Affinage

RRN3

RNA polymerase I-specific transcription initiation factor RRN3 · UniProt Q9NYV6

Length
651 aa
Mass
74.1 kDa
Annotated
2026-06-10
40 papers in source corpus 32 papers cited in narrative 32 extracted findings
Cross-family judge vs UniProt: tie faithfulness: 7/8 claims corpus-supported (88%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RRN3 (TIF-IA in mammals, Rrn3p in yeast) is an essential, growth-regulated RNA polymerase I (Pol I) transcription initiation factor that couples ribosomal RNA synthesis to the physiological state of the cell (PMID:4070001, PMID:8413268, PMID:11265758). It acts as a stoichiometric bridge: RRN3 binds directly to Pol I—principally through the RPA43/A43 subunit and at an interface located between the AC40/19 and A14/43 subcomplexes—to convert an inactive Pol I dimer into an initiation-competent monomer, and simultaneously contacts the promoter-bound core factor/SL1 (via Rrn6 and the TAF(I)95/TAF(I)68 subunits) to recruit polymerase to the rDNA promoter (PMID:8670901, PMID:11032814, PMID:12393749, PMID:21940764, PMID:27418309). RRN3 also possesses an intrinsic, separable DNA-binding domain (residues ~382–400) that is required for transcription independently of its protein–protein contacts (PMID:23393135). Functioning stoichiometrically rather than catalytically, RRN3 is required for forming the first phosphodiester bonds but is then released from Pol I after initiation; its CK2-dependent phosphorylation at S170/172 triggers this release to permit elongation, and FCP1 dephosphorylation regenerates the active factor for new rounds of initiation (PMID:8413268, PMID:12646563, PMID:18559419). RRN3 activity is governed by a multi-kinase phosphorylation code that integrates nutrient, growth-factor, and stress signals: ERK/RSK phosphorylation at S633/S649 and mTOR-dependent phosphorylation at S44 activate it, whereas S199 and JNK2-mediated T200 phosphorylation inactivate it and drive its translocation away from nucleoli (PMID:12620228, PMID:15004009, PMID:15805466). Akt-CK2 and LKB1 signaling further regulate its stability and nuclear/nucleolar localization (PMID:24297901, PMID:26506235). Loss of RRN3 is embryonic lethal in mice and triggers nucleolar stress, L11–MDM2-dependent p53 activation, and apoptosis (PMID:15989966). Beyond canonical Pol I initiation, RRN3 participates in NF-κB nucleolar stress signaling, senescence (via an ATM-regulated interaction with the cargo receptor p62/SQSTM1), and a non-canonical nuclear role in alternative polyadenylation of autophagy mRNAs (PMID:29873780, PMID:41271632, PMID:41466483).

Mechanistic history

Synthesis pass · year-by-year structured walk · 20 steps
  1. 1985 High

    Established the existence of a growth-dependent factor required for accurate Pol I initiation, framing rRNA synthesis as physiologically regulated rather than constitutive.

    Evidence Partial purification of TIF-IA and in vitro transcription reconstitution with purified factors

    PMID:4070001

    Open questions at the time
    • Did not identify the molecular nature of the factor
    • No mechanism for how activity tracks growth state
  2. 1990 High

    Showed TIF-IA behaves like a Pol I 'sigma factor', physically associating with the polymerase to license promoter-specific initiation, and linked Pol I phosphorylation to initiation competence.

    Evidence Biochemical co-fractionation, in vitro reconstitution, and phosphatase treatment of Pol I

    PMID:2390974

    Open questions at the time
    • Did not define which subunit mediates the contact
    • Phospho-target on Pol I/TIF-IA not mapped
  3. 1993 High

    Defined TIF-IA as a 75 kDa monomer acting at the catalytic step of initiation and released afterward, distinguishing it from stable preinitiation complex components.

    Evidence Purified factor reconstitution, template commitment, and single-round transcription assays

    PMID:8413268

    Open questions at the time
    • Direct binding interface not resolved
    • No molecular clone yet
  4. 1996 High

    Identified yeast Rrn3p as the essential factor that stimulates DNA-independent Pol I recruitment to the promoter, establishing the genetically tractable ortholog.

    Evidence Genetic complementation, in vitro transcription with purified Rrn3p, Sarkosyl single-round assays

    PMID:8670901

    Open questions at the time
    • Pol I subunit contact unknown
    • Conservation to mammals not yet shown
  5. 2000 High

    Pinned the Pol I–Rrn3 contact to the A43/RPA43 subunit and demonstrated cross-species functional conservation of RRN3 from yeast to human.

    Evidence Yeast conditional genetics, E. coli co-expression, immuno-EM, cross-species complementation, and human cloning/complementation

    PMID:10758157 PMID:11032814 PMID:11265758

    Open questions at the time
    • Precise A43–Rrn3 interface residues not defined
    • How Rrn3 simultaneously contacts core factor unclear
  6. 2002 High

    Mapped distinct TIF-IA surfaces for Pol I (RPA43/PAF67) versus SL1 (TAF(I)95/68) and showed phosphorylation gates the Pol I interaction, mechanistically linking signaling to bridging function.

    Evidence Deletion mapping, co-IP, and comparison of phosphorylated (Sf9) versus bacterial recombinant protein in binding and transcription assays

    PMID:12015311 PMID:12393749

    Open questions at the time
    • Identity of the activating kinase(s) not established
    • Specific phospho-sites not yet mapped
  7. 2003 High

    Defined the growth-factor arm of regulation (ERK/RSK at S633/S649) and confirmed RRN3 acts stoichiometrically, becoming inactivated upon transcription.

    Evidence Phosphopeptide mapping, kinase assays, S649A mutagenesis, MEK inhibition, and limiting-factor in vitro transcription

    PMID:12620228 PMID:12646563

    Open questions at the time
    • Molecular basis of post-initiation inactivation unresolved
    • How phosphorylation alters the structure not known
  8. 2004 High

    Placed mTOR upstream of Pol I via opposing phospho-sites (activating S44, inactivating S199) controlling both complex formation and nucleocytoplasmic localization.

    Evidence Rapamycin treatment, phospho-mapping, mutagenesis, co-IP, and immunofluorescence

    PMID:15004009

    Open questions at the time
    • S199 kinase identity unknown
    • Transport machinery driving relocalization not defined
  9. 2005 High

    Defined the stress-inactivation arm: JNK2 phosphorylation of T200 disrupts Pol I/SL1 contacts and relocalizes TIF-IA, with genetic KO conferring stress resistance.

    Evidence In vitro kinase assay, phospho-mapping, T200V mutagenesis, co-IP, immunofluorescence, and Jnk2-/- cells

    PMID:15805466

    Open questions at the time
    • How T200 phosphorylation physically blocks both interfaces unclear
  10. 2005 High

    Established that RRN3 is essential for development and that its loss triggers a defined nucleolar-stress/p53 apoptotic program via L11–MDM2.

    Evidence Mouse knockout, conditional MEF depletion, L11–MDM2 and MDM2–p53 co-IP, and p53 RNAi rescue

    PMID:15989966

    Open questions at the time
    • Whether other ribosomal proteins contribute not addressed
    • Tissue-specific requirements not dissected
  11. 2007 High

    Showed Pol I subunits Rpa49/Rpa34 control both Rrn3 recruitment and its release during elongation, and confirmed TOR-dependent recruitment of TIF-IA to rDNA in a metazoan.

    Evidence Yeast genetics/ChIP/epistasis and Drosophila Tif-IA mutant/RNAi/ChIP with TOR epistasis

    PMID:18086878 PMID:18086911

    Open questions at the time
    • Mechanism coupling Rpa49 to Rrn3 release not molecularly defined
  12. 2008 High

    Identified CK2 phosphorylation of S170/172 as the molecular trigger for Rrn3 release from Pol I enabling elongation, with FCP1 reversing it to recycle the factor.

    Evidence Kinase assay, mutagenesis, FRAP, ChIP, co-IP, and covalent tethering to RPA43; plus heparin-resistance recruitment assay distinguishing competent complexes

    PMID:18559419 PMID:18590050

    Open questions at the time
    • How phosphorylation weakens the RPA43 interface structurally not shown
  13. 2011 High

    Provided the first crystal structure (HEAT-repeat fold with a regulatory serine patch) and localized the Pol I binding site, unifying phospho-regulation with structure.

    Evidence X-ray crystallography, phospho-mimetic mutagenesis, in vitro binding, ChIP, and cross-linking/MS

    PMID:21940764

    Open questions at the time
    • Structure of the full Rrn3–Pol I–DNA initiation complex not yet resolved
  14. 2013 High

    Revealed an intrinsic, essential DNA-binding domain in Rrn3 separable from its protein–protein contacts, adding a direct rDNA-engagement function.

    Evidence EMSA, deletion/point mutagenesis, in vitro transcription, yeast complementation, and co-IP

    PMID:23393135

    Open questions at the time
    • Where on the promoter Rrn3 DNA-binding acts is not mapped
  15. 2014 Medium

    Validated the Rrn3–rpa43 interface as a functionally essential, druggable target using a minimal inhibitory peptide.

    Evidence In vitro transcription inhibition, TAT-peptide transduction, and cell division assays

    PMID:25033839

    Open questions at the time
    • Therapeutic specificity and in vivo efficacy not established
  16. 2016 Medium

    Resolved the architecture of how Rrn3 binding monomerizes inactive Pol I dimers into an initiation-competent state, and extended signaling control (Akt-CK2, LKB1, heat-shock CK2) over RRN3 stability and localization.

    Evidence Cryo-EM of yeast Pol I–Rrn3; kinase cascade co-IP/localization (Akt-CK2; LKB1/S636); CK2-dependent heat-shock inactivation analysis

    PMID:24297901 PMID:26506235 PMID:27257073 PMID:27418309

    Open questions at the time
    • Several signaling links rest on single-lab co-IP/localization data
    • Higher-resolution Rrn3–Pol I structure not available
  17. 2017 Medium

    Distinguished UBF/SL1-driven preinitiation complex persistence from Rrn3-dependent Pol I loading, refining the order of assembly at rDNA.

    Evidence Conditional Rrn3 inactivation with high-resolution ChIP-Seq in mouse cells

    PMID:28715449

    Open questions at the time
    • How UBF-bound PIC transitions to an Rrn3-loaded competent state mechanistically unclear
  18. 2018 Medium

    Placed TIF-IA degradation upstream of NF-κB nucleolar stress signaling, broadening RRN3's role beyond transcription into stress sensing.

    Evidence RNAi, CDK4 inhibition, S44 mutagenesis, and IP in ex vivo culture

    PMID:29873780

    Open questions at the time
    • Degradation machinery (E3 ligase) not identified
    • Direct link from TIF-IA loss to NF-κB activation not fully traced
  19. 2025 Medium

    Uncovered a non-canonical nuclear function: S199-phosphorylated RRN3 relocates to the nucleoplasm to regulate alternative polyadenylation of autophagy mRNAs, repurposing a Pol I factor as an RNA-processing regulator under nutrient stress.

    Evidence Long-read RNA-seq, PAR-CLIP, subcellular fractionation, S199 mutagenesis, and xenografts in ovarian cancer cells

    PMID:41271632

    Open questions at the time
    • Single-lab finding without independent confirmation
    • How nuclear RRN3 engages APA machinery is undefined
    • Generality beyond ovarian cancer unknown
  20. 2026 Medium

    Identified an ATM-regulated p62/SQSTM1 interaction controlling TIF-IA accumulation in senescence, where TIF-IA drives nucleolar phenotype, SASP, and ROS independently of cell-cycle arrest.

    Evidence Conditional genetic manipulation in multiple mouse senescence models, TIF-IA–p62 co-IP, and ATM inhibition

    PMID:41466483

    Open questions at the time
    • Mechanism linking p62 sequestration to RRN3 stability not detailed
    • Single-lab finding

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the full set of regulatory phosphorylations is structurally integrated to switch RRN3 between Pol I-bound, released, relocalized, and non-canonical RNA-binding states remains unresolved.
  • No structure of phosphorylated RRN3 or the complete initiation complex on DNA
  • Kinases for several sites (e.g., S199) unidentified
  • Mechanistic basis of nuclear RNA-processing role undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0140110 transcription regulator activity 3 GO:0140223 general transcription initiation factor activity 3 GO:0003677 DNA binding 1 GO:0003723 RNA binding 1
Localization
GO:0005634 nucleus 3 GO:0005654 nucleoplasm 3 GO:0005730 nucleolus 3 GO:0005829 cytosol 2
Pathway
R-HSA-162582 Signal Transduction 3 R-HSA-74160 Gene expression (Transcription) 3 R-HSA-8953897 Cellular responses to stimuli 3 R-HSA-5357801 Programmed Cell Death 1
Partners
FCP1PAF67RPA43RRN6SQSTM1TAF1ATAF1B
Complex memberships
Pol I–Rrn3 initiation complex

Evidence

Reading pass · 32 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1985 TIF-IA is a growth-dependent transcription factor that co-purifies with RNA polymerase I and is required for accurate and efficient Pol I transcription initiation in vitro; its amount or activity fluctuates with the physiological state of cells (absent in quiescent cells). Partial purification of TIF-IA; in vitro transcription reconstitution with purified factors Nucleic acids research High 4070001
1990 TIF-IA physically associates with RNA polymerase I (converting it into a transcriptionally active holoenzyme capable of initiating at the rDNA promoter) and behaves analogously to a bacterial sigma factor: it is present in limiting amounts, associates with Pol I, is required for initiation, and is separable from the polymerase at certain salt conditions. Dephosphorylation of Pol I abolishes in vitro transcription initiation without affecting non-specific polymerizing activity. Biochemical co-fractionation, in vitro transcription reconstitution, phosphatase treatment of Pol I The EMBO journal High 2390974
1993 Purified TIF-IA is a 75 kDa monomeric polypeptide that directly interacts with RNA Pol I and is a bona fide transcription initiation factor; preinitiation complexes can assemble without TIF-IA but formation of the first phosphodiester bonds requires TIF-IA; after initiation, TIF-IA is released from the initiation complex and can facilitate transcription from templates bearing preinitiation complexes lacking TIF-IA. Murine TIF-IA complements both mouse and human growth-inhibited cell extracts. Purified factor reconstitution, template commitment assay, in vitro transcription with purified components Molecular and cellular biology High 8413268
1996 Yeast Rrn3p is an essential RNA Pol I transcription factor that directly interacts with Pol I independently of DNA template; pre-incubation of Rrn3p with purified Pol I stimulates formation of a Sarkosyl-resistant pre-initiation complex, indicating Rrn3p stimulates Pol I recruitment to the promoter. Rrn3p is not part of the stable pre-initiation complex that supports multiple rounds of transcription. Genetic complementation (rrn3 mutant extracts), immunoaffinity purification, in vitro transcription with purified Rrn3p, template commitment assay, single-round transcription with Sarkosyl The EMBO journal High 8670901
1997 Yeast RRN3 is a multicopy suppressor of the cbf5-1 temperature-sensitive mutation; the cbf5-1 mutant shows a defect in rRNA biosynthesis at restrictive temperatures, placing RRN3 in a genetic pathway with CBF5/nucleolar function. High-copy suppressor screen, genetic epistasis in yeast Molecular and cellular biology Medium 9315678
2000 Yeast Pol I subunit A43 directly interacts with Rrn3: conditional mutations in A43 disrupt the Pol I–Rrn3 transcriptionally competent complex; the two proteins form a stable complex when co-expressed in E. coli; overexpression of Rrn3 suppresses A43 mutant phenotype; A43 and Rrn3 show synthetic lethality; immunoelectron microscopy confirms their co-localization within the Pol I–Rrn3 complex. Rrn3 also contacts the C-terminus of Rrn6 (core factor subunit) via affinity chromatography. Conditional yeast genetics, co-expression in E. coli, synthetic lethality, immunoelectron microscopy, two-hybrid screen, affinity chromatography The EMBO journal High 11032814
2000 Human TIF-IA is the mammalian ortholog of yeast Rrn3p: recombinant TIF-IA interacts with Pol I in the absence of template DNA, augments Pol I transcription in vivo, and rescues transcription in extracts from growth-arrested cells in vitro. Molecular cloning, in vitro transcription complementation assay, in vivo transcription augmentation EMBO reports High 11265758
2000 Human Rrn3 functionally rescues a yeast RRN3 disruption strain in vivo; a point mutation in a conserved amino acid compromises function of both yeast and human factors, confirming functional conservation across eukaryotes. Cross-species genetic complementation in yeast, site-directed mutagenesis Proceedings of the National Academy of Sciences of the United States of America High 10758157
2002 TIF-IA is associated with a fraction of TIF-IB/SL1 and initiation-competent Pol I. Nutrient starvation, density arrest, and cycloheximide inactivate TIF-IA and impair its association with Pol I. Deletion mapping shows that TIF-IA amino acids 512–609 interact with Pol I subunits RPA43 and PAF67, while residues 411–415 (LARAK motif) are required for association with TAF(I)95 and TAF(I)68 (SL1 subunits). Co-immunoprecipitation, deletion mutant mapping, in vitro interaction assays EMBO reports Medium 12393749
2002 Phosphorylation state of mammalian Rrn3 regulates its interaction with the rpa43 subunit of RNA Pol I and hence rDNA transcription: cycloheximide inhibits Rrn3 phosphorylation and causes its dissociation from Pol I; Rrn3 produced in Sf9 cells (phosphorylated) but not in bacteria interacts with rpa43 in vitro; neither dephosphorylated nor bacterially-produced Rrn3 restores transcription in cycloheximide-treated cell extracts. Co-immunoprecipitation, in vitro binding assay (Sf9 vs. bacterial recombinant protein), in vitro transcription complementation, phosphatase treatment The Journal of biological chemistry High 12015311
2003 ERK and RSK kinases phosphorylate TIF-IA at S633 and S649 in response to growth factor signaling; replacement of S649 with alanine inactivates TIF-IA, inhibits pre-rRNA synthesis, and retards cell growth. PD98059 (MEK inhibitor) blocks TIF-IA activation, confirming MAPK-dependent regulation. Phosphopeptide mapping, site-directed mutagenesis, in vitro kinase assay, PD98059 inhibitor treatment, cell growth assay Molecular cell High 12620228
2003 Mammalian Rrn3 functions stoichiometrically (not catalytically) in rDNA transcription: Rrn3 becomes inactivated during transcription reactions, dissociates from Pol I upon transcription, and the inactivated form cannot form a stable complex with Pol I. In vitro transcription assay with limiting factor analysis, sequential transcription reactions, co-immunoprecipitation The Journal of biological chemistry Medium 12646563
2004 mTOR regulates Pol I transcription through TIF-IA: rapamycin (mTOR inhibitor) inactivates TIF-IA, impairs transcription-initiation complex formation, and causes translocation of TIF-IA from nucleus to cytoplasm. Mechanistically, rapamycin causes hypophosphorylation of S44 and hyperphosphorylation of S199; S44 phosphorylation activates TIF-IA while S199 phosphorylation inactivates it. Rapamycin treatment, phosphopeptide mapping, site-directed mutagenesis, co-immunoprecipitation (TIF-IA with Pol I and SL1), immunofluorescence localization Genes & development High 15004009
2005 JNK2 inactivates TIF-IA under stress by phosphorylating it at T200; this phosphorylation impairs TIF-IA interaction with Pol I and TIF-IB/SL1, abrogates initiation complex formation, and causes translocation of TIF-IA from nucleolus to nucleoplasm. T200V substitution or Jnk2 knockout prevents inactivation/translocation and confers stress-resistance of Pol I transcription. In vitro kinase assay, phosphopeptide mapping, site-directed mutagenesis, co-immunoprecipitation, immunofluorescence, genetic knockout (Jnk2-/-) Genes & development High 15805466
2005 Genetic inactivation of TIF-IA in mice causes embryonic lethality (before/at E9.5). Conditional Cre-mediated depletion in MEFs leads to nucleolar disruption, cell cycle arrest, p53 upregulation, and apoptosis. Elevated p53 results from increased binding of ribosomal protein L11 to MDM2, decreasing MDM2–p53 and MDM2–p19(ARF) interactions. RNAi-mediated loss of p53 rescues proliferation arrest and apoptosis. Homologous recombination knockout in mice, Cre-mediated conditional depletion in MEFs, RNAi, co-immunoprecipitation (L11–MDM2, MDM2–p53), immunofluorescence Molecular cell High 15989966
2007 In yeast, Pol I subunits Rpa49 and Rpa34 control both the recruitment of Rrn3 to the rDNA promoter and its release during elongation: rpa49 mutants lacking the C-terminus reduce polymerase occupancy and strongly impair Rrn3 release from elongating Pol I; this elongation defect is bypassed by an N-terminal deletion of Rpa43 (rpa43-35,326), placing Rpa43–Rrn3 interaction downstream of Rpa49 function. Yeast genetics (deletion/point mutants), ChIP, 6-azauracil/mycophenolate sensitivity, epistasis analysis Molecular and cellular biology Medium 18086878
2007 Drosophila TIF-IA is required for rRNA synthesis and cell growth in vivo; the TOR pathway regulates TIF-IA recruitment to rDNA; TIF-IA overexpression maintains rRNA transcription when TOR activity is reduced, placing TIF-IA genetically downstream of TOR in growth control. Drosophila genetic analysis (Tif-IA null mutants), RNAi knockdown, epistasis with TOR pathway, ChIP (TIF-IA occupancy at rDNA) The Journal of cell biology High 18086911
2008 CK2 phosphorylates TIF-IA at S170/172, triggering release of TIF-IA from Pol I after transcription initiation, which is required for transcription elongation. Inhibition of S170/172 phosphorylation or covalent tethering of TIF-IA to RPA43 inhibits rDNA transcription, perturbs nucleolar structure, and causes cell cycle arrest. Dephosphorylation of S170/172 by FCP1 phosphatase facilitates TIF-IA reassociation with Pol I for new rounds of transcription. In vitro kinase assay, site-directed mutagenesis, FRAP, ChIP, co-immunoprecipitation, chemical crosslinking (TIF-IA tethered to RPA43) Molecular and cellular biology High 18559419
2008 Mammalian Rrn3 is required for formation of a transcription-competent preinitiation complex: Pol I can be recruited to the rDNA template in the absence of active Rrn3 but the resulting complex cannot initiate transcription; the functional Rrn3-containing complex is ~5-fold more heparin-resistant than the non-functional complex. Novel ChIP-like template recruitment assay, heparin challenge, in vitro transcription Gene expression Medium 18590050
2009 TIF-IA dynamically shuttles between cytoplasm, nucleoplasm, and nucleolus with a mean nucleolar residence time of ~30 s; the majority of TIF-IA is in cytoplasm/nucleus with only ~7% in nucleoli at steady state. Import from cytoplasm to nucleus is ~3-fold faster than export, suggesting active importin/exportin-mediated transport. Upon ribotoxic stress, TIF-IA is released from nucleoli with a half-time of ~24 min, downstream of JNK2 activation as the rate-limiting step. Live-cell fluorescence microscopy (GFP-TIF-IA), FRAP, kinetic modeling, JNK2 activity time-course Biochimica et biophysica acta Medium 19450626
2011 Crystal structure of yeast Rrn3 reveals a unique HEAT repeat fold with a surface serine patch. Phosphorylation of this serine patch represses human Pol I transcription; a phospho-mimetic mutation of the patch prevents Rrn3 binding to Pol I in vitro and reduces cell growth and Pol I gene occupancy in vivo. Cross-linking places the Rrn3 binding site on Pol I between subcomplexes AC40/19 and A14/43. X-ray crystallography, in vitro Pol I binding assay, mutagenesis (phospho-mimetic), ChIP, cell growth assay, protein cross-linking/mass spectrometry Genes & development High 21940764
2013 Rrn3 is a DNA-binding protein; a domain (residues 382–400) with similarity to the HSF2 DNA-binding domain is required for DNA binding. Mutation or deletion of this domain abolishes DNA binding and transcription in vitro and fails to complement a yeast rrn3-ts mutant, while the mutants retain interaction with rpa43 and SL1, demonstrating that DNA binding is an independent and essential function of Rrn3. Electrophoretic mobility shift assay (EMSA), deletion and point mutagenesis, in vitro transcription, yeast complementation, co-immunoprecipitation The Journal of biological chemistry High 23393135
2013 Activated Akt enhances rRNA synthesis by phosphorylating CK2α on a threonine near its N-terminus, which in turn phosphorylates TIF-IA; activated Akt also stabilizes TIF-IA (preventing degradation), induces its translocation to the nucleolus, and enhances its interaction with Pol I. Co-immunoprecipitation, kinase assays (Akt→CK2α→TIF-IA), RNAi knockdown, pharmacological inhibition (AZD8055, rapamycin), subcellular fractionation/immunofluorescence Proceedings of the National Academy of Sciences of the United States of America Medium 24297901
2014 A conserved 22 amino-acid peptide within rpa43 is necessary and sufficient for the Rrn3–rpa43 interaction; this peptide inhibits rDNA transcription in vitro and inhibits Pol I transcription and cell division when delivered intracellularly, confirming that the Rrn3–rpa43 interface is functionally essential. In vitro transcription inhibition assay, peptide transduction (TAT-coupled), cell division assay, in silico conservation analysis Molecular cancer research Medium 25033839
2016 Cryo-EM structure of the yeast Pol I–Rrn3 complex at 4.8 Å resolution reveals how Rrn3 binding converts an inactive Pol I dimer into an initiation-competent monomer. Cryo-electron microscopy structural analysis Nature communications High 27418309
2016 Heat shock inactivates TIF-IA by inhibiting CK2-dependent phosphorylation at S170/172, repressing rRNA synthesis; this is mechanistically distinct from PAPAS lncRNA-mediated chromatin changes (CHD4/NuRD) but both mechanisms together shut down rDNA transcription under thermo-stress. Phosphorylation analysis (S170/172), CK2 inhibition, co-immunoprecipitation (CHD4–PAPAS), ChIP, in vitro transcription Nucleic acids research Medium 27257073
2016 Conditional inactivation of Rrn3 by genetic depletion leads to loss of Pol I occupancy at rDNA but a unique Enhancer Boundary Complex (CTCF/Cohesin) and UBF-bound preinitiation complexes persist independently of Rrn3 or ongoing transcription; preinitiation complex formation is driven by UBF independently of transcription. Conditional genetic inactivation (mouse cells), high-resolution ChIP-Seq PLoS genetics Medium 28715449
2018 TIF-IA degradation (dependent on UBF/p14ARF and S44 phosphorylation status) is a novel upstream event in NF-κB nucleolar stress signaling; specific NF-κB-activating stresses induce TIF-IA degradation, preceded by increased nucleolar size, and blocking TIF-IA degradation blocks stress effects on nucleolar size and NF-κB activation. CDK4 inhibition mimics this pathway. RNAi knockdown, pharmacological inhibition (CDK4 inhibitor), site-directed mutagenesis (S44), immunoprecipitation, ex vivo tissue culture assay Nucleic acids research Medium 29873780
2016 LKB1 kinase promotes cell survival under uridine-depleted (AICAR-treated) conditions by maintaining TIF-IA nuclear accumulation and TIF-IA-mediated pre-rRNA synthesis; LKB1 kinase activity (but not kinase-dead mutant) is required for TIF-IA nuclear translocation; a S636D (phospho-mimetic) TIF-IA mutant cannot rescue AICAR-induced apoptosis whereas wild-type or S636A can, placing S636 as a regulatory phosphorylation site. RNAi knockdown, mutant overexpression (S636A/S636D), subcellular fractionation, cell viability assay, LKB1 reconstitution in LKB1-null cells Oncotarget Medium 26506235
2025 Under nutrient stress, phosphorylation of RRN3 at S199 is sufficient to divert RRN3 from nucleolus to nuclear plasma, where RRN3 regulates alternative polyadenylation (APA) of autophagy-related mRNAs (e.g., OPTN), enhancing their stability and promoting autophagy in ovarian cancer cells. Long-read RNA sequencing, PAR-CLIP, subcellular fractionation, site-directed mutagenesis (S199 phosphorylation), in vivo xenograft experiments Cell death & disease Medium 41271632
2026 In senescence, TIF-IA accumulates in the nucleus and nucleolus as an early event; this accumulation is not required for cell cycle arrest but is essential for phenotypic changes to nucleoli, the SASP, and stable senescence. In proliferating cells, TIF-IA binds the cargo receptor p62 (SQSTM1); ATM activation during senescence disrupts this interaction, allowing TIF-IA accumulation. TIF-IA accumulation also elevates ROS levels. Conditional genetic manipulation, multiple mouse senescence models, co-immunoprecipitation (TIF-IA–p62), ATM inhibitor treatment, immunofluorescence Aging cell Medium 41466483
2024 Time-resolved binding assays show that CF (core factor) uses a two-step mechanism (binding + isomerization) to recognize the rDNA promoter; CF-mediated recruitment of the Pol I–Rrn3 complex to the promoter is inefficient, with Pol I rapidly dissociating after recruitment. Biochemical binding kinetics (time-resolved), biophysical assays, molecular dynamics simulation (yeast system) bioRxivpreprint Low bio_10.1101_2024.10.30.621142

Source papers

Stage 0 corpus · 40 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2004 mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes & development 385 15004009
2005 Genetic inactivation of the transcription factor TIF-IA leads to nucleolar disruption, cell cycle arrest, and p53-mediated apoptosis. Molecular cell 219 15989966
2003 ERK-dependent phosphorylation of the transcription initiation factor TIF-IA is required for RNA polymerase I transcription and cell growth. Molecular cell 219 12620228
2005 The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-IA and down-regulates rRNA synthesis. Genes & development 176 15805466
2000 The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3. The EMBO journal 147 11032814
1990 A growth-dependent transcription initiation factor (TIF-IA) interacting with RNA polymerase I regulates mouse ribosomal RNA synthesis. The EMBO journal 114 2390974
2000 TIF-IA, the factor mediating growth-dependent control of ribosomal RNA synthesis, is the mammalian homolog of yeast Rrn3p. EMBO reports 113 11265758
1996 RRN3 gene of Saccharomyces cerevisiae encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. The EMBO journal 108 8670901
1985 Growth-dependent regulation of rRNA synthesis is mediated by a transcription initiation factor (TIF-IA). Nucleic acids research 94 4070001
1997 The yeast nucleolar protein Cbf5p is involved in rRNA biosynthesis and interacts genetically with the RNA polymerase I transcription factor RRN3. Molecular and cellular biology 92 9315678
2000 RNA polymerase I transcription factor Rrn3 is functionally conserved between yeast and human. Proceedings of the National Academy of Sciences of the United States of America 91 10758157
2011 Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes & development 88 21940764
2002 Multiple interactions between RNA polymerase I, TIF-IA and TAF(I) subunits regulate preinitiation complex assembly at the ribosomal gene promoter. EMBO reports 82 12393749
2007 Drosophila TIF-IA is required for ribosome synthesis and cell growth and is regulated by the TOR pathway. The Journal of cell biology 81 18086911
2002 Rrn3 phosphorylation is a regulatory checkpoint for ribosome biogenesis. The Journal of biological chemistry 75 12015311
2007 Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription. Molecular and cellular biology 71 18086878
1993 Function of the growth-regulated transcription initiation factor TIF-IA in initiation complex formation at the murine ribosomal gene promoter. Molecular and cellular biology 70 8413268
2013 Akt activation enhances ribosomal RNA synthesis through casein kinase II and TIF-IA. Proceedings of the National Academy of Sciences of the United States of America 66 24297901
2008 Phosphorylation by casein kinase 2 facilitates rRNA gene transcription by promoting dissociation of TIF-IA from elongating RNA polymerase I. Molecular and cellular biology 66 18559419
2017 A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription. PLoS genetics 65 28715449
2016 Heat shock represses rRNA synthesis by inactivation of TIF-IA and lncRNA-dependent changes in nucleosome positioning. Nucleic acids research 55 27257073
2016 RNA polymerase I-Rrn3 complex at 4.8 Å resolution. Nature communications 55 27418309
2013 DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription. The Journal of biological chemistry 34 23393135
2003 Rrn3 becomes inactivated in the process of ribosomal DNA transcription. The Journal of biological chemistry 30 12646563
2018 Identification of a novel TIF-IA-NF-κB nucleolar stress response pathway. Nucleic acids research 23 29873780
2016 TIF-IA: An oncogenic target of pre-ribosomal RNA synthesis. Biochimica et biophysica acta 22 27641688
2014 TIF-IA-dependent regulation of ribosome synthesis in drosophila muscle is required to maintain systemic insulin signaling and larval growth. PLoS genetics 22 25356674
2014 Selective inhibition of rDNA transcription by a small-molecule peptide that targets the interface between RNA polymerase I and Rrn3. Molecular cancer research : MCR 21 25033839
2008 Mammalian Rrn3 is required for the formation of a transcription competent preinitiation complex containing RNA polymerase I. Gene expression 20 18590050
2007 Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene. BMC molecular biology 19 18047649
2009 Dynamic subcellular partitioning of the nucleolar transcription factor TIF-IA under ribotoxic stress. Biochimica et biophysica acta 13 19450626
2016 LKB1 promotes cell survival by modulating TIF-IA-mediated pre-ribosomal RNA synthesis under uridine downregulated conditions. Oncotarget 9 26506235
2022 Rrn3 gene knockout affects ethanol-induced locomotion in adult heterozygous zebrafish. Psychopharmacology 4 35006303
2015 TIF-IA and Ebp1 regulate RNA synthesis in T cells. Blood 2 25883228
2025 NSH76: a selective inhibitor of RRN3 and RNA polymerase I transcription with potential for cancer therapy. Journal of translational medicine 1 41116164
2005 The association of TIF-IA and polymerase I mediates promoter recruitment and regulation of ribosomal RNA transcription in Acanthamoeba castellanii. Gene expression 1 16358415
2026 Loss of p62 Binding Allows TIF-IA Accumulation in Senescence, Which Promotes Phenotypic Changes to Nucleoli and the Senescence Associated Secretory Phenotype. Aging cell 0 41466483
2026 Early growth response 1 promotes RNA polymerase I-directed transcription and cancer growth by activating RRN3 expression. Communications biology 0 41507426
2026 Clinical significance and functional characterization of RRN3 in gastric cancer: insights from pan-cancer analysis and experimental validation. Frontiers in oncology 0 42211503
2025 Nutrient stress diverts RRN3 from rRNA transcription to alternative polyadenylation of autophagy mRNAs in ovarian cancer. Cell death & disease 0 41271632

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