EYA4 has two supported molecular roles. PMID:19606496(https://pubmed.ncbi.nlm.nih.gov/19606496/), abstract Results, reports EYA4–SIX3 co-immunoprecipitation, SIX3-dependent nuclear recruitment and cooperative reporter-gene activation. The committed UniProt O95677 CC:SUBUNIT independently curates this functional interaction with experimental evidence from that paper. These positive results support DNA-binding transcription factor binding and transcriptional coactivation. Full Methods and historical construct sequences remain unavailable: the literal GOA partner Q62233 denotes mouse Six3, and no purified human–human binary-affinity assay or isoform-resolved result is claimed. The earlier generic-binding-only interpretation overlooked the explicitly reported functional assay.
The 2024 phosphatase study, Methods for protein purification and phosphatase assays, directly measures human EYA4 residues 367–639 on PLK1-pY425, PLK1-pY445 and H2AX-pY142 peptides. The described purification uses poly-His/TVMV tagging, Ni-NTA, Fast Q and Superdex 75; the inspected Methods do not identify the expression host. This isolated domain matches current isoforms 1 and 2, without establishing equivalent activity for all full-length isoforms.
The same study's Results and Figure 2 distinguish EYA4-specific perturbation from EYA1 depletion and pan-EYA inhibition. EYA4 depletion reduces PLK1-pT210 relative to total PLK1 and reduces phosphorylation of TCTP and CDC25C, with a nonsignificant CyclinB result. The EYA4 catalytic mutant and docking mutants support coupling between EYA4 phosphatase activity and PLK1 activation. EYA4 therefore performs the dephosphorylation step in positive regulation of protein kinase activity; PLK1 performs the downstream kinase reactions. No kinase activity is assigned to EYA4. Figure 1G and the Figure 3 Results connect endogenous G2 centrosomal EYA4 with centrosomal PLK1, pericentrin accumulation and centrosome separation. The isolated pY445 PRM comparison is a nonsignificant trend; predicted PLK1 conformational changes remain a model. Selected main text and captions were read, without new experimental-image or supplementary-data inspection.
The process comparator check was mixed. Complete human CDC25A/B/C GOA captures had 62/70/66 records, emphasizing mitotic transitions rather than GO:0045860 or its descendants. PTPRA and PTPN11 also lacked that specific queried process, whereas PTPRC had a GO:0045860 NAS annotation. These records do not establish a universal phosphatase convention or an overlooked EYA4 annotation. The process assessment rests on EYA4's actual catalytic step and the orthogonal human PLK1-activity readouts. The proposed NEW process uses GO:0071902, positive regulation of protein serine/threonine kinase activity, to represent the known PLK1 kinase class more precisely than its parent GO:0045860. The initiation-specific GO:0032147 is not asserted. No O95677 entry was found in the committed GO-CAM index. Comparator absence alone is not used to claim a missed annotation.
HPA EYA4 independently supports nucleoplasm with approved HPA004805 immunofluorescence in HeLa, Rh30 and U2OS. The complete 89-residue antigen matches isoform 5, while the other isoforms share 62/63-residue segments; staining is not isoform-resolved. Broad nucleus annotations can refine to nucleoplasm. The cytoplasm rows remain non-core because the diffuse distribution associated with SIX3-dependent shuttling is not reducible to the G2 centrosomal pool. The separately measured centrosomal pool now also has its own NEW annotation, supported by the human-cell experiment rather than by narrowing a broader distribution assertion.
PAINT PTHR10190 retains the verified 639-residue human EYA4 leaf PTN002468882. Positive IBDs at PTN000022641 support phosphatase, nuclear, differentiation and DNA-repair-regulatory roles; PTN002565156 supports embryonic morphogenesis and inner-ear development. No target-path NOT was found. Changed donor lists between imported GOA and current PAINT remain version differences, not reasons to reject the ancestral placement. The H2AX-pY142 peptide assay corroborates the repair inference, but the Eya1/3 cellular study and UniProt's EYA1-derived CC:FUNCTION statement are not direct EYA4 cellular repair experiments.
Developmental sources retain their distinct scopes. Mouse Eya4 deletion, Results, gives birth-stage palate maturation delay and later middle-ear/eustachian-tube abnormalities. Zebrafish eya4 perturbation, Methods and Results, uses two splice-blocking morpholinos, mismatch controls, otic/canal/hair-cell endpoints and downstream atp1b2b rescue. The publisher-provided original preview was read through ResearchGate. These data support conserved developmental participation without direct EYA4 DNA binding. Embryonic morphogenesis is an is_a descendant of anatomical structure morphogenesis; inner ear development is not, so only the former replaces the broad TAS term. The rat IEP experiment in PMID:11159937(https://pubmed.ncbi.nlm.nih.gov/11159937/) remains unread beyond metadata and abstract.
PMID:9887327(https://pubmed.ncbi.nlm.nih.gov/9887327/) remains abstract-only. Predominantly craniofacial/dermamyotome/limb expression does not exclude ocular expression, and the negative ODD screen does not test visual processing. The original TAS visual-perception support therefore remains UNDECIDED. Later developmental evidence can refine morphology without retroactively verifying that old paper. No claim that the gene name caused the annotation is established.
Five alternative-splicing isoforms are preserved exactly. UniProt predicts low isoform 3 abundance through nonsense-mediated decay; the prediction is not a measured abundance result. Tissue and disease sections support heart/skeletal-muscle enrichment, DFNA10 hearing loss and CMD1J cardiomyopathy. These facts inform the standalone description, while isoform-function uncertainty is addressed in the questions and proposed experiments.
The campaign's standing instruction adds no publication quotations. References, claim-level locators and access limits remain explicit; the quotation validator is not represented as having tested absent quotations. Current QuickGO returns the same 16 EYA4 contexts and lacks the UniProt-listed GO:2001240 record; these independent source versions are preserved without refreshing or overwriting the imported files. No provider deep-research result is fabricated or relabeled from these notes.
Three NEW rows make the already supported functions and location explicit: centrosome (IDA, PMID:38360978 Figure 1G), transcription coactivator activity (IDA, the primary reporter assay reported in PMID:19606496, corroborated by the experimentally curated target UniProt record), and positive regulation of protein serine/threonine kinase activity (IMP, PMID:38360978 Figure 2, catalytic-mutant comparisons and the independent Figure 4C chemistry). The coactivation proposal does not pretend that unavailable historical Methods or construct sequences have been verified. No new publication quotation is added. All sixteen imported source objects and their decisions remain preserved; only two cytoplasm explanations are revised to rest directly on distribution biology.
The kinase process passes the participation test because EYA4 supplies the catalytic dephosphorylation step. The proposed GO:0071902 is a more specific descendant of the review's previous GO:0045860; only the specific term is proposed, and the core uses the same identifier. No other proposed or imported term is its ancestor or descendant. The comparator evidence is mixed: three CDC25 phosphatases lack this branch, whereas the inspected PTPRC record carries GO:0045860 (NAS, PMID:15275963). This does not establish a systematic convention excluding phosphatases, and it is not the evidence for the EYA4 claim.
Current official records mark GO:0071902 and GO:0045860 as obsoletion candidates, not obsolete terms. This prospective ontology status is retained as a question about future representation; it is not misreported as current invalidity or ignored. The demonstrated mechanism and the explicit limits on the pY445 measurement remain the biological basis of the proposal.
The cytoplasm decisions do not depend on an ontology-closure argument. A fresh typed QuickGO ancestry query on 2026-10-25 still returned no GO:0005737 in the centrosome closure. That is the bounded current-service result, not a claim about all historical GO releases. The imported distribution evidence independently supports the retained non-core cytoplasm decisions.
The coactivator proposal uses IDA because PMID:19606496 reports the authors' own transcriptional reporter experiment. Under the GO evidence guide, evidence class describes the experiment supporting the annotation; availability of the original Methods does not convert direct experimental evidence into TAS. The abstract and target UniProt record support this bounded assignment. The original Methods and historical construct sequences remain unavailable, the recorded partner Q62233 is mouse Six3, and equivalent activity of all five human EYA4 products remains unestablished. No additional RNA polymerase II process is proposed by extrapolating the EYA1 review: the available EYA4 abstract does not resolve the assay details needed for that extension.
GO:0071902 is retained because it is currently non-obsolete and describes the demonstrated EYA4 catalytic contribution to increased PLK1 activity. The candidate-for-obsoletion flag remains explicit; it does not supply a replacement term or invalidate the measured mechanism. The existing question preserves this future representation issue without adding a redundant parent or an initiation-specific claim.
The literal-comma and percent-encoded-comma forms of the typed centrosome ancestry request were both tested on 2026-10-25. Both returned HTTP 200 with identical eleven-ancestor results, neither containing GO:0005737. Encoding therefore did not explain this particular service result. This observation remains bounded to the captured current responses, and the cytoplasm decisions continue to rest independently on the distribution evidence.