While auditing the existing review, found that both the top-level description
and the core_functions entry for GO:0010484 (histone H3 acetyltransferase
activity) already asserted that RTT109 "prevents DNA-RNA hybrid accumulation" /
contributes to "R-loop suppression" through H3K14/H3K23 acetylation, but no
reference anywhere in the file actually cited or quoted the paper establishing
this. The gene's own working file RTT109-CURATION-REVIEW.md (an untracked
scratch document in this folder) explicitly flagged this: "R-loop/DNA-RNA
hybrid prevention not explicitly annotated but supported (NEW annotation
should be added)" -- but that follow-up was never done in the actual
RTT109-ai-review.yaml.
Identified and fetched the source paper: PMID:35866610, Cañas et al. 2022,
Genetics, "A role for the Saccharomyces cerevisiae Rtt109 histone
acetyltransferase in R-loop homeostasis and associated genome instability"
PMID:35866610. Full text now cached at
publications/PMID_35866610.md via ai-gene-review fetch-pmid.
Checked whether an existing GO term could be used for a direct NEW
existing_annotations entry (as done for e.g. ROF1's filamentous-growth
annotation). Searched QuickGO for "R-loop" and "DNA-RNA hybrid": the only
R-loop process term is GO:0062176 (R-loop processing), whose definition is
explicitly R-loop disassembly -- the opposite direction from what RTT109
does (RTT109 loss increases R-loop levels; RTT109 activity prevents their
formation). No term for "negative regulation of R-loop formation" exists in
GO. Per project convention (never force a mismatched id onto a real finding),
recorded this as a proposed_new_terms entry instead, with PMID:35866610 as
support and GO:0006325 (chromatin organization, already used elsewhere in
this review) as a defensible proposed_parent.
Also added PMID:35866610 to references: with a reference_review (HIGH
relevance, VERIFIED -- PubMed/PMC-verified, full text cached) and attached
supported_by provenance to the GO:0010484 core-function block that was
making the previously-uncited claim.
No other issues found in this review during this audit pass. The bulk of the
70 existing_annotations entries (H3K56/K9/K27/K14/K23 acetyltransferase
activity, chromatin assembly, DNA damage response, etc.) are well-supported
by the cited literature and internally consistent.