Affinage

CTR9

RNA polymerase-associated protein CTR9 homolog · UniProt Q6PD62

Length
1173 aa
Mass
133.5 kDa
Annotated
2026-04-28
28 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CTR9 is the TPR-domain scaffold subunit of the PAF1 complex (PAF1C), functioning as a central organizer of RNA Polymerase II-coupled transcription elongation and co-transcriptional chromatin modification. Its TPR module heterodimerizes with PAF1 to nucleate PAF1C assembly, and disruption of this interface abolishes complex formation, histone H3K4me3 and H3K36me3 deposition, and yeast viability (PMID:30228257, PMID:11884586). CTR9 restrains Polycomb-mediated H3K27me3 by maintaining PRC2 subtype equilibrium (PRC2.2 over PRC2.1), regulates NELF/SPT5-dependent elongation pausing at stimulus-responsive loci such as c-Fos, controls ERα stability and genome-wide ERα/RNAPII chromatin occupancy in estrogen signaling, and is itself targeted for proteasomal degradation via SIAH1-mediated K48-linked polyubiquitination (PMID:35137163, PMID:23593388, PMID:26494790, PMID:37038329). De novo CTR9 missense variants cause a neurodevelopmental disorder, with patient-derived mutations showing enhanced PAF1 binding affinity and dominant-negative effects in zebrafish (PMID:35717577).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 1996 Medium

    Establishing CTR9 as a TPR-repeat nuclear phosphoprotein whose SH2-binding C-terminal region governs nuclear localization answered the fundamental question of domain architecture and subcellular targeting.

    Evidence Biochemical purification, cDNA cloning, and deletion-mutant transfection with SH2 binding assays in mammalian cells

    PMID:8636124

    Open questions at the time
    • SH2-binding partners in vivo not identified
    • phosphorylation sites not mapped
    • no connection yet to transcription machinery
  2. 2002 High

    Identification of Ctr9 as a stoichiometric subunit of the Paf1/RNAPII complex, distinct from Mediator, resolved how CTR9 connects to the transcription machinery and established genetic epistasis with PAF1.

    Evidence Tandem affinity purification and mass spectrometry from yeast, plus ctr9Δ paf1Δ double-mutant epistasis

    PMID:11884586

    Open questions at the time
    • Structural basis of Ctr9–Paf1 interaction unknown
    • mechanism of RNAPII association not defined
  3. 2013 Medium

    Demonstration that CTR9 occupies coding regions to maintain an elongation block at stimulus-responsive genes (c-Fos, Il17a) and that its dissociation is cytokine/JAK2-dependent revealed a locus-specific transcriptional pausing function beyond general elongation.

    Evidence ChIP, siRNA knockdown, JAK2 inhibitor treatment in mammalian cells; Th17 polarization and in vivo lentiviral overexpression in collagen-induced arthritis model

    PMID:23593388 PMID:24420920

    Open questions at the time
    • Whether JAK2 directly phosphorylates CTR9 or acts indirectly is unresolved
    • mechanism of selective locus occupancy unknown
  4. 2013 Medium

    Ctr9 knockdown in mouse embryos causing loss of H3K36me3 and lineage specification failure, phenocopied by Setd2 knockdown, placed CTR9/PAF1C upstream of H3K36me3 deposition in a developmental context.

    Evidence siRNA knockdown in mouse preimplantation embryos with immunofluorescence for histone marks and lineage marker expression

    PMID:24036311

    Open questions at the time
    • Whether CTR9 directly recruits SETD2 or acts indirectly through elongation is unclear
    • not tested whether H3K4me3 is also affected in embryos
  5. 2015 Medium

    Discovery that CTR9 stabilizes ERα protein and promotes genome-wide ERα/RNAPII chromatin occupancy showed that CTR9 functions as a master regulator of estrogen-dependent transcription in breast cancer cells.

    Evidence siRNA knockdown, ChIP, protein stability assays in ERα-positive breast cancer cells; extended by genome-wide ChIP-seq

    PMID:26494790 PMID:27829357

    Open questions at the time
    • Mechanism by which CTR9 stabilizes ERα protein not defined
    • whether this is PAF1C-dependent or an independent CTR9 function is unresolved
  6. 2015 Medium

    Identification of a direct CTR9–dopamine transporter (DAT) interaction at the plasma membrane that enhances DAT surface trafficking and dopamine uptake revealed an unexpected extranuclear function for CTR9.

    Evidence Yeast two-hybrid, GST pulldown, co-immunoprecipitation, dopamine uptake assay, and deletion mutagenesis in mammalian cells

    PMID:26048990

    Open questions at the time
    • Physiological relevance in dopaminergic neurons not demonstrated
    • fraction of CTR9 at the plasma membrane not quantified
    • not independently replicated
  7. 2016 Medium

    Cross-species rescue of Drosophila ctr9 null lethality by human CTR9 cDNA, along with loss of H3K4me3, established deep functional conservation of CTR9's role in histone modification.

    Evidence Drosophila null mutant, immunofluorescence, ChIP for H3K4me3, human cDNA rescue

    PMID:27678520

    Open questions at the time
    • Whether PAF1C composition is identical in Drosophila is not fully resolved
    • genome-wide histone mark changes not profiled
  8. 2018 High

    Crystal structures of human and yeast Ctr9/Paf1 subcomplexes defined the TPR-mediated heterodimerization interface essential for PAF1C assembly, histone methylation, and viability, resolving the structural basis of the complex.

    Evidence X-ray crystallography, in vitro binding assays, interface-disrupting mutagenesis with in vivo histone modification analysis

    PMID:30228257

    Open questions at the time
    • Full PAF1C structure with all five subunits not yet determined at atomic resolution
    • how the Ctr9-Paf1 dimer interfaces with RNAPII structurally remains incomplete
  9. 2018 Medium

    Showing that Paf1 and Ctr9 specifically suppress telomeric repeat-containing RNA (TERRA) levels through both transcription and degradation pathways expanded CTR9's role to telomere biology.

    Evidence Genetic deletion in yeast, Northern blot/RT-PCR for TERRA, double-mutant epistasis with Sir4, Rat1, and Trf4

    PMID:29145644

    Open questions at the time
    • Direct mechanism of TERRA suppression (transcriptional vs. degradation) not separated for Ctr9
    • relevance to mammalian telomere biology not tested
  10. 2022 Medium

    Genome-wide expansion of H3K27me3 upon CTR9 loss was traced to a PRC2 subtype switch (PRC2.2→PRC2.1), explaining how PAF1C antagonizes Polycomb repression and revealing a therapeutic vulnerability to PRC2 inhibitors.

    Evidence Inducible CTR9 knockdown, quantitative histone profiling, ChIP-seq for H3K27me3, PRC2 subtype characterization in human cells; corroborated by EZH2 inhibitor rescue in mesenchymal stem cells

    PMID:35137163 PMID:36383652

    Open questions at the time
    • How CTR9/PAF1C mechanistically controls PRC2 subtype equilibrium is unknown
    • whether this is transcription-dependent or a direct chromatin mechanism is unresolved
  11. 2022 Medium

    De novo CTR9 missense variants were linked to neurodevelopmental disorder, with gain-of-PAF1-affinity mutations acting dominant-negatively in zebrafish, establishing CTR9 as a disease gene.

    Evidence Patient variant identification, pull-down affinity assays (mutant vs. WT), zebrafish ctr9 knockout and rescue with mutant human cDNA

    PMID:35717577

    Open questions at the time
    • Precise downstream molecular pathways disrupted by gain-of-affinity mutations not defined
    • patient cohort is small
    • no mouse model of patient mutations
  12. 2023 Medium

    Identification of SIAH1 as an E3 ligase that K48-polyubiquitinates CTR9 for proteasomal degradation defined the first regulated turnover mechanism for CTR9 protein.

    Evidence Yeast two-hybrid, co-immunoprecipitation, in vivo ubiquitination assay, proteasome inhibitor treatment in hepatocellular carcinoma cells

    PMID:37038329

    Open questions at the time
    • Signals that trigger SIAH1-mediated CTR9 degradation not identified
    • lysine residues on CTR9 targeted by SIAH1 not mapped
    • physiological contexts beyond HCC not tested

Open questions

Synthesis pass · forward-looking unresolved questions
  • The mechanism by which CTR9/PAF1C controls PRC2 subtype switching, the structural basis for full PAF1C–RNAPII engagement, and the physiological significance of extranuclear CTR9 functions remain unresolved.
  • Full atomic structure of PAF1C bound to RNAPII elongation complex not available
  • CTR9–DAT interaction not validated in primary neurons
  • How patient gain-of-affinity mutations alter transcription and chromatin globally is unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 4 GO:0005198 structural molecule activity 2
Localization
GO:0005634 nucleus 2 GO:0005886 plasma membrane 1
Pathway
R-HSA-74160 Gene expression (Transcription) 5 R-HSA-4839726 Chromatin organization 4 R-HSA-1266738 Developmental Biology 2
Partners
CDC73ESR1LEO1PAF1RTF1SIAH1SLC6A3
Complex memberships
PAF1 complex (PAF1C)

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2002 Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex, distinct from the Srb-mediator form of Pol II holoenzyme; Ctr9 associates with Paf1, Cdc73, and Pol II as shown by tandem affinity purification and mass spectrometry; deletion of CTR9 leads to severe pleiotropic phenotypes similar to PAF1 deletion, and genetic epistasis shows ctr9Δ paf1Δ double mutants are not additive, placing them in the same pathway. Tandem affinity purification, mass spectrometry, genetic epistasis (double mutant analysis) Molecular and cellular biology High 11884586
2018 Crystal structures of human and yeast Ctr9/Paf1 subcomplexes reveal they assemble into heterodimers via an interface between the tetratricopeptide repeat (TPR) module of Ctr9 and Paf1; disruption of this Ctr9/Paf1 interaction abolishes overall Paf1C assembly and is essential for yeast viability; disruption of this interaction also greatly reduces histone H3 methylation in vivo. Crystal structure determination, in vitro binding assays, in vivo mutagenesis, histone modification analysis Nature communications High 30228257
1996 CTR9 (p150TSP) is a nuclear phosphoprotein containing multiple tetratricopeptide repeat (TPR) domains; the TPR module mediates homotypic protein-protein interactions; the C-terminal serine/glutamic acid-rich region binds SH2 domains in a serine/threonine phosphorylation-dependent manner; the SH2-binding domain is required for nuclear localization. Biochemical purification, cDNA cloning, transfection with deletion mutants, SH2 binding assays The Journal of biological chemistry Medium 8636124
2013 CTR9 (as part of PAFc) constitutively associates with the 5'-coding region of the c-Fos locus and maintains an elongation block; upon IL-6 stimulation, CTR9 dissociates from the locus in a JAK2 kinase-dependent manner; CTR9 depletion reduces NELF association and enhances SPT5 and CDK9 recruitment at c-Fos, promoting transcription elongation. ChIP assay, siRNA knockdown, pharmacological inhibitor (JAK2 inhibitor AG-490), RNA Pol II phospho-form analysis PloS one Medium 23593388
2013 Ctr9 knockdown in mouse preimplantation embryos causes loss of histone H3K36me3, failure of lineage specification at the blastocyst stage, and aberrant expression of imprinted genes; these phenotypes are phenocopied by knockdown of Setd2 (H3K36 methyltransferase) or Rtf1, placing Ctr9 upstream or in the same pathway as H3K36me3 deposition. siRNA knockdown in mouse embryos, immunofluorescence for histone modifications, lineage marker expression analysis, epistasis with Setd2 and Rtf1 Developmental biology Medium 24036311
2014 CTR9 occupies the coding region of the Il17a gene in naive T cells and functions as a transcriptional repressor of IL-17; upon Th17-polarizing conditions or IL-6 stimulation, CTR9 dissociates from the Il17a locus; CTR9 depletion enhances IL-17 expression and Th17 differentiation, while CTR9 overexpression in vivo (via lentivirus) reduces CD4+IL-17+ T cells and ameliorates collagen-induced arthritis. ChIP assay, siRNA knockdown, lentivirus-mediated overexpression in vivo, flow cytometry Journal of immunology Medium 24420920
2015 Ctr9 is identified as a direct binding partner of the dopamine transporter (DAT) via yeast two-hybrid; confirmed by GST pulldown and co-immunoprecipitation in vivo; Ctr9 co-localizes with DAT at the plasma membrane in co-expressing mammalian cells; Ctr9 interaction with DAT (requiring residues YKF in the DAT C-terminus) increases DAT-mediated dopamine uptake by raising the number of DAT transporters at the plasma membrane; the SH2 domain of Ctr9 is required for its nuclear localization. Yeast two-hybrid, GST pulldown, co-immunoprecipitation, dopamine uptake assay, deletion mutagenesis, 3D modeling The Journal of biological chemistry Medium 26048990
2015 Ctr9 knockdown in ERα-positive breast cancer cells almost completely abolishes estrogen-regulated transcriptional response; mechanistically, Ctr9 enhances ERα protein stability, promotes recruitment of ERα and RNAPII to target loci, and stimulates transcription elongation and transcription-coupled histone modifications. siRNA knockdown, ChIP assay, gene expression analysis, protein stability assay Genes & development Medium 26494790
2016 Genome-wide ChIP-seq shows that Ctr9 knockdown dramatically decreases global occupancy of ERα and RNAPII at ERα target genes in estrogen-treated breast cancer cells, demonstrating that Ctr9 controls ERα-target gene expression by regulating global chromatin occupancy of both ERα and RNAPII, independent of other PAFc subunits. ChIP-seq, siRNA knockdown, genome-wide analysis BMC genomics Medium 27829357
2018 In yeast, Paf1 and Ctr9 (core subunits of the PAF1 complex) specifically maintain low levels of telomere repeat-containing RNA (TERRA); double mutant analysis shows Paf1 and Ctr9 affect TERRA independently of Sir4, Rat1, and Trf4; both transcription and RNA degradation mechanisms are implicated. Genetic deletion, Northern blot/RT-PCR for TERRA, double mutant epistasis analysis Nucleic acids research Medium 29145644
2022 CTR9 depletion causes genome-wide expansion of H3K27me3 and increased PRC2 recruitment to chromatin; mechanistically, CTR9 loss triggers a switch from the less active PRC2.2 subtype to the more active PRC2.1 subtype, thereby controlling H3K27me3 levels and distribution; CTR9 knockdown cells become hypersensitive to PRC2 inhibitors. Inducible/stable CTR9 KD cell lines, quantitative histone modification profiling, ChIP-seq for H3K27me3, PRC2 subtype characterization Nucleic acids research Medium 35137163
2022 CTR9 counteracts EZH2-mediated H3K27me3 deposition in human mesenchymal stem cells; CTR9 knockdown increases H3K27me3, impairs BMP-2 secretion and BMP-SMAD pathway activation, and blocks osteochondral differentiation; EZH2 inhibitors partially rescue differentiation defects of CTR9 KD cells; BMP-2 supplementation rescues osteogenic differentiation. siRNA knockdown, EZH2 inhibitor rescue, BMP-2 supplementation rescue, in vivo ectopic osteogenesis assay, transcriptome analysis Science advances Medium 36383652
2023 SIAH1 interacts with CTR9 (identified by yeast two-hybrid and confirmed by co-immunoprecipitation) and promotes K48-linked polyubiquitination of CTR9, leading to its proteasomal degradation; SIAH1 thereby inhibits CTR9-driven epithelial-mesenchymal transition in hepatocellular carcinoma cells. Yeast two-hybrid, co-immunoprecipitation, ubiquitination assay, proteasome inhibitor treatment Carcinogenesis Medium 37038329
2016 Drosophila CTR9 homolog (CG2469) localizes to cell nuclei and is enriched in histone locus bodies; loss of Drosophila Ctr9 reduces global H3K4me3 levels; both human and Drosophila Ctr9 localize to nuclei of Drosophila cells, and human CTR9 cDNA rescues the lethality of Drosophila ctr9 null mutants, demonstrating functional conservation. Null mutation, immunofluorescence, ChIP for H3K4me3, human cDNA rescue experiment G3 (Bethesda, Md.) Medium 27678520
2022 De novo CTR9 missense variants in patients with neurodevelopmental disorder show stronger affinity to PAF1 protein in pull-down assays compared to wild-type CTR9; zebrafish ctr9 knockout causes motor defects and telencephalon enlargement; human CTR9 mutant proteins fail to rescue ctr9-knockout zebrafish motor phenotype, and overexpression of mutant CTR9 mRNA causes telencephalon enlargement, indicating dominant-negative or gain-of-function interference with normal CTR9 activity. Pull-down assay (mutant vs. wild-type affinity), zebrafish knockout, rescue experiment with human mutant cDNA, mRNA overexpression Human molecular genetics Medium 35717577

Source papers

Stage 0 corpus · 28 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Molecular and cellular biology 204 11884586
2014 Germline mutations in the PAF1 complex gene CTR9 predispose to Wilms tumour. Nature communications 76 25099282
2018 Paf1 and Ctr9 subcomplex formation is essential for Paf1 complex assembly and functional regulation. Nature communications 37 30228257
2013 CTR9/PAF1c regulates molecular lineage identity, histone H3K36 trimethylation and genomic imprinting during preimplantation development. Developmental biology 34 24036311
2015 Ctr9, a key subunit of PAFc, affects global estrogen signaling and drives ERα-positive breast tumorigenesis. Genes & development 29 26494790
2016 Ctr9, a Key Component of the Paf1 Complex, Affects Proliferation and Terminal Differentiation in the Developing Drosophila Nervous System. G3 (Bethesda, Md.) 25 27520958
1996 p150TSP, a conserved nuclear phosphoprotein that contains multiple tetratricopeptide repeats and binds specifically to SH2 domains. The Journal of biological chemistry 20 8636124
2018 Paf1 and Ctr9, core components of the PAF1 complex, maintain low levels of telomeric repeat containing RNA. Nucleic acids research 18 29145644
2022 CTR9 drives osteochondral lineage differentiation of human mesenchymal stem cells via epigenetic regulation of BMP-2 signaling. Science advances 16 36383652
2017 Identification of a novel CTR9 germline mutation in a family with Wilms tumor. European journal of medical genetics 15 29292210
2016 Drosophila CG2469 Encodes a Homolog of Human CTR9 and Is Essential for Development. G3 (Bethesda, Md.) 14 27678520
2022 The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium. Nucleic acids research 12 35137163
2021 Transcriptional regulator CTR9 promotes hepatocellular carcinoma progression and metastasis via increasing PEG10 transcriptional activity. Acta pharmacologica Sinica 12 34876700
2015 Ctr9, a Protein in the Transcription Complex Paf1, Regulates Dopamine Transporter Activity at the Plasma Membrane. The Journal of biological chemistry 11 26048990
2022 MicroRNA-17-3p is upregulated in psoriasis and regulates keratinocyte hyperproliferation and pro-inflammatory cytokine secretion by targeting <em>CTR9</em>. European journal of histochemistry : EJH 10 35016493
2014 Transcriptional regulator CTR9 inhibits Th17 differentiation via repression of IL-17 expression. Journal of immunology (Baltimore, Md. : 1950) 10 24420920
2013 CTR9, a component of PAF complex, controls elongation block at the c-Fos locus via signal-dependent regulation of chromatin-bound NELF dissociation. PloS one 9 23593388
2021 CTR9-mediated JAK2/STAT3 pathway promotes the proliferation, migration, and invasion of human glioma cells. Journal of clinical laboratory analysis 8 34369006
2016 Systematic identification of Ctr9 regulome in ERα-positive breast cancer. BMC genomics 8 27829357
2023 SIAH1/CTR9 axis promotes the epithelial-mesenchymal transition of hepatocellular carcinoma. Carcinogenesis 7 37038329
2022 Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder. Genetics in medicine : official journal of the American College of Medical Genetics 7 35499524
2012 Proteome analysis of a CTR9 deficient yeast strain suggests that Ctr9 has function(s) independent of the Paf1 complex. Biochimica et biophysica acta 4 22446411
2025 Paralog-Dependent Specialization of Paf1C Subunit, Ctr9, for Sex Chromosome Gene Regulation and Male Germline Differentiation in Drosophila. Genes to cells : devoted to molecular & cellular mechanisms 3 40763999
2024 Ctr9 promotes virulence of Candida albicans by regulating methionine metabolism. Virulence 2 39316797
2022 De novo non-synonymous CTR9 variants are associated with motor delay and macrocephaly: human genetic and zebrafish experimental evidence. Human molecular genetics 1 35717577
2024 Novel CTR9 germline pathogenic splice site variant in siblings with Wilms tumor from Tanzania. European journal of medical genetics 0 39293508
2007 [The effect of recombinant TSBP on protein kinase A activity]. Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi 0 18232488
2006 [Fusion expression and affinity purification of a human novel gene tsbp in eukaryotic cells]. Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology 0 16948892