Affinage

PRPF3

U4/U6 small nuclear ribonucleoprotein Prp3 · UniProt O43395

Length
683 aa
Mass
77.5 kDa
Annotated
2026-06-10
26 papers in source corpus 11 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PRPF3 is an essential pre-mRNA splicing factor that functions as a core protein of the U4/U6 di-snRNP and is required for assembly and integrity of the U4/U6.U5 tri-snRNP (PMID:9404889, PMID:9326489). It forms a stable, RNA-independent complex with the Prp4 homolog (PRPF4) and a cyclophilin, binding the C-terminal WD-repeat β-propeller of Prp4 (PMID:9404889, PMID:9826507). Structurally, PRPF3 uses a bipartite RNA-binding region — an expanded ferredoxin-like fold that recognizes the U6 snRNA 3' single-stranded overhang and a preceding peptide that binds the U4/U6 stem II duplex — to assemble cooperatively with Snu13 and Prp31 on U4/U6 di-snRNA, inhibit Brr2-mediated U4/U6 unwinding, and thereby bridge U4/U6 and U5 within the tri-snRNP (PMID:26161500). During spliceosome assembly its middle domain is engaged by SPF30, which simultaneously binds U2AF35, linking 3' splice site recognition to tri-snRNP addition (PMID:18211889). PRPF3 is essential for development, as homozygous loss is embryonic lethal in mice and lethal to zebrafish eye cells (PMID:18552388). Dominant missense mutations (T494M, P493S) cause autosomal dominant retinitis pigmentosa not through haploinsufficiency but via a gain-of-function mechanism: the T494M mutant forms toxic nuclear aggregates specifically in photoreceptor cells, disrupts splicing-factor distribution, and triggers apoptosis (PMID:11773002, PMID:17517693, PMID:18552388); intronic splice variants disrupting PRPF3 splicing also cause dominant RP (PMID:42211691). Beyond constitutive splicing, nuclear PRPF3 directs alternative splicing of FANCI toward DNA-repair-competent variants after ionizing radiation, and its protein stability is regulated by the interacting partner TMEM43 (PMID:35260078, PMID:37168687).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1997 High

    Established that PRPF3 is a bona fide spliceosomal protein, defining its physical context as a stable U4/U6-associated complex with the Prp4 homolog and a cyclophilin.

    Evidence Biochemical purification and peptide sequencing from HeLa cells with co-purification analysis

    PMID:9404889

    Open questions at the time
    • Did not define the RNA contacts or domain architecture mediating snRNP association
    • Functional consequence of the cyclophilin in the complex not resolved
  2. 1997 High

    Defined PRPF3's functional role by showing the yeast ortholog is required for stable U4/U6 snRNP formation and tri-snRNP assembly, without which spliceosome assembly fails.

    Evidence Heat-inactivation of prp3 mutant yeast with snRNA Northern analysis and in vitro/in vivo splicing assays

    PMID:9326489

    Open questions at the time
    • Did not establish the molecular mechanism by which Prp3 stabilizes U4/U6
    • Direct RNA-binding activity not shown
  3. 1998 Medium

    Mapped the direct PRPF3–PRPF4 interaction interface, localizing Prp3 binding to the C-terminal WD-repeat domain of Prp4.

    Evidence Yeast two-hybrid, in vitro immunoprecipitation, deletion/point mutation analysis and structural modelling

    PMID:9826507

    Open questions at the time
    • Single-lab mapping without a co-crystal structure
    • Functional requirement of the interface for splicing not directly tested
  4. 2002 Medium

    Linked PRPF3 to human disease by identifying conserved missense mutations co-segregating with autosomal dominant retinitis pigmentosa.

    Evidence Genomic sequencing and family linkage/co-segregation analysis across multiple families

    PMID:11773002

    Open questions at the time
    • No biochemical mechanism for how mutations cause photoreceptor disease
    • Did not distinguish loss-of-function from gain-of-function
  5. 2007 Medium

    Resolved the disease mechanism as photoreceptor-specific gain-of-function, showing T494M mutant PRPF3 forms toxic nuclear aggregates that disrupt splicing factors and trigger apoptosis.

    Evidence Immunofluorescence/co-localization in transfected cells and human retina, apoptosis and inhibitor assays

    PMID:17517693

    Open questions at the time
    • Why aggregation is photoreceptor-restricted not explained
    • Aggregate composition and clearance pathway not defined
  6. 2008 High

    Genetically confirmed that RP is not caused by haploinsufficiency and demonstrated PRPF3 is essential for early development.

    Evidence Gene-trap knockout mouse and zebrafish with retinal histology, ERG, Western blotting, and survival analysis

    PMID:18552388

    Open questions at the time
    • Did not model the dominant aggregate phenotype in vivo
    • Compensatory upregulation mechanism not detailed
  7. 2008 Medium

    Placed PRPF3 in the spliceosome assembly pathway by showing SPF30 bridges it to U2AF35, coupling 3' splice site recognition to tri-snRNP recruitment.

    Evidence Co-immunoprecipitation and GST pulldown with domain constructs

    PMID:18211889

    Open questions at the time
    • Functional consequence of disrupting the bridge on splicing not tested
    • Stoichiometry within assembling spliceosome unknown
  8. 2015 High

    Provided the structural and mechanistic basis for PRPF3 function, defining a bipartite RNA-binding region that bridges U4/U6 and U5 and inhibits Brr2 unwinding.

    Evidence X-ray crystallography, RNA-binding and Brr2 unwinding assays, yeast mutagenesis with splicing/tri-snRNP readouts

    PMID:26161500

    Open questions at the time
    • Did not connect the structural mechanism to the RP aggregation phenotype
    • Regulation of Brr2 inhibition timing in the catalytic cycle not addressed
  9. 2022 Medium

    Identified post-translational regulation of PRPF3 by TMEM43, linking PRPF3 stability to a cancer-promoting signaling axis.

    Evidence Co-IP/mass spectrometry, knockdown in vitro and in xenografts, cell cycle analysis

    PMID:35260078

    Open questions at the time
    • Mechanism of TMEM43-mediated stabilization (e.g. degradation pathway) not defined
    • Whether splicing activity mediates the cancer phenotype not established
  10. 2023 Medium

    Extended PRPF3 function to regulated alternative splicing, showing nuclear PRPF3 drives DNA-repair-competent FANCI variants after irradiation and modulates radiosensitivity.

    Evidence Co-IP, immunofluorescence, RT-PCR splicing assays and knockdown with radiation-sensitivity and cell cycle readouts

    PMID:37168687

    Open questions at the time
    • How TXNL4B directs PRPF3 toward FANCI splicing is unclear
    • Single-lab finding without independent confirmation
  11. 2026 Medium

    Demonstrated that intronic non-canonical splice variants in PRPF3 cause dominant RP and are amenable to antisense correction.

    Evidence Dual fluorescence reporter assay in HEK293T with FACS quantification and U7snRNA-AON rescue

    PMID:42211691

    Open questions at the time
    • Rescue shown only in a cell-based reporter, not in patient tissue or animal models
    • Cell-type specificity of the pathogenic mechanism not addressed

Open questions

Synthesis pass · forward-looking unresolved questions
  • How PRPF3's defined splicing functions mechanistically connect to the photoreceptor-specific toxicity of RP mutants and to its non-canonical roles in cancer and DNA damage remains unresolved.
  • No structural explanation for why T494M aggregates only in photoreceptors
  • Whether non-spliceosomal PRPF3 roles share its RNA-binding mechanism is unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140098 catalytic activity, acting on RNA 2 GO:0003723 RNA binding 1 GO:0098772 molecular function regulator activity 1
Localization
GO:0005634 nucleus 2 GO:0005654 nucleoplasm 1
Pathway
R-HSA-8953854 Metabolism of RNA 3 R-HSA-73894 DNA Repair 1
Partners
PRPF31PRPF4PRPF8SNU13SPF30TMEM43TXNL4BU2AF35
Complex memberships
U4/U6 di-snRNPU4/U6.U5 tri-snRNP

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1997 Human PRPF3 (hPrp3) is a component of a stable protein complex with the human Prp4 homolog and a cyclophilin, and this complex is associated with U4/U6 snRNPs purified from HeLa cells. The complex behaves as a single species throughout purification, indicating tight association independent of RNA. Biochemical purification from HeLa cells, peptide sequencing, full-length cDNA cloning, co-purification analysis RNA (New York, N.Y.) High 9404889
1997 Yeast Prp3p is a component of the U4/U6 snRNP and U4/U6.U5 tri-snRNP; heat inactivation of Prp3p leads to loss of free U6 snRNPs and tri-snRNPs, accumulation of free U4 snRNA, and failure of spliceosome assembly from prespliceosomes, establishing Prp3p as required for stable U4/U6 snRNP formation and tri-snRNP assembly. Genetic heat-inactivation of prp3 mutant yeast, snRNA analysis (Northern blotting), splicing assays in vitro and in vivo RNA (New York, N.Y.) High 9326489
1998 Yeast Prp4 interacts directly with yeast Prp3 through the C-terminal WD-repeat (beta-propeller) domain of Prp4; deletion analysis and point mutations mapped the Prp3-binding surface to the C-terminal half of Prp4, and a small basic-rich N-terminal region of Prp4 is essential for cell viability. Yeast two-hybrid system, in vitro immunoprecipitation, deletion and point-mutation analysis, 3D structural modelling Journal of molecular biology Medium 9826507
2002 Two missense mutations (T494M and P493S) in the 11th exon of HPRP3 (PRPF3) co-segregate with autosomal dominant retinitis pigmentosa in multiple families; the altered residues are highly conserved across all known Prp3 orthologs, implicating this domain in the splicing function essential for photoreceptor survival. Genomic sequencing, haplotype analysis with SNPs, family linkage/co-segregation analysis Human molecular genetics Medium 11773002
2007 Wild-type PRPF3 co-localizes with small nuclear ribonucleoproteins (snRNPs) and SC35-marked nuclear speckles. The RP-causing T494M mutant PRPF3 forms abnormally large nuclear aggregates specifically in photoreceptor cells, triggers apoptosis in those cells, and disrupts the distribution of other splicing factors; this aggregation is not seen in non-photoreceptor cells. Immunofluorescence/co-localization in transfected cells and human retina sections, apoptosis assays, transcriptional/translational/proteasome inhibition experiments Human molecular genetics Medium 17517693
2008 Heterozygous Prpf3 knockout mice do not show photoreceptor degeneration, establishing that RP18 is not caused by haploinsufficiency. Compensatory upregulation of the wild-type allele maintains near-normal Prpf3 levels. Homozygous knockout is embryonic lethal in mice and causes high cell death in zebrafish eyes, confirming Prpf3 is essential for early development. Gene-trap knockout mouse and zebrafish generation, retinal histology, ERG, Western blotting, RT-PCR splicing assay, survival analysis Investigative ophthalmology & visual science High 18552388
2008 SPF30 bridges a simultaneous interaction between U2AF35 (prespliceosome) and hPrp3 (tri-snRNP component) via its N-terminal domain binding U2AF35 and its C-terminus binding a middle domain of hPrp3, potentially linking 3' splice site recognition to tri-snRNP addition during spliceosome assembly. Co-immunoprecipitation, GST pulldown assays with defined domain constructs The Journal of biological chemistry Medium 18211889
2015 Prp3 contains a bipartite RNA-binding region: an expanded ferredoxin-like fold that recognizes the 3'-single-stranded overhang of U6 snRNA, and a preceding peptide that binds the U4/U6 stem II duplex. This composite dsRNA/ssRNA binding region assembles cooperatively with Snu13 and Prp31 on U4/U6 di-snRNAs, inhibits Brr2-mediated U4/U6 unwinding in vitro, and mutations disrupting RNP contacts cause tri-snRNP assembly and splicing defects in vivo. Prp3 thus bridges U4/U6 and U5 in the tri-snRNP. X-ray crystallography, biochemical RNA-binding assays, in vitro Brr2 unwinding assay, mutational analysis in yeast with splicing and tri-snRNP assembly readouts, phylogenetic analysis eLife High 26161500
2022 TMEM43 physically interacts with PRPF3 (identified by co-IP/mass spectrometry) and stabilizes PRPF3 protein levels; TMEM43-mediated stabilization of PRPF3 promotes pancreatic cancer progression through the RAP2B/ERK signaling axis. Co-immunoprecipitation followed by protein mass spectrometry, knockdown experiments in vitro and in vivo (xenograft), cell cycle analysis Cellular & molecular biology letters Medium 35260078
2023 TXNL4B interacts with PRPF3 and co-localizes with it in the nucleus after ionizing radiation. Nuclear PRPF3 promotes alternative splicing of FANCI toward variants FANCI-12 and FANCI-13, and facilitates interaction of PRP31 and PRP8 with the spliceosome core; inhibition of PRPF3 suppresses FANCI-12 production, impairs DNA damage repair, induces G2/M arrest, and increases radiosensitivity. Co-immunoprecipitation, immunofluorescence co-localization, alternative splicing assays (RT-PCR), knockdown with functional radiation-sensitivity readouts, cell cycle analysis MedComm Medium 37168687
2026 A novel heterozygous intronic non-canonical splice variant in PRPF3 causes dominant retinitis pigmentosa by disrupting normal splicing; antisense oligonucleotides (AONs delivered via U7 snRNA cassettes) can rescue normal splicing and restore gene function in a HEK293T dual fluorescence reporter assay, demonstrating the pathogenicity of the splice variant. Dual fluorescence reporter assay in HEK293T cells, FACS quantification of splicing rescue, co-transfection of U7snRNA-AON constructs Molecular therapy. Nucleic acids Medium 42211691

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Mutations in HPRP3, a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa. Human molecular genetics 194 11773002
1988 The primary structures of six human salivary acidic proline-rich proteins (PRP-1, PRP-2, PRP-3, PRP-4, PIF-s and PIF-f). The Biochemical journal 97 3196309
2003 Mutations in the pre-mRNA splicing-factor genes PRPF3, PRPF8, and PRPF31 in Spanish families with autosomal dominant retinitis pigmentosa. Investigative ophthalmology & visual science 82 12714658
1997 A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs. RNA (New York, N.Y.) 76 9404889
2002 Tandem mass spectrometry for structural characterization of proline-rich proteins: application to salivary PRP-3. Analytical chemistry 49 12199583
2011 Temporal and tissue specific regulation of RP-associated splicing factor genes PRPF3, PRPF31 and PRPC8--implications in the pathogenesis of RP. PloS one 44 21283520
2015 A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing. eLife 43 26161500
1997 The yeast Prp3 protein is a U4/U6 snRNP protein necessary for integrity of the U4/U6 snRNP and the U4/U6.U5 tri-snRNP. RNA (New York, N.Y.) 40 9326489
2007 Mutations in splicing factor PRPF3, causing retinal degeneration, form detrimental aggregates in photoreceptor cells. Human molecular genetics 36 17517693
1998 Functional and structural characterization of the prp3 binding domain of the yeast prp4 splicing factor. Journal of molecular biology 33 9826507
2008 Decreased levels of the RNA splicing factor Prpf3 in mice and zebrafish do not cause photoreceptor degeneration. Investigative ophthalmology & visual science 30 18552388
2008 EPS15R, TASP1, and PRPF3 are novel disease candidate genes targeted by HNF4alpha splice variants in hepatocellular carcinomas. Gastroenterology 28 18395097
1996 A ninth locus (RP18) for autosomal dominant retinitis pigmentosa maps in the pericentromeric region of chromosome 1. Human molecular genetics 28 8842740
2010 Variable phenotypic expressivity in a Swiss family with autosomal dominant retinitis pigmentosa due to a T494M mutation in the PRPF3 gene. Molecular vision 21 20309403
2022 TMEM43 promotes pancreatic cancer progression by stabilizing PRPF3 and regulating RAP2B/ERK axis. Cellular & molecular biology letters 17 35260078
2008 Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3. The Journal of biological chemistry 15 18211889
1992 Preparation of DNA topoisomers by RP-18 high-performance liquid chromatography. Analytical biochemistry 12 1443600
2011 Comparison of monolithic and 1.8-μm RP-18 silica capillary columns using chromatographic data and mass spectrometric identification scores for proteins. Journal of separation science 10 21648078
2004 Clinical features of a Japanese family with autosomal dominant retinitis pigmentosa associated with a Thr494Met mutation in the HPRP3 gene. Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie 8 15085354
2024 Integrative analysis based on ATAC-seq and RNA-seq reveals a novel oncogene PRPF3 in hepatocellular carcinoma. Clinical epigenetics 7 39501301
1998 Refined genetic mapping of autosomal dominant retinitis pigmentosa locus RP18 reduces the critical region to 2 cM between D1S442 and D1S2858 on chromosome 1q. Human genetics 7 9600251
2023 TXNL4B regulates radioresistance by controlling the PRP3-mediated alternative splicing of FANCI. MedComm 6 37168687
2009 Differential display reveals a novel pig gene, PRPF3, which is differentially expressed in Large White versus Wujin skeletal muscle tissues. Molecular biology reports 2 19757174
2017 PRPF3-Associated Autosomal Dominant Retinitis Pigmentosa and CYP4V2-Associated Bietti's Crystalline Corneoretinal Dystrophy Coexist in a Multigenerational Chinese Family. Journal of ophthalmology 1 28848678
2026 FACS-based dual fluorescence reporter assay demonstrates efficacy of antisense oligonucleotide therapy of novel PRPF3 intronic splice variant. Molecular therapy. Nucleic acids 0 42211691
1984 [Deletions of plasmid pRP3.1ts12 derived from RP1 leading to the suppression of the thermosensitive ts12 mutation and mucoid phenotype induction in Escherichia coli K-12]. Genetika 0 6370789

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