C0P8M6 (cDNA clone MIP05908p) is the 86-residue protein predicted from the short Pcf11-RC transcript of the Drosophila Pcf11 (Inr-a, CG10228) locus, and is identical in sequence to the FlyBase-derived isoform C entry E1JH69. It shares only residues 1-62 with the 573-residue and ~1950-residue Pcf11 products, so it carries about the first third of the RNA polymerase II CTD-interacting domain (CID, residues 11-146 in the longer products) followed by a unique 24-residue C-terminal tail. It lacks the rest of the CID and every region C-terminal to it. A protein corresponding to Pcf11-RC was not detected in testis extracts with an antibody raised against residues 1-283, even though the RC transcript is abundant. Its activity and location are therefore unknown, and it is not known whether it is translated. The long Pcf11 proteins encoded by the same gene are nuclear, chromatin-associated components of cleavage factor II (with Cbc). They promote RNA polymerase II transcription termination by bridging the polymerase CTD to the nascent transcript and dismantling paused elongation complexes, and they regulate poly(A)-site choice. None of these activities has been shown for, or can be structurally inferred for, the 86-residue product.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000993 RNA polymerase II complex binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Family-level InterPro2GO transfer to a product that keeps only about a third of the CID. Reason: IPR045154 (PCF11-like) is a family signature, and CTD binding is a real property of the full-length Drosophila Pcf11, which binds the CTD and nascent RNA (PMID:16387654). That activity is carried by the complete CID helical bundle (residues 11-146 in the longer products). C0P8M6 shares only residues 1-62 with them and then ends in a unique 24-residue tail (file:DROME/Pcf11/Pcf11-bioinformatics/RESULTS-rereview.md), and the Genes Dev study describes the CID as only partially present in the RC product. A truncated helical bundle is not expected to fold into a CTD-binding module, and the RC protein has not been detected in vivo. The term is correct for the gene but over-annotated on this product. Supporting Evidence: PMID:39111825 PCF11 has a CID (Pol II C-terminal binding domain) present in both the PCF11-long and the 63 kDa PCF11-RB isoforms but only partially present in the short protein encoded by PCF11-RC. file:DROME/Pcf11/Pcf11-bioinformatics/RESULTS-rereview.md C0P8M6 retains residues 11-62 of the CID (about 38% of it) plus an unrelated C-terminal tail. PMID:16387654 dPcf11 forms a bridge between the CTD and RNA. |
| GO:0003723 RNA binding | IDA PMID:16387654 Pcf11 is a termination factor in Drosophila that dismantles ... | UNDECIDED | Summary: A valid gene-level experimental result whose attachment to the 86-residue RC product cannot be verified. Reason: Zhang and Gilmour showed that Drosophila Pcf11 bridges the CTD to nascent RNA, so RNA binding is well supported for the gene. FlyBase made this annotation at gene level and it is carried onto C0P8M6. Only the abstract is cached, and it does not say which construct was assayed. It is very unlikely to have been the 86-residue RC product, since the RC protein has not been detected and lacks most of the CID and all C-terminal regions. The curator's experimental call for the gene is not disputed. Whether this exact product binds RNA is undetermined, so the row is left UNDECIDED rather than accepted as a function of C0P8M6. Supporting Evidence: PMID:16387654 dPcf11 forms a bridge between the CTD and RNA. PMID:39111825 no protein product corresponding to PCF11-RC was observed despite a seemingly high level of the PCF11-RC transcript isoform detected by snRNA-seq of Drosophila testis tissue |
| GO:0003729 mRNA binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Family-level transfer of an RNA-binding activity the truncated product has no region to carry. Reason: In Pcf11 proteins RNA contact is made by regions outside the N-terminal CID. Reconstituted mammalian CFII places RNA binding in the Pcf11 zinc fingers (PMID:30139799), which lie well C-terminal to the CID. C0P8M6 ends at residue 86 and keeps only residues 1-62 of the shared sequence. The family signature cannot transfer an activity whose structural basis is absent from this product. Supporting Evidence: file:DROME/Pcf11/Pcf11-bioinformatics/RESULTS-rereview.md C0P8M6 has none of the regions C-terminal to the CID that the longer products carry. PMID:39111825 PCF11 has a CID (Pol II C-terminal binding domain) present in both the PCF11-long and the 63 kDa PCF11-RB isoforms but only partially present in the short protein encoded by PCF11-RC. |
| GO:0006369 termination of RNA polymerase II transcription | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: True of the Pcf11 gene but not supported for this truncated, undetected product. Reason: Drosophila Pcf11 is a termination factor: RNAi causes Pol II readthrough at hsp70, and the protein dismantles elongation complexes in a CTD-dependent manner (PMID:16387654). The mechanism requires CTD binding and RNA contact, and C0P8M6 has neither the complete CID nor the C-terminal regions. The RC protein was also not detected in testis, so there is no evidence that this product takes part in termination. The family-level IEA is therefore an over-annotation of this accession. It should stay on the long isoforms. Supporting Evidence: PMID:16387654 We show that Pcf11 is directly involved in termination in Drosophila. PMID:39111825 no protein product corresponding to PCF11-RC was observed despite a seemingly high level of the PCF11-RC transcript isoform detected by snRNA-seq of Drosophila testis tissue |
| GO:0010467 gene expression | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: An uninformative ARBA process term for a product with no demonstrated activity. Reason: This is an ARBA machine-learning association. Gene expression is a very high-level parent of the specific termination and 3'-end processing roles of full-length Pcf11, and none of those roles can be attributed to the 86-residue RC product, which lacks the functional regions and has not been detected as a protein. Supporting Evidence: PMID:39111825 no protein product corresponding to PCF11-RC was observed despite a seemingly high level of the PCF11-RC transcript isoform detected by snRNA-seq of Drosophila testis tissue |
| GO:0031124 mRNA 3'-end processing | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: CFII-dependent 3'-end processing belongs to the long Pcf11 isoforms, not the RC product. Reason: Pcf11-containing CFII regulates poly(A)-site choice in Drosophila spermatocytes, and Cbc co-immunoprecipitated with the >250 kDa long Pcf11 forms (PMID:39111825). Pcf11 homologs bind Cbc/Clp1 through a region near the C terminus that C0P8M6 lacks. Yeast Pcf11 3'-end processing also depends on regions separable from CTD binding (PMID:12727883). The 86-residue product has none of these regions, so the family-level IEA overstates it. Supporting Evidence: PMID:39111825 PCF11 homologs in mammals and yeast have been shown to bind Cbc homologs through a region close to the C terminus of PCF11 file:DROME/Pcf11/Pcf11-bioinformatics/RESULTS-rereview.md C0P8M6 has none of the regions C-terminal to the CID that the longer products carry. |
| GO:0032991 protein-containing complex | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: An uninformative ARBA location; the CFII complex has been shown only for the long isoforms. Reason: The only Drosophila Pcf11 complex shown experimentally is CFII with Cbc, recovered with the >250 kDa long Pcf11 forms. Cbc binding maps to the Pcf11 C-terminal region that C0P8M6 lacks, and neither the ~70 kDa RB form nor any RC product was recovered. The generic term is not supported for this product. Supporting Evidence: PMID:39111825 Immunoprecipitation with anti-HA antibodies from extracts of testes from flies homozygous for HA:cbc coimmunoprecipitated the >250 kDa band from the PCF11 isoforms, consistent with the Cbc and PCF11 proteins interacting in a complex |
Loading supporting content…
Download this section (compressed HTML)Q: Should the gene-level FlyBase experimental annotations for Pcf11 be carried onto the 86-residue RC product (C0P8M6/E1JH69), or only onto the long and RB isoforms whose sequences contain the full CID?
Experiment: Tag the unique C-terminal tail of the RC product at the endogenous locus, or use ribosome profiling of testis and embryo, to test whether the 86-residue protein is made. If it is, test recombinant RC protein for binding to Ser2/Ser5-phosphorylated CTD peptides beside the full CID (residues 1-149).
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: It is unknown whether the Pcf11-RC transcript is translated into a stable 86-residue protein in vivo, and if so what that protein does.
OPEN BIOLOGY WHOLLY_DARK
What is known: The RC product shares Pcf11 residues 1-62, which contain about a third of the CID, and has a unique 24-residue tail. A protein of the expected size was not seen in testis with an N-terminal antibody, although the RC transcript is abundant.
What would resolve it: Ribosome profiling or tagged-allele detection of the RC product, followed by CTD-binding and localization assays if it is made.
Provenance (the field's own admissions):
Loading supporting content…
Download this section (compressed HTML)Protein 1 of cleavage and polyadenylation factor 1 (Pcf11) encodes an RNA binding protein involved in RNA splicing regulation.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)