Pinto, I., Wu, W.-H., Na, J. G„ and Hampsey, M. (1994). Characterization of sua7 mutations defines a domain of TFIIB involved in transcription start site selection in yeast. J. Biol. Chem. 269, 30569-30573.

Poon, D., and Weil, P. A. (1993). Immunopurification of yeast TATA-binding protein and associated factors. Presence of transcription factor IIIB transcriptional activity. J. Biol. Chem. 268, 15325-15328.

Prelich, G. (2002). RNA polymerase II carboxy-terminal domain kinases: emerging clues to their function. Eukaryot. Cell 1, 153-162.

Pugh, B. F., and Tjian, R. (1990). Mechanism of transcriptional activation by Spl: evidence for coactivators. Cell 61, 1187-1197. Pugh, B. F., and Tjian, R. (1991). Transcription from a TATA-less promoter requires a multisubunit TFIID complex. Genes Dev. 5, 1935-1945.

Pugh, B. F. (2000). Control of gene expression through regulation of the TATA-binding protein. Gene 255, 1-14. Ranish, J. A., Lane, W. S., and Hahn, S. (1992). Isolation of two genes that encode subunits of the yeast transcription factor IIA. Science 255, 1127-1229.

Ranish, J. A., Yudkovsky, N., and Hahn, S. (1999). Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes Dev. 13, 49-63. Ranish, J. A., Hahn, S., Lu, Y., Yi, E. C., Li, X.-J., Eng, J., and Aebersold, R. (2004). Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat. Genet. 56,707-713.

Reid, J., Murray, I., Watt, K., Betney, R., and McEwan, I. J. (2002). The androgen receptor interacts with multiple regions of the large subunit of general transcription factor TFIIF. J. Biol. Chem. 277, 41247-41253.

Reinberg, D., and Roeder, R. G. (1987). Factors involved in specific transcription by mammalian RNA polymerase II. Purification and functional analysis of initiation factors IIB and HE. J. Biol. Chem. 262, 3310-3321.

Reinberg, D., Horikoshi, M., and Roeder, R. G. (1987). Factors involved in specific transcription in mammalian RNA polymerase II. Functional analysis of initiation factors IIA and IID and identification of a new factor operating at sequences downstream of the initiation site. J. Biol. Chem. 262, 3322-3330. Robert, F., Douziech, M., Forget, D., Egly, J.-M., Greenblatt, J., Burton, Z. F., and Coulombe, B. (1998). Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. Mol. Cell. 2, 341-351.

Roberts, S. G. E., Ha, I., Maldonado, E., Reinberg, D., and Green, M. R. (1993). Interaction between an acidic activator and transcription factor TFIIB is required for transcriptional activation. Nature 363, 741-744.

Robinson, M. M., Yatherajam, G., Ranallo, R. T., Brie, A., Paule, M. R., and Stargell, L. A. (2005). Mapping and functional characterization of the TAF11 interaction with TFIIA. Mol. Cell. Biol. 25, 945-957.

Rochette-Egly, C., Adam, S., Rossignol, M., Egly, J.-M., and Chambon, P. (1997). Stimulation of RARa activation function AF-1 through binding to the general transcription factor TFIIH and phosphorylation by CDK7. Cell 90, 97-107. Rodriguez, C. R., Cho, E.-J., Keogh, M.-C., Moore, C. L., Greenleaf, A. L., and Buratowski, S. (2000). Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. Mol. Cell. Biol. 20, 104-112.

Roeder, R. G., and Rutter, W. J. (1969). Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms. Nature 224, 234-237.

Roeder, R. G., and Rutter, W. J. (1970). Specific nucleolar and nucleoplasmic RNA polymerases. Proc. Natl. Acad. Sci. USA 65, 675-682.

Rossignol, M., Kolb-Cheynel, I., and Egly, J.-M. (1997). Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH. EMBO J. 16, 1628-1637. Sanders, S. L„ Garbett, K. A., and Weil, P. A. (2002). Molecular characterization of Saccharomyces cerevisiae TFIID. Mol. Cell. Biol. 22, 6000-6013.

Sauer, F., Fondell, J. D., Ohkuma, Y., Roeder, R. G., and Jackie, H. (1995). Control of transcription by Kriippel through interactions with TFIIB and TFIIE(3. Nature 375, 162-164. Sawadogo, M., and Roeder, R. G. (1985a). Factors involved in specific transcription by human RNA polymerase II: analysis by a rapid and quantitative in vitro assay. Proc. Natl. Acad. Sci. USA 82, 4394-4398.

Sawadogo, M., and Roeder, R. G. (1985b). Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell 43, 165-175. Schaeffer, L., Roy, R., Humbert, S., Moncollin, V., Vermeulen, W„ Hoeijmakers, J. H. J., Chambon, P., and Egly, J.-M. (1993). DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor. Science 260, 58-63.

Schaeffer, L., Moncollin, V., Roy, R., Staub, A., Mezzina, M., Sarasin, A., Weeda, G., Hoeijmakers, J. H. J., and Egly, J.-M. (1994). The ERCC2/DNA repair protein is associated with the class II BTF2/TFIIH transcription factor. EMBO J. 13, 2388-2392.

Schroeder, S. C., Schwer, B., Shuman, S„ and Bentley, D. (2000). Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14, 435-2440.

Selleck, W., Howley, R., Fang, Q., Podolny, V., Fried, M. G.,

Buratowski, S., and Tan, S. (2001). A histone fold TAF octamer within the yeast TFIID transcriptional coactivator. Nat. Struct. Biol. 8, 695-700.

Serizawa, H., Conaway, J. W., and Conaway, R. C. (1994). An oligomeric form of the large subunit of transcription factor (TF) IIE activates phosphorylation of the RNA polymerase II carboxyl-terminal domain by TFIIH. J. Biol. Chem. 269, 20750-20756.

Shao, H., Revach, M., Moshonov, S., Tzuman, Y., Gazit, K., Albeck, S., Unger, T., and Dikstein, R. (2005). Core promoter binding by histone-like TAF complexes. Mol. Cell. Biol. 25, 206-219.

Shilatifard, A., Conaway, R. C., and Conaway, J. W. (2003). The RNA polymerase II elongation complex. Annu. Rev. Biochem. 12, 693-715.

Shim, E. Y., Walker, A. K„ Shi, Y„ and Blackwell, T. K. (2002). CDK-9/cyclin T (P-TEFb) is required in two postinitiation pathways for transcription in the C. elegans embryo. Genes Dev. 16, 2135-2146.

Sklar, V. E. F., Schwartz, L. B., and Roeder, R. G. (1975). Distinct molecular structures of nuclear class I, II, and III DNA-dependent RNA polymerases. Proc. Natl. Acad. Sci. USA 72, 348-352.

Smale, S. T. (1997). Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim. Biophys. Acta 1351, 73-88.

Solow, S., Salunek, M., Ryan, R., and Lieberman, P. M. (2001). TAF,,250 phosphorylates human transcription factor IIA on serine residues important for TBP binding and transcription activity. J. Biol. Chem. 276, 15886-15892. Sopta, M., Carthew, R. W., and Greenblatt, J. (1985). Isolation of three proteins that bind to mammalian RNA polymerase II. J. Biol. Chem. 260, 10353-10360.

Sopta, M., Burton, Z. F., and Greenblatt, J. (1989). Structure and associated DNA-helicase activity of a general transcription initiation factor that binds to RNA polymerase II. Nature 341, 410-414.

Stargell, L. A., Moqtaderi, Z., Dorris, D. R, Ogg, R. C., and Struhl, K. (2000). TFIIA has activator-dependent and core promoter functions in vivo. J. Biol. Chem. 275, 12374-12380. Sumimoto, H., Ohkuma, Y., Sinn, E., Kato, H., Shimasaki, S., Horikoshi, M., and Roeder, R. G. (1991). Conserved sequence motifs in the small subunit of human general transcription factor TFIIE. Nature 354, 401-404.

Sun, X., Ma, D., Sheldon, M., Yeung, K., and Reinberg, D. (1994). Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription. Genes Dev. 8, 2336-2348.

Svejstrap, J. Q„ Vichi, P., and Egly, J.-M. (1996). The multiple roles of transcription/repair factor TFIIH. Trends Biochem. Sci. 21, 346-350.

Tan, S., Garrett, K. P., Conaway, R. C., and Conaway, J. W.

(1994). Cryptic DNA-binding domain in the C terminus of RNA polymerase II general transcription factor RAP30. Proc. Natl. Acad. Sci. USA 91, 9808-9812.

Tan, S., Hunziker, Y., Sargent, D. F., and Richmond, T. J. (1996). Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature 381, 127-134.

Tan, Q., Linask, K. L„ Ebright, R. H„ and Woychik, N. A. (2000). Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes Dev. 14, 339-348. Tanese, N., Pugh, B. F., and Tjian, R. (1991). Coactivators for a proline-rich activator purified from the multisubunit human TFIID complex. Genes Dev. 5, 2212-2224. Tantin, D., and Carey, M. (1994). A heteroduplex template circumvents the energetic requirement for ATP during activated transcription by RNA polymerase II. J. Biol. Chem. 269, 17397-17400.

Thomas, M. C., and Chiang, C.-M. (2005). E6 oncoprotein represses p53-dependent gene activation via inhibition of protein acetylation independently of inducing p53 degradation. Mol. Cell 17, 251-264.

Tora, L. (2002). A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes Dev. 16, 673-675. Tsai, F. T. F„ and Sigler, P. B. (2000). Structural basis of preinitiation comples assembly on human pol II promoters. EMBO J. 19, 25-36.

Ulmasov, T„ Larkin, R. M„ and Guilfoyle, T. J. (1996). Association between 36- and 13.6-kDa a-like subunits of Arabidopsis thaliana RNA polymerase II. J. Biol. Chem. 271, 5085-5094.

Upadhyaya, A. B„ Lee, S. H., and DeJong, J. (1999). Identification of a general transcription factor TFIIAa/fS homolog selectively expressed in testis. J. Biol. Chem. 274, 18040-18048. Upadhyaya, A. B., Khan, M., Mou, T.-C., Junker, M., Gray, D. M., and DeJong, J. (2002). The germ cell-specific transcription factor ALF. Structural properties and stabilization of the TATA-binding protein (TBP)-DNA complex. J. Biol. Chem. 277, 34208-34216.

Van Dyke, M. W„ Roeder, R. G., and Sawadogo, M. (1988). Physical analysis of transcriptional preinitiation complex assembly on a class II gene promoter. Science 241, 1335-1338. van Vuuren, A. J., Vermeulen, W., Ma, L., Weeda, G., Appeldoorn, E., Jaspers, N. G., van der Eb, A. J., Bootsma, D., Hoeijmakers, J. H. J., and Humbert, S. (1994). Correction of xeroderma pigmentosum repair defect by basal transcription factor BTF2 (TFIIH). EMBO J. 13, 1645-1653. Verrijzer, C. P., Chen, J.-L., Yokomori, K„ and Tjian, R. (1995). Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell 81, 1115-1125. Verrijzer, C. P., and Tjian, R. (1996). TAFs mediate transcriptional activation and promoter selectivity. Trends

Walker, S. S., Reese, J. C., Apone, L. M., and Green, M. R. (1996). Transcription activation in cells lacking TAFnS. Nature 383, 185-188.

Walker, S. S., Shen, W.-C., Reese, J. C., Apone, L. M., and Green, M. R. (1997). Yeast TAF„145 required for transcription of Gl/S cyclin genes and regulated by the cellular growth state. Cell 90, 607-614.

Wampler, S. L., and Kadonaga, J. T. (1992). Functional analysis of Drosophila transcription factor IIB. Genes Dev. 6, 1542-1552. Wang, W., Gralla, J. D., and Carey, M. (1992). The acidic activator GAL4-AH can stimulate polymerase II transcription by promoting assembly of a closed complex requiring TFIID and TFIIA. Genes Dev. 6, 1716-1727.

Wang, Z., Svejstrup, J. Q., Feaver, W. J., Wu, X., Kornberg, R. D., and Friedberg, E. C. (1994). Transcription factor b (TFIIH) is required during nucleotide-excision repair in yeast. Nature 368, 74-76.

Wang, Z., Buratowski, S., Svejstrup, J. Q., Feaver, W. J., Wu, X., Kornberg, R. D., Donahue, T. F., and Friedberg, E. C. (1995). The yeast TFB1 and SSL1 genes, which encode subunits of transcription factor IIH, are required for nucleotide excision repair and RNA polymerase II transcription. Mol. Cell. Biol. 15, 2288-2293.

Warfield, L., Ranish, J. A., and Hahn, S. (2004). Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA. Genes Dev. 18, 1022-1034.

Watanabe, T., Hayashi, K., Tanaka, A., Furumoto, T., Hanaoka, F., and Ohkuma, Y. (2003). The carboxy terminus of the small subunit of TFIIE regulates the transition from transcription initiation to elongation by RNA polymerase II. Mol. Cell. Biol. 23, 2914-2926.

Wei, W., Dotjsuren, D., Lin, Y., Qin, W., Nomura, T., Hayashi, N., and Murakami, S. (2001). Direct interaction between subunit RAP30 of the transcription factor IIF (TFIIF) and RNA polymerase subunit 5, which contributes to the association between TFIIF and RNA polymerase II. J. Biol. Chem. 276, 12266-12273.

Weil, P. A., Luse, D. S„ Segall, J., and Roeder, R. G. (1979). Selective and accurate initiation of transcription at the Ad2 major late promotor in a soluble system dependent on purified RNA polymerase II and DNA. Cell 18, 469-484. Weinmann, R., Raskas, H. J., and Roeder, R. G. (1974). Role of DNA-dependent RNA polymerases II and III in transcription of the adenovirus genome late in productive infection. Proc. Natl. Acad. Sci USA 71, 3426-3439.

Weinmann, R., and Roeder, R. G. (1974). Role of DNA-dependent RNA polymerase III in the transcription of the tRNA and 5S RNA genes. Proc. Natl. Acad. Sci. USA 71, 1790-1794. Weiss, S., and Gladstone, L. (1959). A mammalian system for the incorporation of cytidine triphosphate into ribonucleic acid. J.

Wilson, C. J., Chao, D. M., Imbalzano, A. N., Schnitzler, G. R., Kingston, R. E., and Young, R. A. (1996). RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell 84, 235-244.

Wolner, B. S., and Gralla, J. D. (2001). TATA-flanking sequences influence the rate and stability of TATA-binding protein and TFIIB binding. J. Biol. Chem. 276, 6260-6266. Workman, J. L., and Roeder, R. G. (1987). Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell 51, 613-622.

Woychik, N. A., Liao, S. M., Kolodziej, P. A., and Young, R. A. (1990). Subunits shared by eukaryotic nuclear RNA polymerases. Genes Dev. 4, 313-323.

Woychik, N. A., McKune, K., Lane, W. S., and Young, R. A. (1993). Yeast RNA polymerase II subunit RPB11 is related to a subunit shared by RNA polymerase I and III. Gene Expr. 3, 77-82.

Woychik, N. A., and Hampsey, M. (2002). The RNA polymerase II machinery: structure illuminates function. Cell 108, 453-463. Wu, S.-Y., and Chiang, C.-M. (1998). Properties of PC4 and an RNA polymerase II complex in directing activated and basal transcription in vitro. J. Biol. Chem. 273, 12492-12498. Wu, S.-Y., Kershnar, E., and Chiang, C.-M. (1998). TAFlrindependent activation mediated by human TBP in the presence of the positive cofactor PC4. EMBO J. 17, 4478-4490. Wu, S.-Y., Thomas, M. C., Hou, S. Y., Likhite, V., and Chiang, C.-M. (1999). Isolation of mouse TFIID and functional characterization of TBP and TFIID in mediating estrogen receptor and chromatin transcription. J. Biol. Chem. 274, 23480-23490.

Wu, S.-Y., and Chiang, C.-M. (2001a). TATA-binding protein-associated factors enhance the recruitment of RNA polymerase II by transcriptional activators. J. Biol. Chem. 276, 34235-34243. Wu, S.-Y., and Chiang, C.-M. (2001b). Expression and purification of epitope-tagged multisubunit protein complexes from mammalian cells. Current Protocols in Molecular Biology, Unit 16.22.1-16.22.17.

Wu, S.-Y., Zhou, T., and Chiang, C.-M. (2003). Human mediator enhances activator-facilitated recruitment of RNA polymerase II and promoter recognition by TATA-binding protein (TBP) independently of TBP-associated factors. Mol. Cell. Biol. 23, 6229-6242.

Wu, W.-H., and Hampsey, M. (1999). An activation-specific role for transcription factor TFIIB in vivo. Proc. Natl. Acad. Sci. USA 96, 2764-2769.

Xie, X., Kokubo, T., Cohen, S. L., Mirza, U. A., Hoffmann, A., Chait, B. T„ Roeder, R. G., Nakatani, Y„ and Burley, S. K. (1996). Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature 380, 316-322. Xing, I., Sheppard, H. M., Corneillie, S. I., and Liu, X. (2001).

p53 stimulates TFIID-TFIIA-promoter complex assembly and p53-T antigen complex inhibits TATA binding protein-TATA interaction. Mol. Cell. Biol. 21, 3652-3661. Yamashita, S., Wada, K., Horikoshi, M., Gong, D.-W., Kokubo, T., Hisatake, K., Yokotani, N., Malik, S., Roeder, R. G., and Nakatani, Y. (1992). Isolation and characterization of a cDNA encoding Drosophila transcription factor TFIIB. Proc. Natl. Acad. Sci. USA 89, 2839-2843.

Yamashita, S., Hisatake, K., Kokubo, T., Doi, K., Roeder, R. G., Horikoshi, M., and Nakatani, Y. (1993). Transcription factor TFIIB sites important for interaction with promoter-bound TFIID. Science 261, 463-466.

Yan, Q., Moreland, R. J., Conaway, J. W., and Conaway, R. C. (1999). Dual roles for transcription factor IIF in promoter escape by RNA polymerase II. J. Biol. Chem. 274, 25668-35675. Yankulov, K. Y., and Bentley, D. L. (1997). Regulation of CDK7 substrate specificity by MAT1 and TFIIH. EMBO J. 16, 1638-1646.

Yeo, M„ Lin, P. S„ Dahmus, M. E„ and Gill, G. N. (2003). A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5. J. Biol. Chem. 278, 26078-26085.

Yokomori, K., Admon, A., Goodrich, J. A., Chen, J.-L., and Tjian, R. (1993). Drosophila TFIIA-L is processed into two subunits that are associated with the TBP/TAF complex. Genes Dev. 7, 2235-2245.

Yong, C., Mitsuyasu, H., Chun, Z., Oshiro, S., Hamasaki, N., and Kitajima, S. (1998). Structure of the human transcription factor TFIIF revealed by limited proteolysis with trypsin. FEBS Lett. 435, 191-194.

Young, R. A. (1991). RNA polymerase II. Annu. Rev. Biochem 60, 689-715.

Yuiyev, A., Patturajan, M., Litingtung, Y., Joshi, R. V., Gentile, C., Gebara, M., and Corden, J. L. (1996). The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl. Acad. Sci. USA 93, 6975-6980.

Zhou, M., Halanski, M. A., Radonovich, M. F., Kashanchi, F., Peng, J., Price, D. H„ and Brady, J. N. (2000). Tat modifies the activity of CDK9 to phosphorylate serine 5 of the RNA polymerase II carboxyl-terminal domain during human immunodeficiency virus type 1 transcription. Mol. Cell. Biol. 20, 5077-5086.

Zhou, Q„ Lieberman, P. M„ Boyer, T. G„ and Berk, A. J. (1992). Holo-TFIID supports transcriptional stimulation by diverse activators and from a TATA-less promoter. Genes Dev. 6, 1964-1974.

Zhu, A., and Kuziora, M. A. (1996). Homeodomain interaction with the P subunit of the general transcription factor TFIIE. J. Biol. Chem. 271, 20993-20996.

Ziegler, L. M., Khaperskyy, D. A., Ammerman, M. L., and Ponticelli, A. S. (2003). Yeast RNA polymerase II lacking the Rpb9 subunit is impaired for interaction with transcription factor IIF. J. Biol. Chem. 278,48950-48956.

Zurita, M., and Merino, C. (2003). The transcriptional complexity of the TFIIH complex. Trends Genet. 19, 578-584.

0 0

Post a comment