-1a and -1c. Mol. Cell. Biol. 24, 8288-8300
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 8288-8300
    • Toth, J.I.1    Datta, S.2    Athanikar, J.N.3    Freedman, L.P.4    Osborne, T.F.5
  • 124
    • 0037043739 scopus 로고    scopus 로고
    • A component of the ARC/mediator complex required for TGF β/Nodal signalling
    • Kato, Y., Habas, R., Katsuyama, Y., Naar, A. M. and He, X. (2002) A component of the ARC/mediator complex required for TGF β/Nodal signalling. Nature 418, 641-646
    • (2002) Nature , vol.418 , pp. 641-646
    • Kato, Y.1    Habas, R.2    Katsuyama, Y.3    Naar, A.M.4    He, X.5
  • 126
    • 0037177573 scopus 로고    scopus 로고
    • Transcription control by E1A and MAP kinase pathway via Sur2 mediator subunit
    • Stevens, J. L., Cantin, G. T., Wang, G., Shevchenko, A. and Berk, A. J. (2002) Transcription control by E1A and MAP kinase pathway via Sur2 mediator subunit. Science 296, 755-758
    • (2002) Science , vol.296 , pp. 755-758
    • Stevens, J.L.1    Cantin, G.T.2    Wang, G.3    Shevchenko, A.4    Berk, A.J.5
  • 127
    • 0842310355 scopus 로고    scopus 로고
    • Ras induces mediator complex exchange on C/EBP β
    • Mo, X. M., Kowenz-Leutz, E., Xu, H. and Leutz, A. (2004) Ras induces mediator complex exchange on C/EBP β. Mol. Cell 13, 241-250
    • (2004) Mol. Cell , vol.13 , pp. 241-250
    • Mo, X.M.1    Kowenz-Leutz, E.2    Xu, H.3    Leutz, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.