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POLR2C

DNA-directed RNA polymerase II subunit RPB3 · UniProt P19387

Length
275 aa
Mass
31.4 kDa
Annotated
2026-06-10
18 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: tie faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

POLR2C (RPB3) is the third-largest, alpha-like core subunit of RNA polymerase II and is essential for assembly of the holoenzyme and for mRNA transcription (PMID:2685562). It is present at one copy per polymerase and nucleates RNAPII assembly by heterodimerizing with RPB11 through conserved alpha-homology regions, deletion of which abolishes its incorporation into the enzyme (PMID:9556554, PMID:15987790); within the assembled polymerase it directly contacts the beta-homologue Rpb2 (PMID:9738888). Structure-based mutagenesis partitions RPB3 into terminal conserved regions required for assembly and central eukaryote-specific regions required for activator-dependent transcription, the latter mapping to a structurally conserved surface homologous to the bacterial alpha CAP-interaction site (PMID:10673505, PMID:11453250). Through this eukaryote-specific region RPB3 serves as a docking point that recruits sequence-specific transcription factors—including myogenin, ATF4, and Snail—to the polymerase, thereby coupling RNAPII to myogenic differentiation, stress-responsive transactivation, and Snail-driven E-cadherin repression and epithelial-mesenchymal transition (PMID:12207009, PMID:12860379, PMID:25211001). Its incorporation into the nascent Rpb3 subcomplex is chaperoned by Gpn2 and Rba50 (PMID:29661922).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1989 High

    Established that RPB3 is an essential gene whose product is required for the very assembly of RNA polymerase II, defining it as a core structural subunit rather than an accessory factor.

    Evidence Temperature-sensitive rpb3 mutant with immunological RNAPII depletion and mRNA measurement in yeast

    PMID:2685562

    Open questions at the time
    • Did not resolve which RPB3 domains drive assembly
    • No structural placement within the enzyme
  2. 1998 High

    Defined the stoichiometry and assembly determinants, showing one RPB3 copy per polymerase and that conserved alpha-homology regions are obligatory for incorporation.

    Evidence Immunoaffinity/nickel-chelate purification of tagged RNAPII plus deletion mutagenesis; two-hybrid mapping of the Rpb2 contact

    PMID:9556554 PMID:9738888

    Open questions at the time
    • Rpb2 contact mapped only by two-hybrid, no biochemical confirmation
    • Order of subunit addition not established
  3. 1999 Medium

    Localized assembly-critical mutations to conserved region A and showed RPB11 overexpression suppresses the phenotype, pinpointing the RPB3–RPB11 subassembly as the key step.

    Evidence Random mutagenesis and overexpression suppression analysis in fission yeast

    PMID:10503538

    Open questions at the time
    • Single-lab genetic analysis
    • Structural basis of the RPB3–RPB11 interface not resolved here
  4. 2001 Medium

    Functionally separated RPB3's assembly role from its transcription-activation role, mapping assembly to terminal conserved regions and activator-dependent transcription to central eukaryote-specific regions B and C.

    Evidence In vitro GAL4-VP16 activator-dependent transcription with rpb3 mutant extracts; earlier structure-based C92R/A159G mutagenesis defining the conserved activation surface

    PMID:10673505 PMID:11453250

    Open questions at the time
    • Direct activator contacts at the surface not biochemically demonstrated
    • Single lab
  5. 2005 Medium

    Showed the RPB3–RPB11 heterodimer initiates assembly and that the heterodimerization interface diverged between yeast and humans, refining the molecular basis of polymerase nucleation.

    Evidence In vitro heterodimerization assays with human and yeast truncation mutants

    PMID:15987790

    Open questions at the time
    • No structural model of the human interface
    • Functional consequence of interface divergence untested
  6. 2014 Medium

    Extended RPB3's role to factor recruitment, establishing that its eukaryote-specific surface (Sud/N-terminus) directly binds sequence-specific transcription factors to couple RNAPII to differentiation, stress, and EMT programs.

    Evidence Yeast two-hybrid, reciprocal Co-IP, and dominant-negative fragment assays for myogenin, ATF4, and Snail across muscle differentiation and HCC models

    PMID:12207009 PMID:12860379 PMID:25211001

    Open questions at the time
    • Interactions shown largely in single-lab systems
    • How factor binding at RPB3 mechanistically alters transcription is unresolved
  7. 2018 Medium

    Identified dedicated assembly chaperones, showing Gpn2 and Rba50 cooperatively build the Rpb3 subcomplex during RNAPII biogenesis.

    Evidence Co-IP, pulldown, and loss-of-function with RNAPII assembly readout

    PMID:29661922

    Open questions at the time
    • Structural mechanism of chaperone-assisted assembly unknown
    • Single lab
  8. 2025 Medium

    Revealed a role for the RPB3 elongation-complex surface in transcription termination, where residue K9 forms a salt-bridge surface regulating Hrp1 binding and NNS-dependent terminator readthrough.

    Evidence Allele-specific mutagenesis and suppressor selection in HRP1 with transcriptome readthrough assays in yeast (preprint)

    PMID:bio_10.1101_2025.05.07.652672

    Open questions at the time
    • Preprint, not peer-reviewed
    • Direct Rpb3-K9–Hrp1 contact not structurally confirmed
    • Relevance to human termination untested

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the eukaryote-specific factor-recruitment surface of RPB3 mechanistically integrates with the core enzyme to modulate initiation, elongation, and termination remains unresolved.
  • No structural model of factor-bound RPB3 within the holoenzyme
  • Human relevance of yeast termination findings untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 4 GO:0005198 structural molecule activity 2
Localization
GO:0005634 nucleus 1
Pathway
R-HSA-74160 Gene expression (Transcription) 2
Partners
ATF4GPN2IGFBP3MYOGENINPOLR2BPOLR2JRBA50SNAIL
Complex memberships
RNA polymerase II

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1989 RPB3 (POLR2C) is an essential single-copy gene encoding the third-largest subunit of RNA polymerase II; a temperature-sensitive rpb3 mutant prevented RNA polymerase II assembly, depleted functional enzyme, and reduced mRNA levels, demonstrating RPB3 is required for RNAPII assembly and mRNA transcription. Temperature-sensitive mutant analysis, immunological depletion of RNAPII, mRNA level measurement Molecular and cellular biology High 2685562
1998 Rpb3 (POLR2C) is present at a stoichiometry of one copy per RNA polymerase II molecule; deletion of either alpha-homology region (amino acids 29–55 or 226–267) abolishes Rpb3 assembly into RNAPII in vivo. Immunoaffinity and nickel-chelate chromatography of His6-tagged and untagged Rpb3-containing RNAPII; deletion mutagenesis The Journal of biological chemistry High 9556554
1998 Rpb3 (POLR2C) contacts Rpb2 (the beta-homologue) at the conserved region H of Rpb2, as mapped by two-hybrid screening using fission yeast subunit fragments. Yeast two-hybrid system with truncation fragments of Rpb1 and Rpb2 Molecular & general genetics : MGG Medium 9738888
1999 Temperature-sensitive and cold-sensitive mutations in fission yeast rpb3 map to four conserved regions (A–D); cold-sensitive mutations in region A disrupt RNAPII assembly, and the Ts phenotype is suppressed by overexpression of Rpb11 (the pairing partner of Rpb3), establishing that Rpb3 mutations primarily affect the Rpb3–Rpb11 subassembly. Random mutagenesis, temperature/cold-sensitive growth assays, overexpression suppression analysis Molecular & general genetics : MGG Medium 10503538
2000 Amino acid substitutions C92R and A159G in yeast RPB3 (POLR2C) specifically impair activator-dependent transcription without affecting basal transcription; homology modeling on the bacterial alpha-NTD crystal structure places residues 92–95 and 159–162 adjacent in 3D space, corresponding to the CAP activator-interaction surface of the bacterial alpha subunit, indicating a structurally conserved activation surface in RPB3. Alanine-scanning and targeted mutagenesis, activator-dependent transcription assays, homology modeling on bacterial alpha-NTD crystal structure Genes & development High 10673505
2001 In vitro functional analysis of fission yeast Rpb3 mutants shows that mutations in terminal conserved regions A and D impair RNAPII assembly, while mutations in central eukaryote-specific regions B and C reduce activator (GAL4-VP16)-dependent transcription without equivalent assembly defects, functionally partitioning assembly from activated transcription roles within Rpb3. In vitro GAL4-VP16 activator-dependent transcription system using S. pombe cell extracts from rpb3 mutants, heat treatment assays Current genetics Medium 11453250
2001 The interaction site of Rpb2 with Rpb3 in fission yeast RNAPII was mapped to the C-terminal region of Rpb2 (amino acids 902–989, encoded by base 2701–2966 of Rpb2 cDNA) using two-hybrid analysis. Yeast two-hybrid system with Rpb2 deletion fragments; beta-galactosidase activity assay Wei sheng wu xue bao = Acta microbiologica Sinica Low 12552808
2002 Human RPB3 (POLR2C) interacts with the myogenic transcription factor myogenin via a specific RPB3 region not homologous to the prokaryotic alpha subunit; this interaction involves the basic HLH region of myogenin but not other HLH factors (MyoD, Myf5, MRF4); coimmunoprecipitation confirmed that myogenin contacts the RNAPII complex through RPB3; a dominant-negative RPB3 fragment (Sud) counteracts myogenin transactivation and muscle differentiation. Yeast two-hybrid screening, coimmunoprecipitation, dominant-negative overexpression, muscle differentiation assays FASEB journal Medium 12207009
2003 Human RPB3 (POLR2C) interacts with the transcription factor ATF4 via an RPB3-specific region (Sud) not homologous to the prokaryotic alpha subunit; RPB3 enhances ATF4 transactivation activity, and the Sud dominant-negative fragment markedly inhibits ATF4 transactivation. Yeast two-hybrid, transactivation assays with dominant-negative RPB3 fragment FEBS letters Medium 12860379
2005 RPB3 (POLR2C) forms a heterodimer with RPB11 that initiates RNAPII assembly; in yeast, the C-terminal region of RPB11 is critical for heterodimerization, whereas in humans the conserved N-terminal alpha-motifs dominate the RPB3–RPB11 interface, indicating that the heterodimerization interface has diverged during evolution. In vitro heterodimerization assays comparing human and yeast RPB3/RPB11 truncation mutants Nucleic acids research Medium 15987790
2006 IGFBP-3 interacts with Rpb3 (POLR2C) in rat myoblasts; the interaction requires the MBD/NLS epitope of IGFBP-3 (a NLS mutant does not associate with Rpb3); interaction was confirmed by coimmunoprecipitation with specific antisera. Yeast two-hybrid library screening with IGFBP-3 deletion mutants; coimmunoprecipitation with specific antisera Endocrinology Medium 16455777
2014 Rpb3 (POLR2C) binds directly to the transcription factor Snail via its N-terminus; this interaction downregulates E-cadherin and induces epithelial-mesenchymal transition (EMT) in hepatocellular carcinoma cells; the N-terminal fragment of Rpb3 acts as a dominant negative blocking Rpb3–Snail binding and inhibiting proliferation and migration in Rpb3-high-expression HCC cells. Co-IP/direct binding assay, E-cadherin expression assay, dominant-negative N-terminus overexpression, cell proliferation/migration assays, xenograft tumor growth Oncotarget Medium 25211001
2018 Gpn2 and Rba50 directly participate in assembly of the Rpb3 (POLR2C) subcomplex during RNAPII biogenesis: Gpn2 interacts with Rpb12, Rba50 interacts with Rpb3, Gpn2 and Rba50 interact with each other, and loss of function of either disrupts Rpb3 subcomplex assembly and subsequent RNAPII biogenesis. Co-IP, pulldown assays, loss-of-function analysis of Gpn2/Rba50 with RNAPII assembly readout Molecular and cellular biology Medium 29661922
2025 A K9E substitution at residue 9 of Rpb3 (POLR2C) causes readthrough of NNS-dependent terminators and cold-sensitive growth in yeast; genetic suppression by an R317G substitution in the RRM2 of Hrp1 (Nab4/CF1B) indicates that Rpb3-K9 forms a salt-bridge interaction surface that regulates binding of the anti-termination factor Hrp1 to the RNAPII elongation complex. Allele-specific mutagenesis, genome-wide suppressor selection, targeted suppressor selection in HRP1, transcriptome readthrough assays bioRxivpreprint Medium bio_10.1101_2025.05.07.652672

Source papers

Stage 0 corpus · 18 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1989 RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus. Molecular and cellular biology 89 2685562
1990 A conjugation-specific gene (cnjC) from Tetrahymena encodes a protein homologous to yeast RNA polymerase subunits (RPB3, RPC40) and similar to a portion of the prokaryotic RNA polymerase alpha subunit (rpoA). Nucleic acids research 51 2112240
2006 Ribonucleic acid polymerase II binding subunit 3 (Rpb3), a potential nuclear target of insulin-like growth factor binding protein-3. Endocrinology 46 16455777
2000 Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes & development 37 10673505
2003 Functional interaction of the subunit 3 of RNA polymerase II (RPB3) with transcription factor-4 (ATF4). FEBS letters 33 12860379
2002 The alpha-like RNA polymerase II core subunit 3 (RPB3) is involved in tissue-specific transcription and muscle differentiation via interaction with the myogenic factor myogenin. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 28 12207009
2017 POLR2C Mutations Are Associated With Primary Ovarian Insufficiency in Women. Journal of the Endocrine Society 26 29367954
2018 Gpn2 and Rba50 Directly Participate in the Assembly of the Rpb3 Subcomplex in the Biogenesis of RNA Polymerase II. Molecular and cellular biology 24 29661922
1998 Rpb3, stoichiometry and sequence determinants of the assembly into yeast RNA polymerase II in vivo. The Journal of biological chemistry 20 9556554
1998 Mapping of Rpb3 and Rpb5 contact sites on two large subunits, Rpb1 and Rpb2, of the RNA polymerase II from fission yeast. Molecular & general genetics : MGG 16 9738888
2005 Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II. Nucleic acids research 14 15987790
2014 Rpb3 promotes hepatocellular carcinoma through its N-terminus. Oncotarget 10 25211001
1999 Isolation and characterization of temperature-sensitive mutations in the gene (rpb3) for subunit 3 of RNA polymerase II in the fission yeast Schizosaccharomyces pombe. Molecular & general genetics : MGG 7 10503538
2001 Functional analysis of RNA polymerase II Rpb3 mutants of the fission yeast Schizosaccharomyces pombe. Current genetics 5 11453250
1991 PCR detection of the MspI polymorphism in the human IRBP gene (RPB3). Nucleic acids research 4 1713667
2023 A biallelic variant in POLR2C is associated with congenital hearing loss and male infertility: Case report. European journal of clinical investigation 1 36576366
2025 POLR2C, HIF1A, CD4, and CREB1 as the identified key regulators in geriatric insomnia: A comprehensive approach using systems biology and machine learning methods. Computational biology and chemistry 0 41289970
2001 [Mapping the interaction site of Rpb2 and Rpb3 subunit of fission yeast RNA polymerase II]. Wei sheng wu xue bao = Acta microbiologica Sinica 0 12552808

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