RPD3 IBA Re-review Notes

PAINT / IBA rows

• GO:0004407 histone deacetylase activity: current PTHR10625 PAINT places this at PANTHER:PTN008143312, a broad class I HDAC node seeded by many experimentally annotated descendants, including budding-yeast RPD3 itself (SGD:S000005274) and HOS2 (SGD:S000003162). Retained as ACCEPT and NO_FAILURE_CORE.
• GO:0031507 heterochromatin formation: current PAINT places this at PANTHER:PTN000743059 from fly Rpd3 and human HDAC1/HDAC2. The transfer crosses a regulatory-sign boundary in budding yeast: Rpd3 is not Sir2 and does not nucleate silent chromatin; Sun and Hampsey showed that "deletion of the SIN3 and RPD3 genes enhances silencing, implying that the Sin3-Rpd3 complex functions to counteract, rather than to establish or maintain, silencing" PMID:10388812, and Zhou et al. showed Rpd3 directly deacetylates H4K5/H4K12 at boundary regions and characterized "the anti-silencing functions of Rpd3p during the formation of heterochromatin boundaries" PMID:19372273. I changed the row to MODIFY with GO:0033696 heterochromatin boundary formation and PROPAGATION_BAD / REGULATORY_SIGN_INVERSION.
• GO:0070210 Rpd3L-Expanded complex: current PTHR10625 PAINT places this at PANTHER:PTN000835673, a fungal node seeded by PomBase SPBC36.05c. This is consistent with Rpd3 as the conserved catalytic subunit of Rpd3L/Sin3-type HDAC complexes and remains ACCEPT / NO_FAILURE_CORE.

2025-2026 literature search

PubMed and web searches on 2026-09-28 for Rpd3, Rpd3L, RPD3, Saccharomyces, and yeast found nine 2025-2026 PubMed records. I cached the four direct budding-yeast primary papers and ignored the plant RPD3-type HDAC reviews, a Histoplasma Rpd3 paper, and the bioRxiv preprint that was superseded by the 2026 Cell Reports paper.

• Dai et al. 2025 found that sucrose-activated Tpk2 "phosphorylates Rpd3L catalytic subunit Rpd3 to inhibit its ability to deacetylate Ada3" and phosphorylates Ash1 to reduce the Rpd3L-SAGA interaction PMID:40301306.
• Serrano-Quilez et al. 2025 identified "a functional and physical interaction between Mip6 and the histone deacetylase Rpd3" in heat-shock transcriptional memory PMID:40537058.
• Chong et al. 2026 showed that "the Rpd3L histone deacetylase complex dynamically modulates chromatin state to control replication fork progression and buffer TRCs in Saccharomyces cerevisiae" PMID:42268949.
• Bhattacharya et al. 2026 showed that Rpd3 "mediates nutrient-dependent chromatin reprogramming that coordinates transcriptional shutdown and global acetylation balance during metabolic transitions" PMID:42418323.
• A 2026-10-01 PubMed/web update found Zhao et al. 2026, which solved Rpd3L structures on mono- and di-nucleosome substrates and showed that "dual nucleosome engagement selectively enhances Rpd3L activity and broadens substrate specificity" PMID:42152683.

Current GOA refresh on 2026-10-01

• Forced the RPD3 UniProt/GOA refresh and accepted all seven newly seeded rows: an SGD IMP row for GO:0000727 break-induced replication from a 2025 genome-wide BIR screen; InterPro GO:0004407; GO:0032221 Rpd3S complex from the Rpd3/Sin3 small-complex proteomics reanalysis; GO:0033698 Rpd3L complex from the 2023 Rpd3L cryo-EM structure; the broad ARBA GO:0051052 regulation of DNA metabolic process row; GO:0070211 Snt2C complex; and the direct GO:0141221 histone deacetylase activity, hydrolytic mechanism row from the Rpd3 ER-motif mutagenesis paper.
• Marked 56 old rows as retired: true because their exact source assertions are absent from current GOA. These are five stale automatic parent rows, nine old unqualified duplicate transcription-regulation rows from PMID:20398213/PMID:24358376, and 42 stale generic protein-binding rows from older proteomics snapshots.
• Left the three current IBA rows unchanged biologically: GO:0004407 and GO:0070210 remain sound NO_FAILURE_CORE transfers from PTN008143312 and PTN000835673, while the PTN000743059 GO:0031507 heterochromatin formation row remains a MODIFY to heterochromatin boundary formation because the PAINT node crosses a regulatory-sign boundary in budding yeast.

PR #3787 follow-up

• Rewrote the GO:0000727 break-induced replication IMP row to cite the
  cached RPD3/Rpd3L-specific BIR prose from PMID:41398407 and changed its
  action to KEEP_AS_NON_CORE.
• Changed the broad ARBA GO:0051052 regulation of DNA metabolic process row
  to KEEP_AS_NON_CORE and trimmed its evidence back to the TRC/replication-fork
  Rpd3L paper.
• Normalized the RPD3 gene and IBA_REVIEW history actors from claude-code to
  codex to match the agent and commit provenance.
• Corrected rpd3-current-goa.yaml after those two action flips: final action
  totals are now ACCEPT 95 and KEEP_AS_NON_CORE 7, and both changed rows record
  after: KEEP_AS_NON_CORE.