Affinage

POLR2B

DNA-directed RNA polymerase II subunit RPB2 · UniProt P30876

Length
1174 aa
Mass
133.9 kDa
Annotated
2026-06-10
44 papers in source corpus 11 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

POLR2B (RPB2) is the second-largest subunit of RNA polymerase II and contributes directly to the enzyme's catalytic core and to multiple steps of mRNA synthesis (PMID:15886393). Its conserved active-center residue E791 (E836 in yeast) coordinates NTP and Mg(B) loading, and substitution to alanine impairs both NTP polymerization and intrinsic transcript cleavage at limiting Mg/NTP concentrations (PMID:15886393). Beyond catalysis, the Rpb2 lobe domain functionally interacts with the TFIIB B-finger to govern transcription start-site selection and to support elongation (PMID:15082791), and rpb2 mutations alter transcriptional elongation efficiency that is read out in vivo as shifts toward upstream and internal poly(A) site usage (PMID:14560031, PMID:23355614). The lobe surface also serves as a docking platform for the elongation factor IWS1, whose short linear motifs contact this region to stimulate elongation. RPB2 forms a direct subunit-subunit interface with Rpb3 through its conserved C-terminal region (PMID:9738888, PMID:12552808). Before functioning in the nucleus, RPB2 is assembled with Rpb1 in the cytoplasm in a process requiring the assembly factor Rtr1 acting with Gpn3 and Npa3 (PMID:36190433), and is then trafficked from the cis-Golgi through the ER to the nucleus by TANGO6 in association with COPI vesicles during G1, a route whose disruption causes cytoplasmic accumulation of RPB2 and G1 arrest (PMID:38490996). Distinct rpb2 alleles also couple the polymerase to chromatin and RNA-processing outputs, including RNAi-dependent heterochromatin maintenance via an Elp1-dependent pathway.

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 1998 Low

    Establishing how the two largest polymerase subunits are held together: mapping where Rpb2 contacts Rpb3 defined a physical anchor point within the assembled enzyme.

    Evidence Yeast two-hybrid mapping of S. pombe Rpb2 fragments against Rpb3

    PMID:9738888

    Open questions at the time
    • Single two-hybrid mapping with no orthogonal or structural validation
    • Interface boundaries refined only in later mapping work
    • Does not address functional consequence of disrupting the interface
  2. 2000 Medium

    Connecting Rpb2 to initiation-stage regulators: a genetically interacting rpb2 allele and co-purification placed Ssu72 in physical and functional contact with the polymerase core.

    Evidence Genetic suppressor screen plus co-IP with purified RNAP II in yeast

    PMID:11046131

    Open questions at the time
    • Does not define the direct Rpb2 surface contacted
    • Mechanism of the functional interaction during initiation not resolved
  3. 2001 Low

    Refining the Rpb2-Rpb3 interface to a defined C-terminal segment localized the subunit contact within Rpb2 primary sequence.

    Evidence Yeast two-hybrid mapping with Rpb2 fragment constructs in S. pombe

    PMID:12552808

    Open questions at the time
    • Single-method mapping without structural confirmation
    • No test of whether the segment is necessary for assembly in vivo
  4. 2003 Medium

    Linking Rpb2 to elongation in vivo: rpb2 mutations shifted poly(A) site choice, showing that elongation defects manifest as altered 3'-end processing.

    Evidence In vivo poly(A) site reporter analysis in yeast rpb2 mutants

    PMID:14560031

    Open questions at the time
    • Does not pinpoint which Rpb2 structural element drives the elongation defect
    • Indirect readout of elongation through poly(A) choice
  5. 2004 Medium

    Defining a start-site selection role: the Rpb2 lobe domain was shown to interact functionally with the TFIIB B-finger and to also affect elongation.

    Evidence Genetic suppressor analysis, in vitro run-on and abortive initiation assays, 6-azauracil sensitivity in yeast

    PMID:15082791

    Open questions at the time
    • Physical contact inferred genetically rather than structurally at the time
    • Quantitative contribution to start-site scanning not isolated
  6. 2005 High

    Assigning a catalytic role to a specific Rpb2 residue: E791 was shown to be required for NTP-Mg(B) loading, defining Rpb2's contribution to the active center.

    Evidence Human RNAP II E791A mutant purification with in vitro and in vivo transcription and transcript cleavage assays

    PMID:15886393

    Open questions at the time
    • Does not resolve full coordination geometry of the active site
    • Other Rpb2 active-center residues not systematically tested here
  7. 2011 High

    Testing the necessity of the Rpb2 flap loop/TFIIB interface: its deletion left global initiation, elongation, pausing, and cleavage largely intact, bounding the functional importance of this surface.

    Evidence Flap loop deletion mutant in HEK293 with genome-wide ChIP-seq and multiple in vitro transcription assays

    PMID:21670157

    Open questions at the time
    • A modest pausing effect was masked by TFIIF, leaving its physiological relevance unresolved
    • Negative result does not exclude redundant contributions from adjacent surfaces
  8. 2013 Medium

    Tying elongation rate to stress-responsive 3'-end choice: UV damage redirected RPB2 poly(A) site usage, showing elongation rate governs poly(A) selection on the RPB2 gene itself.

    Evidence Poly(A) site usage analysis, 3'UTR reporters, and mRNA stability assays before/after UV in yeast

    PMID:23355614

    Open questions at the time
    • Whether this autoregulatory behavior generalizes to RPB2 protein levels not established
    • Molecular sensor coupling damage to elongation rate not identified
  9. 2022 Medium

    Defining cytoplasmic assembly of the enzyme: Rtr1, with Gpn3 and Npa3, was shown to be required for proper assembly of Rpb1 and Rpb2 prior to nuclear import.

    Evidence Genetic suppressor analysis, co-IP, localization microscopy, and a catalytically dead Rtr1 mutant in yeast

    PMID:36190433

    Open questions at the time
    • Order and stoichiometry of assembly intermediates not fully resolved
    • How phosphatase-independent Rtr1 promotes assembly mechanistically unclear
  10. 2023 Low

    Connecting RPB2 to tumor cell growth: POLR2B knockdown suppressed glioblastoma proliferation and altered a downstream target, linking the subunit to a disease-relevant transcriptional output.

    Evidence shRNA knockdown, proliferation and xenograft assays, RNA-seq identifying DDIT4 in GBM cells

    PMID:37423037

    Open questions at the time
    • Phenotype may reflect general loss of polymerase function rather than specific regulation
    • DDIT4 regulation not shown to be direct
    • Single lab without rescue controls
  11. 2024 Medium

    Resolving how RPB2 reaches the nucleus: TANGO6 captures RPB2 in the cis-Golgi via COPI vesicles and routes it through the ER to the nucleus during G1.

    Evidence Co-IP, live-cell imaging of RPB2 trafficking, cell cycle analysis, and conditional TANGO6 perturbation in mouse HSCs

    PMID:38490996

    Open questions at the time
    • How RPB2 is loaded onto the Golgi/COPI route is not defined
    • Relationship between this trafficking step and cytoplasmic Rtr1-dependent assembly not integrated
  12. 2025 Medium

    Extending Rpb2 function to chromatin silencing: a gain-of-function rpb2-N44Y allele impaired RNAi-dependent heterochromatin through an Elp1-dependent pathway.

    Evidence CRISPR mutagenesis, genetic epistasis with elp1/elp3 deletions, siRNA and heterochromatin reporter assays in S. pombe (preprint)

    Open questions at the time
    • Preprint, single lab
    • Direct biochemical link between Rpb2-N44Y and Elp1 chromatin function not established
  13. 2025 Medium

    Structurally defining elongation- and splicing-factor docking on Rpb2: cryo-EM placed IWS1 SLiMs and the U1-70K RRM on the RPB2 lobe domain.

    Evidence Cryo-EM of Pol II complexes plus SLiM deletion and in vitro elongation assays; co-IP in yeast (preprints)

    Open questions at the time
    • Preprints, single labs
    • Human U1-70K-RPB2 contact partly relies on a referenced prior structure
    • Functional importance of the splicing contact in cells not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • How cytoplasmic Rtr1-dependent assembly, Golgi/COPI-TANGO6 trafficking, and nuclear catalytic function are temporally and mechanistically integrated into a single biogenesis pathway for RPB2 remains unresolved.
  • No unified model linking assembly, trafficking, and nuclear loading
  • Regulation of RPB2 biogenesis across the cell cycle incompletely defined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2 GO:0003677 DNA binding 1 GO:0140098 catalytic activity, acting on RNA 1
Localization
GO:0005634 nucleus 1 GO:0005794 Golgi apparatus 1 GO:0005829 cytosol 1
Pathway
R-HSA-74160 Gene expression (Transcription) 3 R-HSA-8953854 Metabolism of RNA 3
Partners
IWS1RPB3RTR1SSU72TANGO6TFIIBU1-70K
Complex memberships
RNA polymerase II

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 Ssu72 physically interacts with purified RNA Pol II (containing Rpb2 subunit) as shown by co-immunoprecipitation, and a suppressor allele rpb2-100 (R512C in homology block D) was identified that genetically interacts with ssu72-2, defining Ssu72 as a factor that physically and functionally interacts with the RNAP II core machinery during transcription initiation. Genetic suppressor screen, co-immunoprecipitation with purified RNAP II, in vivo transcription assays Molecular and cellular biology Medium 11046131
2003 Mutations in the RPB2 subunit of RNA Pol II (along with SPT5 and TFIIS) cause increased utilization of internal and upstream poly(A) sites in yeast, indicating that transcriptional elongation defects leading to pausing or arrest can be visualized in vivo through poly(A) site choice, and that RPB2 plays a role in transcriptional elongation efficiency. In vivo gene expression analysis using poly(A) site reporter genes in yeast rpb2 mutants Molecular and cellular biology Medium 14560031
2004 A functional interaction between the B-finger domain of TFIIB and the lobe domain of Rpb2 (G369S substitution) was identified through genetic suppressor analysis. The Rpb2 lobe-jaw region defines a novel role for Rpb2 in transcription start site selection, and the sua7-3 rpb2-101 double mutant was sensitive to 6-azauracil in vivo and to NTP substrate depletion in vitro, linking Rpb2 lobe domain to elongation as well. Genetic suppressor screen, in vitro promoter-specific run-on transcription, abortive initiation assay, 6-azauracil sensitivity Molecular and cellular biology Medium 15082791
2005 The highly conserved Rpb2 residue E791 (human RNAP II; E836 in yeast) is involved in NTP and Mg(B) binding at the active center. The E791A substitution mutant showed impaired transcription activity at low NTP concentrations both in vitro and in vivo, and decreased NTP polymerization and transcript cleavage activities at low Mg concentrations, implicating this residue in NTP-Mg(B) loading into the active site. Affinity purification of human RNAP II E791A mutant, in vitro transcription assay, in vivo transcription assay, transcript cleavage assay at varying Mg and NTP concentrations Nucleic acids research High 15886393
2011 Deletion of the RPB2 flap loop (Δ873-884) in human RNAP II, which removes the TFIIB interaction interface, had no detectable effect on global transcription initiation, RNAP II occupancy, promoter escape, productive elongation, promoter binding, abortive initiation, TFIIS-stimulated transcript cleavage, or NELF/DSIF inhibition in vitro. A modest effect on elongation and pausing was suppressed by TFIIF. Genome-wide ChIP-seq in HEK293 cells expressing flap loop deletion mutant, in vitro transcription and abortive initiation assays, TFIIS cleavage assay, NELF/DSIF pausing assay Molecular and cellular biology High 21670157
1998 Two-hybrid analysis using S. pombe RNAP II subunits mapped an Rpb3 contact site within the conserved region H of Rpb2 (the beta-subunit homology region conserved among all RNA polymerases), establishing a direct physical interaction between Rpb2 and Rpb3 within the polymerase complex. Yeast two-hybrid assay with fission yeast Rpb2 fragments Molecular & general genetics Low 9738888
2001 Two-hybrid mapping in S. pombe identified the Rpb2-Rpb3 interaction site at the C-terminal region of Rpb2, within amino acids 902–989 (encoded by base 2701–2966 of Rpb2 cDNA). Yeast two-hybrid assay with Rpb2 fragment constructs Wei sheng wu xue bao (Acta Microbiologica Sinica) Low 12552808
2013 UV damage regulates alternative polyadenylation of the RPB2 gene in yeast: in normally growing cells, the proximal poly(A) site is preferentially used; after UV damage and transcription recovery, the distal poly(A) site is preferentially used. The 3'UTR of RPB2 is sufficient for this regulation, and the rate of transcription elongation (not initiation) is an important determinant of poly(A) site choice. RNA analysis of poly(A) site usage before and after UV damage, 3'UTR reporter constructs, mRNA stability assays Nucleic acids research Medium 23355614
2022 Rtr1 is directly required for assembly of the two largest RNAP II subunits (Rpb1 and Rpb2). Deletion of RTR1 leads to cytoplasmic clumping of RNAP II subunits. Rtr1 coordinates with Gpn3 and Npa3 assembly factors; overexpression of RTR1 suppresses cytoplasmic clump formation of RNAP II subunit in a gpn3-9 mutant. This function does not require Rtr1 phosphatase catalytic activity. Genetic suppressor analysis, co-immunoprecipitation, fluorescence microscopy of RNAP II subunit localization, analysis of catalytically inactive Rtr1 mutant FASEB journal Medium 36190433
2024 TANGO6 associates with COPI vesicles and captures RPB2 in the cis-Golgi during G1 phase, then carries RPB2 to the ER and subsequently to the nucleus. Functional disruption of TANGO6 causes cytoplasmic accumulation of RPB2 and G1 cell cycle arrest. Conditional depletion or overexpression of TANGO6 in mouse hematopoietic stem cells compromises or expands hematopoiesis. Co-immunoprecipitation, live cell fluorescence imaging, cell cycle analysis (PI staining), conditional knockout/overexpression in mouse hematopoietic stem cells Nature communications Medium 38490996
2023 Knockdown of POLR2B (RPB2) by shRNA suppresses GBM tumor cell growth in vitro and in vivo in a xenograft model, and RNA sequencing identified DDIT4 (DNA damage-inducible transcript 4) as a downstream transcriptional target regulated by RPB2 in glioblastoma cells. shRNA knockdown, cell proliferation assay, xenograft mouse model, RNA sequencing, GO and GSEA analysis Biochemical and biophysical research communications Low 37423037
2025 A gain-of-function mutation in the Rpb2 subunit of Pol II (rpb2-N44Y in S. pombe) reduces RNAi-dependent heterochromatin. The heterochromatin defects of rpb2-N44Y require Elongator Protein 1 (Elp1); loss of Elp1 (but not other Elongator subunits such as Elp3) suppresses these defects independently of the mcm5s2U34 tRNA modification, revealing an Elp1 chromatin function downstream of or parallel to Rpb2. CRISPR site-directed mutagenesis, genetic epistasis with elp1/elp3 deletions, siRNA quantification, heterochromatin reporter assays in S. pombe bioRxivpreprint Medium
2025 Cryo-EM mapping showed that IWS1 short linear motifs (SLiMs) in its intrinsically disordered C-terminal region directly contact the RPB2 lobe domain of Pol II. Functional assays demonstrated that IWS1 interactions with the RPB2 lobe and ELOF1 are required for IWS1-dependent transcription elongation stimulation, while IWS1 recruitment depends on the RPB1 jaw domain and downstream DNA binding. Cryo-electron microscopy structure determination, deletion mutagenesis of SLiMs, in vitro transcription elongation assays bioRxivpreprint Medium
2025 In yeast, Prp40 (not U1-70K) is the predominant mediator of U1 snRNP interaction with Pol II; multiple domains of Prp40 interact with Pol II independently of the CTD. In humans, the cryo-EM structure showed that U1-70K RRM domain directly interacts with the RPB2 subunit of Pol II, mediating co-transcriptional splicing coupling. Co-immunoprecipitation in yeast, cryo-EM structure of human U1 snRNP–Pol II complex, domain deletion analysis bioRxivpreprint Low

Source papers

Stage 0 corpus · 44 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2005 Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). Molecular phylogenetics and evolution 379 15737578
2013 Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal genetics and biology : FG & B 280 23357352
2004 Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Molecular phylogenetics and evolution 277 15288074
2006 Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Molecular phylogenetics and evolution 262 17081773
2005 Lower level relationships in the mushroom genus Cortinarius (Basidiomycota, Agaricales): a comparison of RPB1, RPB2, and ITS phylogenies. Molecular phylogenetics and evolution 84 16085431
2005 Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA. Molecular phylogenetics and evolution 59 15904853
2006 Ribosomal and RPB2 DNA sequence analyses suggest that Sporidesmium and morphologically similar genera are polyphyletic. Mycological research 55 16908125
2003 In vivo evidence that defects in the transcriptional elongation factors RPB2, TFIIS, and SPT5 enhance upstream poly(A) site utilization. Molecular and cellular biology 53 14560031
2000 Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae. Molecular and cellular biology 53 11046131
2015 The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities. Molecular ecology resources 45 26287723
2008 Molecular phylogeny of RPB2 gene reveals multiple origin, geographic differentiation of H genome, and the relationship of the Y genome to other genomes in Elymus species. Molecular phylogenetics and evolution 41 18262439
2006 Phylogenetic utility of protein (RPB2, beta-tubulin) and ribosomal (LSU, SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota, Fungi). Antonie van Leeuwenhoek 39 17072532
2004 Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation. Molecular and cellular biology 38 15082791
2004 RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids. Molecular phylogenetics and evolution 36 15223030
1996 Transcription-coupled and global genome repair in the Saccharomyces cerevisiae RPB2 gene at nucleotide resolution. Nucleic acids research 32 8836174
2007 Molecular evolution and genome divergence at RPB2 gene of the St and H genome in Elymus species. Plant molecular biology 30 17551673
2000 Discovery of paralogous nuclear gene sequences coding for the second-largest subunit of RNA polymerase II (RPB2) and their phylogenetic utility in gentianales of the asterids. Molecular biology and evolution 26 10908634
2006 RNA polymerase II gene (RPB2) encoding the second largest protein subunit in Phaeosphaeria nodorum and P. avenaria. Mycological research 25 17020806
1993 Cloning and sequence determination of the Schizosaccharomyces pombe rpb2 gene encoding the subunit 2 of RNA polymerase II. Nucleic acids research 25 8441660
2014 Transcription-independent functions of an RNA polymerase II subunit, Rpb2, during genome rearrangement in the ciliate, Oxytricha trifallax. Genetics 24 24793090
2014 Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies. Mycologia 24 24898532
2005 Molecular phylogeny of the palm genus Chamaedorea, based on the low-copy nuclear genes PRK and RPB2. Molecular phylogenetics and evolution 24 16249101
2010 Pleurotus eryngii species complex: sequence analysis and phylogeny based on partial EF1α and RPB2 genes. Fungal biology 22 20943152
2011 The RPB2 flap loop of human RNA polymerase II is dispensable for transcription initiation and elongation. Molecular and cellular biology 21 21670157
2004 Paralogy and orthology in the MALVACEAE rpb2 gene family: investigation of gene duplication in hibiscus. Molecular biology and evolution 21 15084680
2009 Phylogeny of Litsea and related genera (Laureae-Lauraceae) based on analysis of rpb2 gene sequences. Journal of plant research 18 19219578
2006 Phylogeny and a new species of Sparassis (Polyporales, Basidiomycota): evidence from mitochondrial atp6, nuclear rDNA and rpb2 genes. Mycologia 17 17139851
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
2013 UV damage regulates alternative polyadenylation of the RPB2 gene in yeast. Nucleic acids research 15 23355614
2013 TNFRSF10A-LOC389641 rs13278062 but not REST-C4orf14-POLR2B-IGFBP7 rs1713985 was found associated with age-related macular degeneration in a Chinese population. Investigative ophthalmology & visual science 14 24235014
2012 Multiple origins of allopolyploid wheatgrass Elymus caninus revealed by RPB2, PepC and TrnD/T genes. Molecular phylogenetics and evolution 14 22617317
2011 Evaluation of partial tef1, rpb2, and nLSU sequences for identification of isolates representing Armillaria calvescens and Armillaria gallica from northeastern North America. Fungal biology 14 21802054
2006 Duplication and paralog sorting of RPB2 and RPB1 genes in core eudicots. Molecular phylogenetics and evolution 14 17208015
2005 The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II. Nucleic acids research 13 15886393
2016 Phylogenetic relationship of two popular edible Pleurotus in China, Bailinggu (P. eryngii var. tuoliensis) and Xingbaogu (P. eryngii), determined by ITS, RPB2 and EF1α sequences. Molecular biology reports 10 27075657
2022 Rtr1 is required for Rpb1-Rpb2 assembly of RNAPII and prevents their cytoplasmic clump formation. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 6 36190433
2023 The RNA polymerase II subunit B (RPB2) functions as a growth regulator in human glioblastoma. Biochemical and biophysical research communications 4 37423037
2022 Phylogenetic relationship of Fusarium species isolated from keratitis using TEF1 and RPB2 gene sequences. Iranian journal of microbiology 4 37124860
2025 Protein Coding Low-Copy rpb2 and ef1-α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy. Ecology and evolution 3 40260151
2024 TANGO6 regulates cell proliferation via COPI vesicle-mediated RPB2 nuclear entry. Nature communications 2 38490996
2020 The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (Arecaceae). Physiology and molecular biology of plants : an international journal of functional plant biology 2 32943823
2012 Arnica (Asteraceae) phylogeny revisited using RPB2: complex patterns and multiple d-paralogues. Molecular phylogenetics and evolution 1 22425730
2025 Correction to "Protein Coding Low-Copy rpb2 and ef1-α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy". Ecology and evolution 0 40589596
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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