30
Views
52
CrossRef citations to date
0
Altmetric
Article

Spn1 Regulates the Recruitment of Spt6 and the Swi/Snf Complex during Transcriptional Activation by RNA Polymerase II

, , , &
Pages 1393-1403 | Received 20 Sep 2007, Accepted 27 Nov 2007, Published online: 27 Mar 2023

REFERENCES

  • Adelman, K., M. T. Marr, J. Werner, A. Saunders, Z. Ni, E. D. Andrulis, and J. T. Lis. 2005. Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol. Cell 17:103–112.
  • Adkins, M. W., and J. K. Tyler. 2006. Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Mol. Cell 21:405–416.
  • Andrulis, E. D., E. Guzman, P. Doring, J. Werner, and J. T. Lis. 2000. High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. Genes Dev. 14:2635–2649.
  • Awrey, D. E., N. Shimasaki, C. Koth, R. Weilbaecher, V. Olmsted, S. Kazanis, X. Shan, J. Arellano, C. H. Arrowsmith, C. M. Kane, and A. M. Edwards. 1998. Yeast transcript elongation factor (TFIIS), structure and function. II: RNA polymerase binding, transcript cleavage, and read-through. J. Biol. Chem. 273:22595–22605.
  • Awrey, D. E., R. G. Weilbaecher, S. A. Hemming, S. M. Orlicky, C. M. Kane, and A. M. Edwards. 1997. Transcription elongation through DNA arrest sites. A multistep process involving both RNA polymerase II subunit RPB9 and TFIIS. J. Biol. Chem. 272:14747–14754.
  • Bernstein, B. E., C. L. Liu, E. L. Humphrey, E. O. Perlstein, and S. L. Schreiber. 2004. Global nucleosome occupancy in yeast. Genome Biol. 5:R62.
  • Boeke, J. D., J. Trueheart, G. Natsoulis, and G. R. Fink. 1987. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 154:164–175.
  • Bortvin, A., and F. Winston. 1996. Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272:1473–1476.
  • Bregman, D. B., L. Du, S. van der Zee, and S. L. Warren. 1995. Transcription-dependent redistribution of the large subunit of RNA polymerase II to discrete nuclear domains. J. Cell Biol. 129:287–298.
  • Burckin, T., R. Nagel, Y. Mandel-Gutfreund, L. Shiue, T. A. Clark, J. L. Chong, T. H. Chang, S. Squazzo, G. Hartzog, and M. Ares, Jr. 2005. Exploring functional relationships between components of the gene expression machinery. Nat. Struct. Mol. Biol. 12:175–182.
  • Bushnell, D. A., K. D. Westover, R. E. Davis, and R. D. Kornberg. 2004. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 angstroms. Science 303:983–988.
  • Cairns, B. R., Y. J. Kim, M. H. Sayre, B. C. Laurent, and R. D. Kornberg. 1994. A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. Proc. Natl. Acad. Sci. USA 91:1950–1954.
  • Cheng, C., and P. A. Sharp. 2003. RNA polymerase II accumulation in the promoter-proximal region of the dihydrofolate reductase and gamma-actin genes. Mol. Cell. Biol. 23:1961–1967.
  • Costa, P. J., and K. M. Arndt. 2000. Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics 156:535–547.
  • Davie, J. K., and C. M. Kane. 2000. Genetic interactions between TFIIS and the Swi-Snf chromatin-remodeling complex. Mol. Cell. Biol. 16:5960–5973.
  • Endoh, M., W. Zhu, J. Hasegawa, H. Watanabe, D. K. Kim, M. Aida, N. Inukai, T. Narita, T. Yamada, A. Furuya, H. Sato, Y. Yamaguchi, S. S. Mandal, D. Reinberg, T. Wada, and H. Handa. 2004. Human Spt6 stimulates transcription elongation by RNA polymerase II in vitro. Mol. Cell. Biol. 24:3324–3336.
  • Exinger, F., and F. Lacroute. 1992. 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 22:9–11.
  • Feaver, W. J., O. Gileadi, Y. Li, and R. D. Kornberg. 1991. CTD kinase associated with yeast RNA polymerase II initiation factor b. Cell 67:1223–1230.
  • Fischbeck, J. A., S. M. Kraemer, and L. A. Stargell. 2002. SPN1, a conserved yeast gene identified by suppression of a post-recruitment defective yeast TATA-binding protein mutant. Genetics 162:1605–1616.
  • Formosa, T., P. Eriksson, J. Wittmeyer, J. Ginn, Y. Yu, and D. Stillman. 2001. Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. EMBO J. 20:3506–3517.
  • Gavin, A. C., M. Bosche, R. Krause, P. Grandli, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A. M. Michon, C. M. Cruciat, M. Remor, C. Hofert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–146.
  • Geng, F., Y. Cao, and B. C. Laurent. 2001. Essential roles of Snf5p in Snf-Swi chromatin remodeling in vivo. Mol. Cell. Biol. 21:4311–4320.
  • Govind, C. K., S. Yoon, H. Qiu, S. Govind, and A. G. Hinnebusch. 2005. Simultaneous recruitment of coactivators by Gcn4p stimulates multiple steps of transcription in vivo. Mol. Cell. Biol. 25:5626–5638.
  • Guarente, L., B. Lalonde, P. Gifford, and E. Alani. 1984. Distinctly regulated tandem upstream activation sites mediate catabolite repression of the CYC1 gene of S. cerevisiae. Cell 36:503–511.
  • Guarente, L., and T. Mason. 1983. Heme regulates transcription of the cyc1 gene of S. cerevisiae via an upstream activation site. Cell 32:1279–1286.
  • Guenther, M. G., S. S. Levine, L. A. Boyer, R. Jaenisch, and R. A. Young. 2007. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88.
  • Hampsey, M. 1997. A review of phenotypes in Saccharomyces cerevisiae. Yeast 13:1099–1133.
  • Happel, A. M., M. S. Swanson, and F. Winston. 1991. The SNF2, SNF5, and SNF6 genes are required for Ty transcription in Saccharomyces cerevisiae. Genetics 128:69–77.
  • Hartzog, G. A., T. Wada, H. Handa, and F. Winston. 1998. Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev. 12:357–369.
  • Hirsch, J. P., and S. A. Henry. 1986. Expression of the Saccharomyces cerevisiae inositol-1-phosphate synthase (INO1) gene is regulated by factors that affect phospholipid synthesis. Mol. Cell. Biol. 6:3320–3328.
  • Kaplan, C. D., L. Laprade, and F. Winston. 2003. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301:1096–1099.
  • Kettenberger, H., K. J. Armache, and P. Cramer. 2004. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16:955–965.
  • Kim, H. J., S. H. Jeong, J. H. Heo, S. J. Jeong, S. T. Kim, H. D. Youn, J. W. Han, H. W. Lee, and E. J. Cho. 2004. mRNA capping enzyme activity is coupled to an early transcription elongation. Mol. Cell. Biol. 24:6184–6193.
  • Kim, M., S. H. Ahn, N. J. Krogan, J. F. Greenblatt, and S. Buratowski. 2004. Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO J. 23:354–364.
  • Kim, T. H., L. O. Barrera, M. Zheng, C. Qu, M. A. Singer, T. A. Richmond, Y. Wu, R. D. Green, and B. Ren. 2005. A high-resolution map of active promoters in the human genome. Nature 436:876–880.
  • Kim, Y., and D. J. Clark. 2002. SWI/SNF-dependent long-range remodeling of yeast HIS3 chromatin. Proc. Natl. Acad. Sci. USA 99:15381–15386.
  • Komarnitsky, P., E. J. Cho, and S. Buratowski. 2000. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14:2452–2460.
  • Krogan, N. J. M., M. Kim, S. H. Ahn, G. Zhong, M. S. Kobor, G. Cagney, A. Emili, A. Shilatifard, S. Buratowski, and J. F. Greenblatt. 2002. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22:6979–6992.
  • Krumm, A., T. Meulia, M. Brunvand, and M. Groudine. 1992. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev. 6:2201–2213.
  • Kulish, D., and K. Struhl. 2001. TFIIS enhances transcriptional elongation through an artificial arrest site in vivo. Mol. Cell. Biol. 21:4162–4168.
  • Kuras, L., and K. Struhl. 1999. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399:609–613.
  • Laribee, R. N., N. J. Krogan, T. Xiao, Y. Shibata, T. R. Hughes, J. F. Greenblatt, and B. D. Strahl. 2005. BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Curr. Biol. 15:1487–1493.
  • Laurent, B. C., and M. Carlson. 1992. Yeast SNF2/SWI2, SNF5, and SNF6 proteins function coordinately with the gene-specific transcriptional activators GAL4 and bicoid. Genes Dev. 6:1707–1715.
  • Laurent, B. C., M. A. Treitel, and M. Carlson. 1991. Functional interdependence of the yeast SNF2, SNF5, and SNF6 proteins in transcriptional activation. Proc. Natl. Acad. Sci. USA 88:2687–2691.
  • Lee, C. K., Y. Shibata, B. Rao, B. D. Strahl, and J. D. Lieb. 2004. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36:900–905.
  • Lindstrom, D. L., S. L. Squazzo, N. Muster, T. A. Burckin, K. C. Wachter, C. A. Emigh, J. A. McCleery, J. R. R. Yates, and G. A. Hartzog. 2003. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23:1368–1378.
  • Liu, Z., Z. Zhou, G. Chen, and S. Bao. 2007. A putative transcriptional elongation factor hIws1 is essential for mammalian cell proliferation. Biochem. Biophys. Res. Commun. 353:47–53.
  • Lu, H., L. Zawel, L. Fisher, J.-M. Egly, and D. Reinberg. 1992. Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II. Nature 358:641–645.
  • Malagon, F., A. H. Tong, B. K. Shafer, and J. N. Strathern. 2004. Genetic interactions of DST1 in Saccharomyces cerevisiae suggest a role of TFIIS in the initiation-elongation transition. Genetics 166:1215–1227.
  • Mandal, S. S., H. Cho, S. Kim, K. Cabane, and D. Reinberg. 2002. FCP1, a phosphatase specific for the heptapeptide repeat of the largest subunit of RNA polymerase II, stimulates transcription elongation. Mol. Cell. Biol. 22:7543–7552.
  • Martens, C., B. Krett, and P. Laybourn. 2001. RNA polymerase II and TBP occupy the repressed CYC1 promoter. Mol. Microbiol. 40:1009–1019.
  • Martens, J. A., and F. Winston. 2003. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13:136–142.
  • Mason, P. B., and K. Struhl. 2005. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell 17:831–840.
  • Meinhart, A., T. Kamenski, S. Hoeppner, S. Baumli, and P. Cramer. 2005. A structural perspective of CTD function. Genes Dev. 19:1401–1415.
  • Moqtaderi, Z., J. D. Yale, K. Struhl, and S. Buratowski. 1996. Yeast homologues of higher eukaryotic TFIID subunits. Proc. Natl. Acad. Sci. USA 93:14654–14658.
  • Morillo-Huesca, M., M. Vanti, and S. Chavez. 2006. A simple in vivo assay for measuring the efficiency of gene length-dependent processes in yeast mRNA biogenesis. FEBS J. 273:756–769.
  • Mueller, C. L., and J. A. Jaehning. 2002. Ctr9, Rft1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol. Cell. Biol. 22:1971–1980.
  • Myers, L. C., and R. D. Kornberg. 2000. Mediator of transcriptional regulation. Annu. Rev. Biochem. 69:729–749.
  • Patturajan, M., R. J. Schulte, B. M. Sefton, R. Berezney, M. Vincent, O. Bensaude, S. L. Warren, and J. L. Corden. 1998. Growth-related changes in phosphorylation of yeast RNA polymerase II. J. Biol. Chem. 273:4689–4694.
  • Peterson, C. L., and I. Herskowitz. 1992. Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell 68:573–583.
  • Phatnani, H. P., and A. L. Greenleaf. 2006. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20:2922–2936.
  • Prather, D. M., E. Larschan, and F. Winston. 2005. Evidence that the elongation factor TFIIS plays a role in transcription initiation at GAL1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 25:2650–2659.
  • Ptashne, M. 2003. Regulated recruitment and cooperativity in the design of biological regulatory systems. Philos. Trans. A 361:1223–1234.
  • Ptashne, M. 2005. Regulation of transcription: from lambda to eukaryotes. Trends Biochem. Sci. 30:275–279.
  • Radonjic, M., J. Andrau, P. Lijnzaad, P. Kemmeren, T. Kockelkorn, D. van Leenen, N. van Berkum, and F. Holstege. 2005. Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol. Cell 18:171–183.
  • Reines, D., M. J. Chamberlin, and C. M. Kane. 1989. Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a block to transcription in a human gene in vitro. J. Biol. Chem. 264:10799–10809.
  • Reppas, N. B., J. T. Wade, G. M. Church, and K. Struhl. 2006. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol. Cell 24:747–757.
  • Riles, L., R. J. Shaw, M. Johnston, and D. Reines. 2004. Large-scale screening of yeast mutants for sensitivity to the IMP dehydrogenase inhibitor 6-azauracil. Yeast 21:241–248.
  • Schaeffer, L., R. Roy, S. Humbert, V. Moncollin, W. Vermeulen, J. H. Hoeijmakers, P. Chambon, and J. M. Egly. 1993. DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor. Science 260:58–63.
  • Schroeder, S. C., B. Schwer, S. Shuman, and D. Bentley. 2000. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14:2435–2440.
  • Schroeder, S. C., D. A. Zorio, B. Schwer, S. Shuman, and D. Bentley. 2004. A function of yeast mRNA cap methyltransferase, Abd1, in transcription by RNA polymerase II. Mol. Cell 13:377–387.
  • Sekinger, E. A., Z. Moqtaderi, and K. Struhl. 2005. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell 18:735–748.
  • Serizawa, H., J. Conaway, and R. Conaway. 1993. Phosphorylation of C-terminal domain of RNA polymerase II is not required in basal transcription. Nature 363:371–374.
  • Serizawa, H., R. C. Conaway, and J. W. Conaway. 1992. A carboxyl-terminal-domain kinase associated with RNA polymerase I transcription factor d from rat liver. Proc. Natl. Acad. Sci. USA 89:7476–7480.
  • Sherman, F., J. W. Stewart, E. Margoliash, J. Parker, and W. Campbell. 1966. The structural gene for yeast cytochrome C. Proc. Natl. Acad. Sci. USA 55:1498–1504.
  • Squazzo, S. L., P. J. Costa, D. L. Lindstrom, K. E. Kumer, R. Simic, J. L. Jennings, A. J. Link, K. M. Arndt, and G. A. Hartzog. 2002. The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J. 21:1764–1774.
  • Stevens, M., E. De Clercq, and J. Balzarini. 2006. The regulation of HIV-1 transcription: molecular targets for chemotherapeutic intervention. Med. Res. Rev. 26:595–625.
  • Stolinski, L. A., D. M. Eisenmann, and K. M. Arndt. 1997. Indentification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:4490–4500.
  • Strahl-Bolsinger, S., A. Hecht, K. Luo, and M. Grunstein. 1997. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11:83–93.
  • Wada, T., T. Takagi, Y. Yamaguchi, A. Ferdous, T. Imai, S. Hirose, S. Sugimoto, K. Yano, G. A. Hartzog, F. Winston, S. Buratowski, and H. 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.
  • Westover, K. D., D. A. Bushnell, and R. D. Kornberg. 2004. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303:1014–1016.
  • Winston, F., and M. Carlson. 1992. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet. 8:387–391.
  • Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Boeke, H. Bussey, A. M. Chu, C. Connelly, K. Davis, F. Dietrich, S. W. Dow, M. El Bakkoury, F. Foury, S. H. Friend, E. Gentalen, G. Giaever, J. H. Hegemann, T. Jones, M. Laub, H. Liao, R. W. Davis, et al. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901–906.
  • Yamaguchi, Y., T. Wada, D. Watanabe, T. Takagi, J. Hasegawa, and H. Handa. 1999. Structure and function of the human transcription elongation factor DSIF. J. Biol. Chem. 274:8085–8092.
  • Yin, Y. W., and T. A. Steitz. 2002. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 298:1387–1395.
  • Yoh, S. M., H. Cho, L. Pickle, R. M. Evans, and K. A. Jones. 2007. The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. Genes Dev. 21:160–174.
  • Zanton, S. J., and B. F. Pugh. 2006. Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev. 20:2250–2265.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.