Gene Symbol: RPB9
Description: DNA-directed RNA polymerase II core subunit RPB9
Alias: SSU73, DNA-directed RNA polymerase II core subunit RPB9
Species: Saccharomyces cerevisiae S288c

Top Publications

  1. Furter Graves E, Hall B, Furter R. Role of a small RNA pol II subunit in TATA to transcription start site spacing. Nucleic Acids Res. 1994;22:4932-6 pubmed
    ..Here, the yeast SHI wild-type gene has been isolated by complementation and shown to be identical to RPB9, the gene encoding a small subunit of RNA polymerase II...
  2. Woychik N, Liao S, Kolodziej P, Young R. Subunits shared by eukaryotic nuclear RNA polymerases. Genes Dev. 1990;4:313-23 pubmed
  3. Flores A, Briand J, Gadal O, Andrau J, Rubbi L, Van Mullem V, et al. A protein-protein interaction map of yeast RNA polymerase III. Proc Natl Acad Sci U S A. 1999;96:7815-20 pubmed
    ..Together with parallel interaction studies based on dosage-dependent suppression of conditional mutants, our data suggest a model of the pol III preinitiation complex. ..
  4. Cramer P, Bushnell D, Fu J, Gnatt A, Maier Davis B, Thompson N, et al. Architecture of RNA polymerase II and implications for the transcription mechanism. Science. 2000;288:640-9 pubmed
    ..Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center...
  5. Van Mullem V, Wery M, Werner M, Vandenhaute J, Thuriaux P. The Rpb9 subunit of RNA polymerase II binds transcription factor TFIIE and interferes with the SAGA and elongator histone acetyltransferases. J Biol Chem. 2002;277:10220-5 pubmed
    b>Rpb9 is a small subunit of yeast RNA polymerase II participating in elongation and formed of two conserved zinc domains. rpb9 mutants are viable, with a strong sensitivity to nucleotide-depleting drugs...
  6. Chen X, Ruggiero C, Li S. Yeast Rpb9 plays an important role in ubiquitylation and degradation of Rpb1 in response to UV-induced DNA damage. Mol Cell Biol. 2007;27:4617-25 pubmed
    b>Rpb9, a nonessential subunit of RNA polymerase II (Pol II), has multiple transcription-related functions in Saccharomyces cerevisiae, including transcription elongation and transcription-coupled repair (TCR)...
  7. Li S, Ding B, Chen R, Ruggiero C, Chen X. Evidence that the transcription elongation function of Rpb9 is involved in transcription-coupled DNA repair in Saccharomyces cerevisiae. Mol Cell Biol. 2006;26:9430-41 pubmed
    b>Rpb9, a small nonessential subunit of RNA polymerase II, has been shown to have multiple transcription-related functions in Saccharomyces cerevisiae...
  8. Sun Z, Tessmer A, Hampsey M. Functional interaction between TFIIB and the Rpb9 (Ssu73) subunit of RNA polymerase II in Saccharomyces cerevisiae. Nucleic Acids Res. 1996;24:2560-6 pubmed
    Recessive mutations in the SSU71, SSU72 and SSU73 genes of Saccharomyces cerevisiae were identified as either suppressors or enhancers of a TFIIB defect (sua7-1) that confers both a cold-sensitive growth phenotype and a downstream shift ..
  9. Ghazy M, Brodie S, Ammerman M, Ziegler L, Ponticelli A. Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II. Mol Cell Biol. 2004;24:10975-85 pubmed
    ..These results provide direct evidence for the involvement of S. cerevisiae TFIIF in the mechanism of transcription start site utilization and support the view that a TFIIF-RNA polymerase II interaction is a determinant in this process. ..

More Information


  1. Wery M, Shematorova E, Van Driessche B, Vandenhaute J, Thuriaux P, Van Mullem V. Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. EMBO J. 2004;23:4232-42 pubmed
    ..mutants were sensitive to nucleotide-depleting drugs and epistatic to null mutants of the RNA polymerase II subunit Rpb9, suggesting that their elongation defects are mediated by Rpb9...
  2. Kruk J, Dutta A, Fu J, Gilmour D, Reese J. The multifunctional Ccr4-Not complex directly promotes transcription elongation. Genes Dev. 2011;25:581-93 pubmed publisher
    ..Our comprehensive analysis shows that Ccr4-Not directly regulates transcription, and suggests it does so by promoting the resumption of elongation of arrested RNAPII when it encounters transcriptional blocks in vivo. ..
  3. Chang M, Bellaoui M, Boone C, Brown G. A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc Natl Acad Sci U S A. 2002;99:16934-9 pubmed
    ..These genes may promote replication fork stability or processivity during encounters between replication forks and DNA damage. ..
  4. Li S, Smerdon M. Rpb4 and Rpb9 mediate subpathways of transcription-coupled DNA repair in Saccharomyces cerevisiae. EMBO J. 2002;21:5921-9 pubmed
    b>Rpb9, a non-essential subunit of RNA polymerase II, mediates a transcription-coupled repair (TCR) subpathway in Saccharomyces cerevisiae. This subpathway initiates at the same upstream site as the previously identified Rad26 subpathway...
  5. Czeko E, Seizl M, Augsberger C, Mielke T, Cramer P. Iwr1 directs RNA polymerase II nuclear import. Mol Cell. 2011;42:261-6 pubmed publisher
    ..Iwr1 function is Pol II specific, transcription independent, and apparently conserved from yeast to human. ..
  6. Hemming S, Jansma D, Macgregor P, Goryachev A, Friesen J, Edwards A. RNA polymerase II subunit Rpb9 regulates transcription elongation in vivo. J Biol Chem. 2000;275:35506-11 pubmed
    RNA polymerase II lacking the Rpb9 subunit uses alternate transcription initiation sites in vitro and in vivo and is unable to respond to the transcription elongation factor TFIIS in vitro...
  7. Nesser N, Peterson D, Hawley D. RNA polymerase II subunit Rpb9 is important for transcriptional fidelity in vivo. Proc Natl Acad Sci U S A. 2006;103:3268-73 pubmed
    ..In contrast, strains containing a deletion of RPB9, which encodes a small core subunit of Pol II, were found to engage in error-prone transcription...
  8. Owiti N, Lopez C, Singh S, Stephenson A, Kim N. Def1 and Dst1 play distinct roles in repair of AP lesions in highly transcribed genomic regions. DNA Repair (Amst). 2017;55:31-39 pubmed publisher
    ..Overall, Def1 and Dst1 mediate very different outcomes in response to AP-induced transcription arrest. ..
  9. Sigurdsson S, Dirac Svejstrup A, Svejstrup J. Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability. Mol Cell. 2010;38:202-10 pubmed publisher
    ..Our results suggest that transcription problems leading to backtracking are frequent in vivo and that reactivation of backtracked RNAPII is crucial for transcription. ..
  10. Donaldson I, Friesen J. Zinc stoichiometry of yeast RNA polymerase II and characterization of mutations in the zinc-binding domain of the largest subunit. J Biol Chem. 2000;275:13780-8 pubmed
    ..Core activity of the mutant enzyme was reduced 20-fold. We conclude that mutations in the zinc-binding domain can reduce core activity without altering the association of any of the subunits required for this activity. ..
  11. Porrúa O, Libri D. A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat Struct Mol Biol. 2013;20:884-91 pubmed publisher
    ..We also show that termination is inhibited by RNA-DNA hybrids. Our results elucidate the role of Sen1p in controlling pervasive transcription. ..
  12. Niesser J, Wagner F, Kostrewa D, Mühlbacher W, Cramer P. Structure of GPN-Loop GTPase Npa3 and Implications for RNA Polymerase II Assembly. Mol Cell Biol. 2015;36:820-31 pubmed publisher
    ..These results suggest that GPN-loop GTPases are assembly chaperones for Pol II and other protein complexes. ..
  13. Ruprich Robert G, Wery M, Després D, Boulard Y, Thuriaux P. Crucial role of a dicarboxylic motif in the catalytic center of yeast RNA polymerases. Curr Genet. 2011;57:327-34 pubmed publisher
    ..Rpb2-E(836) and the funnel domain are not found among the RNA-dependent eukaryotic RNA polymerases and may thus represent a specific adaptation to double-stranded DNA templates. ..
  14. Schaft D, Roguev A, Kotovic K, Shevchenko A, Sarov M, Shevchenko A, et al. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res. 2003;31:2475-82 pubmed
    ..Since SET2 is also a histone methyltransferase, these results suggest a role for histone 3 lysine 36 methylation in transcriptional elongation. ..
  15. Sayre M, Tschochner H, Kornberg R. Reconstitution of transcription with five purified initiation factors and RNA polymerase II from Saccharomyces cerevisiae. J Biol Chem. 1992;267:23376-82 pubmed
    ..TFIIA failed to substitute for any purified factor or to stimulate transcription with the complete set of factors, indicating that its function in crude extracts is primarily as an anti-inhibitor. ..
  16. Lehmann E, Brueckner F, Cramer P. Molecular basis of RNA-dependent RNA polymerase II activity. Nature. 2007;450:445-9 pubmed
    ..The RdRP activity of Pol II provides a missing link in molecular evolution, because it suggests that Pol II evolved from an ancient replicase that duplicated RNA genomes. ..
  17. Gaillard H, Tous C, Botet J, González Aguilera C, Quintero M, Viladevall L, et al. Genome-wide analysis of factors affecting transcription elongation and DNA repair: a new role for PAF and Ccr4-not in transcription-coupled repair. PLoS Genet. 2009;5:e1000364 pubmed publisher
  18. Takagi Y, Calero G, Komori H, Brown J, Ehrensberger A, Hudmon A, et al. Head module control of mediator interactions. Mol Cell. 2006;23:355-64 pubmed
    ..The head module evidently controls Mediator-RNA polymerase II and Mediator-promoter interactions. ..
  19. Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nat Commun. 2017;8:15741 pubmed publisher
    ..We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. ..
  20. Zaros C, Briand J, Boulard Y, Labarre Mariotte S, Garcia Lopez M, Thuriaux P, et al. Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases. Nucleic Acids Res. 2007;35:634-47 pubmed
    ..The large intervening segment of Rpb1 is held across the DNA Cleft by Rpb9, consistent with the synergy observed for rpb5 mutants and rpb9Delta or its RNA polymerase I rpa12Delta counterpart...
  21. Li S, Chen X, Ruggiero C, Ding B, Smerdon M. Modulation of Rad26- and Rpb9-mediated DNA repair by different promoter elements. J Biol Chem. 2006;281:36643-51 pubmed
    Rad26, the yeast homologue of human Cockayne syndrome group B protein, and Rpb9, a nonessential subunit of RNA polymerase II, have been shown to mediate two subpathways of transcription-coupled DNA repair in yeast...
  22. Koyama H, Ueda T, Ito T, Sekimizu K. Novel RNA polymerase II mutation suppresses transcriptional fidelity and oxidative stress sensitivity in rpb9Delta yeast. Genes Cells. 2010;15:151-9 pubmed publisher
    We previously reported that transcription elongation factor S-II and RNA polymerase II subunit Rpb9 maintain transcriptional fidelity and contribute to oxidative stress resistance in yeast...
  23. Wong J, Ingles C. A compromised yeast RNA polymerase II enhances UV sensitivity in the absence of global genome nucleotide excision repair. Mol Gen Genet. 2001;264:842-51 pubmed
  24. Tatum D, Li W, Placer M, Li S. Diverse roles of RNA polymerase II-associated factor 1 complex in different subpathways of nucleotide excision repair. J Biol Chem. 2011;286:30304-13 pubmed publisher
    ..To our best knowledge, among the NER-modulating factors documented so far, Paf1C appears to have the most diverse functions in different NER pathways or subpathways. ..
  25. Mosley A, Pattenden S, Carey M, Venkatesh S, Gilmore J, Florens L, et al. Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation. Mol Cell. 2009;34:168-78 pubmed publisher
    ..Functional characterization of Rtr1 reveals its role as a CTD phosphatase essential for the S5-to-S2-P transition. ..
  26. Lisica A, Engel C, Jahnel M, Roldán Ã, Galburt E, Cramer P, et al. Mechanisms of backtrack recovery by RNA polymerases I and II. Proc Natl Acad Sci U S A. 2016;113:2946-51 pubmed publisher
    ..Taken together, we identify distinct backtrack recovery strategies of Pol I and Pol II, shedding light on the evolution of cellular functions of these key enzymes. ..
  27. Felipe Abrio I, Lafuente Barquero J, García Rubio M, Aguilera A. RNA polymerase II contributes to preventing transcription-mediated replication fork stalls. EMBO J. 2015;34:236-50 pubmed publisher
    ..Three specific alleles of the RNAPII core, rpb1-1, rpb1-S751F and rpb9∆, cause a defect in replication fork progression, compensated for by additional origin firing, as the main ..
  28. Deshpande S, Sadhale P, Vijayraghavan U. Involvement of S. cerevisiae Rpb4 in subset of pathways related to transcription elongation. Gene. 2014;545:126-31 pubmed publisher
    ..interaction of rpb4? with mutants in many transcription elongation factors such as Paf1, Spt4, Dst1, Elp3 and Rpb9. We demonstrate that, Rpb4 interacts functionally with Paf1 to affect the transcription elongation of the FKS1 gene...
  29. Tan Q, Prysak M, Woychik N. Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Mol Cell Biol. 2003;23:3329-38 pubmed
    ..The association of Rpb4/Rpb7 with Rpb6 suggests that analogous subunits of each RNA polymerase impart class-specific functions through a conserved core subunit. ..
  30. Holbein S, Wengi A, Decourty L, Freimoser F, Jacquier A, Dichtl B. Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation. RNA. 2009;15:837-49 pubmed publisher
    ..Finally, chemical-genetic profiling revealed genome-wide pathways linked to cordycepin activity and identified novel genes involved in poly(A) homeostasis. ..
  31. Kasahara K, Ohyama Y, Kokubo T. Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region. Nucleic Acids Res. 2011;39:4136-50 pubmed publisher
    ..This novel mechanism ensures accurate transcriptional initiation by delineating the 5'- and 3'-boundaries of the PIC assembly zone. ..
  32. Babbarwal V, Fu J, Reese J. The Rpb4/7 module of RNA polymerase II is required for carbon catabolite repressor protein 4-negative on TATA (Ccr4-not) complex to promote elongation. J Biol Chem. 2014;289:33125-30 pubmed publisher
    ..The interplay between Ccr4-Not and Rpb4/7 described here suggests a mechanism for how the cell coordinates mRNA synthesis and decay. ..
  33. Shaw R, Wilson J, Smith K, Reines D. Regulation of an IMP dehydrogenase gene and its overexpression in drug-sensitive transcription elongation mutants of yeast. J Biol Chem. 2001;276:32905-16 pubmed
    ..These findings show that yeast possess a conserved system that gauges nucleotide pools and cell growth rate and responds through a uniquely regulated member of the IMD gene family. ..
  34. Daulny A, Geng F, Muratani M, Geisinger J, Salghetti S, Tansey W. Modulation of RNA polymerase II subunit composition by ubiquitylation. Proc Natl Acad Sci U S A. 2008;105:19649-54 pubmed publisher
    ..Our data demonstrate that ubiquitylation can directly alter the subunit composition of a core component of the transcriptional machinery and provide a paradigm for how ubiquitin can influence gene activity. ..
  35. Koyama H, Ito T, Nakanishi T, Sekimizu K. Stimulation of RNA polymerase II transcript cleavage activity contributes to maintain transcriptional fidelity in yeast. Genes Cells. 2007;12:547-59 pubmed
    ..b>Rpb9, a small subunit of RNA polymerase II, enhances the cleavage stimulation activity of S-II...
  36. McCann T, Guo Y, McDonald W, Tansey W. Antagonistic roles for the ubiquitin ligase Asr1 and the ubiquitin-specific protease Ubp3 in subtelomeric gene silencing. Proc Natl Acad Sci U S A. 2016;113:1309-14 pubmed publisher
    ..We suggest that control of pol II by nonproteolytic ubiquitylation provides a mechanism to enforce silencing by transient and reversible inhibition of pol II activity at subtelomeric chromatin. ..
  37. González Aguilera C, Tous C, Babiano R, de la Cruz J, Luna R, Aguilera A. Nab2 functions in the metabolism of RNA driven by polymerases II and III. Mol Biol Cell. 2011;22:2729-40 pubmed publisher
  38. Kozmin S, Jinks Robertson S. The mechanism of nucleotide excision repair-mediated UV-induced mutagenesis in nonproliferating cells. Genetics. 2013;193:803-17 pubmed publisher
    ..The requirement for specific DNA-damage checkpoint proteins suggests roles in recruiting and/or activating factors required to fill such gaps. ..
  39. Choi D, Min M, Kim M, Lee R, Kwon S, Bae S. Hrq1 facilitates nucleotide excision repair of DNA damage induced by 4-nitroquinoline-1-oxide and cisplatin in Saccharomyces cerevisiae. J Microbiol. 2014;52:292-8 pubmed publisher
    ..Overexpression of Hrq1K318A helicase-deficient protein rendered mutant cells more sensitive to 4-NQO and cisplatin, suggesting that helicase activity is required for the proper function of Hrq1 in NER. ..
  40. Kaster B, Knippa K, Kaplan C, Peterson D. RNA Polymerase II Trigger Loop Mobility: INDIRECT EFFECTS OF Rpb9. J Biol Chem. 2016;291:14883-95 pubmed publisher
    b>Rpb9 is a conserved RNA polymerase II (pol II) subunit, the absence of which confers alterations to pol II enzymatic properties and transcription fidelity...
  41. Luo J, Fishburn J, Hahn S, Ranish J. An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function. Mol Cell Proteomics. 2012;11:M111.008318 pubmed publisher
    ..As such, it is an attractive approach to study the topology of protein complexes. ..
  42. Silver H, Nissley J, Reed S, Hou Y, Johnson E. A role for SUMO in nucleotide excision repair. DNA Repair (Amst). 2011;10:1243-51 pubmed publisher
    ..excision repair (NER) pathway, and suggested that they participate both in global genome repair (GGR) and in the Rpb9-dependent subpathway of transcription-coupled repair (TCR), but have minimal role in Rad26-dependent TCR...
  43. Jensen T, Boulay J, Olesen J, Colin J, Weyler M, Libri D. Modulation of transcription affects mRNP quality. Mol Cell. 2004;16:235-44 pubmed
    ..Our results suggest that efficient mRNP assembly is under a kinetic control that is influenced by the rate of transcription. ..
  44. Kettenberger H, Armache K, Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell. 2004;16:955-65 pubmed
    ..Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling. ..
  45. Chen X, Ding B, Lejeune D, Ruggiero C, Li S. Rpb1 sumoylation in response to UV radiation or transcriptional impairment in yeast. PLoS ONE. 2009;4:e5267 pubmed publisher
    ..Our results demonstrate a novel covalent modification of Rpb1 in response to UV induced DNA damage or transcriptional impairment, and unravel an important link between the modification and the DNA damage checkpoint response. ..
  46. Malagon F, Tong A, Shafer B, Strathern J. Genetic interactions of DST1 in Saccharomyces cerevisiae suggest a role of TFIIS in the initiation-elongation transition. Genetics. 2004;166:1215-27 pubmed
    ..This stimulatory activity of TFIIS, which is dependent upon Rpb9, facilitates the resumption of transcription elongation when the polymerase stalls or arrests...
  47. Li W, Selvam K, Rahman S, Li S. Sen1, the yeast homolog of human senataxin, plays a more direct role than Rad26 in transcription coupled DNA repair. Nucleic Acids Res. 2016;44:6794-802 pubmed publisher
    ..Our results indicate that Sen1 plays a more direct role than Rad26 in TCR. ..
  48. Koyama H, Sumiya E, Nagata M, Ito T, Sekimizu K. Transcriptional repression of the IMD2 gene mediated by the transcriptional co-activator Sub1. Genes Cells. 2008;13:1113-26 pubmed publisher
    ..These results suggest that the transcriptional co-activator Sub1 also has a role in transcriptional repression during transcription initiation in vivo. ..
  49. Villanyi Z, Ribaud V, Kassem S, Panasenko O, Pahi Z, Gupta I, et al. The Not5 subunit of the ccr4-not complex connects transcription and translation. PLoS Genet. 2014;10:e1004569 pubmed publisher
    ..Hence taken together our results show that Not5 interconnects translation and transcription. ..
  50. Walmacq C, Kireeva M, Irvin J, Nedialkov Y, Lubkowska L, Malagon F, et al. Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II. J Biol Chem. 2009;284:19601-12 pubmed publisher
    b>Rpb9 is a small non-essential subunit of yeast RNA polymerase II located on the surface on the enzyme...
  51. Gibney P, Fries T, Bailer S, Morano K. Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins. Eukaryot Cell. 2008;7:938-48 pubmed publisher
    ..The core RNAPII subunits RPB5, RPB7, and RPB9 were isolated as potent high-copy-number suppressors of the rtr1Delta temperature-sensitive growth phenotype, and ..
  52. Kolodziej P, Woychik N, Liao S, Young R. RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol Cell Biol. 1990;10:1915-20 pubmed
    ..These results more precisely define the subunit composition and phosphorylation of a eucaryotic RNA polymerase II enzyme. ..