Yeast epigenetics and histone inheritance

Reviewing GO annotations for the writers, erasers, readers, chaperones and remodelers of S. cerevisiae chromatin

AI Gene Review · projects/YEAST_EPIGENETICS_HISTONE_INHERITANCE · mature

Bottom line

  • 28 genes reviewed: 1,373 existing annotations plus 11 proposed NEW rows.
  • Current action split: 828 ACCEPT, 184 KEEP_AS_NON_CORE, 305 REMOVE, 22 MODIFY, 19 MARK_AS_OVER_ANNOTATED, 15 UNDECIDED, 11 NEW.
  • 270 of the 305 removals are generic protein binding rows; CLR4, a fission yeast H3K9 methyltransferase with no budding yeast ortholog, is dropped from scope.

The biology: write a state, then copy it

Why this set

  • Yeast silent chromatin (HML/HMR, telomeres) is the best-worked example of a self-propagating chromatin state.
  • Each gene class carries a typical annotation risk: HATs and HDACs get substrate-level terms by homology; SIR proteins pick up replication terms from ORC relatives; complex subunits get complex-level functions.
  • The genes are well studied, so errors can be judged against direct experiments.

What the reviews decided

Example decisions

  • REMOVE SAS2 GO:0035267 NuA4 histone acetyltransferase complex (IBA): SAS2 is in the SAS complex, not NuA4.
  • REMOVE SIR3 GO:0006270 DNA replication initiation (IBA): SIR3 restrains origin activity; it does not start replication.
  • MARK_AS_OVER_ANNOTATED DOT1 GO:0008168 methyltransferase activity (IEA): the specific H3K79 term says more.
  • UNDECIDED 7 HST1 rows: Sir2-like inferences and experimental rows that need the full text.

What a review looks like

SAS2 review page: the description records the SAS complex and its H4K16/H3K14 substrates.

Status and next steps

  • ✅ Reviewed: 28 intended genes in genes/yeast/ (HATs, HDACs, SIR, HMTs, FACT/CAF-1/ASF1/RTT109, SWI/SNF, CHD1, RCO1, PHD1)
  • ✅ Chromatin assembly factor CAF-1: RLF2 (alias CAC1), CAC2 and MSI1 are now reviewed. The old genes/yeast/CAF1/ folder was the CCR4-NOT deadenylase, now renamed POP2 and outside this project
  • ✅ CLR4 dropped: S. cerevisiae has no H3K9 methylation or Clr4/SUV39 ortholog, so the scope stays at 28 budding yeast genes

Read more: projects/YEAST_EPIGENETICS_HISTONE_INHERITANCE.md