Essential nucleolar RNA cytidine acetyltransferase, the sole enzyme in eukaryotes that installs N4-acetylcytidine (ac4C) on RNA. It is the human ortholog of bacterial TmcA and yeast Kre33, and combines an N-terminal helicase/ATPase module with a GNAT-fold N-acetyltransferase domain, so that the reaction consumes both acetyl-CoA and ATP. Its established substrates are 18S rRNA, where it acetylates cytidines in helix 34 and helix 45 (C1842 in human) with snoRNA guidance, and serine and leucine tRNAs, where acetylation of C12 in the D-arm requires the adaptor THUMPD1. NAT10 is a constituent of the nucleolar small-subunit (SSU) processome and is required for early pre-rRNA cleavages and 40S subunit biogenesis; it is nucleolar in interphase and relocates to the midbody in telophase. Whether NAT10 also deposits ac4C on mRNA at physiologically meaningful levels is disputed: antibody-based and reduction-based base-resolution mapping report widespread, position-dependent mRNA acetylation that modulates translation, while an independent chemical base-resolution method finds ac4C essentially confined to rRNA and tRNA in human cells, detectable in mRNA only upon enzyme overexpression, and the two groups have published mutually contradictory reanalyses of each other's data. NAT10 has also been reported to acetylate lysine residues in histones, microtubules and other proteins, but those assays largely used a truncated enzyme lacking the RNA-binding module and the in vivo relevance of a protein-lysine acetyltransferase activity is unresolved. The protein is overexpressed in many cancers, is inhibited by the small molecule remodelin, and its loss causes ribosome-biogenesis defects, slowed growth and cytokinesis failure.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0051392 tRNA cytidine N4-acetyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic transfer of the conserved tRNA ac4C-writer activity, matching direct experimental work on human NAT10 with its adaptor THUMPD1. Reason: Core molecular function. The PAINT node is seeded by yeast Kre33 (SGD:S000005076), E. coli TmcA (UniProtKB:P76562) and archaeal TmcA (UniProtKB:Q5JHC6); the eukaryotic activity was demonstrated directly in human cells, so the transfer is not the only support. Supporting Evidence: PMID:25653167 We demonstrate that yeast Kre33 and human NAT10 are RNA cytosine acetyltransferases with, surprisingly, specificity toward both 18S rRNA and tRNAs. tRNA acetylation requires the intervention of a specific and conserved adaptor: yeast Tan1/human THUMPD1. |
| GO:1990883 18S rRNA cytidine N-acetyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic transfer of the 18S rRNA ac4C-writer activity, which is the best-established function of this family. Reason: Core molecular function, independently demonstrated in human cells. Q9H0A0 appearing in its own WITH/FROM is expected - its experimental annotation is one of the descendant evidences behind the IBD node - and is not circular. Supporting Evidence: PMID:25411247 Here we report that NAT10 is an ATP-dependent RNA acetyltransferase responsible for formation of N(4)-acetylcytidine (ac(4)C) at position 1842 in the terminal helix of mammalian 18 S rRNA. |
| GO:0051391 tRNA acetylation | IBA GO_REF:0000033 | ACCEPT | Summary: The biological process matching the tRNA acetyltransferase activity. Reason: Core process; human NAT10 acetylates serine and leucine tRNAs with THUMPD1. Supporting Evidence: PMID:25653167 Specific eukaryotic tRNAs, including leucine and serine in yeast, are acetylated at position 12 (46). |
| GO:0032040 small-subunit processome | IBA GO_REF:0000033 | ACCEPT | Summary: NAT10 is a constituent of the nucleolar SSU processome, confirmed structurally in human cells. Reason: Core location; independently supported by cryo-EM of human SSU processomes. Supporting Evidence: PMID:34516797 The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. |
| GO:0106162 mRNA cytidine N-acetyltransferase activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic transfer of an mRNA ac4C-writer activity whose existence in human cells is actively disputed between two base-resolution mapping methods. Reason: Retained but demoted. The WITH/FROM set is AGI_LocusCode:AT1G10490, PANTHER:PTN000100786, UniProtKB:Q5JHC6 and UniProtKB:Q9H0A0. Q5JHC6 is TMCA_THEKO, the Thermococcus kodakarensis enzyme - precisely the lineage in which transcriptome-wide mRNA ac4C is uncontested (PMID:32555463), while the same study failed to detect ac4C in human mRNA except upon enzyme overexpression. Q9H0A0 in its own WITH/FROM reflects its human IDAs and is expected, not circular. No propagation failure is asserted: the node placement is defensible and the human IDAs exist. The demotion reflects that the human substrate claim rests on methods whose specificity is contested in print (PMID:38640895 versus PMID:38640896), whereas the 18S rRNA and tRNA activities are not in doubt. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:Q5JHC6 · TMCA_THEKO (Thermococcus kodakarensis TmcA/Nat10) SUPPORTS TRANSFER Archaeal donor; archaeal mRNA ac4C is well established and uncontested, unlike the human case. UniProtKB:Q9H0A0 · NAT10 (human, the target itself) SUPPORTS TRANSFER Self-inclusion is expected - the human IDAs are descendant evidence behind the IBD node, not circular support. AGI_LocusCode:AT1G10490 · Arabidopsis thaliana NAT10 ortholog UNRESOLVED Plant donor not inspected in detail here. PANTHER:PTN000100786 · PAINT ancestral node SUPPORTS TRANSFER Supporting Evidence: PMID:32555463 In human and yeast mRNAs, ac4C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. |
| GO:0002101 tRNA wobble cytosine modification | IBA GO_REF:0000033 | MODIFY | Summary: Over-propagated from the bacterial donor. The wobble position is the bacterial TmcA target; eukaryotic NAT10 acetylates C12 in the tRNA D-arm, not the wobble base. Reason: The only experimental donor in WITH/FROM is UniProtKB:P76562, verified at UniProt as TMCA_ECOLI "tRNA(Met) cytidine acetyltransferase TmcA", which acetylates the wobble cytidine of elongator tRNA-Met. The eukaryotic enzyme has a different site specificity: NAT10/THUMPD1 acetylate position 12 of serine and leucine tRNAs, in the D-arm. The generic tRNA acetylation term is correct for human; the wobble-specific term is not. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE LINEAGE OR TAXON MISMATCH Sources checked: UniProtKB:P76562 · TmcA (Escherichia coli K12) SUPPORTS SOURCE BUT NOT TARGET Bacterial TmcA acetylates the wobble C34 of elongator tRNA-Met; the eukaryotic orthologue's tRNA target is C12 in the D-arm, so the site-specific term does not transfer. PANTHER:PTN000100786 · PAINT ancestral node SUPPORTS TRANSFER The node correctly carries tRNA acetylation; only the wobble-specific scoping is wrong for the animal clade. Proposed replacements: tRNA acetylation Supporting Evidence: PMID:25411247 In bacteria, ac 4 C is present at the wobble position of elongator tRNA Met PMID:25653167 Specific eukaryotic tRNAs, including leucine and serine in yeast, are acetylated at position 12 (46). |
| GO:1904812 rRNA acetylation involved in maturation of SSU-rRNA | IBA GO_REF:0000033 | ACCEPT | Summary: The precise biological process for the 18S rRNA acetyltransferase activity. Reason: Core process; NAT10 depletion causes accumulation of the 30S pre-rRNA and loss of ac4C1842. Supporting Evidence: PMID:25411247 RNAi-mediated knockdown of NAT10 resulted in growth retardation of human cells, and this was accompanied by high-level accumulation of the 30 S precursor of 18 S rRNA, suggesting that ac(4)C1842 formation catalyzed by NAT10 is involved in rRNA processing and ribosome biogenesis. |
| GO:0000154 rRNA modification | IEA GO_REF:0000104 | ACCEPT | Summary: Generic parent of the specific rRNA acetylation process. Reason: Correct, though uninformative next to GO:1904812, which this gene also carries. |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: NAT10 has an N-terminal helicase/ATPase module and the acetyl transfer reaction requires ATP hydrolysis. Reason: Mechanistically real and required for the core activity; UniProt annotates ATP-binding residues at 287-296 and 470, and ac4C formation in vitro needed both ATP and acetyl-CoA. Supporting Evidence: PMID:25411247 Here we report that NAT10 is an ATP-dependent RNA acetyltransferase responsible for formation of N(4)-acetylcytidine (ac(4)C) at position 1842 in the terminal helix of mammalian 18 S rRNA. |
| GO:0005730 nucleolus | IEA GO_REF:0000120 | ACCEPT | Summary: NAT10 is predominantly nucleolar in interphase. Reason: Core location, supported by multiple independent methods. |
| GO:0008080 N-acetyltransferase activity | IEA GO_REF:0000120 | MODIFY | Summary: Correct but far too general; the specific RNA cytidine acetyltransferase terms are available and already on this gene. Reason: A GNAT-family parent term that carries no information about the substrate. Replace with the substrate-specific RNA acetyltransferase terms. Proposed replacements: 18S rRNA cytidine N-acetyltransferase activity tRNA cytidine N4-acetyltransferase activity |
| GO:0016072 rRNA metabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: Generic ancestor of the specific rRNA acetylation and SSU maturation processes. Reason: Correct but uninformative; retained as a true parent. |
| GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups | IEA GO_REF:0000002 | MODIFY | Summary: An InterPro-derived grandparent term with no substrate information. Reason: Correct in kind but far too general for an enzyme whose specific activity is experimentally defined. Proposed replacements: 18S rRNA cytidine N-acetyltransferase activity |
| GO:0030496 midbody | IEA GO_REF:0000044 | ACCEPT | Summary: NAT10 relocalizes to the mitotic midbody in telophase. Reason: Well-documented secondary location, supported experimentally and by immunofluorescence curation. |
| GO:0042274 ribosomal small subunit biogenesis | IEA GO_REF:0000104 | ACCEPT | Summary: NAT10 is required for 40S subunit production via the SSU processome and early pre-rRNA cleavages. Reason: Core biological process. |
| GO:0051391 tRNA acetylation | IEA GO_REF:0000104 | ACCEPT | Summary: The biological process matching the tRNA acetyltransferase activity. Reason: Core process; human NAT10 acetylates serine and leucine tRNAs with THUMPD1. |
| GO:0051392 tRNA cytidine N4-acetyltransferase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea reaction mapping (RHEA:53876) for tRNA cytidine acetylation. Reason: Core molecular function; the Rhea reaction matches the experimentally demonstrated chemistry. |
| GO:0106162 mRNA cytidine N-acetyltransferase activity | IEA GO_REF:0000116 | KEEP AS NON CORE | Summary: Rhea reaction mapping (RHEA:58480) that follows from UniProt's acceptance of the disputed mRNA substrate claim. Reason: This IEA is downstream of the same contested primary literature as the IDAs (UniProt cites PMID:30449621 and PMID:35679869 for this catalytic activity). Retained for consistency with the experimental rows, but not core while the existence of physiological mRNA ac4C in human cells is unresolved. |
| GO:0140640 catalytic activity, acting on a nucleic acid | IEA GO_REF:0000117 | MODIFY | Summary: Very high-level ARBA term. Reason: True but essentially contentless for a protein with a precisely defined catalytic activity. Proposed replacements: 18S rRNA cytidine N-acetyltransferase activity |
| GO:1904812 rRNA acetylation involved in maturation of SSU-rRNA | IEA GO_REF:0000002 | ACCEPT | Summary: The precise biological process for the 18S rRNA acetyltransferase activity. Reason: Core process, matching the experimental data on ac4C1842 and pre-rRNA processing. |
| GO:1990883 18S rRNA cytidine N-acetyltransferase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea reaction mapping (RHEA:51424) for 18S rRNA cytidine acetylation. Reason: Core molecular function; matches the demonstrated ATP- and acetyl-CoA-dependent chemistry. |
| GO:0005515 protein binding | IPI PMID:25653167 Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine ... | REMOVE | Summary: Bare protein binding (with THUMPD1); carries no functional information. Reason: Per project guidance, GO:0005515 is uninformative. The biologically meaningful content of this interaction - THUMPD1 as the tRNA-binding adaptor required for tRNA acetylation - is already captured by GO:0051392 and GO:0051391. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | REMOVE | Summary: Bare protein binding from a large-scale interactome map. Reason: Per project guidance, GO:0005515 is uninformative. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Ma... | REMOVE | Summary: Bare protein binding from crosslinking mass spectrometry of nuclei. Reason: Per project guidance, GO:0005515 is uninformative. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | REMOVE | Summary: Bare protein binding from a proteome-scale interaction network. Reason: Per project guidance, GO:0005515 is uninformative. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | REMOVE | Summary: Bare protein binding from a multimodal cell-map study. Reason: Per project guidance, GO:0005515 is uninformative. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005730 nucleolus | NAS PMID:34516797 Nucleolar maturation of the human small subunit processome. | ACCEPT | Summary: Nucleolar localization asserted in the context of SSU processome curation. Reason: Core location, consistent with all other evidence. |
| GO:0030490 maturation of SSU-rRNA | NAS PMID:34516797 Nucleolar maturation of the human small subunit processome. | ACCEPT | Summary: NAT10 acts within the SSU processome during maturation of 18S rRNA. Reason: Core process, structurally and biochemically supported. Supporting Evidence: PMID:34516797 The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. |
| GO:0032040 small-subunit processome | NAS PMID:34516797 Nucleolar maturation of the human small subunit processome. | ACCEPT | Summary: NAT10 is a component of the human SSU processome. Reason: Core complex membership. |
| GO:0005730 nucleolus | IDA GO_REF:0000052 | ACCEPT | Summary: Immunofluorescence localization to the nucleolus (HPA). Reason: Core location. |
| GO:0030496 midbody | IDA GO_REF:0000052 | ACCEPT | Summary: Immunofluorescence localization to the midbody (HPA). Reason: Corroborates the published telophase relocalization. |
| GO:0030496 midbody | EXP PMID:19303003 NAT10, a nucleolar protein, localizes to the midbody and reg... | ACCEPT | Summary: NAT10 concentrates in the mitotic midbody during telophase. Reason: Direct experimental localization; a real secondary site, and residues 702-1025 are required for it. Supporting Evidence: PMID:19303003 we demonstrated that NAT10 (N-acetyltransferase 10, NAT10) is not only predominantly distributed in the nucleolus in interphase, but is also concentrated in the mitotic midbody during telophase. |
| GO:1990883 18S rRNA cytidine N-acetyltransferase activity | EXP PMID:25411247 Human NAT10 is an ATP-dependent RNA acetyltransferase respon... | ACCEPT | Summary: Direct demonstration that NAT10 forms ac4C1842 in 18S rRNA, requiring both ATP and acetyl-CoA. Reason: The single best-supported molecular function of this protein, and the anchor of the whole review. Supporting Evidence: PMID:25411247 Here we report that NAT10 is an ATP-dependent RNA acetyltransferase responsible for formation of N(4)-acetylcytidine (ac(4)C) at position 1842 in the terminal helix of mammalian 18 S rRNA. |
| GO:0006417 regulation of translation | IDA PMID:35679869 Direct epitranscriptomic regulation of mammalian translation... | KEEP AS NON CORE | Summary: Translation is modulated by ac4C in a position-dependent way - stimulated within coding sequences, inhibited when present in 5' UTRs and Kozak contexts. Reason: Retained, and the unsigned "regulation" term is the right one because the same study finds effects in both directions. Demoted to non-core because the annotation derives from the mRNA-ac4C mapping whose specificity is disputed (PMID:38640895 versus PMID:38640896); note also that NAT10 loss cripples 40S biogenesis, so translational phenotypes after NAT10 depletion are expected on either model of the mRNA question. Supporting Evidence: PMID:35679869 Although cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5' UTRs impacts protein synthesis at the level of initiation. |
| GO:0106162 mRNA cytidine N-acetyltransferase activity | IDA PMID:35679869 Direct epitranscriptomic regulation of mammalian translation... | KEEP AS NON CORE | Summary: Base-resolution RedaC:T-seq assignment of ac4C to human mRNA, contradicted by an independent base-resolution method and the subject of a published dispute that remains unresolved. Reason: GOA carries both sides of this question only implicitly, so it is stated here. Arango et al. report position-dependent ac4C in HeLa mRNA by RedaC:T-seq (PMID:35679869), building on antibody-based acRIP-seq (PMID:30449621). Sas-Chen et al., using chemical base-resolution ac4C-seq, find ac4C confined to rRNA and tRNA in human cells and inducible in mRNA only by enzyme overexpression (PMID:32555463, method in PMID:33772246). The two groups then published back-to-back reanalyses of the same data reaching opposite conclusions (PMID:38640895 "No evidence for ac4C within human mRNA upon data reassessment" versus PMID:38640896 "Detection of ac4C in human mRNA is preserved upon data reassessment"), and neither was retracted. This is an experimental annotation whose full text I have not read, so it is kept, not removed; but it is not core while the substrate class itself is contested, in contrast to the 18S rRNA and tRNA activities, which are not in doubt. A sizeable 2025-2026 disease literature (e.g. PMID:41956987, PMID:42315153, PMID:42592486) asserts NAT10-dependent mRNA ac4C on named transcripts using the contested assay class without engaging the dispute; it adds volume, not independent methodological support. Supporting Evidence: PMID:35679869 Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. PMID:32555463 In human and yeast mRNAs, ac4C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. |
| GO:0000154 rRNA modification | TAS Reactome:R-HSA-6790901 | ACCEPT | Summary: Reactome pathway assertion of rRNA modification. Reason: Correct, though uninformative next to GO:1904812, which this gene also carries. |
| GO:0032040 small-subunit processome | IDA PMID:34516797 Nucleolar maturation of the human small subunit processome. | ACCEPT | Summary: Cryo-EM of maturing human SSU processomes places NAT10 within the particle. Reason: Core complex membership, structurally resolved. Supporting Evidence: PMID:34516797 We report the high-resolution cryo–electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms. |
| GO:0042274 ribosomal small subunit biogenesis | IDA PMID:34516797 Nucleolar maturation of the human small subunit processome. | ACCEPT | Summary: NAT10 acts in early 40S subunit maturation. Reason: Core biological process. |
| GO:0005515 protein binding | IPI PMID:31722219 CCDC84 Acetylation Oscillation Regulates Centrosome Duplicat... | REMOVE | Summary: Bare protein binding (with CCDC84/CENATAC). Reason: Per project guidance, GO:0005515 is uninformative. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0006473 protein acetylation | IDA PMID:31722219 CCDC84 Acetylation Oscillation Regulates Centrosome Duplicat... | KEEP AS NON CORE | Summary: NAT10 reported as the acetyltransferase setting CCDC84/CENATAC lysine 31 acetylation, opposed by SIRT1. Reason: Kept - it is an experimental annotation and CLAUDE.md forbids overruling one whose full text I have not read - but explicitly non-core, and notably GOA carries no protein-lysine acetyltransferase molecular function for NAT10, which is the right state of affairs. Reported protein-lysine acetylation activities (histones, alpha-tubulin, TP53, MDM2, and most recently histone H3 via a GSDMC scaffold in PMID:42176271) were largely measured in vitro with a truncated construct (aa 164-834) that lacks the N-terminal helicase/RNA-binding module required for the RNA reaction; the converse control, whether full-length NAT10 acetylates protein substrates, has not been done cleanly. UniProt reaches the same conclusion, stating that the relevance of the protein lysine acetyltransferase activity is unsure in vivo. Because NAT10 loss collapses 40S biogenesis, indirect routes to altered protein acetylation are not excluded. Supporting Evidence: PMID:31722219 the acetylation state of CCDC84 at lysine 31 is regulated by the deacetylase SIRT1 and the acetyltransferase NAT10 PMID:25411247 It remains to be determined whether full-length NAT10 has efficient and specific lysine acetyltransferase activity toward histones or other proteins. |
| GO:0010824 regulation of centrosome duplication | IDA PMID:31722219 CCDC84 Acetylation Oscillation Regulates Centrosome Duplicat... | KEEP AS NON CORE | Summary: Via CCDC84/CENATAC acetylation, NAT10 is reported to modulate SASS6 degradation and centriole number. Reason: Real experimental observation but peripheral to the enzyme's RNA-modifying role, and dependent on the same unresolved protein-acetyltransferase question. |
| GO:0008080 N-acetyltransferase activity | EXP PMID:25411247 Human NAT10 is an ATP-dependent RNA acetyltransferase respon... | MODIFY | Summary: Correct but far too general; the substrate-specific terms are available and already on this gene. Reason: This very paper defines the specific activity (18S rRNA cytidine acetylation), so the generic parent should be replaced. Proposed replacements: 18S rRNA cytidine N-acetyltransferase activity tRNA cytidine N4-acetyltransferase activity |
| GO:0008080 N-acetyltransferase activity | EXP PMID:25653167 Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine ... | MODIFY | Summary: Correct but far too general; the substrate-specific terms are available and already on this gene. Reason: This paper defines both the 18S rRNA and the tRNA specificity, so the generic parent should be replaced. Proposed replacements: 18S rRNA cytidine N-acetyltransferase activity tRNA cytidine N4-acetyltransferase activity |
| GO:0045727 positive regulation of translation | IDA PMID:30449621 Acetylation of Cytidine in mRNA Promotes Translation Efficie... | MODIFY | Summary: Signed as positive, but the same laboratory later showed that ac4C in 5' UTRs and Kozak contexts inhibits initiation, so the direction is not uniform. Reason: The regulatory sign is not general. PMID:30449621 reported that acetylated mRNAs are stabilised and better translated, but PMID:35679869 showed the effect is position-dependent and can be inhibitory. The unsigned parent is the honest term, and this gene already carries it. Proposed replacements: regulation of translation Supporting Evidence: PMID:30449621 mRNA acetylation was further demonstrated to enhance substrate translation in vitro and in vivo. PMID:35679869 Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. |
| GO:0106162 mRNA cytidine N-acetyltransferase activity | IDA PMID:30449621 Acetylation of Cytidine in mRNA Promotes Translation Efficie... | KEEP AS NON CORE | Summary: Antibody-based (acRIP-seq) assignment of ac4C to human mRNA; the founding observation of the contested mRNA substrate claim. Reason: Same adjudication as the PMID:35679869 row, kept consistent across all four GO:0106162 annotations. This is the acRIP-seq study, i.e. antibody-based rather than base-resolution, and antibody specificity for ac4C is exactly what the subsequent chemical mapping (PMID:32555463) called into question. It is an experimental annotation and is therefore retained rather than removed, but it is not core. The strongest part of this paper that survives the dispute is the demonstration that NAT10 loss destabilises and reduces translation of a defined mRNA cohort - a phenotype that does not by itself establish direct mRNA acetylation, since NAT10 loss also cripples 40S biogenesis. Supporting Evidence: PMID:30449621 Ablation of NAT10 reduced ac4C detection at the mapped mRNA sites and was globally associated with target mRNA downregulation. |
| GO:0005697 telomerase holoenzyme complex | IDA PMID:18082603 Purification of human telomerase complexes identifies factor... | MARK AS OVER ANNOTATED | Summary: NAT10 co-purified with telomerase as an associated NTPase, which the paper itself distinguishes from holoenzyme components. Reason: The study explicitly reserves "holoenzyme component" for the three core H/ACA proteins that are essential for RNP accumulation, and describes NAT10 among two NTPases that merely associate preferentially with active enzyme. Co-purification of an abundant nucleolar RNA-binding enzyme with an H/ACA RNP is not strong evidence of stable complex membership. Not removed, since it is an experimental annotation, but flagged as an over-annotation. Supporting Evidence: PMID:18082603 All three core H/ACA-motif binding proteins are telomerase holoenzyme components essential for RNP accumulation. |
| GO:0070182 DNA polymerase binding | IPI PMID:18082603 Purification of human telomerase complexes identifies factor... | KEEP AS NON CORE | Summary: Interaction with TERT (UniProtKB:O14746), which is formally an RNA-dependent DNA polymerase, so the term is technically applicable. Reason: Technically correct but a bare binding term that conveys little about NAT10's function; the interaction was detected in a telomerase affinity purification and its functional significance is unclear. |
| GO:0005730 nucleolus | IDA PMID:18082603 Purification of human telomerase complexes identifies factor... | ACCEPT | Summary: Direct localization of NAT10 to the nucleolus. Reason: Core location. |
| GO:0032211 negative regulation of telomere maintenance via telomerase | IMP PMID:18082603 Purification of human telomerase complexes identifies factor... | KEEP AS NON CORE | Summary: Overexpression of NAT10 shortened telomeres; the phenotype is a gain-of-function observation, not a loss-of-function one. Reason: Retained as an experimental annotation, but the supporting phenotype is telomere shortening upon overexpression of NAT10 (and equally of GNL3L and two hnRNPs), which does not establish that endogenous NAT10 negatively regulates telomerase. This also sits awkwardly beside the older report that NAT10/hALP activates TERT transcription, i.e. the two literatures assign opposite signs. Peripheral to the enzyme's core RNA-modifying role. Supporting Evidence: PMID:18082603 Curiously, overexpression of either associated hnRNP protein (hnRNP C and hnRNP U) or either NTPase protein (NAT10 and GNL3L) induced telomere shortening. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6790987 | KEEP AS NON CORE | Summary: Generic nuclear compartment assignment from a Reactome reaction. Reason: Not wrong, but NAT10 is predominantly nucleolar; the nucleolus annotations are the informative ones. |
| GO:0000781 chromosome, telomeric region | HDA PMID:19135898 Purification of proteins associated with specific genomic Lo... | KEEP AS NON CORE | Summary: Recovered in a proteomic pull-down of telomeric chromatin (PICh). Reason: High-throughput locus-proteomics hit for an abundant nucleolar RNA-binding protein; plausible but peripheral and not independently corroborated as a site of action. |
| GO:0016020 membrane | HDA PMID:19946888 Defining the membrane proteome of NK cells. | MARK AS OVER ANNOTATED | Summary: Recovered in an NK-cell membrane proteome. Reason: NAT10 is a soluble nucleolar protein with no transmembrane segment, signal peptide or lipid anchor in UniProt. A membrane-fraction proteomics hit is almost certainly co-fractionation, and the bare "membrane" term is in any case uninformative. |
| GO:0003723 RNA binding | HDA PMID:22658674 Insights into RNA biology from an atlas of mammalian mRNA-bi... | KEEP AS NON CORE | Summary: Recovered as a poly(A)-RNA-interacting protein in an mRNA-interactome capture experiment. Reason: True and mechanistically relevant - substrate binding is intrinsic to the acetyltransferase - but a generic parent term. Worth noting that this class of experiment is part of what originally motivated the search for mRNA ac4C. |
| GO:0003723 RNA binding | HDA PMID:22681889 The mRNA-bound proteome and its global occupancy profile on ... | KEEP AS NON CORE | Summary: Recovered in a second, independent mRNA-bound proteome study. Reason: True but generic; the specific RNA substrate relationships are captured by the acetyltransferase terms. |
| GO:0005634 nucleus | NAS PMID:11214970 Prediction of the coding sequences of unidentified human gen... | ACCEPT | Summary: Author statement in a large-scale cDNA sequencing paper. Reason: Correct but general; the nucleolus annotations are the informative ones. |
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Download this section (compressed HTML)Q: Does endogenous human mRNA carry N4-acetylcytidine at stoichiometries that matter biologically, or is the reported mRNA ac4C an artefact of antibody cross-reactivity and sequencing-mismatch analysis? This is the single question that decides whether GO:0106162 is a real molecular function of human NAT10 or an over-annotation. PMID:32555463 and PMID:38640895 find no evidence; PMID:30449621, PMID:35679869 and PMID:38640896 defend the opposite conclusion on the same data. GOA currently records the positive side only (IDA, IBA, IEA), with no NOT annotation representing the negative result.
Suggested experts: Schraga Schwartz, Shalini Oberdoerffer, Jordan L Meier
Q: If human mRNA ac4C exists, is it deposited by NAT10 acting directly on mRNA, or is it a low-level by-product of an enzyme whose targeting machinery is built for rRNA and tRNA? NAT10's two validated substrates are each selected by a dedicated adaptor (snoRNAs for 18S rRNA, THUMPD1 for tRNA). No comparable targeting factor has been identified for mRNA, which would be expected if mRNA acetylation were a programmed activity rather than opportunistic modification at accessible motifs.
Suggested experts: Denis L J Lafontaine, Sunny Sharma, Tsutomu Suzuki
Q: Is full-length NAT10 a genuine protein-lysine acetyltransferase in cells, or are the reported histone, tubulin, TP53, MDM2 and CENATAC acetylation events indirect? Nearly all positive in vitro results used a construct (aa 164-834) that lacks the helicase/RNA-binding module required for the RNA reaction, and UniProt flags the in vivo relevance as unsure. A 2026 report that GSDMC scaffolds NAT10 onto chromatin to drive histone H3 acetylation (PMID:42176271) revives the question but does not settle it, since it is a chromatin and knockdown study rather than an enzymology one.
Suggested experts: Tsutomu Suzuki, Jianguo Chen, Denis L J Lafontaine
Q: How much of the phenotype attributed to NAT10-mediated mRNA ac4C in the disease literature is actually a consequence of impaired 40S ribosome biogenesis? NAT10 depletion and remodelin treatment both compromise ribosome production, which globally perturbs mRNA stability and translation. Studies that infer direct mRNA acetylation of a named transcript from a NAT10-knockdown phenotype plus an ac4C-RIP signal cannot separate the two routes without a catalytically dead rescue and an orthogonal, antibody-independent site measurement.
Suggested experts: Denis L J Lafontaine, Sebastian Klinge
Experiment: Quantitative LC-MS/MS of ac4C in rigorously purified, rRNA- and tRNA-depleted poly(A) RNA from wild-type and NAT10-knockout human cells, with isotope-labelled ac4C standards, reported as mol ac4C per mol cytidine. A shared, blinded sample set analysed by both the Schwartz and Oberdoerffer laboratories plus a third independent group would settle the abundance question without relying on either sequencing chemistry. The dispute is entirely about indirect readouts (antibody enrichment, chemical reduction, mismatch calling), so a direct mass measurement on the same material is the arbiter neither reanalysis can supply.
Hypothesis: If endogenous human mRNA carries physiologically meaningful ac4C, a direct mass measurement on rigorously purified poly(A) RNA will detect it above the NAT10-knockout background; if the sequencing signals are artefactual, it will not.
Type: quantitative mass spectrometry of modified nucleosides
Experiment: Site-specific validation of a handful of the most confidently called mRNA ac4C sites (for example the DUSP1 CDS sites C327/C330/C331 reported in PMID:41956987) by an antibody-free, single-site assay in unperturbed cells, together with a catalytically inactive NAT10 rescue. This converts a transcriptome-wide statistical claim into a testable single-molecule claim, and distinguishes catalysis from the indirect effects of losing the protein.
Hypothesis: Individual high-confidence mRNA ac4C sites are genuine, NAT10-catalysed modifications and will be lost upon expression of a catalytically dead NAT10.
Type: single-site RNA modification assay with catalytic-mutant rescue
Experiment: Reconstitute acetyl transfer in vitro with full-length recombinant NAT10, comparing an rRNA substrate, a tRNA/THUMPD1 substrate, a naked mRNA fragment and a recombinant protein substrate (histone H3, alpha-tubulin, CENATAC) side by side under identical acetyl-CoA and ATP conditions, and repeat with the aa 164-834 truncation. This directly tests whether the protein-lysine activity is an artefact of truncation and measures the relative efficiency of mRNA versus the validated RNA substrates on one enzyme preparation.
Hypothesis: The reported protein-lysine acetyltransferase activity is an artefact of using a truncated enzyme, and full-length NAT10 will acetylate RNA substrates but not protein substrates under identical conditions.
Type: in vitro acetyltransferase assay with matched substrates and constructs
Experiment: Separate ribosome-biogenesis effects from putative mRNA effects by comparing acute NAT10 degradation (degron) against expression of a NAT10 point mutant that retains 18S rRNA acetylation but is impaired for mRNA binding, scoring polysome profiles, Ribo-seq and mRNA half-lives. This provides the missing control in essentially all of the disease literature, where NAT10 loss simultaneously removes the 40S biogenesis function.
Hypothesis: Translational and mRNA-stability phenotypes attributed to mRNA ac4C are largely secondary to loss of 40S ribosome biogenesis.
Type: degron plus separation-of-function mutant with polysome profiling and Ribo-seq
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