Affinage

C9ORF78

Splicing factor C9orf78 · UniProt Q9NZ63

Length
289 aa
Mass
33.7 kDa
Annotated
2026-06-09
12 papers in source corpus 4 papers cited in narrative 4 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

C9ORF78 is a late-stage splicing regulatory protein that engages the spliceosome to control alternative splice-site selection (PMID:25245948, PMID:35241646). Its fission yeast ortholog Tls1 associates with the spliceosome remodeling helicase Brr2 and governs splicing of a defined subset of mRNAs, including shelterin components whose missplicing drives telomeric heterochromatin and telomere-length defects; human C9ORF78 likewise associates with the spliceosome (PMID:25245948). Mechanistically, C9ORF78 binds tightly to the C-terminal helicase cassette of BRR2, wrapping around it in a manner mutually exclusive with the B-complex protein FBP21, thereby defining a multi-factor trafficking site on the helicase; it additionally contacts other spliceosomal factors including the 3'-splice-site-regulating helicase PRPF22, and its depletion shifts NAGNAG 3'-splice-site usage and causes BRR2-dependent exon skipping (PMID:35241646). Beyond splicing, a subpopulation of C9ORF78 localizes to centromeres/kinetochores during mitosis where it co-localizes with ACA, Mad1, and Ndc80, accumulates upon mitotic checkpoint activation, and is required for accurate chromosome segregation (PMID:35167828). C9ORF78 also forms a complex with FAM50A at its S121 residue to enhance ASNS transcription and asparagine biosynthesis, promoting breast cancer brain metastasis (PMID:40531994).

Mechanistic history

Synthesis pass · year-by-year structured walk · 4 steps
  1. 2014 High

    Established that C9ORF78's conserved function lies in spliceosome-associated regulation of a specific mRNA subset, by showing the fission yeast ortholog Tls1 binds Brr2 and controls shelterin splicing with downstream chromatin consequences.

    Evidence Protein purification/MS, RNA-seq, and genetic cDNA-rescue epistasis in fission yeast, with human C9ORF78 spliceosome association also shown

    PMID:25245948

    Open questions at the time
    • Direct biochemical mechanism of human C9ORF78 within the spliceosome not resolved here
    • Whether human C9ORF78 regulates an orthologous mRNA set is untested
  2. 2022 High

    Defined the molecular mechanism of C9ORF78 as a late-stage splicing factor that occupies a multi-factor trafficking site on BRR2 to control 3'-splice-site choice and exon inclusion.

    Evidence In vitro binding, cryo-EM of the C9ORF78/FBP21-BRR2 helicase cassette, AP-MS, RNA UV-crosslinking, and siRNA knockdown with BRR2-dependency test

    PMID:35241646

    Open questions at the time
    • Functional consequence of competition with FBP21 in vivo not defined
    • Role of PRPF22 contact in splice-site selection unresolved
  3. 2022 Medium

    Revealed an unexpected mitotic role by showing a C9ORF78 subpopulation localizes to centromeres/kinetochores and is required for faithful chromosome segregation.

    Evidence GFP-tagging/immunofluorescence with centromere/kinetochore markers, siRNA knockdown mitotic-defect readout, and E2F1/N-Myc overexpression Western blot

    PMID:35167828

    Open questions at the time
    • No reconstitution or structural confirmation of a centromere interaction
    • Mechanism linking splicing role to segregation function unknown
    • Direct binding partner at the kinetochore not identified
  4. 2025 Medium

    Connected C9ORF78 to a metabolic-transcriptional axis by showing it complexes with FAM50A to drive ASNS transcription and asparagine biosynthesis in cancer.

    Evidence Co-IP with S121 site mapping, ASNS transcription and asparagine synthesis assays, and genetic/pharmacological perturbation with metastasis readout

    PMID:40531994

    Open questions at the time
    • Single-lab finding without reciprocal structural validation
    • Mechanism by which the complex enhances ASNS transcription undefined
    • Relationship between this transcriptional role and the spliceosomal function unclear

Open questions

Synthesis pass · forward-looking unresolved questions
  • How C9ORF78's distinct activities — late-stage splicing regulation, mitotic centromere localization, and FAM50A-dependent transcriptional control — are integrated into one protein's biology remains unresolved.
  • No unifying model connecting splicing, segregation, and metabolic roles
  • Tissue- and context-specific functions not delineated

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 1
Localization
GO:0005634 nucleus 1 GO:0005694 chromosome 1
Pathway
R-HSA-8953854 Metabolism of RNA 2
Partners
BRR2FAM50AFBP21PRPF22
Complex memberships
spliceosome

Evidence

Reading pass · 4 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2014 The fission yeast ortholog of C9ORF78, Tls1, associates with the spliceosome subunit Brr2 (as shown by protein purification and mass spectrometry). Tls1 regulates splicing of a subset of mRNAs including the shelterin components rap1+ and poz1+; missplicing of these components causes telomeric heterochromatin defects and altered telomere length in tls1Δ cells. Epistasis experiments (replacing rap1+ and poz1+ with cDNAs) confirmed that missplicing of shelterin mRNAs is the mechanistic cause of heterochromatin defects. The human homologue C9ORF78 was also shown to associate with the spliceosome. Protein purification and mass spectrometry (Tls1 interactors), RNA sequencing (splicing analysis), genetic epistasis (cDNA rescue experiments), deletion library screen Nucleic Acids Research High 25245948
2022 C9ORF78 tightly interacts with BRR2 (a spliceosome remodeling helicase) in vitro. Cryo-EM structures reveal that C9ORF78 and the spliceosomal B complex protein FBP21 wrap around the C-terminal helicase cassette of BRR2 in a mutually exclusive manner, defining a multi-factor trafficking site. Affinity purification/mass spectrometry and RNA UV-crosslinking identified additional C9ORF78 interactors in spliceosomes, including the 3'-splice site regulating helicase PRPF22. Knockdown of C9ORF78 leads to alternative NAGNAG 3'-splice site usage and exon skipping, with the exon skipping dependent on BRR2. C9ORF78 is established as a late-stage splicing regulatory protein. In vitro binding assay, cryo-EM structure determination, affinity purification/mass spectrometry, RNA UV-crosslinking, siRNA knockdown with RNA-seq splicing analysis Nature Communications High 35241646
2022 GFP-tagged and endogenous C9ORF78 localizes to nuclei in interphase but, unexpectedly, a subpopulation co-localizes with kinetochore/centromere markers ACA, Mad1, and Ndc80 in mitotic cells. C9ORF78 levels at centromere/kinetochore increase upon mitotic checkpoint activation. Knockdown of C9ORF78 caused mitotic defects (chromosome segregation errors). Protein abundance is dramatically reduced in confluent/serum-deprived cells and re-expressed upon serum stimulation; overexpression of E2F1 or N-Myc elevated C9ORF78 expression, suggesting these transcription factors mediate serum-dependent upregulation. GFP tagging and immunofluorescence, co-localization with centromere/kinetochore markers (ACA, Mad1, Ndc80), siRNA knockdown with mitotic defect readout, overexpression of E2F1/N-Myc with Western blot Experimental Cell Research Medium 35167828
2025 C9ORF78 forms a complex with FAM50A specifically at the S121 residue of C9ORF78, and this complex enhances ASNS (asparagine synthetase) transcription and accelerates asparagine biosynthesis, facilitating breast cancer brain metastasis. Co-immunoprecipitation (FAM50A-C9ORF78 complex), site-specific interaction mapping (S121 residue), ASNS transcription assay, asparagine synthesis assay, genetic suppression and pharmacological inhibition with metastasis readout Science Advances Medium 40531994

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Large scale identification of human hepatocellular carcinoma-associated antigens by autoantibodies. Journal of immunology (Baltimore, Md. : 1950) 160 12097419
2010 Combined interphase fluorescence in situ hybridization elucidates the genetic heterogeneity of T-cell acute lymphoblastic leukemia in adults. Haematologica 35 20065082
2019 Hepatocellular carcinoma-associated antigen 59 of Haemonchus contortus modulates the functions of PBMCs and the differentiation and maturation of monocyte-derived dendritic cells of goats in vitro. Parasites & vectors 20 30871600
2014 Tls1 regulates splicing of shelterin components to control telomeric heterochromatin assembly and telomere length. Nucleic acids research 16 25245948
2019 Combined Use of Indirect ELISA and Western Blotting with Recombinant Hepatocellular Carcinoma-Associated Antigen 59 Is a Potential Immunodiagnostic Tool for the Detection of Prepatent Haemonchus contortus Infection in Goat. Animals : an open access journal from MDPI 14 31412573
2022 A multi-factor trafficking site on the spliceosome remodeling enzyme BRR2 recruits C9ORF78 to regulate alternative splicing. Nature communications 10 35241646
2021 Haemonchus contortus hepatocellular carcinoma-associated antigen 59 with poly (lactic-co-glycolic acid): A promising nanovaccine candidate against Haemonchus contortus infection. Veterinary parasitology 10 33677347
2021 Nanoparticles of Chitosan/Poly(D,L-Lactide-Co-Glycolide) Enhanced the Immune Responses of Haemonchus contortus HCA59 Antigen in Model Mice. International journal of nanomedicine 10 33981142
2024 AGO2-RIP-Seq reveals miR-34/miR-449 cluster targetome in sinonasal cancers. PloS one 5 38215077
2025 FAM50A drives breast cancer brain metastasis through interaction with C9ORF78 to enhance ʟ-asparagine production. Science advances 4 40531994
2022 C9ORF78 partially localizes to centromeres and plays a role in chromosome segregation. Experimental cell research 2 35167828
2026 Transcriptome and functional analyses reveal key regulators of flowering time in Camellia sinensis. Plant physiology and biochemistry : PPB 0 42235246

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