Affinage

PRPF4

U4/U6 small nuclear ribonucleoprotein Prp4 · UniProt O43172

Length
522 aa
Mass
58.4 kDa
Annotated
2026-06-10
14 papers in source corpus 12 papers cited in narrative 12 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

PRPF4 (SNRNP60/HPrp4p) is a WD-repeat protein that forms a seven-bladed beta-propeller and functions as a structural component of the U4/U6.U5 tri-snRNP, where it remains stably associated with the U4/U6 snRNP even under salt conditions that dissociate the tri-snRNP (PMID:9257651). It is recruited to the U4/U6 snRNP through a direct interaction with PRPF3 (Hprp3p): the central region of PRPF3 is necessary and sufficient for binding PRPF4, and this interaction is required for the complex to associate with U4/U6 snRNAs (PMID:9328476, PMID:11971898). The intrinsically disordered N-terminus of PRPF4 additionally engages cyclophilin H (PPIH) through a bipartite, two-site interaction (PMID:28935721). The functional importance of these contacts is established by adRP-causing variants: PRPF4 p.R192H disrupts the PRPF4–PRPF3 interface and prevents tri-snRNP integration, behaving as a functional null, while p.Pro315Leu acts through dominant-negative effects on tri-snRNP component levels, together causing autosomal dominant retinitis pigmentosa via haploinsufficiency and dominant-negative mechanisms (PMID:24419317, PMID:25383878). Consistent with a broad role in splicing, zebrafish prpf4 loss impairs spliceosome assembly and pre-mRNA splicing (including slc25a39), activates ATM/CHK2-p53-dependent DNA-damage and cell-cycle arrest responses, and disrupts downstream Fgf, Wnt/β-catenin, and chemokine signaling, leading to apoptosis in neural and erythroid lineages (PMID:30174136, PMID:41360772). A distinct CDK-like kinase paralog (hPRP4/Prp4p) phosphorylates Elk-1 downstream of EGF and the splicing factor Prp1p, linking kinase activity to splicing and cell-cycle progression (PMID:10799319, PMID:11252721).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1997 High

    Identifying PRPF4 as a salt-stable U4/U6 snRNP component established it as a core structural subunit of the tri-snRNP rather than a transient factor, and the WD-repeat architecture predicted a beta-propeller scaffold.

    Evidence Immunoaffinity purification, cDNA cloning/sequencing, and homology analysis of the human U4/U6-60kD protein

    PMID:9257651

    Open questions at the time
    • Did not define which surface of the propeller mediates snRNP contacts
    • No direct binding partner identified at this stage
  2. 1997 Medium

    Demonstrating a physical PRPF4–PRPF3 interaction and PRPF3's co-precipitation with U4/U6/U5 snRNAs placed both proteins together in the tri-snRNP and pointed to PRPF3 as the link to the snRNP.

    Evidence Co-immunoprecipitation, antibody pulldown, and snRNA co-precipitation

    PMID:9328476

    Open questions at the time
    • Did not map the minimal interaction region
    • Single lab, no thermodynamic quantification
  3. 2002 High

    Mapping the PRPF3 central region as necessary and sufficient for PRPF4 binding, and showing this interaction is required for U4/U6 snRNA association, established that PRPF3 recruits PRPF4 onto the snRNP.

    Evidence Deletion-mutant co-IP, isothermal titration calorimetry, and primer extension in HeLa nuclear extracts

    PMID:11971898

    Open questions at the time
    • No atomic structure of the PRPF3–PRPF4 interface
    • Did not address PPIH contribution
  4. 2017 Medium

    Resolving that PPIH binds the intrinsically disordered PRPF4 N-terminus at two distinct sites defined a second, bipartite assembly contact distinct from the PRPF3 interface.

    Evidence Recombinant reconstitution, point-mutation uncoupling of binding sites, and biophysical/NMR characterization

    PMID:28935721

    Open questions at the time
    • In vitro only; cellular requirement of each site untested
    • No structure of the full PRPF4–PPIH–PRPF3 module
  5. 2014 High

    Two disease variants clarified how PRPF4 dysfunction causes adRP: R192H abolishes PRPF3 binding and tri-snRNP integration (functional null/haploinsufficiency), while P315L acts dominant-negatively, linking the assembly biochemistry directly to human pathology.

    Evidence Binding/integration assays in human cells plus zebrafish overexpression, morpholino knockdown, and equivalent-mutation rescue

    PMID:24419317 PMID:25383878

    Open questions at the time
    • Why a ubiquitously expressed splicing factor causes a retina-specific phenotype is unresolved
    • Dominant-negative mechanism not reconstituted biochemically
  6. 2018 Medium

    Genetic prpf4 loss in zebrafish showed that splicing failure has tissue-level consequences, coupling impaired spliceosome assembly to p53-dependent apoptosis and disrupted Fgf/Wnt/chemokine signaling.

    Evidence Gene-trap mutant with p53 rescue, RNA-Seq splicing analysis, and pathway analysis

    PMID:30174136

    Open questions at the time
    • Whether disrupted signaling is direct or secondary to global mis-splicing unclear
    • Specific mis-spliced effector transcripts not defined
  7. 2025 Medium

    Refined zebrafish analysis connected prpf4 loss to ATM/CHK2-p53-driven cell-cycle arrest and to a specific splicing defect in slc25a39, providing concrete molecular routes from splicing failure to lineage-specific (erythroid) defects.

    Evidence prpf4 mutant cell-cycle FACS, DNA-damage markers, RNA-Seq splice-site analysis, and slc25a39 expression

    PMID:41360772

    Open questions at the time
    • Causal link between DNA damage and which mis-spliced transcripts is not established
    • Relevance to mammalian/human erythropoiesis untested
  8. 2000 Medium

    A CDK-like kinase paralog (hPRP4) was shown to phosphorylate Elk-1 at Thr-417 downstream of EGF/forskolin, defining a signaling/transcription role separate from the WD-repeat splicing protein.

    Evidence Kinase assays in COS-7 cells with site-specific phosphorylation and Elk-1 luciferase reporter

    PMID:10799319

    Open questions at the time
    • This concerns the CDK-like kinase paralog, not the WD-repeat PRPF4
    • Single study, no in vivo confirmation
  9. 2001 Medium

    S. pombe Prp4p kinase activity was shown to be required for splicing and to phosphorylate the splicing factor Prp1p, linking the kinase ortholog to spliceosome function and cell-cycle progression.

    Evidence In vitro kinase reconstitution with Prp1p, yeast two-hybrid, in vivo labeling, and genetic analysis

    PMID:11252721

    Open questions at the time
    • Fission-yeast ortholog; mammalian relevance to WD-repeat PRPF4 unclear
    • Substrate set beyond Prp1p undefined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How tri-snRNP assembly biochemistry translates into a retina-restricted disease phenotype, and whether the kinase-associated signaling functions reflect PRPF4 itself or a distinct paralog, remain unresolved.
  • No atomic-resolution structure of the PRPF4–PRPF3–PPIH assembly module
  • Tissue specificity of adRP unexplained
  • Identity/separation of WD-repeat PRPF4 versus CDK-like kinase functions not clarified within the corpus

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0008092 cytoskeletal protein binding 2 GO:0005198 structural molecule activity 1
Localization
GO:0005634 nucleus 2
Pathway
R-HSA-8953854 Metabolism of RNA 3 R-HSA-1643685 Disease 2
Partners
PPIHPRPF3
Complex memberships
U4/U6 snRNPU4/U6.U5 tri-snRNP

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1997 Human U4/U6-60kD protein (PRPF4/SNRNP60) was identified as a component of the U4/U6.U5 tri-snRNP that specifically associates with U4/U6 snRNP even at salt concentrations where the tri-snRNP complex dissociates; its primary structure contains seven WD repeats, predicting a beta-propeller topology homologous to G-protein beta subunits. Immunoaffinity chromatography, cDNA cloning and sequencing, sequence homology analysis RNA (New York, N.Y.) High 9257651
1997 Hprp3p and Hprp4p interact with each other; Hprp3p co-immunoprecipitates with U4, U6, and U5 snRNAs, placing both proteins in the U4/U6.U5 tri-snRNP; the first 100 amino acids of Hprp3p are not essential for the Hprp3p–Hprp4p interaction. Co-immunoprecipitation, antibody pulldown, snRNA co-precipitation Human molecular genetics Medium 9328476
2002 The central region of Hprp3p (lacking N-terminal 194 aa or C-terminal 240 aa) is necessary and sufficient for binding Hprp4p; this Hprp3p–Hprp4p interaction is required for association of the complex with U4/U6 snRNAs, indicating that Hprp3p recruits Hprp4p to the U4/U6 snRNP. Co-immunoprecipitation, isothermal titration calorimetry, primer extension analysis, bacterial and mammalian expression of deletion mutants The Journal of biological chemistry High 11971898
2000 Human hPRP4, a CDK-like kinase homologous to S. pombe Prp4p, is activated by EGF or forskolin treatment and phosphorylates Elk-1 at Thr-417 (a site distinct from other MAPKs), leading to Elk-1 transactivation; this demonstrates a signaling/transcription-factor activation function for hPRP4 beyond splicing. Kinase activity assay in COS-7 cells, EGF/forskolin stimulation, site-specific phosphorylation analysis, luciferase reporter (Elk-1 trans-activation) Biochemical and biophysical research communications Medium 10799319
2001 S. pombe Prp4p kinase activity is required for pre-mRNA splicing in vivo; Prp4p phosphorylates the non-SR splicing factor Prp1p in vitro and interacts with Prp1p in two-hybrid assays; loss of Prp4p kinase activity impairs G1-S and G2-M cell cycle progression. In vitro kinase assay with bacterially expressed Prp1p, yeast two-hybrid, in vivo phosphorylation labeling, genetic analysis EMBO reports Medium 11252721
2002 The deubiquitinating enzyme Ubp21p of S. pombe stabilizes a mutant form of Prp4p kinase; Ubp21 was identified as a high-copy suppressor of a mutation in the ALKHP motif of Prp4p's kinase subdomain XI, indicating that ubiquitin-mediated proteolysis regulates Prp4p steady-state levels. High-copy suppressor screen, mutational analysis of kinase domain, Ubp21 characterization Molecular genetics and genomics Low 11919719
2014 The PRPF4 p.Pro315Leu variant causes dominant-negative effects: overexpression in cells upregulates tri-snRNP components (PRPF4 itself included) and alters SC35 splicing-factor localization as a compensatory response; overexpression of mutant but not wild-type PRPF4 causes retinal deformities in zebrafish and worsens phenotypes in prpf4 morphants, establishing PRPF4 as a U4/U6-U5 tri-snRNP component whose dysfunction leads to adRP via haploinsufficiency and dominant-negative mechanisms. Luciferase promoter assay, overexpression in fibroblasts and HeLa cells, SC35 immunostaining, zebrafish overexpression and morpholino knockdown Human molecular genetics Medium 24419317
2014 The PRPF4 p.R192H variant disrupts the binding interface between PRPF4 and PRPF3, preventing PRPF4 from integrating into the tri-snRNP; introduction of the equivalent mutation in zebrafish prpf4 causes complete loss of function in vivo, and the variant behaves as a functional null (haploinsufficiency) in a human cell line. Biochemical binding assays (co-IP/pulldown), cell-line tri-snRNP integration assay, zebrafish in vivo functional rescue experiments PloS one High 25383878
2017 PPIH (cyclophilin H) binds the N-terminus of PRPF4 at two distinct interaction sites (bipartite binding); the N-terminal region of PRPF4 is intrinsically disordered and does not adopt secondary structure upon PPIH binding; mutations in both sites are required to abrogate complex formation. Recombinant protein expression and purification, complex formation assay, mutational analysis (point mutations uncoupling binding sites), NMR/biophysical characterization The Biochemical journal Medium 28935721
2018 In zebrafish, prpf4 loss-of-function leads to p53-dependent apoptosis in neural cells and defects in posterior lateral line primordium (pLLP) migration; RNA-Seq shows prpf4 deficiency impairs spliceosome assembly, causes compensatory upregulation of spliceosomal genes, and alters pre-mRNA splicing; Fgf, Wnt/β-catenin, and chemokine signaling pathways are disrupted. Gene-trap zebrafish mutant, p53 rescue experiments, RNA-Seq splicing analysis, signaling pathway analysis Journal of genetics and genomics Medium 30174136
2019 PRPF4 knockdown in breast cancer cell lines reduces proliferation, migration, invasion, and induces apoptosis; microarray analysis indicates reduced phosphorylation of p38 MAPK associated with decreased expression of PPIP5K1, PPIPK2, and YWHAE, placing PRPF4 upstream of p38 MAPK signaling. Stable shRNA knockdown in MCF7 and MDA-MB-468 cells, colony formation assay, migration/invasion assays, microarray, Western blot for p38 MAPK phosphorylation Molecular and cellular probes Low 31445970
2025 In zebrafish, prpf4 mutation causes DNA damage and activates the ATM/CHK2-p53 signaling pathway, arresting early erythrocytes at S and G2/M phases and inducing apoptosis; separately, prpf4 mutation causes skipped-exon splicing defects including in slc25a39 pre-mRNA, reducing slc25a39 mRNA and impairing late erythrocyte maturation. Zebrafish prpf4 mutant analysis, cell cycle assay (FACS), DNA damage markers, RNA-Seq splice-site analysis, slc25a39 expression analysis Cell death discovery Medium 41360772

Source papers

Stage 0 corpus · 14 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2014 PRPF4 mutations cause autosomal dominant retinitis pigmentosa. Human molecular genetics 108 24419317
1997 The human U4/U6 snRNP contains 60 and 90kD proteins that are structurally homologous to the yeast splicing factors Prp4p and Prp3p. RNA (New York, N.Y.) 62 9257651
2014 Identification of a PRPF4 loss-of-function variant that abrogates U4/U6.U5 tri-snRNP integration and is associated with retinitis pigmentosa. PloS one 36 25383878
2001 Fission yeast Prp4p kinase regulates pre-mRNA splicing by phosphorylating a non-SR-splicing factor. EMBO reports 33 11252721
1997 Identification and characterization of human genes encoding Hprp3p and Hprp4p, interacting components of the spliceosome. Human molecular genetics 33 9328476
2002 Central region of the human splicing factor Hprp3p interacts with Hprp4p. The Journal of biological chemistry 28 11971898
2019 PRPF4 is a novel therapeutic target for the treatment of breast cancer by influencing growth, migration, invasion, and apoptosis of breast cancer cells via p38 MAPK signaling pathway. Molecular and cellular probes 15 31445970
2000 Characterization of hPRP4 kinase activation: potential role in signaling. Biochemical and biophysical research communications 15 10799319
2017 The spliceosomal proteins PPIH and PRPF4 exhibit bi-partite binding. The Biochemical journal 9 28935721
2018 prpf4 is essential for cell survival and posterior lateral line primordium migration in zebrafish. Journal of genetics and genomics = Yi chuan xue bao 8 30174136
2019 Suppression of PRPF4 regulates pluripotency, proliferation, and differentiation in mouse embryonic stem cells. Cell biochemistry and function 6 31502671
2002 The deubiquitinating enzyme Ubp21p of fission yeast stabilizes a mutant form of protein kinase Prp4p. Molecular genetics and genomics : MGG 6 11919719
2025 PRPF4 Knockdown Suppresses Glioblastoma Progression via the p38 MAPK and ERK Signaling Pathways. Anticancer research 1 39890169
2025 Prpf4 sequentially regulates the expansion and maturation of erythrocyte through distinct mechanisms. Cell death discovery 0 41360772

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