A Region within the RAP74 Subunit of Human Transcription Factor IIF Is Critical for Initiation but Dispensable for Complex Assembly

REFERENCES

• Amouyal, M., and J. Buc 1987. Topological unwinding of strong and weak promoters by RNA polymerase. A comparison between the lac wild-type and the UV5 sites of Escherichia coli. J. Mol. Biol. 195:795–808.
   PubMedGoogle Scholar
• Aso, T., H. A. Vasavada, T. Kawaguchi, F. J. Germino, S. Ganguly, S. Kitajima, S. M. Weissman, and J. Yasukochi 1992. Characterization of cDNA for the large subunit of the transcription initiation factor TFIIF. Nature 355:461–464.
   PubMedGoogle Scholar
• Conaway, J. W., and J. Conaway 1989. A multisubunit transcription factor essential for accurate initiation by RNA polymerase II. J. Biol. Chem. 264:2357–2362.
   PubMedGoogle Scholar
• Conaway, R. C., K. P. Garrett, J. P. Hanley, and J. Conaway 1991. Mechanism of promoter selection by RNA polymerase II: mammalian transcription factors alpha and beta gamma promote entry of polymerase into the preinitiation complex. Proc. Natl. Acad. Sci. USA 88:6205–6209.
   PubMedGoogle Scholar
• Coulombe, B., and J. Burton 1998. DNA bending and wrapping around RNA polymerase: a revolutionary model to describe transcriptional mechanisms. Microbiol. Mol. Biol. Rev. 63:457–478.
   Google Scholar
• deHaseth, P. L., M. L. Zupancic, M. T. Record Jr.. 1998. RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J. Bacteriol. 180:3019–3025.
   PubMed Web of Science ®Google Scholar
• Finkelstein, A., C. F. Kostrub, J. Li, D. P. Chavez, B. Q. Wang, S. M. Fang, J. Greenblatt, and J. Burton 1992. A cDNA encoding RAP74, a general initiation factor for transcription by RNA polymerase II. Nature 355:464–467.
   PubMedGoogle Scholar
• Flores, O., I. Ha, and J. Reinberg 1990. Factors involved in specific transcription by mammalian RNA polymerase II. Purification and subunit composition of transcription factor IIF. J. Biol. Chem. 265:5629–5634.
   PubMed Web of Science ®Google Scholar
• Flores, O., H. Lu, M. Killeen, J. Greenblatt, Z. F. Burton, and J. Reinberg 1991. The small subunit of transcription factor IIF recruits RNA polymerase II into the preinitiation complex. Proc. Natl. Acad. Sci. USA 88:9999–10003.
   PubMedGoogle Scholar
• Forget, D., F. Robert, G. Grondin, Z. F. Burton, J. Greenblatt, and J. Coulombe 1997. RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box. Proc. Natl. Acad. Sci. USA 94:7150–7155.
   PubMedGoogle Scholar
• Gamper, H. B., and J. Hearst 1982. A topological model for transcription based on unwinding angle analysis of E. coli RNA polymerase binary, initiation and ternary complexes. Cell 29:81–90.
   PubMed Web of Science ®Google Scholar
• Gong, D. W., S. Hasegawa, K. Wada, R. G. Roeder, Y. Nakatani, and J. Horikoshi 1992. Elucidation of three putative structural subdomains by comparison of primary structure of Xenopus and human RAP74. Nucleic Acids Res. 20:6736.
   PubMedGoogle Scholar
• Goodrich, J. A., and J. Tjian 1994. Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell 77:145–156.
   PubMedGoogle Scholar
• Ha, I., W. S. Lane, and J. Reinberg 1991. Cloning of a human gene encoding the general transcription initiation factor IIB. Nature 352:689–695.
   PubMedGoogle Scholar
• Hampsey, M. 1998. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62:465–503.
   PubMed Web of Science ®Google Scholar
• Hawley, D. K., and J. Roeder 1985. Separation and partial characterization of three functional steps in transcription initiation by human RNA polymerase II. J. Biol. Chem. 260:8163–8172.
   PubMedGoogle Scholar
• Henry, N. L., A. M. Campbell, W. J. Feaver, D. Poon, P. A. Weil, and J. Kornberg 1994. TFIIF-TAF-RNA polymerase II connection. Genes Dev. 8:2868–2878.
   PubMed Web of Science ®Google Scholar
• Hodo, H. G., and J. Blatti 1977. Purification using polyethylenimine precipitation and low molecular weight subunit analyses of calf thymus and wheat germ DNA-dependent RNA polymerase II. Biochemistry 16:2334–2343.
   PubMed Web of Science ®Google Scholar
• Holstege, F. C., D. Tantin, M. Carey, P. C. van der Vliet, and J. Timmers 1995. The requirement for the basal transcription factor IIE is determined by the helical stability of promoter DNA. EMBO J. 14:810–819.
   PubMed Web of Science ®Google Scholar
• Holstege, F. C., P. C. van der Vliet, and J. Timmers 1996. Opening of an RNA polymerase II promoter occurs in two distinct steps and requires the basal transcription factors IIE and IIH. EMBO J. 15:1666–1677.
   PubMedGoogle Scholar
• Jiang, Y., S. T. Smale, and J. Gralla 1993. A common ATP requirement for open complex formation and transcription at promoters containing initiator or TATA elements. J. Biol. Chem. 268:6535–6540.
   PubMedGoogle Scholar
• Juo, Z. S., T. K. Chiu, P. M. Leiberman, I. Baikalov, A. J. Berk, and J. Dickerson 1996. How proteins recognize the TATA box. J. Mol. Biol. 261:239–254.
   PubMed Web of Science ®Google Scholar
• Kephart, D. D., M. P. Price, Z. F. Burton, A. Finkelstein, J. Greenblatt, and J. Price 1993. Cloning of a Drosophila cDNA with sequence similarity to human transcription factor RAP74. Nucleic Acids Res. 21:1319.
   PubMedGoogle Scholar
• Kephart, D. D., B. Q. Wang, Z. F. Burton, and J. Price 1994. Functional analysis of Drosophila factor 5 (TFIIF), a general transcription factor. J. Biol. Chem. 269:13536–13543.
   PubMedGoogle Scholar
• Killeen, M., B. Coulombe, and J. Greenblatt 1992. Recombinant TBP, transcription factor IIB, and RAP30 are sufficient for promoter recognition by mammalian RNA polymerase II. J. Biol. Chem. 267:9463–9466.
   PubMedGoogle Scholar
• Kim, T. K., T. Lagrange, Y. H. Wang, J. D. Griffith, D. Reinberg, and J. Ebright 1997. Trajectory of DNA in the RNA polymerase II transcription preinitiation complex. Proc. Natl. Acad. Sci. USA 94:12268–12273.
   PubMedGoogle Scholar
• Kitajima, S., Y. Tanaka, T. Kawaguchi, T. Nagaoka, S. M. Weissman, and J. Yasukochi 1990. A heteromeric transcription factor required for mammalian RNA polymerase II. Nucleic Acids Res. 18:4843–4849.
   PubMedGoogle Scholar
• Lei, L., and Z. F. Burton. Submitted for publication.
   Google Scholar
• Lei, L., D. Ren, A. Finkelstein, and J. Burton 1998. Functions of the N- and C-terminal domains of human RAP74 in transcriptional initiation, elongation, and recycling of RNA polymerase II. Mol. Cell. Biol. 18:2130–2142.
   PubMedGoogle Scholar
• Marshall, N. F., and J. Price 1992. Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol. Cell. Biol. 12:2078–2090.
   PubMed Web of Science ®Google Scholar
• Maxon, M. E., J. A. Goodrich, and J. Tjian 1994. Transcription factor IIE binds preferentially to RNA polymerase IIa and recruits TFIIH: a model for promoter clearance. Genes Dev. 8:515–524.
   PubMed Web of Science ®Google Scholar
• Orphanides, G., T. Lagrange, and J. Reinberg 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657–2683.
   PubMed Web of Science ®Google Scholar
• Pan, G., and J. Greenblatt 1994. Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site. J. Biol. Chem. 269:30101–30104.
   PubMed Web of Science ®Google Scholar
• Parvin, J. D., and J. Sharp 1993. DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell 73:533–540.
   PubMed Web of Science ®Google Scholar
• Parvin, J. D., B. M. Shykind, R. E. Meyers, J. Kim, and J. Sharp 1994. Multiple sets of basal factors initiate transcription by RNA polymerase II. J. Biol. Chem. 269:18414–18421.
   PubMedGoogle Scholar
• Peterson, M. G., J. Inostroza, M. E. Maxon, O. Flores, A. Admon, D. Reinberg, and J. Tjian 1991. Structure and functional properties of human general transcription factor IIE. Nature 354:369–373.
   PubMedGoogle Scholar
• Polyakov, A., E. Severinova, and J. Darst 1995. Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83:365–373.
   PubMedGoogle Scholar
• Robert, F., M. Douziech, D. Forget, J.-M. Egly, J. Greenblatt, Z. F. Burton, and J. Coulombe 1998. Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. Mol. Cell 2:341–351.
   PubMedGoogle Scholar
• Roeder, R. G. 1996. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 21:327–335.
   PubMed Web of Science ®Google Scholar
• Rost, B., C. Sander, and J. Schneider 1994. PHD—an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10:53–60.
   PubMedGoogle Scholar
• Sawadogo, M., and J. Roeder 1985. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell 43:165–175.
   PubMed Web of Science ®Google Scholar
• Shapiro, D. J., P. A. Sharp, W. W. Wahli, and J. Keller 1988. A high-efficiency HeLa cell nuclear transcription extract. DNA 7:47–55.
   PubMedGoogle Scholar
• Sun, X., D. Ma, M. Sheldon, K. Yeung, and J. Reinberg 1994. Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription. Genes Dev. 8:2336–2348.
   PubMedGoogle Scholar
• Sun, Z. W., and J. Hampsey 1995. Identification of the gene (SSU71/TFG1) encoding the largest subunit of transcription factor TFIIF as a suppressor of a TFIIB mutation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 92:3127–3131.
   PubMed Web of Science ®Google Scholar
• Tan, S., T. Aso, R. C. Conaway, and J. Conaway 1994. Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II. J. Biol. Chem. 269:25684–25691.
   PubMed Web of Science ®Google Scholar
• Timmers, H. T. 1994. Transcription initiation by RNA polymerase II does not require hydrolysis of the beta-gamma phosphoanhydride bond of ATP. EMBO J. 13:391–399.
   PubMedGoogle Scholar
• Tyree, C. M., C. P. George, L. M. Lira-DeVito, S. L. Wampler, M. E. Dahmus, L. Zawel, and J. Kadonaga 1993. Identification of a minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II. Genes Dev. 7:1254–1265.
   PubMed Web of Science ®Google Scholar
• Wada, T., T. Takagi, Y. Yamaguchi, A. Ferdous, T. Imai, S. Hirose, S. Sugimoto, K. Yano, G. Hartzog, F. Winston, S. Buratowski, and J. Handa 1998. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12:343–356.
   PubMed Web of Science ®Google Scholar
• Wang, B. Q., and J. Burton 1995. Functional domains of human RAP74 including a masked polymerase binding domain. J. Biol. Chem. 270:27035–27044.
   PubMedGoogle Scholar
• Wang, B. Q., C. F. Kostrub, A. Finkelstein, and J. Burton 1993. Production of human RAP30 and RAP74 in bacterial cells. Protein Expr. Purif. 4:207–214.
   PubMedGoogle Scholar
• Wang, B. Q., L. Lei, and J. Burton 1994. Importance of codon preference for production of human RAP74 and reconstitution of the RAP30/74 complex. Protein Expr. Purif. 5:476–485.
   PubMedGoogle Scholar
• Wang, W., M. Carey, and J. Gralla 1992. Polymerase II promoter activation: closed complex formation and ATP-driven start site opening. Science 255:450–453.
   PubMed Web of Science ®Google Scholar
• Xie, Z., and J. Price 1997. Drosophila Factor 2, an RNA polymerase II transcript release factor, has DNA-dependent ATPase activity. J. Biol. Chem. 272:31902–31907.
   PubMedGoogle Scholar
• Yamaguchi, Y., T. Takagi, T. Wada, K. Yano, A. Furuya, S. Sugimoto, J. Hasegawa, and J. Handa 1999. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97:41–51.
   PubMed Web of Science ®Google Scholar
• Yokomori, K., C. P. Verrijzer, and J. Tjian 1998. An interplay between TATA box-binding protein and transcription factors IIE and IIA modulates DNA binding and transcription. Proc. Natl. Acad. Sci. USA 95:6722–6727.
   PubMedGoogle Scholar