ESA1 curation notes

Update 2026-09-02

Batch audit of the existing ESA1-ai-review.yaml. The review is otherwise thorough
(63 GOA lines all reviewed, sound REMOVE/KEEP_AS_NON_CORE calls), but one citation in
core_functions[0].supported_by was wrong:

• The entry cited PMID:11742990 ("The Saccharomyces cerevisiae Set1 complex includes
  an Ash2 homologue and methylates histone 3 lysine 4", Roguev et al. 2001 EMBO J) with
  supporting_text equal to that paper's own title, offered as support for ESA1's core
  histone-acetyltransferase molecular function (GO:0004402) plus its involvement in
  transcription regulation (GO:0006357) and DNA repair (GO:0006281).
• publications/PMID_11742990.md (cached abstract) is about the Set1/COMPASS
  H3K4-methyltransferase complex and does not mention ESA1/Esa1 anywhere
  PMID:11742990 — an unrelated methyltransferase complex, not the
  NuA4/Esa1 acetyltransferase this review is about. This is a genuine miscitation (right
  format, wrong paper), not merely a weak citation.
• Fixed by replacing it with PMID:9520405 ("ESA1 is a histone acetyltransferase that
  is essential for growth in yeast", Smith et al. 1998 PNAS), which is already used
  elsewhere in this review's existing_annotations (GO:0004402 IMP evidence line) and
  directly supports the claim: PMID:9520405.
• No other content, actions, or GO terms were changed. PMID:31699900 (crotonylation)
  remains as the second supported_by entry, unchanged.

Everything else reviewed (all existing_annotations, the description, and the rest of
core_functions) was judged sound and evidence-backed; no further changes made in this
pass. Note: this gene directory also carries several non-standard files
(ESA1-CURATION-ANALYSIS.md, ESA1-CURATION-SUMMARY.md, ESA1-ai-review-CURATED.yaml,
ESA1-ANNOTATION-TRIAGE.tsv, README-CURATION.md, FILES-INDEX.md,
ESA1-DECISIONS-OVERVIEW.txt, ESA1-CURATION-COMPLETE.md) left over from an earlier
curation pass; left untouched here since removing/consolidating them is outside the
scope of this citation fix.

2026-10-01 current-GOA / IBA review

• Refreshed ESA1 from current UniProt/GOA before editing. Current GOA has 76
  live rows after the header; the refresh expanded the YAML from 63 to 86 rows
  by adding 23 current assertions that were absent from the older review.
• Preserved 10 historical source assertions as retired: true: the old generic
  GO:0004402 IBA, four old UniProt keyword rows under GO_REF:0000043, one
  broad ARBA stress row, and three old consolidated IntAct GO:0005515 rows
  whose exact source signatures are absent from the current GOA export.
• Checked interpro/panther/PTHR10615/PTHR10615-paint.tsv. Six live IBA rows
  still trace to the broad MYST/KAT ancestor PANTHER:PTN004172926; the newly
  materialized GO:0010485 histone H4 acetyltransferase activity IBA row traces
  to the fungal Esa1/NuA4 node PANTHER:PTN000834946. Both placements match
  yeast Esa1 biology, and the ESA1 self-donors are direct experimental seeds,
  not circularity.
• Resolved the new rows conservatively. New direct GO:0004402 HAT rows, NuA4
  and Piccolo complex rows, the broad DNA-damage response row, the
  protein-lysine-acetyltransferase row, the histone H4 IBA, and the
  crotonyltransferase row were accepted. The ComplexPortal nucleosome part_of
  row was removed because NuA4/Piccolo bind nucleosome substrates but Esa1 is
  not part of a nucleosome. The fission-yeast ISS
  GO:0106226 peptide 2-hydroxyisobutyryltransferase activity row remains
  UNDECIDED pending source-side review.
• Converted all generic GO:0005515 protein binding rows to REMOVE. The
  IntAct interactions may be real, but the bare binding rows add no functional
  information beyond Esa1's NuA4/Piccolo complex membership and catalytic
  annotations.
• Searched 2024-2026 literature for exact yeast ESA1/NuA4/Tip60 updates. The
  2024 NuA4/Pah1/nuclear-shape paper (PMID:38961766) extends the existing
  lipid-metabolism/Pah1 context, and the 2025 Gcn5/Esa1/RSC-occupancy paper
  (PMID:40958614) fits the existing chromatin/transcription-regulation calls.
  The 2025 Piccolo NuA4 cryo-EM study (PMID:40100634) and the 2026
  NuA4/Sfp1/ribosome-biogenesis paper (PMID:42103225) are additional context.
  None justify new ESA1 GO rows beyond the accepted acetyltransferase,
  complex, chromatin, and Pol II transcription-regulation assertions.

2026-11-01 review response

• Corrected the UniProtKB:O94446 ISS source from fission-yeast Mst2 to
  fission-yeast Mst1. O94446 is mst1 in PTHR10615:SF218, the same ESA1
  subfamily as budding-yeast Esa1, not the mst2/KAT7 member in SF161.
• Re-read the GO:0010629 negative regulation of gene expression ARBA row
  against the retained PMID:16436512 rDNA/telomeric silencing rows. The broad
  negative-regulation parent is true enough to keep as non-core, rather than a
  false ARBA-only transfer, because Esa1 directly participates in Pol II
  silencing at telomeres and rDNA even though NuA4 is predominantly a positive
  transcriptional regulator.
• Reclassified the GO:0008270 zinc ion binding RCA row as non-core structural
  zinc coordination by the MYST zinc finger, and marked the NAS
  GO:0006351 DNA-templated transcription row as over-annotated beside the
  accepted, more specific Pol II transcription-regulation rows.
• Replaced generic HAT and crotonyltransferase snippets in the H4
  acetyltransferase core-function support with H4-specific evidence from
  PMID:17274630 and PMID:12353039.
• Followed up on the PR re-review by moving the GO:0008270 zinc ion binding
  support to the exact UniProt FT ZN_FING 195..220 feature, narrowing the
  GO:0010629 and generic GO:0004402 explanations so they match their
  actions, adding GO:0140068 histone crotonyltransferase activity to
  core_functions, and reconciling esa1-current-goa.yaml action counts.
• Restored the curated UniProt ESA1 substrate range to the description,
  generic GO:0004402 reasons, and H4 core-function prose: H4 K5/K8/K12/K16
  remain the dominant and most specific Piccolo NuA4 acetylation sites, but the
  broader HAT rows are also supported by curated H3K14, H2BK16, H2AK4/7, and
  H2A.ZK14 acetylation assertions.
• Reframed the crotonyltransferase core function as Piccolo NuA4-mediated
  contribution to GO:0140068, matching Fellows et al.'s in-vitro
  heterotrimer assay and in-vivo Esa1-N-FRB depletion result.
• Revisited two ESA1 rows that had diverged from main: the live
  ComplexPortal GO:0000786 nucleosome assertion should be MODIFY to
  GO:0031491 nucleosome binding, because the structural evidence supports
  NuA4/Piccolo binding to nucleosome substrates but not Esa1 being part of the
  nucleosome; the broad NAS GO:0006351 DNA-templated transcription row stays
  MARK_AS_OVER_ANNOTATED, because the accepted GO:0006357 Pol II
  transcription-regulation rows already capture the specific Esa1 role.