Genomes and Genes
Gene Symbol: RPB2
Description: DNA-directed RNA polymerase II core subunit RPB2
Alias: RPB150, RPO22, SIT2, SOH2, DNA-directed RNA polymerase II core subunit RPB2
Species: Saccharomyces cerevisiae S288c
- Grünberg S, Warfield L, Hahn S. Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening. Nat Struct Mol Biol. 2012;19:788-96 pubmed publisher..Right-handed threading of DNA through the Ssl2 binding groove, combined with the fixed position of upstream promoter DNA, leads to DNA unwinding and the open state. ..
- Eichner J, Chen H, Warfield L, Hahn S. Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex. EMBO J. 2010;29:706-16 pubmed publisher..Consistent with this mechanism, mutations far from the enzyme active site, which alter the binding of either structured TFIIF domains to Pol II, have similar defects in transcription start site usage. ..
- Lennon J, Wind M, Saunders L, Hock M, Reines D. Mutations in RNA polymerase II and elongation factor SII severely reduce mRNA levels in Saccharomyces cerevisiae. Mol Cell Biol. 1998;18:5771-9 pubmed..Using yeast lacking SII and bearing a conditional allele of RPB2, the gene encoding the second largest subunit of RNA polymerase II, we describe a genetic interaction between SII ..
- 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. ..
- 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. ..
- Konopka C, Locke M, Gallagher P, Pham N, Hart M, Walker C, et al. A yeast model for polyalanine-expansion aggregation and toxicity. Mol Biol Cell. 2011;22:1971-84 pubmed publisher..Thus longer expansions may have a different mechanism for toxicity. We think that this difference underscores the potential need to examine the cytotoxic mechanisms of both long and short expansions in models of expansion disorders. ..
- Murray S, Udupa R, Yao S, Hartzog G, Prelich G. Phosphorylation of the RNA polymerase II carboxy-terminal domain by the Bur1 cyclin-dependent kinase. Mol Cell Biol. 2001;21:4089-96 pubmed..These results identify Bur1 as a fourth S. cerevisiae CTD kinase and provide striking functional similarities between Bur1 and metazoan P-TEFb. ..
- 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. ..
- 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. ..
- Terzi N, Churchman L, Vasiljeva L, Weissman J, Buratowski S. H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway. Mol Cell Biol. 2011;31:3569-83 pubmed publisher..We speculate that Set1 promotes proper early termination by the Nrd1-Nab3-Sen1 complex by affecting the kinetics of Pol II transcription in early elongation. ..
- 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. ..
- 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. ..
- 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. ..
- Scafe C, Nonet M, Young R. RNA polymerase II mutants defective in transcription of a subset of genes. Mol Cell Biol. 1990;10:1010-6 pubmed..The transcriptional defects exhibited by one of these Ino- mutants (rpb2-2) were further investigated...
- Kaplan C, Holland M, Winston F. Interaction between transcription elongation factors and mRNA 3'-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. J Biol Chem. 2005;280:913-22 pubmed..Overall, these results provide new evidence for a connection between the transcription elongation factor Spt6 and 3'-end formation in vivo. ..
- Kolodziej P, Woychik N, Liao S, Young R. RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol Cell Biol. 1990;10:1915-20 pubmed..Immunoprecipitation from 32P-labeled cell extracts revealed that three of the subunits, RPB1, RPB2, and RPB6, are phosphorylated in vivo...
- Domecq C, Kireeva M, Archambault J, Kashlev M, Coulombe B, Burton Z. Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II. Protein Expr Purif. 2010;69:83-90 pubmed publisher..In this work, we demonstrate a method to generate and purify site-directed mutants in the second largest (Rpb2) RNAP II subunit from yeast, using a tandem affinity purification tag...
- Felipe Abrio I, Lafuente Barquero J, GarcÃa Rubio M, Aguilera A. RNA polymerase II contributes to preventing transcription-mediated replication fork stalls. EMBO J. 2015;34:236-50 pubmed publisher..Our results imply that the RNAPII or ancillary factors actively help prevent transcription-associated genome instability. ..
- 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. ..
- Suh M, Meyer P, Gu M, Ye P, Zhang M, Kaplan C, et al. A dual interface determines the recognition of RNA polymerase II by RNA capping enzyme. J Biol Chem. 2010;285:34027-38 pubmed publisher..Our results indicate that the dual interface based on combining PCI1 and PCI2 is required for directing CE to Pol II elongation complexes. ..
- Feaver W, Svejstrup J, Henry N, Kornberg R. Relationship of CDK-activating kinase and RNA polymerase II CTD kinase TFIIH/TFIIK. Cell. 1994;79:1103-9 pubmed..We show that human CAK possesses the CTD kinase activity characteristic of TFIIH. ..
- 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
- 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..catalytic center of yeast RNA polymerase II and III contains an acidic loop borne by their second largest subunit (Rpb2-(832)GYNQED(837), Rpc128-(764)GYDIED(769)) and highly conserved in all cellular and viral DNA-dependent RNA ..
- Somesh B, Sigurdsson S, Saeki H, Erdjument Bromage H, Tempst P, Svejstrup J. Communication between distant sites in RNA polymerase II through ubiquitylation factors and the polymerase CTD. Cell. 2007;129:57-68 pubmed..These data reveal the specificity and mechanism of RNAPII ubiquitylation and demonstrate that E2s can play a crucial role in substrate recognition. ..
- 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. ..
- Li J, Moazed D, Gygi S. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem. 2002;277:49383-8 pubmed..Together, our results suggest that Set2 through association with the elongating form of RNA polymerase II plays an important role in transcription elongation. ..
- Reyes Reyes M, Hampsey M. Role for the Ssu72 C-terminal domain phosphatase in RNA polymerase II transcription elongation. Mol Cell Biol. 2007;27:926-36 pubmed..Mutations in RPB1 and RPB2, the genes encoding the two largest subunits of RNAP II, were identified as suppressors of ssu72-2...
- 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. ..
- Costa P, Arndt K. Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics. 2000;156:535-47 pubmed..Collectively, our results suggest that Rtf1 may function as a novel transcription elongation factor in yeast. ..
- 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..A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing ..
- 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. ..
- 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. ..
- Chang M, French Cornay D, Fan H, Klein H, Denis C, Jaehning J. A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol Cell Biol. 1999;19:1056-67 pubmed..Our observation that the Mpk1p kinase is fully active in a paf1Delta strain indicates that the Paf1p-Cdc73p complex may function downstream of the Pkc1p-Mpk1p cascade to regulate the expression of a subset of yeast genes. ..
- CieÅ›la M, MakaÅ‚a E, PÅ‚onka M, Bazan R, Gewartowski K, Dziembowski A, et al. Rbs1, a new protein implicated in RNA polymerase III biogenesis in yeast Saccharomyces cerevisiae. Mol Cell Biol. 2015;35:1169-81 pubmed publisher..Additionally, Rbs1 interacts with the Crm1 exportin and shuttles between the cytoplasm and nucleus. We postulate that Rbs1 binds to the Pol III complex or subcomplex and facilitates its translocation to the nucleus. ..
- 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..and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit...
- Fong N, Saldi T, Sheridan R, Cortázar M, Bentley D. RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction. Mol Cell. 2017;66:546-557.e3 pubmed publisher..These results demonstrate that pol II dynamics help govern the decision between sense and divergent antisense transcription. ..
- Denis C, Chiang Y, Cui Y, Chen J. Genetic evidence supports a role for the yeast CCR4-NOT complex in transcriptional elongation. Genetics. 2001;158:627-34 pubmed..deletion of ccr4 resulted in severe synthetic effects with mutations or deletions in the known elongation factors RPB2, TFIIS, and SPT16...
- Mueller C, Jaehning J. Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol Cell Biol. 2002;22:1971-80 pubmed..We suggest that lack of Paf1 results in a defective complex and a block in transcription, which is relieved by removal of Leo1 or Rtf1. ..
- 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. ..
- Sheffer A, Varon M, Choder M. Rpb7 can interact with RNA polymerase II and support transcription during some stresses independently of Rpb4. Mol Cell Biol. 1999;19:2672-80 pubmed..When RPB7 is overexpressed, more Rpb7 assembles with Pol IIDelta4, enough to permit appropriate transcription also under some stress conditions. ..
- Gilbert T, McDaniel S, Byrum S, Cades J, Dancy B, Wade H, et al. A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions. Mol Cell Proteomics. 2014;13:2883-95 pubmed publisher..Collectively, these studies define a new form of the NuA3 complex that associates with H3K36me3 to effect transcriptional elongation. MS data are available via ProteomeXchange with identifier PXD001156. ..
- 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..the critical part of Rpb9 is limited to a N-terminal half that contacts the lobe of the second largest subunit (Rpb2) and forms a beta-addition motif with the "jaw" of the largest subunit (Rpb1)...
- Martin C, Young R. KEX2 mutations suppress RNA polymerase II mutants and alter the temperature range of yeast cell growth. Mol Cell Biol. 1989;9:2341-9 pubmed..These results indicate that the KEX2 protease, whose only known substrates are hormone precursors, can have an important influence on RNA polymerase II and the temperature-dependent growth properties of yeast cells. ..
- Jimeno González S, Schmid M, Malagon F, Haaning L, Jensen T. Rat1p maintains RNA polymerase II CTD phosphorylation balance. RNA. 2014;20:551-8 pubmed publisher..allele is synthetic lethal with the rpb1-E1103G mutation, causing increased RNAPII speed, and is suppressed by the rpb2-10 mutation, causing slowed transcription...
- 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. ..
- Niesser J, Wagner F, Kostrewa D, MÃ¼hlbacher 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. ..
- 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. ..
- Chen B, Hampsey M. Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation. Mol Cell Biol. 2004;24:3983-91 pubmed..Suppression of the R78C Csm(-) phenotype identified a functional interaction between TFIIB and the Rpb2 subunit of RNAP II and defined a novel role for Rpb2 in start site selection...
- Chen H, Hahn S. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell. 2004;119:169-80 pubmed..The TFIIF subunit Tfg1 was found in close proximity to the TFIIB B finger, linker, and core domains, suggesting that these two factors closely cooperate during initiation. ..
- 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. ..
- 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. ..
- Fan H, Klein H. Characterization of mutations that suppress the temperature-sensitive growth of the hpr1 delta mutant of Saccharomyces cerevisiae. Genetics. 1994;137:945-56 pubmed..The SOH1 gene has been cloned and sequenced. The null allele is 10-fold increased for recombination as measured by deletion of a leu2 direct repeat. ..
- 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
- Arndt K, Styles C, Fink G. A suppressor of a HIS4 transcriptional defect encodes a protein with homology to the catalytic subunit of protein phosphatases. Cell. 1989;56:527-37 pubmed..Two of these suppressors, SIT1 and SIT2, are encoded by RPB1 and RPB2, the genes for the two largest subunits of RNA polymerase II...
- Kvint K, Uhler J, Taschner M, Sigurdsson S, Erdjument Bromage H, Tempst P, et al. Reversal of RNA polymerase II ubiquitylation by the ubiquitin protease Ubp3. Mol Cell. 2008;30:498-506 pubmed publisher..In agreement with this, cells with compromised DNA repair are better equipped to survive UV damage when UPB3 is deleted. ..
- Pearson E, Moore C. The evolutionarily conserved Pol II flap loop contributes to proper transcription termination on short yeast genes. Cell Rep. 2014;9:821-8 pubmed publisher..We propose a model in which the flap loop coordinates a binding equilibrium between the competing termination factors Pcf11 and Nrd1 to Pol II during termination of short RNA synthesis. ..
- 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. ..
- Baranes Bachar K, Baranes Bacher K, Khalaila I, Ivantsiv Y, Lavut A, Voloshin O, et al. New interacting partners of the F-box protein Ufo1 of yeast. Yeast. 2008;25:733-43 pubmed publisher..We show directly that the UIMs are crucial for Ufo1 ubiquitylation in vivo, indicating that they facilitate turnover of SCF Ufo1 complexes. This allows recycling of the core subunits of the SCF complex and cell cycle progression. ..
- Pappas D, Hampsey M. Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae. Mol Cell Biol. 2000;20:8343-51 pubmed..One suppressor is allelic to RPB2, the gene encoding the second-largest subunit of RNA polymerase II (RNAP II)...
- Garrido Godino A, García López M, Navarro F. Correct assembly of RNA polymerase II depends on the foot domain and is required for multiple steps of transcription in Saccharomyces cerevisiae. Mol Cell Biol. 2013;33:3611-26 pubmed publisher..Finally, our data help clarify the mechanisms governing the assembly and stability of RNA pol II. ..
- 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..of interactions 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...
- 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. ..
- 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. ..
- 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