MARCHF6-DT encodes PACMP (PAR-amplifying and CtIP-maintaining micropeptide), a 44-amino-acid human microprotein translated from a small ORF in a transcript previously annotated as a long noncoding RNA (CTD-2256P15.2), the divergent transcript of MARCHF6 on chromosome 5. The peptide is predicted to be intrinsically disordered, with a strongly arginine/lysine-rich C-terminal half. PACMP localises to the nucleolus and to chromatin, and is recruited to sites of DNA damage by binding damage-induced poly(ADP-ribose) chains through its basic residues. It has two reported activities in the DNA damage response: it binds KLHL15, the substrate adaptor of a CUL3 ubiquitin ligase, and blocks KLHL15 association with the end-resection factor CtIP (RBBP8), thereby preventing CtIP ubiquitination and degradation; and it binds PAR chains and PARP1 to enhance PARP1-dependent poly(ADP-ribosyl)ation. Depletion of PACMP lowers CtIP levels and PARylation, inhibits tumour growth, and sensitises cancer cells to PARP, ATR and CDK4/6 inhibitors, ionizing radiation, epirubicin and camptothecin. All functional data come from a single study.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | MODIFY | Summary: Interaction of PACMP with PARP1 (P09874) reported in the primary characterisation paper; PACMP enhances PARP1-dependent poly(ADP-ribosyl)ation. Reason: Bare protein binding is uninformative. The partner is the enzyme PARP1, and the interaction is linked to PACMP's enhancement of PARP1 activity, so enzyme binding (GO:0019899) is a more informative term that stays within what the evidence shows. Whether the interaction is direct or bridged by PARP1 auto-PARylation chains is not resolved in the available text, so a PARP1 activator MF is not asserted. Proposed replacements: enzyme binding Supporting Evidence: PMID:35219381 directly binds DNA damage-induced poly(ADP-ribose) chains to enhance PARP1-dependent poly(ADP-ribosyl)ation |
| GO:0005515 protein binding | IPI PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | MODIFY | Summary: Interaction of PACMP with KLHL15 (Q96M94), the substrate-recognition subunit of a CUL3-RING ubiquitin ligase that targets CtIP; PACMP competitively blocks the KLHL15-CtIP association. Reason: Bare protein binding is uninformative. KLHL15 is the substrate adaptor of an E3 ubiquitin ligase complex, and PACMP binding to it prevents CtIP ubiquitination, so ubiquitin protein ligase binding (GO:0031625) captures the interaction. A stronger claim (ubiquitin ligase inhibitor activity, GO:1990948) may be justified by the full text but cannot be verified from the abstract. Proposed replacements: ubiquitin protein ligase binding Supporting Evidence: PMID:35219381 PACMP not only prevents CtIP from ubiquitination through inhibiting the CtIP-KLHL15 association |
| GO:0005694 chromosome | EXP PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | ACCEPT | Summary: PACMP associates with chromatin and is recruited to DNA damage sites via PAR chains. Reason: Experimental localisation by the curators of the primary paper; consistent with PAR-dependent recruitment to damaged chromatin. Site of DNA damage (GO:0090734) is the more specific location. Supporting Evidence: PMID:35219381 directly binds DNA damage-induced poly(ADP-ribose) chains |
| GO:0005694 chromosome | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping (SL-0468 Chromosome) derived from the same experimental data as the EXP row. Reason: Correct mapping, concordant with the experimental annotation. Supporting Evidence: PMID:35219381 directly binds DNA damage-induced poly(ADP-ribose) chains |
| GO:0005730 nucleolus | IDA PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | KEEP AS NON CORE | Summary: UniProt records nucleolar localisation of PACMP from the primary paper. Reason: The nucleolar localisation is accepted from the curators, who read the full text. However, the reported activities (PAR binding, CtIP protection, PARylation enhancement) operate at DNA damage sites; no nucleolus-specific activity is described in the available text, so the is_active_in qualifier is weakly supported and the term is not core. |
| GO:0005730 nucleolus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt SubCell mapping (SL-0188 Nucleolus) derived from the primary paper. Reason: Correct mapping of the curated localisation with the neutral located_in qualifier, but the peptide's reported activities are at DNA damage sites, so the nucleolus is not a core location. |
| GO:0010835 regulation of protein ADP-ribosylation | IDA PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | ACCEPT | Summary: PACMP enhances PARP1-dependent poly(ADP-ribosyl)ation after DNA damage, and its depletion lowers PARylation. Reason: Directly supported. GO has no positive-regulation child of this term (only negative regulation, GO:0010836), so this is the most specific available term. PACMP regulates the activity of PARP1 rather than performing the transfer itself, so a regulation term is correct. Supporting Evidence: PMID:35219381 with a dual function to maintain CtIP abundance and promote poly(ADP-ribosyl)ation PMID:35219381 directly binds DNA damage-induced poly(ADP-ribose) chains to enhance PARP1-dependent poly(ADP-ribosyl)ation |
| GO:0031397 negative regulation of protein ubiquitination | IDA PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | ACCEPT | Summary: PACMP prevents KLHL15-mediated ubiquitination of CtIP by blocking the CtIP-KLHL15 association, maintaining CtIP abundance. Reason: Directly supported and describes one of the two core activities of the peptide. Supporting Evidence: PMID:35219381 PACMP not only prevents CtIP from ubiquitination through inhibiting the CtIP-KLHL15 association |
| GO:0045739 positive regulation of DNA repair | IDA PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | ACCEPT | Summary: By stabilising CtIP and enhancing PARylation, PACMP promotes the DNA damage response; its loss sensitises cells to DNA-damaging agents and DDR inhibitors. Reason: Supported by the curated paper. The CtIP link suggests a more specific role in double-strand break repair/end resection, but that specificity is not stated in the available abstract, so the broader term is retained. Supporting Evidence: PMID:35219381 a lncRNA-derived micropeptide regulates cancer progression and drug resistance by modulating DDR |
| GO:0072572 poly-ADP-D-ribose binding | IDA PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | ACCEPT | Summary: PACMP directly binds DNA damage-induced PAR chains via its arginine-rich C-terminal region (UniProt records that 10A and 4A arginine-to-alanine mutants impair PAR binding). Reason: Direct binding with mutational support; this is the best-defined molecular activity of the peptide and underlies its recruitment to damage sites. Supporting Evidence: PMID:35219381 directly binds DNA damage-induced poly(ADP-ribose) chains |
| GO:0090734 site of DNA damage | IDA PMID:35219381 Micropeptide PACMP inhibition elicits synthetic lethal effec... | ACCEPT | Summary: PACMP is recruited to DNA damage sites through binding to PAR chains. Reason: Core location where both PAR binding and PARylation enhancement take place. Supporting Evidence: PMID:35219381 directly binds DNA damage-induced poly(ADP-ribose) chains to enhance PARP1-dependent poly(ADP-ribosyl)ation |
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Download this section (compressed HTML)Q: Does PACMP inhibit CUL3-KLHL15 ligase activity toward other KLHL15 substrates, or only occlude the CtIP-binding site? The answer decides between ubiquitin ligase inhibitor activity (GO:1990948) and the more neutral ubiquitin protein ligase binding.
Q: Is the PACMP-PARP1 interaction direct, or bridged by PAR chains on auto-modified PARP1? Does PACMP increase PARP1 catalytic activity in a purified system (an enzyme activator activity) or act by stabilising PAR chains?
Q: Does PACMP promote DNA end resection and homologous recombination specifically, as its CtIP-stabilising role predicts, which would support a more specific DNA repair term than positive regulation of DNA repair?
Q: Is the PACMP ORF conserved beyond primates, and has its translation been confirmed independently (ribosome profiling or mass spectrometry) outside the original study?
Experiment: Reconstitute PARP1 automodification in vitro with purified PARP1, damaged DNA and synthetic PACMP peptide (wild type versus the 10A/4A PAR-binding mutants) and measure PAR synthesis kinetics.
Hypothesis: PACMP is a direct activator of PARP1 enzyme activity rather than only a PAR-chain binder.
Type: in vitro enzyme assay
Experiment: Introduce start-codon or frameshift mutations into the endogenous ORF while preserving the transcript, and test CtIP levels, end resection (RPA foci/ssDNA), PARylation and PARP-inhibitor sensitivity.
Hypothesis: PACMP's tumour-suppressive DDR phenotype depends on the peptide rather than the host RNA.
Type: genome editing and DNA repair assays
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