Skip to main content
PMC home page
Genetics logoLink to Genetics
. 2004 Mar;166(3):1215–1227. doi: 10.1534/genetics.166.3.1215

Genetic interactions of DST1 in Saccharomyces cerevisiae suggest a role of TFIIS in the initiation-elongation transition.

Francisco Malagon 1, Amy H Tong 1, Brenda K Shafer 1, Jeffrey N Strathern 1
PMCID: PMC1470799  PMID: 15082542

Abstract

TFIIS promotes the intrinsic ability of RNA polymerase II to cleave the 3'-end of the newly synthesized RNA. This stimulatory activity of TFIIS, which is dependent upon Rpb9, facilitates the resumption of transcription elongation when the polymerase stalls or arrests. While TFIIS has a pronounced effect on transcription elongation in vitro, the deletion of DST1 has no major effect on cell viability. In this work we used a genetic approach to increase our knowledge of the role of TFIIS in vivo. We showed that: (1) dst1 and rpb9 mutants have a synthetic growth defective phenotype when combined with fyv4, gim5, htz1, yal011w, ybr231c, soh1, vps71, and vps72 mutants that is exacerbated during germination or at high salt concentrations; (2) TFIIS and Rpb9 are essential when the cells are challenged with microtubule-destabilizing drugs; (3) among the SDO (synthetic with Dst one), SOH1 shows the strongest genetic interaction with DST1; (4) the presence of multiple copies of TAF14, SUA7, GAL11, RTS1, and TYS1 alleviate the growth phenotype of dst1 soh1 mutants; and (5) SRB5 and SIN4 genetically interact with DST1. We propose that TFIIS is required under stress conditions and that TFIIS is important for the transition between initiation and elongation in vivo.

Full Text

The Full Text of this article is available as a PDF (286.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adam M., Robert F., Larochelle M., Gaudreau L. H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions. Mol Cell Biol. 2001 Sep;21(18):6270–6279. doi: 10.1128/MCB.21.18.6270-6279.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Aguilera Andrés. The connection between transcription and genomic instability. EMBO J. 2002 Feb 1;21(3):195–201. doi: 10.1093/emboj/21.3.195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Alani E., Cao L., Kleckner N. A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics. 1987 Aug;116(4):541–545. doi: 10.1534/genetics.112.541.test. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Allison L. A., Ingles C. J. Mutations in RNA polymerase II enhance or suppress mutations in GAL4. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2794–2798. doi: 10.1073/pnas.86.8.2794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Archambault J., Jansma D. B., Kawasoe J. H., Arndt K. T., Greenblatt J., Friesen J. D. Stimulation of transcription by mutations affecting conserved regions of RNA polymerase II. J Bacteriol. 1998 May;180(10):2590–2598. doi: 10.1128/jb.180.10.2590-2598.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Archambault J., Lacroute F., Ruet A., Friesen J. D. Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II. Mol Cell Biol. 1992 Sep;12(9):4142–4152. doi: 10.1128/mcb.12.9.4142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Asturias F. J., Jiang Y. W., Myers L. C., Gustafsson C. M., Kornberg R. D. Conserved structures of mediator and RNA polymerase II holoenzyme. Science. 1999 Feb 12;283(5404):985–987. doi: 10.1126/science.283.5404.985. [DOI] [PubMed] [Google Scholar]
  8. Awrey D. E., Weilbaecher R. G., Hemming S. A., Orlicky S. M., Kane C. M., Edwards A. M. Transcription elongation through DNA arrest sites. A multistep process involving both RNA polymerase II subunit RPB9 and TFIIS. J Biol Chem. 1997 Jun 6;272(23):14747–14754. doi: 10.1074/jbc.272.23.14747. [DOI] [PubMed] [Google Scholar]
  9. Azad A. K., Stanford D. R., Sarkar S., Hopper A. K. Role of nuclear pools of aminoacyl-tRNA synthetases in tRNA nuclear export. Mol Biol Cell. 2001 May;12(5):1381–1392. doi: 10.1091/mbc.12.5.1381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Badi L., Barberis A. Proteins that genetically interact with the Saccharomyces cerevisiae transcription factor Gal11p emphasize its role in the initiation-elongation transition. Mol Genet Genomics. 2001 Aug;265(6):1076–1086. doi: 10.1007/s004380100505. [DOI] [PubMed] [Google Scholar]
  11. Beach D. L., Salmon E. D., Bloom K. Localization and anchoring of mRNA in budding yeast. Curr Biol. 1999 Jun 3;9(11):569–578. doi: 10.1016/s0960-9822(99)80260-7. [DOI] [PubMed] [Google Scholar]
  12. Bellí G., Garí E., Aldea M., Herrero E. Functional analysis of yeast essential genes using a promoter-substitution cassette and the tetracycline-regulatable dual expression system. Yeast. 1998 Sep 15;14(12):1127–1138. doi: 10.1002/(SICI)1097-0061(19980915)14:12<1127::AID-YEA300>3.0.CO;2-#. [DOI] [PubMed] [Google Scholar]
  13. Bengal E., Flores O., Krauskopf A., Reinberg D., Aloni Y. Role of the mammalian transcription factors IIF, IIS, and IIX during elongation by RNA polymerase II. Mol Cell Biol. 1991 Mar;11(3):1195–1206. doi: 10.1128/mcb.11.3.1195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Bentley D. L. Regulation of transcriptional elongation by RNA polymerase II. Curr Opin Genet Dev. 1995 Apr;5(2):210–216. doi: 10.1016/0959-437x(95)80010-7. [DOI] [PubMed] [Google Scholar]
  15. Bonangelino Cecilia J., Chavez Edna M., Bonifacino Juan S. Genomic screen for vacuolar protein sorting genes in Saccharomyces cerevisiae. Mol Biol Cell. 2002 Jul;13(7):2486–2501. doi: 10.1091/mbc.02-01-0005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Boube M., Faucher C., Joulia L., Cribbs D. L., Bourbon H. M. Drosophila homologs of transcriptional mediator complex subunits are required for adult cell and segment identity specification. Genes Dev. 2000 Nov 15;14(22):2906–2917. doi: 10.1101/gad.17900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Boube Muriel, Joulia Laurent, Cribbs David L., Bourbon Henri-Marc. Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell. 2002 Jul 26;110(2):143–151. doi: 10.1016/s0092-8674(02)00830-9. [DOI] [PubMed] [Google Scholar]
  18. Brachmann C. B., Davies A., Cost G. J., Caputo E., Li J., Hieter P., Boeke J. D. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast. 1998 Jan 30;14(2):115–132. doi: 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2. [DOI] [PubMed] [Google Scholar]
  19. Cadena D. L., Dahmus M. E. Messenger RNA synthesis in mammalian cells is catalyzed by the phosphorylated form of RNA polymerase II. J Biol Chem. 1987 Sep 15;262(26):12468–12474. [PubMed] [Google Scholar]
  20. Cheng Chonghui, Sharp Phillip A. RNA polymerase II accumulation in the promoter-proximal region of the dihydrofolate reductase and gamma-actin genes. Mol Cell Biol. 2003 Mar;23(6):1961–1967. doi: 10.1128/MCB.23.6.1961-1967.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Clark A. B., Dykstra C. C., Sugino A. Isolation, DNA sequence, and regulation of a Saccharomyces cerevisiae gene that encodes DNA strand transfer protein alpha. Mol Cell Biol. 1991 May;11(5):2576–2582. doi: 10.1128/mcb.11.5.2576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Cosma M. P., Panizza S., Nasmyth K. Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF. Mol Cell. 2001 Jun;7(6):1213–1220. doi: 10.1016/s1097-2765(01)00266-0. [DOI] [PubMed] [Google Scholar]
  23. Costa P. J., Arndt K. M. Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics. 2000 Oct;156(2):535–547. doi: 10.1093/genetics/156.2.535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Dagkessamanskaia A., Martin-Yken H., Basmaji F., Briza P., Francois J. Interaction of Knr4 protein, a protein involved in cell wall synthesis, with tyrosine tRNA synthetase encoded by TYS1 in Saccharomyces cerevisiae. FEMS Microbiol Lett. 2001 Jun 12;200(1):53–58. doi: 10.1111/j.1574-6968.2001.tb10692.x. [DOI] [PubMed] [Google Scholar]
  25. Davie J. K., Kane C. M. Genetic interactions between TFIIS and the Swi-Snf chromatin-remodeling complex. Mol Cell Biol. 2000 Aug;20(16):5960–5973. doi: 10.1128/mcb.20.16.5960-5973.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Davis Joshua A., Takagi Yuichiro, Kornberg Roger D., Asturias Francisco A. Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol Cell. 2002 Aug;10(2):409–415. doi: 10.1016/s1097-2765(02)00598-1. [DOI] [PubMed] [Google Scholar]
  27. Dotson M. R., Yuan C. X., Roeder R. G., Myers L. C., Gustafsson C. M., Jiang Y. W., Li Y., Kornberg R. D., Asturias F. J. Structural organization of yeast and mammalian mediator complexes. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14307–14310. doi: 10.1073/pnas.260489497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Evangelista C. C., Jr, Rodriguez Torres A. M., Limbach M. P., Zitomer R. S. Rox3 and Rts1 function in the global stress response pathway in baker's yeast. Genetics. 1996 Apr;142(4):1083–1093. doi: 10.1093/genetics/142.4.1083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Evans D. R., Hemmings B. A. Mutation of the C-terminal leucine residue of PP2Ac inhibits PR55/B subunit binding and confers supersensitivity to microtubule destabilization in Saccharomyces cerevisiae. Mol Gen Genet. 2000 Nov;264(4):425–432. doi: 10.1007/s004380000302. [DOI] [PubMed] [Google Scholar]
  30. Exinger F., Lacroute F. 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr Genet. 1992 Jul;22(1):9–11. doi: 10.1007/BF00351735. [DOI] [PubMed] [Google Scholar]
  31. Fan H. Y., Cheng K. K., Klein H. L. Mutations in the RNA polymerase II transcription machinery suppress the hyperrecombination mutant hpr1 delta of Saccharomyces cerevisiae. Genetics. 1996 Mar;142(3):749–759. doi: 10.1093/genetics/142.3.749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Fan H. Y., Klein H. L. Characterization of mutations that suppress the temperature-sensitive growth of the hpr1 delta mutant of Saccharomyces cerevisiae. Genetics. 1994 Aug;137(4):945–956. doi: 10.1093/genetics/137.4.945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Fish Rachel N., Kane Caroline M. Promoting elongation with transcript cleavage stimulatory factors. Biochim Biophys Acta. 2002 Sep 13;1577(2):287–307. doi: 10.1016/s0167-4781(02)00459-1. [DOI] [PubMed] [Google Scholar]
  34. Fivaz J., Bassi M. C., Pinaud S., Mirkovitch J. RNA polymerase II promoter-proximal pausing upregulates c-fos gene expression. Gene. 2000 Sep 19;255(2):185–194. doi: 10.1016/s0378-1119(00)00340-1. [DOI] [PubMed] [Google Scholar]
  35. Flanagan P. M., Kelleher R. J., 3rd, Sayre M. H., Tschochner H., Kornberg R. D. A mediator required for activation of RNA polymerase II transcription in vitro. Nature. 1991 Apr 4;350(6317):436–438. doi: 10.1038/350436a0. [DOI] [PubMed] [Google Scholar]
  36. Gavin Anne-Claude, Bösche Markus, Krause Roland, Grandi Paola, Marzioch Martina, Bauer Andreas, Schultz Jörg, Rick Jens M., Michon Anne-Marie, Cruciat Cristina-Maria. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002 Jan 10;415(6868):141–147. doi: 10.1038/415141a. [DOI] [PubMed] [Google Scholar]
  37. Gietz R. D., Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988 Dec 30;74(2):527–534. doi: 10.1016/0378-1119(88)90185-0. [DOI] [PubMed] [Google Scholar]
  38. Goldstein A. L., McCusker J. H. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast. 1999 Oct;15(14):1541–1553. doi: 10.1002/(SICI)1097-0061(199910)15:14<1541::AID-YEA476>3.0.CO;2-K. [DOI] [PubMed] [Google Scholar]
  39. Greenblatt J. RNA polymerase II holoenzyme and transcriptional regulation. Curr Opin Cell Biol. 1997 Jun;9(3):310–319. doi: 10.1016/s0955-0674(97)80002-6. [DOI] [PubMed] [Google Scholar]
  40. Gu W., Malik S., Ito M., Yuan C. X., Fondell J. D., Zhang X., Martinez E., Qin J., Roeder R. G. A novel human SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation. Mol Cell. 1999 Jan;3(1):97–108. doi: 10.1016/s1097-2765(00)80178-1. [DOI] [PubMed] [Google Scholar]
  41. Gu W., Powell W., Mote J., Jr, Reines D. Nascent RNA cleavage by arrested RNA polymerase II does not require upstream translocation of the elongation complex on DNA. J Biol Chem. 1993 Dec 5;268(34):25604–25616. [PMC free article] [PubMed] [Google Scholar]
  42. Gustafsson C. M., Myers L. C., Li Y., Redd M. J., Lui M., Erdjument-Bromage H., Tempst P., Kornberg R. D. Identification of Rox3 as a component of mediator and RNA polymerase II holoenzyme. J Biol Chem. 1997 Jan 3;272(1):48–50. doi: 10.1074/jbc.272.1.48. [DOI] [PubMed] [Google Scholar]
  43. Hampsey M., Na J. G., Pinto I., Ware D. E., Berroteran R. W. Extragenic suppressors of a translation initiation defect in the cyc1 gene of Saccharomyces cerevisiae. Biochimie. 1991 Dec;73(12):1445–1455. doi: 10.1016/0300-9084(91)90177-3. [DOI] [PubMed] [Google Scholar]
  44. Hartzog G. A., Wada T., Handa H., Winston F. Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev. 1998 Feb 1;12(3):357–369. doi: 10.1101/gad.12.3.357. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Hubert J. C., Guyonvarch A., Kammerer B., Exinger F., Liljelund P., Lacroute F. Complete sequence of a eukaryotic regulatory gene. EMBO J. 1983;2(11):2071–2073. doi: 10.1002/j.1460-2075.1983.tb01702.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983 Jan;153(1):163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Izban M. G., Luse D. S. SII-facilitated transcript cleavage in RNA polymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments. J Biol Chem. 1993 Jun 15;268(17):12864–12873. [PubMed] [Google Scholar]
  48. Izban M. G., Luse D. S. The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes. J Biol Chem. 1993 Jun 15;268(17):12874–12885. [PubMed] [Google Scholar]
  49. Jackson J. D., Gorovsky M. A. Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants. Nucleic Acids Res. 2000 Oct 1;28(19):3811–3816. doi: 10.1093/nar/28.19.3811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Jona G., Wittschieben B. O., Svejstrup J. Q., Gileadi O. Involvement of yeast carboxy-terminal domain kinase I (CTDK-I) in transcription elongation in vivo. Gene. 2001 Apr 4;267(1):31–36. doi: 10.1016/s0378-1119(01)00389-4. [DOI] [PubMed] [Google Scholar]
  51. Kettenberger Hubert, Armache Karim-Jean, Cramer Patrick. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell. 2003 Aug 8;114(3):347–357. doi: 10.1016/s0092-8674(03)00598-1. [DOI] [PubMed] [Google Scholar]
  52. Kim H., Ko J. P., Kang U. G., Park J. B., Kim H. L., Lee Y. H., Kim Y. S. Electroconvulsive shock reduces inositol 1,4,5-trisphosphate 3-kinase mRNA expression in rat dentate gyrus. J Neurochem. 1994 Nov;63(5):1991–1994. doi: 10.1046/j.1471-4159.1994.63051991.x. [DOI] [PubMed] [Google Scholar]
  53. Kim Y. J., Björklund 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. Cell. 1994 May 20;77(4):599–608. doi: 10.1016/0092-8674(94)90221-6. [DOI] [PubMed] [Google Scholar]
  54. Kireeva M. L., Komissarova N., Kashlev M. Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity. J Mol Biol. 2000 Jun 2;299(2):325–335. doi: 10.1006/jmbi.2000.3755. [DOI] [PubMed] [Google Scholar]
  55. Kireeva M. L., Komissarova N., Waugh D. S., Kashlev M. The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J Biol Chem. 2000 Mar 3;275(9):6530–6536. doi: 10.1074/jbc.275.9.6530. [DOI] [PubMed] [Google Scholar]
  56. Koleske A. J., Young R. A. The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem Sci. 1995 Mar;20(3):113–116. doi: 10.1016/s0968-0004(00)88977-x. [DOI] [PubMed] [Google Scholar]
  57. Komissarova N., Kashlev M. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded. Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1755–1760. doi: 10.1073/pnas.94.5.1755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Krogan Nevan J., Keogh Michael-Christopher, Datta Nira, Sawa Chika, Ryan Owen W., Ding Huiming, Haw Robin A., Pootoolal Jeffrey, Tong Amy, Canadien Veronica. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell. 2003 Dec;12(6):1565–1576. doi: 10.1016/s1097-2765(03)00497-0. [DOI] [PubMed] [Google Scholar]
  59. Krogan Nevan J., Kim Minkyu, Ahn Seong Hoon, Zhong Guoqing, Kobor Michael S., Cagney Gerard, Emili Andrew, Shilatifard Ali, Buratowski Stephen, Greenblatt Jack F. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol. 2002 Oct;22(20):6979–6992. doi: 10.1128/MCB.22.20.6979-6992.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Krogan Nevan J., Kim Minkyu, Tong Amy, Golshani Ashkan, Cagney Gerard, Canadien Veronica, Richards Dawn P., Beattie Bryan K., Emili Andrew, Boone Charles. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003 Jun;23(12):4207–4218. doi: 10.1128/MCB.23.12.4207-4218.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Krumm A., Hickey L. B., Groudine M. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev. 1995 Mar 1;9(5):559–572. doi: 10.1101/gad.9.5.559. [DOI] [PubMed] [Google Scholar]
  62. Labhart P., Morgan G. T. Identification of novel genes encoding transcription elongation factor TFIIS (TCEA) in vertebrates: conservation of three distinct TFIIS isoforms in frog, mouse, and human. Genomics. 1998 Sep 15;52(3):278–288. doi: 10.1006/geno.1998.5449. [DOI] [PubMed] [Google Scholar]
  63. Larochelle Marc, Gaudreau Luc. H2A.Z has a function reminiscent of an activator required for preferential binding to intergenic DNA. EMBO J. 2003 Sep 1;22(17):4512–4522. doi: 10.1093/emboj/cdg427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Lee H., Kraus K. W., Wolfner M. F., Lis J. T. DNA sequence requirements for generating paused polymerase at the start of hsp70. Genes Dev. 1992 Feb;6(2):284–295. doi: 10.1101/gad.6.2.284. [DOI] [PubMed] [Google Scholar]
  65. Lee Y. C., Park J. M., Min S., Han S. J., Kim Y. J. An activator binding module of yeast RNA polymerase II holoenzyme. Mol Cell Biol. 1999 Apr;19(4):2967–2976. doi: 10.1128/mcb.19.4.2967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Lennon J. C., 3rd, Wind M., Saunders L., Hock M. B., Reines D. Mutations in RNA polymerase II and elongation factor SII severely reduce mRNA levels in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Oct;18(10):5771–5779. doi: 10.1128/mcb.18.10.5771. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Li B., Weber J. A., Chen Y., Greenleaf A. L., Gilmour D. S. Analyses of promoter-proximal pausing by RNA polymerase II on the hsp70 heat shock gene promoter in a Drosophila nuclear extract. Mol Cell Biol. 1996 Oct;16(10):5433–5443. doi: 10.1128/mcb.16.10.5433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Li Y., Bjorklund S., Jiang Y. W., Kim Y. J., Lane W. S., Stillman D. J., Kornberg R. D. Yeast global transcriptional regulators Sin4 and Rgr1 are components of mediator complex/RNA polymerase II holoenzyme. Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):10864–10868. doi: 10.1073/pnas.92.24.10864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Lindstrom D. L., Hartzog G. A. Genetic interactions of Spt4-Spt5 and TFIIS with the RNA polymerase II CTD and CTD modifying enzymes in Saccharomyces cerevisiae. Genetics. 2001 Oct;159(2):487–497. doi: 10.1093/genetics/159.2.487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Mizuguchi Gaku, Shen Xuetong, Landry Joe, Wu Wei-Hua, Sen Subhojit, Wu Carl. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 2003 Nov 26;303(5656):343–348. doi: 10.1126/science.1090701. [DOI] [PubMed] [Google Scholar]
  71. Myer V. E., Young R. A. RNA polymerase II holoenzymes and subcomplexes. J Biol Chem. 1998 Oct 23;273(43):27757–27760. doi: 10.1074/jbc.273.43.27757. [DOI] [PubMed] [Google Scholar]
  72. Myers L. C., Kornberg R. D. Mediator of transcriptional regulation. Annu Rev Biochem. 2000;69:729–749. doi: 10.1146/annurev.biochem.69.1.729. [DOI] [PubMed] [Google Scholar]
  73. Nakanishi T., Nakano A., Nomura K., Sekimizu K., Natori S. Purification, gene cloning, and gene disruption of the transcription elongation factor S-II in Saccharomyces cerevisiae. J Biol Chem. 1992 Jul 5;267(19):13200–13204. [PubMed] [Google Scholar]
  74. Nasmyth K., Jansen R. P. The cytoskeleton in mRNA localization and cell differentiation. Curr Opin Cell Biol. 1997 Jun;9(3):396–400. doi: 10.1016/s0955-0674(97)80013-0. [DOI] [PubMed] [Google Scholar]
  75. Nehlin J. O., Carlberg M., Ronne H. Yeast galactose permease is related to yeast and mammalian glucose transporters. Gene. 1989 Dec 28;85(2):313–319. doi: 10.1016/0378-1119(89)90423-x. [DOI] [PubMed] [Google Scholar]
  76. Neugebauer K. M., Roth M. B. Transcription units as RNA processing units. Genes Dev. 1997 Dec 15;11(24):3279–3285. doi: 10.1101/gad.11.24.3279. [DOI] [PubMed] [Google Scholar]
  77. Orphanides G., Wu W. H., Lane W. S., Hampsey M., Reinberg D. The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature. 1999 Jul 15;400(6741):284–288. doi: 10.1038/22350. [DOI] [PubMed] [Google Scholar]
  78. Orr-Weaver T. L., Szostak J. W., Rothstein R. J. Yeast transformation: a model system for the study of recombination. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6354–6358. doi: 10.1073/pnas.78.10.6354. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. Otero G., Fellows J., Li Y., de Bizemont T., Dirac A. M., Gustafsson C. M., Erdjument-Bromage H., Tempst P., Svejstrup J. Q. Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol Cell. 1999 Jan;3(1):109–118. doi: 10.1016/s1097-2765(00)80179-3. [DOI] [PubMed] [Google Scholar]
  80. Pagé Nicolas, Gérard-Vincent Manon, Ménard Patrice, Beaulieu Maude, Azuma Masayuki, Dijkgraaf Gerrit J. P., Li Huijuan, Marcoux José, Nguyen Thuy, Dowse Tim. A Saccharomyces cerevisiae genome-wide mutant screen for altered sensitivity to K1 killer toxin. Genetics. 2003 Mar;163(3):875–894. doi: 10.1093/genetics/163.3.875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. Pal M., McKean D., Luse D. S. Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence. Mol Cell Biol. 2001 Sep;21(17):5815–5825. doi: 10.1128/MCB.21.17.5815-5825.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. 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 Cell. 2001 Jul;8(1):9–19. doi: 10.1016/s1097-2765(01)00296-9. [DOI] [PubMed] [Google Scholar]
  83. Percipalle Piergiorgio, Fomproix Nathalie, Kylberg Karin, Miralles Francesc, Bjorkroth Birgitta, Daneholt Bertil, Visa Neus. An actin-ribonucleoprotein interaction is involved in transcription by RNA polymerase II. Proc Natl Acad Sci U S A. 2003 May 12;100(11):6475–6480. doi: 10.1073/pnas.1131933100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  84. Pinto I., Ware D. E., Hampsey M. The yeast SUA7 gene encodes a homolog of human transcription factor TFIIB and is required for normal start site selection in vivo. Cell. 1992 Mar 6;68(5):977–988. doi: 10.1016/0092-8674(92)90040-j. [DOI] [PubMed] [Google Scholar]
  85. Piruat J. I., Aguilera A. Mutations in the yeast SRB2 general transcription factor suppress hpr1-induced recombination and show defects in DNA repair. Genetics. 1996 Aug;143(4):1533–1542. doi: 10.1093/genetics/143.4.1533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  86. Piruat J. I., Chávez S., Aguilera A. The yeast HRS1 gene is involved in positive and negative regulation of transcription and shows genetic characteristics similar to SIN4 and GAL11. Genetics. 1997 Dec;147(4):1585–1594. doi: 10.1093/genetics/147.4.1585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  87. Plet A., Eick D., Blanchard J. M. Elongation and premature termination of transcripts initiated from c-fos and c-myc promoters show dissimilar patterns. Oncogene. 1995 Jan 19;10(2):319–328. [PubMed] [Google Scholar]
  88. Pokholok Dmitry K., Hannett Nancy M., Young Richard A. Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell. 2002 Apr;9(4):799–809. doi: 10.1016/s1097-2765(02)00502-6. [DOI] [PubMed] [Google Scholar]
  89. Qian X., Gozani S. N., Yoon H., Jeon C. J., Agarwal K., Weiss M. A. Novel zinc finger motif in the basal transcriptional machinery: three-dimensional NMR studies of the nucleic acid binding domain of transcriptional elongation factor TFIIS. Biochemistry. 1993 Sep 28;32(38):9944–9959. doi: 10.1021/bi00089a010. [DOI] [PubMed] [Google Scholar]
  90. Qian X., Jeon C., Yoon H., Agarwal K., Weiss M. A. Structure of a new nucleic-acid-binding motif in eukaryotic transcriptional elongation factor TFIIS. Nature. 1993 Sep 16;365(6443):277–279. doi: 10.1038/365277a0. [DOI] [PubMed] [Google Scholar]
  91. Rappaport J., Reinberg D., Zandomeni R., Weinmann R. Purification and functional characterization of transcription factor SII from calf thymus. Role in RNA polymerase II elongation. J Biol Chem. 1987 Apr 15;262(11):5227–5232. [PubMed] [Google Scholar]
  92. Rasmussen E. B., Lis J. T. Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. J Mol Biol. 1995 Oct 6;252(5):522–535. doi: 10.1006/jmbi.1995.0517. [DOI] [PubMed] [Google Scholar]
  93. Reines D., Chamberlin M. J., Kane C. M. 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. 1989 Jun 25;264(18):10799–10809. [PubMed] [Google Scholar]
  94. Reines D., Conaway R. C., Conaway J. W. Mechanism and regulation of transcriptional elongation by RNA polymerase II. Curr Opin Cell Biol. 1999 Jun;11(3):342–346. doi: 10.1016/S0955-0674(99)80047-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Rudd M. D., Izban M. G., Luse D. S. The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8057–8061. doi: 10.1073/pnas.91.17.8057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Sanders Steven L., Jennings Jennifer, Canutescu Adrian, Link Andrew J., Weil P. Anthony. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol Cell Biol. 2002 Jul;22(13):4723–4738. doi: 10.1128/MCB.22.13.4723-4738.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  97. Santos-Rosa H., Aguilera A. Isolation and genetic analysis of extragenic suppressors of the hyper-deletion phenotype of the Saccharomyces cerevisiae hpr1 delta mutation. Genetics. 1995 Jan;139(1):57–66. doi: 10.1093/genetics/139.1.57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. Santos-Rosa H., Clever B., Heyer W. D., Aguilera A. The yeast HRS1 gene encodes a polyglutamine-rich nuclear protein required for spontaneous and hpr1-induced deletions between direct repeats. Genetics. 1996 Mar;142(3):705–716. doi: 10.1093/genetics/142.3.705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  99. Sarkar S., Azad A. K., Hopper A. K. Nuclear tRNA aminoacylation and its role in nuclear export of endogenous tRNAs in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14366–14371. doi: 10.1073/pnas.96.25.14366. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Sawadogo M., Lescure B., Sentenac A., Fromageot P. Native deoxyribonucleic acid transcription by yeast RNA polymerase--P37 complex. Biochemistry. 1981 Jun 9;20(12):3542–3547. doi: 10.1021/bi00515a037. [DOI] [PubMed] [Google Scholar]
  101. Sawadogo M., Sentenac A., Fromageot P. Interaction of a new polypeptide with yeast RNA polymerase B. J Biol Chem. 1980 Jan 10;255(1):12–15. [PubMed] [Google Scholar]
  102. Schneider E. E., Albert T., Wolf D. A., Eick D. Regulation of c-myc and immunoglobulin kappa gene transcription by promoter-proximal pausing of RNA polymerase II. Curr Top Microbiol Immunol. 1999;246:225–231. doi: 10.1007/978-3-642-60162-0_28. [DOI] [PubMed] [Google Scholar]
  103. Schott Daniel, Huffaker Tim, Bretscher Anthony. Microfilaments and microtubules: the news from yeast. Curr Opin Microbiol. 2002 Dec;5(6):564–574. doi: 10.1016/s1369-5274(02)00369-7. [DOI] [PubMed] [Google Scholar]
  104. Sekimizu K., Nakanishi Y., Mizuno D., Natori S. Purification and preparation of antibody to RNA polymerase II stimulatory factors from Ehrlich ascites tumor cells. Biochemistry. 1979 Apr 17;18(8):1582–1588. doi: 10.1021/bi00575a031. [DOI] [PubMed] [Google Scholar]
  105. Sen R., Nagai H., Shimamoto N. Conformational switching of Escherichia coli RNA polymerase-promoter binary complex is facilitated by elongation factor GreA and GreB. Genes Cells. 2001 May;6(5):389–401. doi: 10.1046/j.1365-2443.2001.00436.x. [DOI] [PubMed] [Google Scholar]
  106. Shilatifard A. Factors regulating the transcriptional elongation activity of RNA polymerase II. FASEB J. 1998 Nov;12(14):1437–1446. doi: 10.1096/fasebj.12.14.1437. [DOI] [PubMed] [Google Scholar]
  107. Shilatifard Ali, Conaway Ronald C., Conaway Joan Weliky. The RNA polymerase II elongation complex. Annu Rev Biochem. 2003 Mar 27;72:693–715. doi: 10.1146/annurev.biochem.72.121801.161551. [DOI] [PubMed] [Google Scholar]
  108. Shu Y., Yang H., Hallberg E., Hallberg R. Molecular genetic analysis of Rts1p, a B' regulatory subunit of Saccharomyces cerevisiae protein phosphatase 2A. Mol Cell Biol. 1997 Jun;17(6):3242–3253. doi: 10.1128/mcb.17.6.3242. [DOI] [PMC free article] [PubMed] [Google Scholar]
  109. Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  110. Stirling D. A., Welch K. A., Stark M. J. Interaction with calmodulin is required for the function of Spc110p, an essential component of the yeast spindle pole body. EMBO J. 1994 Sep 15;13(18):4329–4342. doi: 10.1002/j.1460-2075.1994.tb06753.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  111. Strobl L. J., Eick D. Hold back of RNA polymerase II at the transcription start site mediates down-regulation of c-myc in vivo. EMBO J. 1992 Sep;11(9):3307–3314. doi: 10.1002/j.1460-2075.1992.tb05409.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Sugino A., Nitiss J., Resnick M. A. ATP-independent DNA strand transfer catalyzed by protein(s) from meiotic cells of the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1988 Jun;85(11):3683–3687. doi: 10.1073/pnas.85.11.3683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  113. Svejstrup J. Q., Li Y., Fellows J., Gnatt A., Bjorklund S., Kornberg R. D. Evidence for a mediator cycle at the initiation of transcription. Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6075–6078. doi: 10.1073/pnas.94.12.6075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Svejstrup Jesper Q. Chromatin elongation factors. Curr Opin Genet Dev. 2002 Apr;12(2):156–161. doi: 10.1016/s0959-437x(02)00281-2. [DOI] [PubMed] [Google Scholar]
  115. Takizawa P. A., Sil A., Swedlow J. R., Herskowitz I., Vale R. D. Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast. Nature. 1997 Sep 4;389(6646):90–93. doi: 10.1038/38015. [DOI] [PubMed] [Google Scholar]
  116. Tang H., Liu Y., Madabusi L., Gilmour D. S. Promoter-proximal pausing on the hsp70 promoter in Drosophila melanogaster depends on the upstream regulator. Mol Cell Biol. 2000 Apr;20(7):2569–2580. doi: 10.1128/mcb.20.7.2569-2580.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Tong A. H., Evangelista M., Parsons A. B., Xu H., Bader G. D., Pagé N., Robinson M., Raghibizadeh S., Hogue C. W., Bussey H. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 2001 Dec 14;294(5550):2364–2368. doi: 10.1126/science.1065810. [DOI] [PubMed] [Google Scholar]
  118. Ueno K., Sekimizu K., Mizuno D., Natori S. Antibody against a stimulatory factor of RNA polymerase II inhibits nuclear RNA synthesis. Nature. 1979 Jan 11;277(5692):145–146. doi: 10.1038/277145a0. [DOI] [PubMed] [Google Scholar]
  119. Ujvári Andrea, Pal Mahadeb, Luse Donal S. RNA polymerase II transcription complexes may become arrested if the nascent RNA is shortened to less than 50 nucleotides. J Biol Chem. 2002 Jun 26;277(36):32527–32537. doi: 10.1074/jbc.M201145200. [DOI] [PubMed] [Google Scholar]
  120. Vainberg I. E., Lewis S. A., Rommelaere H., Ampe C., Vandekerckhove J., Klein H. L., Cowan N. J. Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin. Cell. 1998 May 29;93(5):863–873. doi: 10.1016/s0092-8674(00)81446-4. [DOI] [PubMed] [Google Scholar]
  121. Van Mullem Vincent, Wery Maxime, Werner Michel, Vandenhaute Jean, Thuriaux Pierre. The Rpb9 subunit of RNA polymerase II binds transcription factor TFIIE and interferes with the SAGA and elongator histone acetyltransferases. J Biol Chem. 2002 Jan 4;277(12):10220–10225. doi: 10.1074/jbc.M107207200. [DOI] [PubMed] [Google Scholar]
  122. Wach A., Brachat A., Pöhlmann R., Philippsen P. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast. 1994 Dec;10(13):1793–1808. doi: 10.1002/yea.320101310. [DOI] [PubMed] [Google Scholar]
  123. Wada T., Takagi T., Yamaguchi Y., Ferdous A., Imai T., Hirose S., Sugimoto S., Yano K., Hartzog G. A., Winston F. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 1998 Feb 1;12(3):343–356. doi: 10.1101/gad.12.3.343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  124. Waldherr M., Ragnini A., Jank B., Teply R., Wiesenberger G., Schweyen R. J. A multitude of suppressors of group II intron-splicing defects in yeast. Curr Genet. 1993 Oct;24(4):301–306. doi: 10.1007/BF00336780. [DOI] [PubMed] [Google Scholar]
  125. Weeks J. R., Hardin S. E., Shen J., Lee J. M., Greenleaf A. L. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlations with gene activity and transcript processing. Genes Dev. 1993 Dec;7(12A):2329–2344. doi: 10.1101/gad.7.12a.2329. [DOI] [PubMed] [Google Scholar]
  126. Weilbaecher Rodney G., Awrey Donald E., Edwards Aled M., Kane Caroline M. Intrinsic transcript cleavage in yeast RNA polymerase II elongation complexes. J Biol Chem. 2003 Apr 11;278(26):24189–24199. doi: 10.1074/jbc.M211197200. [DOI] [PubMed] [Google Scholar]
  127. Wind M., Reines D. Transcription elongation factor SII. Bioessays. 2000 Apr;22(4):327–336. doi: 10.1002/(SICI)1521-1878(200004)22:4<327::AID-BIES3>3.0.CO;2-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  128. Wu J., Awrey D. E., Edwards A. M., Archambault J., Friesen J. D. In vitro characterization of mutant yeast RNA polymerase II with reduced binding for elongation factor TFIIS. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11552–11557. doi: 10.1073/pnas.93.21.11552. [DOI] [PMC free article] [PubMed] [Google Scholar]
  129. Yarm F., Sagot I., Pellman D. The social life of actin and microtubules: interaction versus cooperation. Curr Opin Microbiol. 2001 Dec;4(6):696–702. doi: 10.1016/s1369-5274(01)00271-5. [DOI] [PubMed] [Google Scholar]
  130. Zabrocki Piotr, Van Hoof Christine, Goris Jozef, Thevelein Johan M., Winderickx Joris, Wera Stefaan. Protein phosphatase 2A on track for nutrient-induced signalling in yeast. Mol Microbiol. 2002 Feb;43(4):835–842. doi: 10.1046/j.1365-2958.2002.02786.x. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES