Regulatory diversity among metazoan co-activator complexes (original) (raw)
References
Levine, M. & Tjian, R. Transcription regulation and animal diversity. Nature424, 147–151 (2003). ArticleCASPubMed Google Scholar
Gruber, T. M. & Gross, C. A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol.57, 441–466 (2003). ArticleCASPubMed Google Scholar
Khorasanizadeh, S. The nucleosome: from genomic organization to genomic regulation. Cell116, 259–272 (2004). ArticleCASPubMed Google Scholar
Lemon, B. D. & Tjian, R. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev.14, 2551–2569 (2000). ArticleCASPubMed Google Scholar
Näär, A. M., Lemon, B. D. & Tjian, R. Transcriptional coactivator complexes. Annu. Rev. Biochem.70, 475–501 (2001). ArticlePubMed Google Scholar
Roth, S. Y., Denu, J. M. & Allis, C. D. Histone acetyltransferases. Annu. Rev. Biochem.70, 81–120 (2001). ArticleCASPubMed Google Scholar
Thompson, C. M., Koleske, A. J., Chao, D. M. & Young, R. A. A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast. Cell73, 1361–1375 (1993). ArticleCASPubMed Google Scholar
Hengartner, C. J. et al. Association of an activator with an RNA polymerase II holoenzyme. Genes Dev.9, 897–910 (1995). ArticleCASPubMed Google Scholar
Kim, Y., Bjorklund, S., Li, Y., Sayre, M. H. & Kornberg, R. D. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell77, 599–608 (1994). ArticleCASPubMed Google Scholar
Malik, S. & Roeder, R. G. Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells. Trends Biochem. Sci.25, 277–283 (2000). ArticleCASPubMed Google Scholar
Mittler, G., Kremmer, E., Timmers, H. T. & Meisterernst, M. Novel critical roles of a human mediator complex for basal RNA polymerase II transcription. EMBO Rep.2, 808–813 (2001). ArticleCASPubMedPubMed Central Google Scholar
Davidson, E. H. Genomic Regulatory Systems: Development and Evolution (Academic Press, New York, 2001). Google Scholar
Rachez, C. & Freedman, L. P. Mediator complexes and transcription. Curr. Opin. Cell Biol.13, 274–280 (2001). ArticleCASPubMed Google Scholar
Taatjes, D. J., Näär, A. M., Andel, F., Nogales, E. & Tjian, R. Structure, function, and activator-induced conformations of the CRSP coactivator. Science295, 1058–1062 (2002). ArticleCASPubMed Google Scholar
Liu, Y., Ranish, J. A., Aebersold, R. & Hahn, S. Yeast nuclear extract contains two major forms of RNA polymerase II mediator complexes. J. Biol. Chem.276, 7169–7175 (2001). ArticleCASPubMed Google Scholar
Francis, N. J. & Kingston, R. E. Mechanisms of transcriptional memory. Nature Rev. Mol. Cell Biol.2, 409–421 (2001). ArticleCAS Google Scholar
Hutchison, C. J. Lamins: building blocks or regulators of gene expression? Nature Rev. Mol. Cell Biol.3, 848–858 (2002). ArticleCAS Google Scholar
Kadonaga, J. T. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell116, 247–257 (2004). ArticleCASPubMed Google Scholar
Lemon, B. D., Inouye, C., King, D. S. & Tjian, R. Selectivity of chromatin-remodeling cofactors for ligand-activated transcription. Nature414, 924–928 (2001). ArticleCASPubMed Google Scholar
Brand, M., Yamamoto, K., Staub, A. & Tora, L. Identification of TATA-binding protein-free TAFII-containing complex subunits suggests a role in nucleosome acetylation and signal transduction. J. Biol. Chem.274, 18285–18289 (1999). ArticleCASPubMed Google Scholar
Wieczorek, E., Brand, M., Jacq, X. & Tora, L. Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II. Nature393, 187–191 (1998). ArticleCASPubMed Google Scholar
Brand, M. et al. UV-damaged DNA-binding protein in the TFTC complex links DNA damage recognition to nucleosome acetylation. EMBO J.20, 3187–3196 (2001). ArticleCASPubMedPubMed Central Google Scholar
Hardy, S. et al. TATA-binding protein-free TAF-containing complex (TFTC) and p300 are both required for efficient transcriptional activation. J. Biol. Chem.277, 32875–32882 (2002). ArticleCASPubMed Google Scholar
Ogryzko, V. V. et al. Histone-like TAFs within the PCAF histone acetylase complex. Cell94, 35–44 (1998). ArticleCASPubMed Google Scholar
Martinez, E. Multi-protein complexes in eukaryotic gene transcription. Plant Mol. Biol.50, 925–947 (2002). ArticleCASPubMed Google Scholar
Mo, X., Kowenz-Leutz, E., Xu, H. & Leutz, A. Ras induces mediator complex exchange on C/EBPβ. Mol. Cell13, 241–250 (2004). ArticleCASPubMed Google Scholar
Borggrefe, T., Davis, R., Erdjument-Bromage, H., Tempst, P. & Kornberg, R. D. A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast. J. Biol. Chem.277, 44202–44207 (2002). ArticleCASPubMed Google Scholar
Holstege, F. C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell95, 717–728 (1998). ArticleCASPubMed Google Scholar
Zhou, R. et al. SOX9 interacts with a component of the human thyroid hormone receptor-associated protein complex. Nucleic Acids Res.30, 3245–3452 (2002). ArticleCASPubMedPubMed Central Google Scholar
Akoulitchev, S., Chuikov, S. & Reinberg, D. TFIIH is negatively regulated by cdk8-containing mediator complexes. Nature407, 102–106 (2000). ArticleCASPubMed Google Scholar
Kuchin, S. & Carlson, M. Functional relationships of Srb10–Srb11 kinase, carboxy-terminal domain kinase CTDK-I, and transcriptional corepressor Ssn6–Tup1. Mol. Cell Biol.18, 1163–1171 (1998). ArticleCASPubMedPubMed Central Google Scholar
Song, W. & Carlson, M. Srb/mediator proteins interact functionally and physically with transcriptional repressor Sfl1. EMBO J.17, 5757–5765 (1998). ArticleCASPubMedPubMed Central Google Scholar
Zaman, Z., Ansari, A. Z., Koh, S. S., Young, R. & Ptashne, M. Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression. Proc. Natl Acad. Sci. USA98, 2550–2554 (2001). ArticleCASPubMedPubMed Central Google Scholar
Zhang, H. & Emmons, S. W. A C. elegans mediator protein confers regulatory selectivity on lineage-specific expression of a transcription factor gene. Genes Dev.14, 2161–2172 (2000). ArticleCASPubMedPubMed Central Google Scholar
Näär, A. M., Taatjes, D. J., Zhai, W., Nogales, E. & Tjian, R. Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation. Genes Dev.16, 1339–1344 (2002). ArticlePubMedPubMed CentralCAS Google Scholar
Brower, C. S. et al. Mammalian mediator subunit mMed8 is an Elongin BC-interacting protein that can assemble with Cul2 and Rbx1 to reconstitute a ubiquitin ligase. Proc. Natl Acad. Sci. USA99, 10353–10358 (2002). ArticleCASPubMedPubMed Central Google Scholar
Chi, Y. et al. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev.15, 1078–1092 (2001). ArticleCASPubMedPubMed Central Google Scholar
Nelson, C., Goto, S., Lund, K., Hung, W. & Sadowski, I. Srb10/Cdk8 regulates yeast filamentous growth by phosphorylating the transcription factor Ste12. Nature421, 187–190 (2003). ArticleCASPubMed Google Scholar
Song, A., Wang, Q., Goebl, M. G. & Harrington, M. A. Phosphorylation of nuclear MyoD is required for its rapid degradation. Mol. Cell. Biol.18, 4994–4999 (1998). ArticleCASPubMedPubMed Central Google Scholar
Hochheimer, A. & Tjian, R. Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. Genes Dev.17, 1309–1320 (2003). ArticleCASPubMed Google Scholar
Freiman, R. N. et al. Requirement of tissue-selective TBP-associated factor TAFII105 in ovarian development. Science293, 2084–2087 (2001). ArticleCASPubMed Google Scholar
Hiller, M. A., Lin, T. Y., Wood, C. & Fuller, M. T. Developmental regulation of transcription by a tissue-specific TAF homolog. Genes Dev.15, 1021–1030 (2001). ArticleCASPubMedPubMed Central Google Scholar
Hochheimer, A., Zhou, S., Zheng, S., Holmes, M. C. & Tjian, R. TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature420, 439–445 (2002). ArticleCASPubMed Google Scholar
Holmes, M. C. & Tjian, R. Promoter-selective properties of the TBP-related factor TRF1. Science288, 867–870 (2000). ArticleCASPubMed Google Scholar
Kaltenbach, L., Horner, M. A., Rothman, J. H. & Mango, S. E. The TBP-like factor CeTLF is required to activate RNA polymerase II transcription during C. elegans embryogenesis. Mol. Cell6, 705–713 (2000). ArticleCASPubMed Google Scholar
Martianov, I. et al. Late arrest of spermiogenesis and germ cell apoptosis in mice lacking the TBP-like TLF/TRF2 gene. Mol. Cell7, 509–515 (2001). ArticleCASPubMed Google Scholar
Veenstra, G. J., Weeks, D. L. & Wolffe, A. P. Distinct roles for TBP and TBP-like factor in early embryonic gene transcription in Xenopus. Science290, 2312–2315 (2000). ArticleCASPubMed Google Scholar
Zhang, D., Penttila, T. L., Morris, P. L. & Roeder, R. G. Spermiogenesis deficiency in mice lacking the Trf2 gene. Science292, 1153–1155 (2001). ArticleCASPubMed Google Scholar
Olave, I., Wang, W., Xue, Y., Kuo, A. & Crabtree, G. R. Identification of a polymorphic, neuron-specific chromatin remodeling complex. Genes Dev.16, 2509–2517 (2002). ArticleCASPubMedPubMed Central Google Scholar
Berti, L. et al. Isolation and characterization of a novel gene from the DiGeorge chromosomal region that encodes for a mediator subunit. Genomics74, 320–332 (2001). ArticleCASPubMed Google Scholar
Ito, M. et al. Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators. Mol. Cell3, 361–370 (1999). ArticleCASPubMed Google Scholar
Yuan, C., Ito, M., Fondell, J. D., Fu, Z. & Roeder, R. G. The TRAP220 component of a thyroid hormone receptor-associated protein (TRAP) coactivator complex interacts directly with nuclear receptors in a ligand-dependent fashion. Proc. Natl Acad. Sci. USA95, 7939–7944 (1998). ArticleCASPubMedPubMed Central Google Scholar
Ito, M., Yuan, C. X., Okano, H. J., Darnell, R. B. & Roeder, R. G. Involvement of the TRAP220 component of the TRAP/SMCC coactivator complex in embryonic development and thyroid hormone action. Mol. Cell5, 683–693 (2000). ArticleCASPubMed Google Scholar
Ge, K. et al. Transcription coactivator TRAP220 is required for PPARγ2-stimulated adipogenesis. Nature417, 563–567 (2002). ArticleCASPubMed Google Scholar
Kato, Y., Habas, R., Katsuyama, Y., Naar, A. & He, X. A component of the ARC/Mediator complex required for TGFβ/Nodal signalling. Nature418, 641–646 (2002). ArticleCASPubMed Google Scholar
Stevens, J. L. et al. Transcription control by E1A and MAP kinase pathway via Sur2 mediator subunit. Science296, 755–758 (2002). ArticleCASPubMed Google Scholar
Ito, M., Okano, H. J., Darnell, R. B. & Roeder, R. G. The TRAP100 component of the TRAP/Mediator complex is essential in broad transcriptional events and development. EMBO J.21, 3464–3475 (2002). ArticleCASPubMedPubMed Central Google Scholar
Albright, S. R. & Tjian, R. TAFs revisited: more data reveal new twists and confirm old ideas. Gene242, 1–13 (2000). ArticleCASPubMed Google Scholar
Kadam, S. & Emerson, B. M. Transcriptional specificity of human SWI/SNF BRG1 and BRM chromatin remodeling complexes. Mol. Cell11, 377–389 (2003). ArticleCASPubMed Google Scholar
Thut, C. J., Chen, J. L., Klemm, R. & Tjian, R. p53 transcriptional activation mediated by coactivators TAFII40 and TAFII60. Science267, 100–104 (1995). ArticleCASPubMed Google Scholar
Chen, J. L., Attardi, L. D., Verrijzer, C. P., Yokomori, K. & Tjian, R. Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell79, 93–105 (1994). ArticleCASPubMed Google Scholar
Butler, J. E. & Kadonaga, J. T. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev.15, 2515–2519 (2001). ArticleCASPubMedPubMed Central Google Scholar
Ohtsuki, S., Levine, M. & Cai, H. N. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev.12, 547–556 (1998). ArticleCASPubMedPubMed Central Google Scholar
Burke, T. W. & Kadonaga, J. T. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev.11, 3020–3031 (1997). ArticleCASPubMedPubMed Central Google Scholar
Chalkley, G. E. & Verrijzer, C. P. DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250–TAF(II)150 complex recognizes the initiator. EMBO J.18, 4835–4845 (1999). ArticleCASPubMedPubMed Central Google Scholar
Kaufman, J., Ahrens, K., Koop, R., Smale, S. T. & Muller, R. CIF150, a human cofactor for transcription factor IID-dependent initiator function. Mol. Cell. Biol.18, 233–239 (1998). Article Google Scholar
Verrijzer, C. P., Chen, J. L., Yokomori, K. & Tjian, R. Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell81, 1115–1125 (1995). ArticleCASPubMed Google Scholar
Hansen, S. K. & Tjian, R. TAFs and TFIIA mediate differential utilization of the tandem Adh promoters. Cell82, 565–575 (1995). ArticleCASPubMed Google Scholar
Davis, J. A., Takagi, Y., Kornberg, R. D. & Asturias, F. A. Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol. Cell10, 409–415 (2002). ArticleCASPubMed Google Scholar
Johnson, K. M., Wang, J., Smallwood, A., Arayata, C. & Carey, M. TFIID and human mediator coactivator complexes assemble cooperatively on promoter DNA. Genes Dev.16, 1852–1863 (2002). ArticleCASPubMedPubMed Central Google Scholar
Borggrefe, T., Davis, R., Bareket-Samish, A. & Kornberg, R. D. Quantitation of the RNA polymerase II transcription machinery in yeast. J. Biol. Chem.276, 47150–47153 (2001). ArticleCASPubMed Google Scholar
Kimura, H., Tao, Y., Roeder, R. G. & Cook, P. R. Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol. Cell. Biol.19, 5383–5392 (1999). ArticleCASPubMedPubMed Central Google Scholar
Chi, T. & Carey, M. Assembly of the isomerized TFIIA–TFIID–TATA ternary complex is necessary and sufficient for gene activation. Genes Dev.10, 2540–2550 (1996). ArticleCASPubMed Google Scholar
Guermah, M., Malik, S. & Roeder, R. G. Involvement of TFIID and USA components in transcriptional activation of the human immunodeficiency virus promoter by NF-κB and Sp1. Mol. Cell. Biol.18, 3234–3244 (1998). ArticleCASPubMedPubMed Central Google Scholar
Kotani, T. et al. Identification of highly conserved amino-terminal segments of dTAFII230 and yTAFII145 that are functionally interchangeable for inhibiting TBP–DNA interactions in vitro and in promoting yeast cell growth in vivo. J. Biol. Chem.273, 32254–32264 (1998). ArticleCASPubMed Google Scholar
Cosma, M. P. Ordered recruitment: gene-specific mechanism of transcription activation. Mol. Cell10, 227–236 (2002). ArticleCASPubMed Google Scholar
Lewis, B. A. & Reinberg, D. The Mediator coactivator complex: functional and physical roles in transcriptional regulation. J. Cell Sci.116, 3667–3675 (2003). ArticleCASPubMed Google Scholar
Lee, D. K., Kim, S. & Lis, J. T. Different upstream transcriptional activators have distinct coactivator requirements. Genes Dev.13, 2934–2939 (1999). ArticleCASPubMedPubMed Central Google Scholar
West, R. W. Jr., Kruger, B., Thomas, S., Ma, J. & Milgrom, E. RLR1 (THO2), required for expressing lacZ fusions in yeast, is conserved from yeast to humans and is a suppressor of SIN4. Gene243, 195–205 (2000). ArticleCASPubMed Google Scholar
Gwack, Y. et al. 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). ArticleCASPubMedPubMed Central Google Scholar
Burakov, D., Wong, C. W., Rachez, C., Cheskis, B. J. & Freedman, L. P. Functional interactions between the estrogen receptor and DRIP205, a subunit of the heteromeric DRIP coactivator complex. J. Biol. Chem.275, 20928–20934 (2000). ArticleCASPubMed Google Scholar
Fondell, J. D., Ge, H. & Roeder, R. G. Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc. Natl Acad. Sci. USA93, 8329–8333 (1996). ArticleCASPubMedPubMed Central Google Scholar
Hittelman, A. B., Burakov, D., Iniguez-Lluhi, J. A., Freedman, L. P. & Garabedian, M. J. Differential regulation of glucocorticoid receptor transcriptional activation via AF-1 associated proteins. EMBO J.18, 5380–5388 (1999). ArticleCASPubMedPubMed Central Google Scholar
Malik, S., Wallberg, A. E., Kang, Y. K. & Roeder, R. G. 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). ArticleCASPubMedPubMed Central Google Scholar
Frade, R., Balbo, M. & Barel, M. RB18A, whose gene is localized on chromosome 17q12-q21.1, regulates in vivo p53 transactivating activity. Cancer Res.60, 6585–6589 (2000). CASPubMed Google Scholar
Lau, J. F., Nusinzon, I., Burakov, D., Freedman, L. P. & Horvath, C. M. Role of metazoan Mediator proteins in interferon-responsive transcription. Mol. Cell. Biol.23, 620–628 (2003). ArticleCASPubMedPubMed Central Google Scholar
Asada, S. et al. External control of Her2 expression and cancer cell growth by targeting a Ras-linked coactivator. Proc. Natl Acad. Sci. USA99, 12747–12752 (2002). ArticleCASPubMedPubMed Central Google Scholar
Mittler, G. et al. A novel docking site on Mediator is critical for activation by VP16 in mammalian cells. EMBO J.22, 6494–6504 (2003). ArticleCASPubMedPubMed Central Google Scholar
Yang, F., DeBeaumont R., Zhou S. & Näär A. M. The activator-recruited cofactor/Mediator coactivator subunit ARC92 is a functionally important target of the VP16 transcriptional activator. Proc. Natl Acad. Sci. USA101, 2339–2344 (2004). ArticleCASPubMedPubMed Central Google Scholar
Park, J. M., Werner, J., Kim, J. M., Lis, J. T. & Kim, Y. J. Mediator, not holoenzyme, is directly recruited to the heat shock promoter by HSF upon heat shock. Mol. Cell8, 9–19 (2001). ArticleCASPubMed Google Scholar
Park, J. M. et al. Signal-induced transcriptional activation by Dif requires the dTRAP80 Mediator module. Mol. Cell. Biol.23, 1358–1367 (2003). ArticleCASPubMedPubMed Central Google Scholar
Eberhardy, S. R. & Farnham, P. J. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J. Biol. Chem.277, 40156–40162 (2002). ArticleCASPubMed Google Scholar
Sato, S. et al. Identification of mammalian mediator subunits with similarities to yeast mediator subunits Srb5, Srb6, Med11, and Rox3. J. Biol. Chem.278, 15123–15127 (2003). ArticleCASPubMed Google Scholar