Genomes and Genes
Gene Symbol: RPB3
Description: DNA-directed RNA polymerase II core subunit RPB3
Alias: DNA-directed RNA polymerase II core subunit RPB3
Species: Saccharomyces cerevisiae S288c
- Chen H, Hahn S. Binding of TFIIB to RNA polymerase II: Mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex. Mol Cell. 2003;12:437-47 pubmed..This surface is best conserved in polymerases that require a TFIIB-like factor. Our results suggest a general mechanism for interaction of TFIIB-like factors and RNA polymerases and a mechanism for the function of the ribbon domain. ..
- Myers L, Gustafsson C, Bushnell D, Lui M, Erdjument Bromage H, Tempst P, et al. The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev. 1998;12:45-54 pubmed..Evidence for human homologs of several mediator proteins, including Med7, points to similar mechanisms in higher cells. ..
- Allepuz Fuster P, MartÃnez FernÃ¡ndez V, Garrido Godino A, Alonso Aguado S, Hanes S, Navarro F, et al. Rpb4/7 facilitates RNA polymerase II CTD dephosphorylation. Nucleic Acids Res. 2014;42:13674-88 pubmed..Based on these and other results, we suggest a model in which Rpb4/7 helps recruit and potentially stimulate the activity of CTD-modifying enzymes, a role that is central to RNAPII function. ..
- Smith Kinnaman W, Berna M, Hunter G, True J, Hsu P, Cabello G, et al. The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae. Mol Biosyst. 2014;10:1730-41 pubmed publisher..Interestingly, we found that the interaction between Rtr1 and RNAPII is decreased in ctk1? strains. We hypothesize that serine-2 CTD phosphorylation is required for Rtr1 recruitment to RNAPII during transcription elongation. ..
- Jedidi I, Zhang F, Qiu H, Stahl S, Palmer I, Kaufman J, et al. Activator Gcn4 employs multiple segments of Med15/Gal11, including the KIX domain, to recruit mediator to target genes in vivo. J Biol Chem. 2010;285:2438-55 pubmed publisher..Gcn4 is distinctive in relying on comparable contributions from multiple segments of Gal11 for efficient recruitment of Mediator in vivo. ..
- Watson A, Edmondson D, Bone J, Mukai Y, Yu Y, Du W, et al. Ssn6-Tup1 interacts with class I histone deacetylases required for repression. Genes Dev. 2000;14:2737-44 pubmed..Strikingly, two of these class I HDACs interact physically with Ssn6-Tup1. These findings suggest that Ssn6-Tup1 actively recruits deacetylase activities to deacetylate adjacent nucleosomes and promote Tup1-histone interactions. ..
- Suh M, Ye P, Zhang M, Hausmann S, Shuman S, Gnatt A, et al. Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD. Proc Natl Acad Sci U S A. 2005;102:17314-9 pubmed..We speculate that Fcp1 interaction with the non-CTD site may mediate its stimulatory effect on transcription elongation reported previously. ..
- Gómez Navarro N, Peiró Chova L, Rodriguez Navarro S, Polaina J, Estruch F. Rtp1p is a karyopherin-like protein required for RNA polymerase II biogenesis. Mol Cell Biol. 2013;33:1756-67 pubmed publisher..is compatible with a role for Rtp1p as an assembly factor that participates in the formation of the Rpb2/Rpb3 subassembly complex and its binding to the Rpb1p-containing subcomplex...
- Sung P, Guzder S, Prakash L, Prakash S. Reconstitution of TFIIH and requirement of its DNA helicase subunits, Rad3 and Rad25, in the incision step of nucleotide excision repair. J Biol Chem. 1996;271:10821-6 pubmed..These studies reveal the differential requirement of Rad3 DNA helicase and CTD kinase activities in damage-specific incision versus RNA polymerase II transcription. ..
- Nouraini S, Archambault J, Friesen J. Rpo26p, a subunit common to yeast RNA polymerases, is essential for the assembly of RNA polymerases I and II and for the stability of the largest subunits of these enzymes. Mol Cell Biol. 1996;16:5985-96 pubmed..Furthermore, A190p and Rpo21p continued to accumulate at low levels under these conditions. We suggest that Rpo26p is essential for the assembly of RNAPI and RNAPII and for the stability of the largest subunits of these enzymes. ..
- 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. ..
- 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. ..
- Soutourina J, Wydau S, Ambroise Y, Boschiero C, Werner M. Direct interaction of RNA polymerase II and mediator required for transcription in vivo. Science. 2011;331:1451-4 pubmed publisher..We identify a direct physical interaction between the Rpb3 Pol II subunit of Saccharomyces cerevisiae and the essential Mediator subunit, Med17...
- Burugula B, Jeronimo C, Pathak R, Jones J, Robert F, Govind C. Histone deacetylases and phosphorylated polymerase II C-terminal domain recruit Spt6 for cotranscriptional histone reassembly. Mol Cell Biol. 2014;34:4115-29 pubmed publisher..Collectively, our results show that a complex network of interactions, involving the Spt6 tSH2 domain, CTD phosphorylation, and histone deacetylases, coordinate the recruitment of Spt6 to transcribed genes in vivo. ..
- Calvo O, Manley J. The transcriptional coactivator PC4/Sub1 has multiple functions in RNA polymerase II transcription. EMBO J. 2005;24:1009-20 pubmed..Our data provide evidence that Rna15 and Sub1 are present along the length of several genes and that Sub1 facilitates elongation by influencing enzymes that modify RNAP II. ..
- Lee Y, Min S, Gim B, Kim Y. A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. Mol Cell Biol. 1997;17:4622-32 pubmed..A database search revealed the existence of MED6-related genes in humans and Caenorhabditis elegans, suggesting that the role of mediator in transcriptional activation is conserved throughout the evolution. ..
- Eyboulet F, Wydau Dematteis S, Eychenne T, Alibert O, Neil H, Boschiero C, et al. Mediator independently orchestrates multiple steps of preinitiation complex assembly in vivo. Nucleic Acids Res. 2015;43:9214-31 pubmed publisher..This study provides an extensive genome-wide view of Mediator's role in PIC formation, suggesting that Mediator coordinates multiple steps of a PIC assembly pathway. ..
- Han S, Lee J, Kang J, Kim Y. Med9/Cse2 and Gal11 modules are required for transcriptional repression of distinct group of genes. J Biol Chem. 2001;276:37020-6 pubmed
- 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. ..
- Sikorski T, Ficarro S, Holik J, Kim T, Rando O, Marto J, et al. Sub1 and RPA associate with RNA polymerase II at different stages of transcription. Mol Cell. 2011;44:397-409 pubmed publisher..We propose that Sub1 and RPA interact with the nontemplate strand of RNApII complexes during initiation and elongation, respectively. ..
- Meinel D, Burkert Kautzsch C, Kieser A, O Duibhir E, Siebert M, Mayer A, et al. Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II. PLoS Genet. 2013;9:e1003914 pubmed publisher..In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment...
- 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..We conclude that Rpb9 supports intra-pol II interactions that modulate TL function and thus pol II enzymatic properties. ..
- Sathianathan A, Ravichandran P, Lippi J, Cohen L, Messina A, Shaju S, et al. The Eaf3/5/7 Subcomplex Stimulates NuA4 Interaction with Methylated Histone H3 Lys-36 and RNA Polymerase II. J Biol Chem. 2016;291:21195-21207 pubmed..Overall, these results reveal the function of Eaf3/5/7 within NuA4 to be important for both NuA4 and RNA polymerase II binding. ..
- Fellows J, Erdjument Bromage H, Tempst P, Svejstrup J. The Elp2 subunit of elongator and elongating RNA polymerase II holoenzyme is a WD40 repeat protein. J Biol Chem. 2000;275:12896-9 pubmed..Generally, different combinations of double and triple ELP gene deletions cause the same phenotypes as single ELP1, ELP2, or ELP3 deletion, providing genetic evidence that the ELP gene products work together in a complex. ..
- 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. ..
- Kurat C, Lambert J, van Dyk D, Tsui K, van Bakel H, Kaluarachchi S, et al. Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein. Genes Dev. 2011;25:2489-501 pubmed publisher..Our study identified the chromatin boundary protein Yta7 as a key regulator that links S-phase kinases with RNAPII function at cell cycle-regulated histone gene promoters. ..
- 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. ..
- Suh H, Ficarro S, Kang U, Chun Y, Marto J, Buratowski S. Direct Analysis of Phosphorylation Sites on the Rpb1 C-Terminal Domain of RNA Polymerase II. Mol Cell. 2016;61:297-304 pubmed publisher..Furthermore, msCTD associated with capping enzyme was enriched for Ser5-P while that bound to the transcription termination factor Rtt103 had higher levels of Ser2-P. These results suggest a relatively sparse and simple "CTD code." ..
- Alonso B, Beraud C, Meguellati S, Chen S, Pellequer J, Armengaud J, et al. Eukaryotic GPN-loop GTPases paralogs use a dimeric assembly reminiscent of archeal GPN. Cell Cycle. 2013;12:463-72 pubmed publisher..These results suggest that all three GPN proteins act at the molecular level in sister chromatid cohesion mechanism as a GPN|GPN complex reminiscent of the homodimeric structure of PAB0955, an archaeal member of GPN-loop GTPase. ..
- Proft M, Struhl K. MAP kinase-mediated stress relief that precedes and regulates the timing of transcriptional induction. Cell. 2004;118:351-61 pubmed
- Suh H, Hazelbaker D, Soares L, Buratowski S. The C-terminal domain of Rpb1 functions on other RNA polymerase II subunits. Mol Cell. 2013;51:850-8 pubmed publisher..Normal CTD functions are not transferred to RNApI or RNApIII by Rbp6-CTD. These results show that, with some spatial constraints, CTD can function even when disconnected from Rpb1. ..
- 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. ..
- Christie K, Awrey D, Edwards A, Kane C. Purified yeast RNA polymerase II reads through intrinsic blocks to elongation in response to the yeast TFIIS analogue, P37. J Biol Chem. 1994;269:936-43 pubmed
- Vasiljeva L, Buratowski S. Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts. Mol Cell. 2006;21:239-48 pubmed..Since Nrd1 is known to bind RNA polymerase II and be important for sn/snoRNA 3' end processing, Nrd1 may link transcription and RNA 3' end formation with surveillance by the exosome. ..
- Chung W, Craighead J, Chang W, Ezeokonkwo C, Bareket Samish A, Kornberg R, et al. RNA polymerase II/TFIIF structure and conserved organization of the initiation complex. Mol Cell. 2003;12:1003-13 pubmed..The structure of the RNAPII/TFIIF complex suggests a model for the organization of a minimal transcription initiation complex. ..
- 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. ..
- 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. ..
- 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..crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them...
- Han S, Lee Y, Gim B, Ryu G, Park S, Lane W, et al. Activator-specific requirement of yeast mediator proteins for RNA polymerase II transcriptional activation. Mol Cell Biol. 1999;19:979-88 pubmed
- Harel Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M. RNA polymerase II subunits link transcription and mRNA decay to translation. Cell. 2010;143:552-63 pubmed publisher..We propose that Rpb4/7, through its interactions at each step in the mRNA lifecycle, represents a class of factors, "mRNA coordinators," which integrate the various stages of gene expression into a system. ..
- Duan R, Rhie B, Ryu H, Ahn S. The RNA polymerase II Rpb4/7 subcomplex regulates cellular lifespan through an mRNA decay process. Biochem Biophys Res Commun. 2013;441:266-70 pubmed
- Kolodziej P, Woychik N, Liao S, Young R. RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol Cell Biol. 1990;10:1915-20 pubmed..cerevisiae by attaching an epitope coding sequence to a well-characterized RNA polymerase II subunit gene (RPB3) and by immunoprecipitating the product of this gene with its associated polypeptides...
- Rosenheck S, Choder M. Rpb4, a subunit of RNA polymerase II, enables the enzyme to transcribe at temperature extremes in vitro. J Bacteriol. 1998;180:6187-92 pubmed..This result suggests that Pol II molecules should be modified in order to recruit Rpb4; the portion of the modified Pol II molecules is small during logarithmic phase and becomes predominant in stationary phase. ..
- Li B, Howe L, Anderson S, Yates J, Workman J. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem. 2003;278:8897-903 pubmed..Collectively, these results suggest that Set2 is involved in regulating transcription elongation through its direct contact with pol II. ..
- Jasiak A, Hartmann H, Karakasili E, Kalocsay M, Flatley A, Kremmer E, et al. Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. J Biol Chem. 2008;283:26423-7 pubmed publisher..We show that the genome-wide occupancy profiles for Rpb7 and the core subunit Rpb3 are essentially identical...
- Nordick K, Hoffman M, BETZ J, Jaehning J. Direct interactions between the Paf1 complex and a cleavage and polyadenylation factor are revealed by dissociation of Paf1 from RNA polymerase II. Eukaryot Cell. 2008;7:1158-67 pubmed publisher..The lack of this connection helps to explain the defects in 3'-end formation observed in the absence of Paf1. ..
- Otero G, Fellows J, Li Y, de Bizemont T, Dirac A, Gustafsson C, et al. Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol Cell. 1999;3:109-18 pubmed..Our data indicate that the transition from transcriptional initiation to elongation involves an exchange of the multiprotein mediator complex for elongator in a reaction coupled to CTD hyperphosphorylation. ..
- Gustafsson C, Myers L, Li Y, Redd M, Lui M, Erdjument Bromage H, et al. Identification of Rox3 as a component of mediator and RNA polymerase II holoenzyme. J Biol Chem. 1997;272:48-50 pubmed
- 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. ..
- Eychenne T, Novikova E, Barrault M, Alibert O, Boschiero C, Peixeiro N, et al. Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture. Genes Dev. 2016;30:2119-2132 pubmed..This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts. ..
- Mirón García M, Garrido Godino A, García Molinero V, Hernández Torres F, Rodriguez Navarro S, Navarro F. The prefoldin bud27 mediates the assembly of the eukaryotic RNA polymerases in an rpb5-dependent manner. PLoS Genet. 2013;9:e1003297 pubmed publisher..Finally, the role of URI seems to be conserved in humans, suggesting conserved mechanisms in RNA pols biogenesis. ..
- 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. ..
- Woychik N, Liao S, Kolodziej P, Young R. Subunits shared by eukaryotic nuclear RNA polymerases. Genes Dev. 1990;4:313-23 pubmed
- Takahashi H, Kasahara K, Kokubo T. Saccharomyces cerevisiae Med9 comprises two functionally distinct domains that play different roles in transcriptional regulation. Genes Cells. 2009;14:53-67 pubmed publisher..Add-back experiments indicate that some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter. ..
- Leblanc B, Benham C, Clark D. An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled. Proc Natl Acad Sci U S A. 2000;97:10745-50 pubmed..The role of transcription factors might be to mark the promoter and to regulate specific melting of promoter DNA. ..
- Thurtle Schmidt D, Dodson A, Rine J. Histone Deacetylases with Antagonistic Roles in Saccharomyces cerevisiae Heterochromatin Formation. Genetics. 2016;204:177-90 pubmed publisher..Additionally, restoration of silencing by Rpd3 was dependent on another sirtuin family member, Hst3, indicating multiple antagonistic roles for deacetylases in S. cerevisiae silencing. ..
- 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. ..
- Benga W, Grandemange S, Shpakovski G, Shematorova E, Kedinger C, Vigneron M. Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II. Nucleic Acids Res. 2005;33:3582-90 pubmedIn Saccharomyces cerevisiae, RNA polymerase II assembly is probably initiated by the formation of the RPB3-RPB11 heterodimer. RPB3 is encoded by a single copy gene in the yeast, mouse and human genomes...
- Yudkovsky N, Ranish J, Hahn S. A transcription reinitiation intermediate that is stabilized by activator. Nature. 2000;408:225-9 pubmed..The scaffold is stabilized in the presence of the activator Gal4-VP16, but not Gal4-AH, suggesting a new role for some activators and Mediator in promoting high levels of transcription. ..
- Bouchoux C, Hautbergue G, Grenetier S, Carles C, Riva M, Goguel V. CTD kinase I is involved in RNA polymerase I transcription. Nucleic Acids Res. 2004;32:5851-60 pubmed..The results suggest that CTDK-I might participate in the regulation of distinct nuclear transcriptional machineries, thus playing a role in the adaptation of the global transcriptional response to growth signalling. ..
- 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. ..
- Rani P, Ranish J, Hahn S. RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation. Mol Cell Biol. 2004;24:1709-20 pubmed..These results suggest that both the Pol II-Med and Pol II-TFIIF complexes can be recruited for transcription initiation but that only the Pol II-TFIIF complex is competent for transcription reinitiation. ..
- Nair D, Kim Y, Myers L. Mediator and TFIIH govern carboxyl-terminal domain-dependent transcription in yeast extracts. J Biol Chem. 2005;280:33739-48 pubmed
- DERMODY J, Buratowski S. Leo1 subunit of the yeast paf1 complex binds RNA and contributes to complex recruitment. J Biol Chem. 2010;285:33671-9 pubmed publisher..Together, these results suggest that association of Paf1C with RNA stabilizes its localization at actively transcribed regions where it influences chromatin structure. ..
- 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. ..
- 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. ..