Affinage

POLR2D

DNA-directed RNA polymerase II subunit RPB4 · UniProt O15514

Length
142 aa
Mass
16.3 kDa
Annotated
2026-06-10
51 papers in source corpus 29 papers cited in narrative 29 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

POLR2D (Rpb4) is a dissociable subunit of RNA polymerase II that, together with Rpb7, forms a heterodimeric subcomplex docking onto the polymerase core and serving as a hub that couples nuclear transcription to cytoplasmic mRNA fate (PMID:15591044, PMID:24802753). The Rpb4/7 subcomplex contacts the core through the N-terminal RNP-like domain of Rpb7 and the N-terminal region of Rpb4 (which engages Rpb2), with Rpb6 providing an additional docking point; Rpb4 augments Rpb7 association with the polymerase, and a major contribution of the module is to position an OB-fold RNA-binding surface near the nascent transcript (PMID:11087726, PMID:16282592, PMID:18056993, PMID:12697831, PMID:10082533). Functionally, Rpb4/7 stabilizes the pre-initiation complex and is required for a post-recruitment step in initiation, supports elongation through long GC-rich units, and stimulates processivity, pausing suppression, and termination via direct RNA contacts (PMID:9545247, PMID:11087726, PMID:18441121, PMID:19906731). Rpb4 facilitates CTD dephosphorylation by promoting recruitment of the Ssu72 and Fcp1 phosphatases, enables gene loop formation by stabilizing the TFIIB–Ssu72 interaction to recycle Pol II for reinitiation, and supports cotranscriptional 3'-end processing and selection between transcription-coupled DNA repair subpathways (PMID:25416796, PMID:11839823, PMID:31304538, PMID:18195044, PMID:12411509). Metabolic labeling and Rpb4–Rpb2 fusion rescue establish that Rpb4 acts primarily in nuclear mRNA synthesis, but the protein is also co-transcriptionally loaded onto mRNAs ('imprinting') and, upon dissociation, accompanies them to the cytoplasm where—regulated by an extensive PTM repertoire and acting through partners such as Puf3 and Pat1—it globally coordinates mRNA stability and decay to buffer mRNA levels against changes in synthesis (PMID:24802753, PMID:30359412, PMID:33094674, PMID:33440147, PMID:27001033). Deletion of RPB4 in yeast produces heat- and cold-sensitive growth and reduced Pol II activity at temperature extremes (PMID:2674672); no human Mendelian disease connection is described in the available corpus.

Mechanistic history

Synthesis pass · year-by-year structured walk · 17 steps
  1. 1989 High

    Established that Rpb4 is a non-essential but functionally important Pol II subunit by showing its loss impairs polymerase activity and growth at temperature extremes.

    Evidence RPB4 gene deletion and in vitro Pol II activity assays in yeast crude extracts

    PMID:2674672

    Open questions at the time
    • Did not define the molecular step Rpb4 affects
    • Mechanism of temperature sensitivity unresolved
  2. 1998 High

    Localized Rpb4/7 to the Pol II cleft and showed it stabilizes the pre-initiation complex, linking the subunit to initiation rather than catalysis alone.

    Evidence 3D EM difference mapping and surface plasmon resonance on yeast Pol II/PIC; in vitro complementation with recombinant Rpb4

    PMID:9545247 PMID:9829926

    Open questions at the time
    • Did not identify the RNA-contacting surface
    • Nature of the postlogarithmic Pol II modification enabling Rpb4 recruitment unknown
  3. 2000 High

    Defined the mechanistic basis of Rpb4/7 action by showing the Rpb7 OB-fold binds single-stranded nucleic acid and is required for a post-recruitment initiation step, separating nucleic-acid binding from complex assembly.

    Evidence Purified Rpb4/7 nucleic-acid binding, OB-fold deletion mutagenesis, and in vitro transcription reconstitution

    PMID:11087726

    Open questions at the time
    • Did not resolve the exact post-recruitment step in vivo
    • Genome-wide relevance not yet established
  4. 2001 High

    Resolved how the Rpb4/7 dimer is organized and how its RNA-binding face is oriented, providing a structural model for nascent transcript engagement, and showed promoter-selective and activation roles for Rpb4.

    Evidence X-ray structure of the archaeal E/F homolog; rpb4Δ promoter-reporter and domain-deletion assays in yeast

    PMID:11382749 PMID:11741548

    Open questions at the time
    • Archaeal model required validation in eukaryotic Pol II
    • Which activators depend on Rpb4 C-terminus not enumerated
  5. 2002 High

    Connected Rpb4 to CTD phosphatase recruitment and to transcription-coupled DNA repair, broadening its role to post-elongation regulation.

    Evidence Fcp1–Rpb4 cross-linking/pulldown with rpb4 shut-off in S. pombe; genetic epistasis of rpb4Δ/rpb9Δ/rad26Δ TCR mutants

    PMID:11839823 PMID:12411509

    Open questions at the time
    • Direct phosphatase recruitment mechanism not structurally defined
    • How Rpb4 discriminates between TCR subpathways unresolved
  6. 2005 High

    Provided the human Rpb4/Rpb7 structure and mapped the conserved RNA-binding surface, confirming evolutionary conservation of the OB-fold mechanism.

    Evidence X-ray crystallography of human Rpb4/7 at 2.7 Å with site-directed mutagenesis and EMSA

    PMID:16282592

    Open questions at the time
    • Human in vivo functions not tested here
    • RNA specificity determinants not defined
  7. 2004 High

    Defined the atomic interface between Rpb4/7 and the Pol II core, explaining how core contact induces conformational changes and how dissociation occurs.

    Evidence X-ray structures of Rpb4/7 (2.3 Å) and the complete 12-subunit Pol II (3.8 Å) with comparative structural analysis

    PMID:15591044

    Open questions at the time
    • Dynamics of regulated dissociation in vivo not captured
    • PTM influence on the interface not addressed
  8. 2003 Medium

    Identified Rpb6 and the Rpb7 N-terminal RNP domain plus the Rpb4 N-terminus as the physical anchors of the subcomplex on the core, and showed Rpb4 augments Rpb7 incorporation.

    Evidence Conditional rpb6 mutagenesis and direct interaction assays; RPB7 overexpression suppression with reciprocal Co-IP; pulldown/complementation mapping

    PMID:10082533 PMID:12697831 PMID:18056993

    Open questions at the time
    • Relative contribution of each contact to assembly kinetics not quantified
    • Single-lab interaction data
  9. 2008 Medium

    Showed genome-wide that complete Pol II including Rpb4/7 traverses transcribed regions and that Rpb4 contributes to elongation of long genes and to cotranscriptional 3'-end processing.

    Evidence ChIP and ChIP-chip of Rpb4/Rpb7 vs Rpb3 in yeast; rpb4Δ poly(A) site mapping and 6-azauracil sensitivity

    PMID:18195044 PMID:18441121 PMID:18667430

    Open questions at the time
    • Mechanism coupling Rpb4 to 3'-end factor recruitment not biochemically reconstituted
    • Single-lab genome-wide datasets
  10. 2009 High

    Demonstrated directly that the Rpb4/7 homolog stimulates elongation processivity and termination through RNA binding, and placed Rpb4 in a mediator-relayed regulatory chain.

    Evidence Recombinant archaeal RNAP in vitro transcription with F/E RNA-binding mutants; Ace2–Med8–Rpb4 two-hybrid and Co-IP in S. pombe

    PMID:19720063 PMID:19906731

    Open questions at the time
    • Archaeal elongation findings need eukaryotic confirmation
    • Mediator chain shown only for cell-separation genes
  11. 2013 Medium

    Showed Rpb4/7 dissociates from Pol II at specific elongation stages tied to CTD phosphorylation state, refining when the module is functionally engaged.

    Evidence Quantitative mass spectrometry and Co-IP across phospho-CTD isoforms

    PMID:23418395

    Open questions at the time
    • Functional consequence of dissociation at elongation not directly tested here
    • Single-lab proteomics
  12. 2014 High

    Established that Rpb4's primary role is in nuclear mRNA synthesis and that it facilitates CTD dephosphorylation and Ccr4-Not-dependent elongation, while coupling synthesis to mRNA decay via buffering.

    Evidence Metabolic RNA labeling with Rpb2-Rpb4 fusion rescue; rpb4Δ phospho-CTD analysis with SSU72/FCP1 genetics; in vitro Ccr4-Not elongation assays

    PMID:24802753 PMID:25315781 PMID:25416796

    Open questions at the time
    • Structural basis for phosphatase recruitment unresolved
    • How nuclear synthesis defect signals to cytoplasmic decay not fully mapped
  13. 2016 Medium

    Linked Rpb4/7 assembly into Pol II to global post-transcriptional control, showing imprinting-dependent modulation of mRNA stability and stress responses.

    Evidence RPB1 foot mutants impairing Rpb4/7 assembly with global transcriptome and mRNA stability analysis

    PMID:27001033

    Open questions at the time
    • Direct imprinting mechanism on individual transcripts not resolved here
    • Single-lab study
  14. 2018 Medium

    Demonstrated that physical dissociation of Rpb4 from Pol II is required for its cytoplasmic mRNA-decay functions, distinguishing nuclear from cytoplasmic roles.

    Evidence Rpb2-Rpb4 fusion expression with mRNA decay, polysome association, and stress-response assays in yeast

    PMID:30359412

    Open questions at the time
    • Proteolytic release mechanism not fully characterized
    • Single-lab study
  15. 2020 Medium

    Identified the co-transcriptional imprinting machinery, showing Rpb4 and Puf3 mutually depend on each other to load onto mRNAs and co-regulate transcript stability.

    Evidence RIP-Seq, Co-IP, ChIP, and genetic interaction analysis of Rpb4 and Puf3 in yeast

    PMID:33094674

    Open questions at the time
    • Generality beyond Puf3-bound transcripts unknown
    • Single-lab dataset
  16. 2021 Medium

    Revealed that a stage-specific PTM code on Rpb4/7 regulates its interactions with Pol II, eIF3, and Pat1 to control its progression through the mRNA life cycle.

    Evidence Mass spectrometry PTM mapping with PTM-mutant functional and interaction analysis

    PMID:33440147

    Open questions at the time
    • Enzymes writing/erasing individual PTMs not identified
    • Causal ordering of PTM transitions not established
  17. 2022 Medium

    Defined an upstream determinant (Rtr1 CTD phosphatase) of Rpb4/7 incorporation and identified RPB4 as a host target hijacked by influenza polymerase, extending its mechanistic reach.

    Evidence RTR1 deletion with Pol II assembly/ChIP and mRNA stability assays; binary complementation and Co-IP of influenza PB2 with human RPB4 plus PB2 mutagenesis

    PMID:35216121 PMID:35336925

    Open questions at the time
    • Structural details of the FluPol–RPB4 interaction not resolved
    • How Rtr1 mechanistically couples CTD state to assembly not defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the Rpb4/7 PTM code and assembly state are integrated in metazoan cells, and whether POLR2D dysfunction underlies human disease, remain unresolved.
  • No human in vivo functional study in the corpus
  • No Mendelian disease link characterized
  • Most mechanistic detail derives from yeast and archaeal systems

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 4 GO:0005198 structural molecule activity 3 GO:0098772 molecular function regulator activity 3 GO:0003677 DNA binding 1
Localization
GO:0005634 nucleus 3 GO:0005829 cytosol 2
Pathway
R-HSA-74160 Gene expression (Transcription) 5 R-HSA-8953854 Metabolism of RNA 4 R-HSA-73894 DNA Repair 1
Partners
EIF3FCP1PAT1POLR2BPOLR2FPOLR2GPUF3SSU72
Complex memberships
RNA polymerase IIRpb4/7 subcomplex

Evidence

Reading pass · 29 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2004 X-ray crystal structure of Rpb4/7 subcomplex determined at 2.3 Å resolution; combined with the 10-subunit Pol II core to refine a 3.8 Å atomic model of complete 12-subunit Pol II. Structural comparison revealed that core-Rpb4/7 interaction induces formation of an α-helix in the linker region of Rpb1 and folding of the Rpb7 tip loop. Details of the interface explain facilitated Rpb4/7 dissociation in a temperature-sensitive Pol II mutant. X-ray crystallography (2.3 Å for subcomplex, 3.8 Å for complete Pol II); structural comparison with core and free Rpb4/7 The Journal of biological chemistry High 15591044
1989 Deletion of RPB4 in S. cerevisiae produces heat- and cold-sensitive cells and markedly reduces RNA polymerase II activity in crude extracts in vitro, establishing that Rpb4 is required for normal Pol II activity especially at temperature extremes, though not essential for enzyme assembly. Gene deletion, in vitro RNA polymerase activity assay in crude extracts Molecular and cellular biology High 2674672
2001 Crystal structure of the archaeal RPB4/7 homolog complex (Methanococcus jannaschii subunits E and F) determined; subunit E has an elongated two-domain structure with two potential RNA-binding motifs; subunit F wraps around one side of subunit E at the domain interface. A structural model was proposed in which the RNA-binding face of RPB7 is positioned to interact with the nascent RNA transcript. X-ray crystallography of archaeal E/F complex Molecular cell High 11741548
2000 Purified yeast Rpb4/7 heterodimer binds single-stranded DNA and RNA via an OB-fold motif in Rpb7. A deletion in the putative OB-fold nucleic acid-binding surface of Rpb7 abolished binding without affecting Rpb4/7 complex stability or its association with polymerase, yet destroyed transcription activity. Rpb4/7 is required for a post-recruitment step in transcription initiation, not for stable promoter binding. Template competition assay, purified Rpb4/7 single-strand nucleic acid-binding assay, Rpb7 deletion mutagenesis, in vitro transcription reconstitution The Journal of biological chemistry High 11087726
2005 Crystal structure of human Rpb4/Rpb7 heterodimer determined at 2.7 Å. Site-directed mutagenesis of conserved solvent-exposed residues in the Rpb7 OB-fold (including the B4-B5 loop) identified an elongated surface region involved in RNA binding, confirmed by EMSA. The homologous archaeal E subunit uses the same surface for RNA binding. X-ray crystallography (2.7 Å), site-directed mutagenesis, electrophoretic mobility shift assay (EMSA) Nucleic acids research High 16282592
1998 3D EM structure of wild-type yeast Pol II located Rpb4 and Rpb7 at the floor of the DNA-binding cleft. Surface plasmon resonance showed that Rpb4/7 stabilize a minimal pre-initiation complex (promoter DNA, TBP, TFIIB, Pol II), suggesting a role in coupling DNA entry into the cleft to cleft closure during promoter-specific transcription. 3D electron microscopy, difference mapping, surface plasmon resonance The EMBO journal High 9545247
2002 Rpb4 plays a dual role in transcription-coupled DNA repair (TCR) in S. cerevisiae: it suppresses the Rpb9-dependent TCR subpathway and facilitates the Rad26-dependent TCR subpathway, demonstrating a regulatory function of Rpb4 in selecting between TCR subpathways. Genetic epistasis analysis using deletion mutants (rpb4Δ, rpb9Δ, rad26Δ combinations); repair assays The EMBO journal High 12411509
2002 In S. pombe, Fcp1 CTD-phosphatase directly interacts with the Rpb4 subunit of Pol II, identified by chemical cross-linking, GST pulldown, and affinity chromatography. Repression of rpb4 expression reduced Fcp1 in the Pol II complex and increased CTD phosphorylation, demonstrating that Rpb4 is required for Fcp1/TFIIF/Pol II complex formation in vivo. Immunoaffinity purification, chemical cross-linking, GST pulldown, affinity chromatography, rpb4 shut-off strain Molecular and cellular biology High 11839823
1998 Rpb4 is required for Pol II enzymatic activity at temperature extremes (10°C and 35°C) but not at moderate temperature (23°C). Addition of recombinant Rpb4 produced in E. coli rescues Pol II activity in extracts from postlogarithmic cells at non-optimal temperatures. Sucrose gradient and immunoprecipitation showed Rpb4 is present in excess over the Pol II complex, and only Pol II from postlogarithmic cells can be rescued, suggesting Pol II must be modified to recruit Rpb4. In vitro promoter-independent transcription assay in cell extracts, recombinant Rpb4 complementation, sucrose gradient sedimentation, immunoprecipitation Journal of bacteriology High 9829926
1999 Rpb7 can interact with Pol II and support transcription independently of Rpb4 when overexpressed, but fewer Rpb7 molecules associate with Pol II lacking Rpb4 than with wild-type Pol II. Reciprocal coimmunoprecipitation confirmed stable interaction of overproduced Rpb7 with Pol IIΔ4. A major role of Rpb4 is to augment Rpb7 binding to Pol II. RPB7 overexpression suppressor screen, reciprocal coimmunoprecipitation Molecular and cellular biology Medium 10082533
2003 A conditional mutation in the shared Rpb6 subunit (Q100R) causes selective loss of Rpb4 and Rpb7 from purified RNA Pol II. Interaction experiments demonstrated a direct association between Rpb6 and Rpb4, identifying Rpb6 as one contact point between the Rpb4/7 subcomplex and Pol II. Conditional rpb6 mutagenesis, Pol II purification, protein interaction assays Molecular and cellular biology Medium 12697831
2008 Chromatin immunoprecipitation of Rpb4 showed it crosslinks throughout transcribed regions genome-wide. Loss of Rpb4 reduces Pol II levels near 3' ends of mRNA genes, decreases cotranscriptional recruitment of 3'-end processing factors, and alters polyadenylation site usage at the RNA14 gene, establishing that Rpb4 contributes to cotranscriptional 3'-end processing. Chromatin immunoprecipitation (ChIP), rpb4Δ strain analysis, polyadenylation site mapping Molecular and cellular biology Medium 18195044
2008 Genome-wide ChIP coupled to tiling microarray analysis showed that Rpb7 occupancy profiles across the genome are essentially identical to core subunit Rpb3, demonstrating that complete Pol II (including Rpb4/7) associates with DNA in vivo throughout the transcription cycle. Chromatin immunoprecipitation coupled to high-resolution tiling microarray (ChIP-chip) The Journal of biological chemistry Medium 18667430
2013 Quantitative proteomics showed that Rpb4/7 dissociate from RNAPII upon interaction with specific transcriptional elongation-associated proteins recruited to the hyperphosphorylated CTD. RNAPII isolated through Rpb7 is depleted in Ser2 CTD phosphorylation, indicating Rpb4/7 are dispensable during specific elongation stages. Quantitative mass spectrometry proteomics, co-immunoprecipitation with phospho-CTD isoforms Molecular & cellular proteomics : MCP Medium 23418395
2014 Metabolic RNA labeling and dynamic transcriptome analysis showed Rpb4 deletion causes a drastic defect in mRNA synthesis compensated by down-regulation of mRNA degradation (mRNA buffering). Covalent fusion of Rpb4 to Pol II core subunit Rpb2 largely restores mRNA synthesis and degradation defects, demonstrating that Rpb4 functions primarily in nuclear mRNA synthesis by Pol II. Metabolic RNA labeling, comparative dynamic transcriptome analysis, Rpb2-Rpb4 fusion protein complementation, rpb4Δ strain The Journal of biological chemistry High 24802753
2014 Deletion of RPB4 or disruption of Rpb4/7 integrity increased phosphorylation of CTD residues Ser2, Ser5, Ser7, and Thr4 of Rpb1. Genetic interactions were found with CTD phosphatases SSU72 and FCP1. Rpb4 is important for association and recruitment of Ssu72 (Ser5P phosphatase) and Fcp1 (Ser2P/Thr4P phosphatase) to the CTD, placing Rpb4/7 as a facilitator of CTD dephosphorylation. rpb4Δ strain phospho-CTD analysis, genetic interaction screens, phosphatase recruitment assays (ChIP) Nucleic acids research Medium 25416796
2014 The Ccr4-Not complex requires the Rpb4/7 module of Pol II to associate with elongation complexes and stimulate Pol II elongation; loss of Rpb4/7 impairs Ccr4-Not-dependent reactivation of arrested elongation complexes. In vitro elongation assays with purified Ccr4-Not complex, rpb4/7 deletion strains The Journal of biological chemistry Medium 25315781
2019 3C analysis showed that gene loop formation is abolished in rpb4Δ cells. RPB4 overexpression rescued gene looping and transcription termination defects of sua7-1 (TFIIB mutant) and ssu72-2, while SSU72 overexpression restored gene loops in rpb4Δ cells. Rpb4 facilitates the TFIIB-Ssu72 interaction required for gene loop formation, promoting Pol II transfer from terminator to promoter for transcription reinitiation. Chromosome conformation capture (3C) assay, genetic suppression analysis, rpb4Δ strain Nucleic acids research Medium 31304538
2009 Using wholly recombinant archaeal RNAP, the F/E complex (RPB4/7 homolog) greatly stimulates RNAP processivity, enhances full-length product formation, reduces pausing, and increases termination at weak termination signals during elongation. F/E mutants defective in RNA binding show reduced stimulatory activity, implicating F/E–RNA interactions as pivotal for elongation and termination. In vitro transcription assay with recombinant archaeal RNAP; F/E mutant variants on synthetic nucleic acid scaffolds Nucleic acids research High 19906731
2001 Rpb4 is required for activated transcription from a subset of promoters in S. cerevisiae; constitutive transcription is largely unaffected. The C-terminal 24 amino acids of Rpb4 are critical for this activation function. Transcriptional activation by artificial TBP recruitment is also defective without Rpb4. rpb4Δ strain, promoter-reporter assays, domain deletion analysis, TBP recruitment assay The Journal of biological chemistry Medium 11382749
2007 Pulldown and complementation assays identified two crucial contact points for Rpb4/7 subcomplex association with the Pol II core: the N-terminal RNP-like domain of Rpb7 and the partially ordered N-terminal region of Rpb4 (interacting with Rpb2). Mutations in Rpb7's N-terminal domain increase dependence on Rpb4 for polymerase interaction. RNA polymerase pulldown assay, complementation analysis, mutagenesis The Journal of biological chemistry Medium 18056993
2021 Rpb4/7 undergoes more than 100 combinations of post-translational modifications (PTMs); the PTM repertoire changes as the mRNA/Rpb4/7 complex progresses through stages of the mRNA life cycle (transcription, export, translation, decay). Specific PTM mutants affect Rpb4 interactions with key regulators (Pol II, eIF3, Pat1) and disrupt mRNA synthesis/decay buffering. Mass spectrometry-based PTM mapping, PTM mutant functional analysis, interaction assays Cell reports Medium 33440147
2018 Rpb4-Rpb2 fusion protein supports normal transcription but adversely affects mRNA decay, cell proliferation, and stress response, demonstrating that dissociation of Rpb4 from Pol II is required for its cytoplasmic roles in mRNA decay regulation. A portion of the fusion protein is proteolytically cleaved to release free functional Rpb4 that binds mRNAs and polysomes. Rpb2-Rpb4 fusion protein expression, mRNA decay assays, polysome association, stress response assays PloS one Medium 30359412
2009 In S. pombe, Med8 mediator subunit interacts with Rpb4, and Ace2 transcriptional activator interacts with Med8; the C-terminal region of Med8 is required for its interaction with Rpb4. This defines a protein interaction chain (Ace2–Med8–Rpb4) that relays transcriptional regulatory signals to Pol II during cell separation. Yeast two-hybrid, co-immunoprecipitation, domain deletion analysis FEBS letters Medium 19720063
2008 Genome-wide ChIP-chip analysis showed Rpb4 is recruited to coding regions of most transcriptionally active genes with extent increasing with gene length. Pol II lacking Rpb4 is defective in transcribing long, GC-rich transcription units, and rpb4Δ cells are sensitive to 6-azauracil, establishing a role for Rpb4 in transcription elongation that is independent of Rpb7. ChIP-chip (genome-wide chromatin immunoprecipitation with microarray), 6-azauracil sensitivity assay, rpb4Δ strain Eukaryotic cell Medium 18441121
2022 Binary complementation assays revealed an interaction between the N-terminal third domain of influenza PB2 and human RPB4. This interaction was confirmed by co-immunoprecipitation and was found with influenza A, B, and C FluPols. The N-half domain of RPB4 is critical for this interaction. PB2 mutants at conserved positions showed strong transcriptional activity defects, suggesting FluPol uses RPB4 to position itself near the 5'-end of nascent host mRNA during cap-snatching. Binary complementation assay, co-immunoprecipitation, PB2 mutagenesis Viruses Medium 35336925
2022 RTR1 deletion increases the amount of chromatin-associated Pol II lacking Rpb4, decreases Rpb4-mRNA imprinting, and consequently increases mRNA stability. Rtr1 (CTD Ser5P phosphatase) mediates proper association of Rpb4/7 with Pol II during assembly, linking CTD phosphorylation state to Rpb4/7 incorporation and downstream mRNA decay regulation. RTR1 deletion strain, Pol II assembly analysis, ChIP, mRNA stability assays International journal of molecular sciences Medium 35216121
2020 RIP-Seq showed Rpb4 associates genome-wide with more than 1400 mRNA targets. Rpb4 and Puf3 RNA-binding protein physically interact, genetically interact, and co-regulate mRNA stability of a shared set of transcripts. Rpb4-mRNA association depends on Puf3 and vice versa. Puf3 associates with chromatin in an Rpb4-dependent manner, establishing a co-transcriptional imprinting mechanism. RIP-Seq, co-immunoprecipitation, genetic interaction analysis, ChIP RNA biology Medium 33094674
2016 RPB1 foot mutations that impair Rpb4/7 assembly into Pol II activate an environmental stress response (ESR) under optimal growth conditions primarily through post-transcriptional regulation dependent on Rpb4-mRNA imprinting, revealing that Rpb4 globally modulates mRNA stability and coordinates transcription with mRNA decay. RPB1 foot mutant strains, global transcriptional analysis, mRNA stability assays, Rpb4/7 assembly analysis Biochimica et biophysica acta Medium 27001033

Source papers

Stage 0 corpus · 51 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2004 Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. The Journal of biological chemistry 187 15591044
1989 RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth. Molecular and cellular biology 166 2674672
2009 NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes & development 116 19204117
2002 Rpb4 and Rpb9 mediate subpathways of transcription-coupled DNA repair in Saccharomyces cerevisiae. The EMBO journal 109 12411509
2001 Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. Molecular cell 90 11741548
2004 Rpb4 and Rpb7: subunits of RNA polymerase II and beyond. Trends in biochemical sciences 87 15544954
2002 Formation of a carboxy-terminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase II (pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fcp1 and the Rpb4 subunit of pol II. Molecular and cellular biology 83 11839823
2000 Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. The Journal of biological chemistry 73 11087726
2008 The Rpb4 subunit of RNA polymerase II contributes to cotranscriptional recruitment of 3' processing factors. Molecular and cellular biology 63 18195044
2005 Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II. Nucleic acids research 59 16282592
1998 Structure of wild-type yeast RNA polymerase II and location of Rpb4 and Rpb7. The EMBO journal 56 9545247
1999 Rpb7 can interact with RNA polymerase II and support transcription during some stresses independently of Rpb4. Molecular and cellular biology 53 10082533
1998 Rpb4, a subunit of RNA polymerase II, enables the enzyme to transcribe at temperature extremes in vitro. Journal of bacteriology 53 9829926
2009 Molecular mechanisms of RNA polymerase--the F/E (RPB4/7) complex is required for high processivity in vitro. Nucleic acids research 48 19906731
2000 Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12. Nucleic acids research 47 11058130
1999 The Rpb4 subunit of fission yeast Schizosaccharomyces pombe RNA polymerase II is essential for cell viability and similar in structure to the corresponding subunits of higher eukaryotes. Molecular and cellular biology 47 10523639
2002 The A14-A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4-Rpb7 pol II subunits. Proceedings of the National Academy of Sciences of the United States of America 43 12407181
2015 Contribution of PRS3, RPB4 and ZWF1 to the resistance of industrial Saccharomyces cerevisiae CCUG53310 and PE-2 strains to lignocellulosic hydrolysate-derived inhibitors. Bioresource technology 42 25974617
1993 A growth rate-limiting process in the last growth phase of the yeast life cycle involves RPB4, a subunit of RNA polymerase II. Journal of bacteriology 39 8407810
2008 Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. The Journal of biological chemistry 38 18667430
2003 An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Molecular and cellular biology 38 12482973
2013 Quantitative proteomics demonstrates that the RNA polymerase II subunits Rpb4 and Rpb7 dissociate during transcriptional elongation. Molecular & cellular proteomics : MCP 37 23418395
2019 RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit. Nucleic acids research 34 31304538
2014 Rpb4 subunit functions mainly in mRNA synthesis by RNA polymerase II. The Journal of biological chemistry 34 24802753
2001 Rpb4, a non-essential subunit of core RNA polymerase II of Saccharomyces cerevisiae is important for activated transcription of a subset of genes. The Journal of biological chemistry 33 11382749
2005 Rpb4 and Rpb7: a sub-complex integral to multi-subunit RNA polymerases performs a multitude of functions. IUBMB life 31 16036568
2003 Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Molecular and cellular biology 31 12697831
2001 Deletion of the RNA polymerase subunit RPB4 acts as a global, not stress-specific, shut-off switch for RNA polymerase II transcription at high temperatures. The Journal of biological chemistry 31 11577101
2014 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. The Journal of biological chemistry 29 25315781
2014 Rpb4/7 facilitates RNA polymerase II CTD dephosphorylation. Nucleic acids research 29 25416796
2010 Cycling through transcription with the RNA polymerase F/E (RPB4/7) complex: structure, function and evolution of archaeal RNA polymerase. Research in microbiology 26 20863887
2008 Genomewide recruitment analysis of Rpb4, a subunit of polymerase II in Saccharomyces cerevisiae, reveals its involvement in transcription elongation. Eukaryotic cell 25 18441121
2009 RNAP subunits F/E (RPB4/7) are stably associated with archaeal RNA polymerase: using fluorescence anisotropy to monitor RNAP assembly in vitro. The Biochemical journal 21 19492989
2012 Rpb4 and Rpb7: multifunctional subunits of RNA polymerase II. Critical reviews in microbiology 19 22917057
2006 The fission yeast Rpb4 subunit of RNA polymerase II plays a specialized role in cell separation. Molecular genetics and genomics : MGG 18 16972065
2016 Rpb1 foot mutations demonstrate a major role of Rpb4 in mRNA stability during stress situations in yeast. Biochimica et biophysica acta 17 27001033
2001 Multiple cellular processes affected by the absence of the Rpb4 subunit of RNA polymerase II contribute to the deficiency in the stress response of the yeast rpb4(delta) mutant. Molecular & general genetics : MGG 17 11254123
2009 The Med8 mediator subunit interacts with the Rpb4 subunit of RNA polymerase II and Ace2 transcriptional activator in Schizosaccharomyces pombe. FEBS letters 13 19720063
2003 The conserved and non-conserved regions of Rpb4 are involved in multiple phenotypes in Saccharomyces cerevisiae. The Journal of biological chemistry 12 14530281
2021 Numerous Post-translational Modifications of RNA Polymerase II Subunit Rpb4/7 Link Transcription to Post-transcriptional Mechanisms. Cell reports 11 33440147
2018 Dissociation of Rpb4 from RNA polymerase II is important for yeast functionality. PloS one 11 30359412
2020 Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast. RNA biology 9 33094674
2007 Unstructured N terminus of the RNA polymerase II subunit Rpb4 contributes to the interaction of Rpb4.Rpb7 subcomplex with the core RNA polymerase II of Saccharomyces cerevisiae. The Journal of biological chemistry 8 18056993
2022 The Influenza Virus RNA-Polymerase and the Host RNA-Polymerase II: RPB4 Is Targeted by a PB2 Domain That Is Involved in Viral Transcription. Viruses 7 35336925
2022 The Association of Rpb4 with RNA Polymerase II Depends on CTD Ser5P Phosphatase Rtr1 and Influences mRNA Decay in Saccharomyces cerevisiae. International journal of molecular sciences 5 35216121
2019 A comparative study of the proteome regulated by the Rpb4 and Rpb7 subunits of RNA polymerase II in fission yeast. Journal of proteomics 4 30862564
2013 The RNA polymerase II Rpb4/7 subcomplex regulates cellular lifespan through an mRNA decay process. Biochemical and biophysical research communications 4 24358479
2009 The dissociable RPB4 subunit of RNA Pol II has vital functions in Drosophila. Molecular genetics and genomics : MGG 4 19921261
2005 Mapping the interaction site of Rpb4 and Rpb7 subunits of RNA polymerase II in Saccharomyces cerevisiae. Biochemical and biophysical research communications 3 15913559
2014 Involvement of S. cerevisiae Rpb4 in subset of pathways related to transcription elongation. Gene 1 24780862
2008 RAM pathway contributes to Rpb4 dependent pseudohyphal differentiation in Saccharomyces cerevisiae. Fungal genetics and biology : FG & B 1 18687406

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