Affinage

ISY1

Pre-mRNA-splicing factor ISY1 homolog · UniProt Q9ULR0

Length
285 aa
Mass
33.0 kDa
Annotated
2026-06-10
23 papers in source corpus 17 papers cited in narrative 17 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

ISY1 is a conserved spliceosomal protein that acts as a subunit of the NineTeen Complex (NTC/Prp19 complex) to govern the first catalytic step of pre-mRNA splicing (PMID:10094305, PMID:16103217). Recruited together with Yju2 by the NTC prior to branching (PMID:33705709), ISY1 cooperates with U6 snRNA and the step-one factors Cwc25 and Yju2 to stabilize docking of the intron branch helix into the catalytic active site, as visualized directly in cryo-EM structures of the post-branching C complex (PMID:16103217, PMID:27459055). Through this active-site role it enforces fidelity of branchpoint and 3'-splice-site selection: ISY1 deletion suppresses the stalled prp16-302 phenotype while degrading 3'-splice-site accuracy in wild-type backgrounds (PMID:16103217). Genetically and physically ISY1 sits at the core of the activated spliceosome, interacting with Cwc21, Cwc2, and Prp8 to position substrate RNA (PMID:19789211, PMID:24848011, PMID:29487104). This splicing function carries direct cellular consequences—efficient splicing of intron-containing alpha-tubulin transcripts depends on ISY1, and its loss can trigger spindle-checkpoint arrest (PMID:12384582). Beyond core splicing, ISY1 has acquired metazoan roles in gene regulation and genome maintenance: it partners with the endonuclease CPSF3 to perform a pri-miRNA cleavage step upstream of the Microprocessor that selectively licenses pro-miRNA production from pri-miR-17~92, a process that controls embryonic stem-cell pluripotency state transitions (PMID:26255770, PMID:29804889); it forms an XAB2-ISY1-PRP19 complex that promotes DNA end resection during homologous-recombination repair of double-strand breaks (PMID:27084940); and it directly binds APE1 to enhance its abasic-site recognition and endonuclease activity in base excision repair (PMID:31887540). ISY1 also contributes to nuclear retention of unspliced HIV-1 RNA as part of the Prp19-associated complex (PMID:33468685).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 1999 Medium

    Established ISY1 as a bona fide splicing factor by showing it associates with spliceosomes and is required for efficient splicing, answering whether the gene had any splicing role at all.

    Evidence Two-hybrid screen, tagged Co-IP recovering U5/U6 snRNAs, and in vivo splicing in ISY1-null yeast

    PMID:10094305

    Open questions at the time
    • Mechanistic step within splicing undefined
    • Low snRNA recovery leaves stable association ambiguous
  2. 2002 Medium

    Linked ISY1 splicing function to a concrete cellular phenotype by showing its loss reduces alpha-tubulin transcript splicing and triggers spindle-checkpoint arrest, demonstrating physiological consequences of impaired splicing.

    Evidence Genetic epistasis with SYF2/NTC20 deletions, cell-cycle and checkpoint assays, protein-level measurement in yeast

    PMID:12384582

    Open questions at the time
    • Phenotype is indirect via specific intron-containing targets
    • Does not define ISY1's molecular step
  3. 2005 High

    Placed ISY1 mechanistically as an NTC subunit that cooperates with U6 snRNA to promote first-step chemistry and enforce branchpoint/3'-splice-site fidelity, defining the catalytic-step it controls.

    Evidence Genetic suppressor screen of prp16-302, growth assays, biochemical NTC fractionation in yeast

    PMID:16103217

    Open questions at the time
    • Structural basis of branchpoint stabilization not yet resolved
    • Human ortholog function not tested here
  4. 2009 Medium

    Refined ISY1's position at the spliceosome core by demonstrating tight genetic, physical, and functional coupling to Cwc21 during splicing activation.

    Evidence Quantitative genetic interaction mapping, MS of TAP-purified complexes, microarray profiling

    PMID:19789211

    Open questions at the time
    • Direct contact interface with Cwc21 not mapped
  5. 2014 Medium

    Showed ISY1 cooperates with Cwc2 to stabilize active-site RNA elements, building the picture of ISY1 as part of an RNA-stabilizing module.

    Evidence Genetic suppressor/synthetic-lethality analysis and biochemical RNA interaction assays in yeast

    PMID:24848011

    Open questions at the time
    • Which RNA elements ISY1 itself contacts not directly demonstrated
  6. 2015 High

    Revealed a non-canonical metazoan function: ISY1 with CPSF3 performs a pri-miRNA cleavage step upstream of the Microprocessor that selectively licenses pro-miRNA biogenesis from pri-miR-17~92.

    Evidence ISY1 loss-of-function with miRNA biogenesis readout and ESC differentiation assays

    PMID:26255770

    Open questions at the time
    • Catalytic versus scaffolding contribution of ISY1 unresolved
    • Generality beyond miR-17~92 cluster unclear
  7. 2016 High

    Provided direct structural proof that Isy1, with Yju2 and Cwc25, stabilizes branch-helix docking into the active site after the first transesterification, converting genetic inference into physical visualization.

    Evidence Cryo-EM of the post-branching C complex at 3.8 Å

    PMID:27459055

    Open questions at the time
    • Conformational dynamics of recruitment/release not captured at this resolution
  8. 2016 Medium

    Extended ISY1 into genome maintenance by defining an XAB2-ISY1-PRP19 complex that promotes DNA end resection during homologous recombination.

    Evidence Truncation mapping, reciprocal Co-IP, siRNA with HR reporter assays, immunofluorescence near γH2AX foci

    PMID:27084940

    Open questions at the time
    • Molecular step ISY1 contributes to resection undefined
    • Single lab without independent replication
  9. 2019 Medium

    Demonstrated a direct ISY1-APE1 interaction that enhances APE1 endonuclease activity and abasic-site recognition in base excision repair, expanding ISY1's DNA-repair repertoire.

    Evidence Co-IP, in vitro BER reconstitution with purified recombinant proteins, endonuclease assays, oxidative-damage induction

    PMID:31887540

    Open questions at the time
    • No independent replication
    • Structural basis of ISY1-APE1 stimulation unknown
  10. 2021 High

    Resolved the temporal logic of ISY1 recruitment, showing it and Yju2 enter via the NTC before branching and that Prp16 remodels the complex after branching, defining when ISY1 acts.

    Evidence Cryo-EM of yeast C complex at 2.8 Å with biochemical splicing assays

    PMID:33705709

    Open questions at the time
    • Fate/release of Isy1 after branching not fully traced
  11. 2021 Medium

    Showed conserved but distinctly pre-organized ISY1-containing complexes by identifying a trypanosome PRP19-related complex (with SYF1/SYF3/PRC3/PRC5) that enters the spliceosome early.

    Evidence RNAi silencing, affinity purification with MS and sucrose-gradient sedimentation, U4 snRNA co-precipitation

    PMID:34850936

    Open questions at the time
    • Whether this pre-organization holds in metazoans untested
  12. 2021 Medium

    Identified ISY1 as a host factor promoting nuclear retention of unspliced HIV-1 RNA, connecting its splicing-associated activity to viral RNA fate.

    Evidence Genome-wide CRISPR screen, targeted CRISPR knockdown, RNA fractionation/quantification

    PMID:33468685

    Open questions at the time
    • Mechanism of retention versus indirect splicing effect not separated
  13. 2025 Medium

    Proposed a metabolic-signaling role in which JMJD5 hydroxylates an ISY1 arginine, enabling ISY1 to bind and inhibit PRMT6, placing ISY1 downstream of JMJD5 enzymatic function.

    Evidence In vitro hydroxylation and binding assays, PRMT6 activity assays, rescue experiments (preprint)

    PMID:bio_10.1101_2025.09.27.678987

    Open questions at the time
    • Preprint without independent replication
    • Hydroxylated residue and structural mechanism not validated in vivo

Open questions

Synthesis pass · forward-looking unresolved questions
  • How ISY1's single fold is partitioned among spliceosomal first-step stabilization, pri-miRNA processing, DNA-repair complexes, and the proposed PRMT6-regulatory axis—and whether these activities are mutually exclusive or coordinated—remains unresolved.
  • No structural model of non-splicing ISY1 complexes
  • Determinants directing ISY1 to distinct partners unknown
  • Cross-talk between splicing and repair pools untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3 GO:0005198 structural molecule activity 2 GO:0098772 molecular function regulator activity 2
Localization
GO:0005634 nucleus 2
Pathway
R-HSA-8953854 Metabolism of RNA 3 R-HSA-73894 DNA Repair 2
Partners
APE1CPSF3CWC2CWC21JMJD5PRMT6PRP19XAB2
Complex memberships
NineTeen Complex (NTC/Prp19 complex)PRP19-related complex (PRC)XAB2-ISY1-PRP19 complex

Evidence

Reading pass · 17 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 Isy1p is a novel splicing factor that associates with spliceosomes throughout the splicing reactions and co-immunoprecipitates low levels of U5 and U6 snRNAs; deletion of ISY1 reduces splicing efficiency in vivo, indicating a role in optimizing pre-mRNA splicing. Two-hybrid screen, tagged protein co-immunoprecipitation with snRNAs, in vivo splicing assay in ISY1 null mutant yeast RNA (New York, N.Y.) Medium 10094305
2002 Mutations in ISY1 combined with SYF2 deletion cause cell cycle arrest due to reduced splicing of intron-containing alpha-tubulin genes (TUB1, TUB3), lowering alpha-tubulin protein levels and triggering spindle checkpoint activation; ISY1 is synthetically lethal with NTC20 deletion. Genetic epistasis (double-mutant analysis), cell cycle arrest assay, spindle checkpoint activation assay, protein level measurement Nucleic acids research Medium 12384582
2005 Isy1p is a subunit of the NineTeen Complex (NTC/Prp19 complex) and acts together with U6 snRNA to promote a spliceosomal conformation favorable for first-step chemistry; deletion of ISY1 suppresses the cold-sensitive prp16-302 phenotype by alleviating stalling and restoring branchpoint fidelity, and also reduces fidelity of 3'-splice site selection in PRP16 wild-type strains. Genetic suppressor screen of prp16-302, growth assays, biochemical spliceosome fractionation showing NTC membership Genes & development High 16103217
2008 ISY1 shows synthetic genetic interactions with TGS1 (trimethylguanosine synthase); deletion of ISY1 combined with tgs1Δ causes synthetic growth defects, placing ISY1 in a functional network with snRNP components and spliceosome assembly factors. Systematic synthetic growth defect screen (genetic interaction mapping) in budding yeast The Journal of biological chemistry Low 18775984
2009 Cwc21 shows strong genetic, physical, and functional interactions with Isy1, supporting a role for Isy1 at the core of the spliceosome in the activation of splicing. Quantitative genetic interaction mapping, mass spectrometry of tandem affinity-purified complexes, microarray profiling RNA (New York, N.Y.) Medium 19789211
2014 Isy1/NTC30 functionally cooperates with the NTC protein Cwc2 during pre-mRNA splicing; genetic interactions between Cwc2 mutations and Isy1 indicate they act together in stabilizing spliceosome active site RNA elements. Genetic interaction analysis (suppressor/synthetic lethality), biochemical RNA interaction assays Nucleic acids research Medium 24848011
2015 ISY1 (spliceosome-associated) and the endonuclease CPSF3 are responsible for pro-miRNA biogenesis from pri-miR-17~92, a processing step upstream of Microprocessor that selectively licenses production of pre-miR-17, -18a, -19a, -20a, and -19b but not miR-92. Loss-of-function (knockdown/knockout) of ISY1 with miRNA biogenesis readout; ESC differentiation assays Cell High 26255770
2016 Cryo-EM structure of the post-branching spliceosome (C complex) at 3.8 Å shows Isy1 (together with step-one factors Yju2 and Cwc25) stabilizes docking of the branch helix into the active site after the first transesterification reaction. Cryo-electron microscopy structural determination at 3.8 Å resolution Nature High 27459055
2016 XAB2 forms a complex with ISY1 and PRP19; this XAB2-ISY1-PRP19 complex promotes end resection in homologous recombination (HR), as shown by ISY1 depletion impairing DSB repair via HR pathways requiring end resection, CtIP hyperphosphorylation, and RAD51 IRIF. The complex localizes to punctate structures adjacent to γH2AX foci. Truncation mutation analysis, co-immunoprecipitation, siRNA knockdown with HR reporter assays, immunofluorescence localization Nucleic acids research Medium 27084940
2018 ISY1 regulates miRNA biogenesis to control ESC pluripotency state transitions; loss- and gain-of-function experiments show ISY1 promotes exit from naive pluripotency and is necessary and sufficient to induce and maintain poised pluripotency through ISY1-dependent miRNAs. Loss-of-function (knockout) and gain-of-function (overexpression) in mouse ESCs, miRNA profiling, chimera formation assay Cell stem cell Medium 29804889
2018 Prp8 genetic interactions with Isy1 (which buttresses the intron branch point) support a role for specific Prp8 residues in substrate positioning and spliceosome activation at the 5' splice site. Genetic interaction analysis between Prp8 mutants and Isy1 in yeast RNA (New York, N.Y.) Low 29487104
2019 ISY1 directly interacts with APE1 (apurinic/apyrimidinic endonuclease 1) and enhances its 5'-3' endonuclease activity, promotes APE1 recognition of abasic sites, and markedly promotes APE1 activity in both short- and long-patch base excision repair (BER) pathways using purified recombinant proteins in a reconstituted BER system. ISY1 expression is induced by oxidative damage. Co-immunoprecipitation, in vitro BER reconstitution with purified recombinant ISY1 and APE1, endonuclease activity assays, oxidative damage induction DNA repair Medium 31887540
2021 Cryo-EM reconstruction of the yeast C-complex spliceosome at 2.8 Å reveals that Yju2 and Isy1 are recruited by the NTC (NineTeen Complex) before branching; after branching, Prp16 remodels Yju2 binding, allowing Yju2 to remain tethered to the NTC in the C* complex while Isy1's role is defined at the branching step. Cryo-electron microscopy at 2.8 Å resolution, biochemical splicing assays Molecular cell High 33705709
2021 ISY1 is a member of a PRP19-related complex (PRC) in trypanosomes that also contains SYF1, SYF3, PRC3, and PRC5; PRC co-precipitates U4 snRNA, indicating it enters the spliceosome prior to the PRP19 complex, demonstrating a conserved but distinct pre-organization of ISY1-containing complexes. Gene silencing (RNAi), affinity purification combined with sucrose gradient sedimentation and mass spectrometry, snRNA co-precipitation Nucleic acids research Medium 34850936
2021 ISY1 (as part of the Prp19-associated complex) promotes nuclear retention of unspliced HIV-1 RNA; CRISPR/Cas knockdown of ISY1 results in more than 20-fold enhancement of unspliced HIV-1 RNA levels in the cytoplasm. Genome-wide CRISPR/Cas screen, CRISPR knockdown, RNA fractionation and quantification mBio Medium 33468685
2021 Rat1 co-immunoprecipitates with Isy1 (among other splicing factors), and Rat1 mutants show reduced recruitment of splicing factors to introns, supporting a role for Isy1 in cotranscriptional splicing complex assembly. Co-immunoprecipitation, mass spectrometry, ChIP-Seq Nucleic acids research Low 33978753
2025 JMJD5 hydroxylates an arginine residue on ISY1; this hydroxylation modification enables ISY1 to bind to and inhibit PRMT6 (Protein Arginine N-methyltransferase 6), reducing PRMT6 activity; this JMJD5-ISY1-PRMT6 signaling pathway is identified as the principal executor of JMJD5's enzymatic function in metabolic regulation. Biochemical hydroxylation assay (JMJD5 on ISY1), binding assay (ISY1-PRMT6), PRMT6 activity assay, rescue experiments (PRMT6 inactivation rescuing JMJD5 loss phenotype) bioRxivpreprint Medium bio_10.1101_2025.09.27.678987

Source papers

Stage 0 corpus · 23 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2016 Cryo-EM structure of the spliceosome immediately after branching. Nature 198 27459055
2005 The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing. Genes & development 94 16103217
2015 A Biogenesis Step Upstream of Microprocessor Controls miR-17∼92 Expression. Cell 82 26255770
2008 Genetic and biochemical analysis of yeast and human cap trimethylguanosine synthase: functional overlap of 2,2,7-trimethylguanosine caps, small nuclear ribonucleoprotein components, pre-mRNA splicing factors, and RNA decay pathways. The Journal of biological chemistry 59 18775984
2018 An Intermediate Pluripotent State Controlled by MicroRNAs Is Required for the Naive-to-Primed Stem Cell Transition. Cell stem cell 56 29804889
2021 Structural basis for conformational equilibrium of the catalytic spliceosome. Molecular cell 46 33705709
2002 Mutations in genes of Saccharomyces cerevisiae encoding pre-mRNA splicing factors cause cell cycle arrest through activation of the spindle checkpoint. Nucleic acids research 44 12384582
1999 The identification and characterization of a novel splicing protein, Isy1p, of Saccharomyces cerevisiae. RNA (New York, N.Y.) 38 10094305
2018 A genetic program mediates cold-warming response and promotes stress-induced phenoptosis in C. elegans. eLife 34 29664006
2009 A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA (New York, N.Y.) 29 19789211
2016 Tetratricopeptide repeat factor XAB2 mediates the end resection step of homologous recombination. Nucleic acids research 25 27084940
2017 The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes. BMC genomics 24 28569192
2021 CRNKL1 Is a Highly Selective Regulator of Intron-Retaining HIV-1 and Cellular mRNAs. mBio 21 33468685
2023 Identifying Genetic Susceptibility in Neonates With Hypoxic-Ischemic Encephalopathy: A Retrospective Case Series. Journal of child neurology 19 36628482
2018 Prp8 positioning of U5 snRNA is linked to 5' splice site recognition. RNA (New York, N.Y.) 15 29487104
2019 The splicing component ISY1 regulates APE1 in base excision repair. DNA repair 14 31887540
2014 Remodeling of U2-U6 snRNA helix I during pre-mRNA splicing by Prp16 and the NineTeen Complex protein Cwc2. Nucleic acids research 13 24848011
2024 Lysine lactylation-based insight to understanding the characterization of cervical cancer. Biochimica et biophysica acta. Molecular basis of disease 9 39025375
2022 Elevated expression of ISY1, APOA-1, SYNE1, MTG1, and MMP10 at HCC initiation: HCC specific protein network involving interactions of key regulators of lipid metabolism, EGFR signaling, MAPK, and splicing pathways. Protoplasma 7 35962262
2021 A termination-independent role of Rat1 in cotranscriptional splicing. Nucleic acids research 6 33978753
2021 A distinct complex of PRP19-related and trypanosomatid-specific proteins is required for pre-mRNA splicing in trypanosomes. Nucleic acids research 5 34850936
2025 Differential expression of lncRNAs and mRNAs in bone marrow-derived mesenchymal stem cells under continuous and intermittent teriparatide treatment. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 2 40609214
2025 ZNF32 histidine 179 and 183 single-site and double-site mutations promote nuclear speckle formation but differentially regulate the proliferation of breast cancer cells. Frontiers in cell and developmental biology 1 40046230

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