PINT87aa is an 87-amino-acid nuclear peptide encoded within the long intergenic non-protein-coding RNA locus LINC-PINT (p53-induced transcript). It is not translated from the linear lncRNA: exon 2 of LINC-PINT is back-spliced into a predominantly cytoplasmic circular RNA (circPINTexon2), from which an internal open reading frame is translated cap-independently via an internal ribosome entry site. The endogenous peptide has been detected by antibody and mass spectrometry. The sequence is arginine-rich, contains a run of seven cysteines, and has no recognised domain outside its own Pfam family. In the nucleus PINT87aa binds the PAF1 subunit of the RNA polymerase II-associated factor (PAF1) complex, co-occupies target promoters with PAF1, and is proposed to retain PAF1 complex at promoters and thereby restrain transcription of PAF1-dependent genes such as CPEB1, SOX2 and MYC; it does not bind DNA itself. It also binds the DNA-binding domain of the forkhead transcription factor FOXM1 and reduces FOXM1-driven transcription of targets including PHB2. Overexpression suppresses proliferation of glioblastoma cells and induces growth arrest, senescence and reduced mitophagy in hepatocellular carcinoma cells; the peptide and its circRNA are expressed in brain, liver, kidney and stomach and are lower in glioblastoma and HCC than in non-tumour tissue. Functions reported for the linear LINC-PINT RNA (e.g. miRNA sponging, chromatin regulator recruitment) are separate from those of the peptide.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:30367041 A peptide encoded by circular form of LINC-PINT suppresses o... | ACCEPT | Summary: PINT87aa overexpression lowers, and knockdown raises, PAF1 occupancy at the CPEB1 promoter; overexpression represses mRNA of PAF1 target genes (CPEB1, SOX2, MYC) in glioblastoma tumour-initiating cells. Knockdown of the linear lncRNA does not affect these targets, so the effect is attributable to the circRNA-encoded peptide. Reason: Gain- and loss-of-function data in the founding paper, together with direct PAF1 binding and promoter co-occupancy, support a role in repressing RNA polymerase II target genes. The independent FOXM1/PHB2 mechanism in HCC (PMID:33754036) points in the same direction. The more specific term negative regulation of transcription elongation by RNA polymerase II (GO:0034244) would go beyond the data, since Pol II elongation or pausing was not measured directly and the anchoring model is stated as an assumption. Caveat - all evidence comes from one research group, mostly with overexpression. Supporting Evidence: PMID:30367041 PINT87aa overexpression or knocking down enhanced or decreased PAF1/CPEB1 promoter affinity, respectively PMID:30367041 The mRNA of PAF1 downstream genes, including CPEB1, SOX-2, c-Myc, etc., was inhibited transcriptionally PMID:30367041 LINC-PINT knockdown in SW1783 and Hs683 cells using specific ASOs increased cell viability but did not alter PAF1 downstream gene mRNA or protein levels PMID:33754036 We confirmed that FOXM1 could promote the transcription of PHB2 and a negative regulatory effect of PINT87aa on PHB2 expression |
| GO:0005515 protein binding | IPI PMID:30367041 A peptide encoded by circular form of LINC-PINT suppresses o... | REMOVE | Summary: Interaction with PAF1 (Q8N7H5), shown by IP-MS, co-IP in 293T cells and a purified-protein binding assay mapping the site to PAF1 residues 150-300. Reason: The PAF1 interaction is well supported and central to the proposed mechanism, but bare protein binding is uninformative. No GO molecular function term fits binding to the PAF1 elongation complex (PAF1 is not a DNA-binding transcription factor, so GO:0140297 does not apply). The biological consequence is captured by GO:0000122 and the nuclear location. Supporting Evidence: PMID:30367041 A direct binding assay using purified proteins further indicated that PINT87aa interacts with the 150–300-aa domain of PAF1 PMID:30367041 Immunoprecipitation further confirmed a mutual PINT87aa/PAF1 interaction in 293T cells |
| GO:0005515 protein binding | IPI PMID:33754036 Cellular senescence in hepatocellular carcinoma induced by a... | MODIFY | Summary: Interaction with the forkhead transcription factor FOXM1 (Q08050), mapped to the FOXM1 DNA-binding domain; co-IP with a GFP-only negative control, and deletion of PINT87aa residues 30-36 abolishes binding. Reason: FOXM1 is a sequence-specific DNA-binding transcription factor and PINT87aa binds its DNA-binding domain, so DNA-binding transcription factor binding is a more informative term than protein binding. The binding is linked to reduced FOXM1-target transcription (PHB2) without change in FOXM1 levels. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:33754036 PINT87aa could bind to the DNA-binding domain of FOXM1, which was confirmed by co-IP results, indicating that PINT87aa-GFP and FOXM1 interacted with each other PMID:33754036 The co-IP results showed no interaction between the truncated PINT87aa-GFP and FOXM1 |
| GO:0005634 nucleus | IDA PMID:30367041 A peptide encoded by circular form of LINC-PINT suppresses o... | ACCEPT | Summary: RFP- and GFP-tagged PINT87aa is concentrated in the nucleus and co-localises with PAF1 there; ChIP shows promoter occupancy. Reason: Direct localisation evidence, consistent with nuclear partners (PAF1 complex, FOXM1) and promoter ChIP. Localisation was shown with tagged, overexpressed peptide; endogenous localisation was not separately imaged. Supporting Evidence: PMID:30367041 Using RFP fusion protein labeling, we found that this peptide was concentrated in nucleus PMID:30367041 Furthermore, GFP-PINT87aa and PAF1 co-localized in the nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0191 Nucleus), based on the same evidence as the IDA row. Reason: Correct mapping, concordant with the experimental annotation. Supporting Evidence: PMID:30367041 Using RFP fusion protein labeling, we found that this peptide was concentrated in nucleus |
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Download this section (compressed HTML)Q: Does PINT87aa act as a transcription corepressor (GO:0003714) in the GO sense, i.e. is it recruited to FOXM1-bound loci and does it reduce FOXM1 occupancy or activity there, or does it sequester FOXM1 off chromatin?
Q: Does PINT87aa slow RNA polymerase II elongation directly (e.g. increased promoter-proximal pausing at PAF1 targets), which would justify the more specific term negative regulation of transcription elongation by RNA polymerase II (GO:0034244)?
Q: How do the PAF1 and FOXM1 interactions relate; are they mediated by the same arginine-rich N-terminal region (PAF1-critical residues R20-S53; FOXM1-binding residues 30-36)?
Q: Has the peptide been detected in independent proteomic or ribosome-profiling datasets, and by laboratories other than the originating group?
Experiment: Mutate the PINT87aa start codon or introduce a frameshift in endogenous circPINTexon2 (preserving back-splicing and RNA levels), then measure PAF1/FOXM1 promoter occupancy, Pol II pausing (PRO-seq) and target expression, with rescue by wild-type versus binding-deficient (delta30-36) peptide.
Hypothesis: PINT87aa, not the circRNA or linear lncRNA, mediates repression of PAF1 and FOXM1 targets.
Type: genome editing with peptide-specific loss of function and rescue
Experiment: Endogenous co-IP and proximity labelling (e.g. TurboID-tagged knock-in) in non-transformed cells (neural progenitors, hepatocytes), avoiding overexpression.
Hypothesis: PINT87aa forms a direct, stoichiometric complex with PAF1 complex and FOXM1 in cells at endogenous levels.
Type: endogenous interaction proteomics
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