Yeast DNA repair and chromatin

Reviewing GO annotations for 26 S. cerevisiae repair and chromatin genes

AI Gene Review · projects/YEAST_DNA_REPAIR_CHROMATIN · in progress

Bottom line

  • The plan covers 26 genes: checkpoint signalling, homologous recombination, FACT and remodelers, mismatch repair, translesion synthesis and dNTP supply.
  • 4 of 26 reviewed, all on the chromatin side: SPT16, POB3, CHD1, SWI1 (203 rows, including 1 proposed NEW term).
  • Current action split: 124 ACCEPT, 24 KEEP_AS_NON_CORE, 50 REMOVE, 2 MODIFY, 1 MARK_AS_OVER_ANNOTATED, 1 UNDECIDED, 1 NEW.

The biology in one picture

Why this set

  • Repair proteins act on chromatin, not naked DNA, so the interesting annotations sit where repair and nucleosome handling meet.
  • FACT (SPT16–POB3) and the remodelers CHD1 and SWI/SNF carry both transcription and repair annotations; the review has to decide which are core.
  • The recombination genes (MRX, RAD51, RAD52, RAD54) are some of the best-characterised proteins in yeast, a strong test for over-annotation.

What the four reviews decided

Example rows

  • REMOVE CHD1 GO:0005739 mitochondrion (two HDA rows): CHD1 is a nuclear remodeler.
  • UNDECIDED CHD1 GO:0140002 histone H3K4me3 reader activity: conflicting yeast literature.
  • REMOVE POB3 GO:0003677 DNA binding (IEA from the SSRP1/POB3 InterPro domain).
  • NEW SWI1 GO:0031491 nucleosome binding, from cryo-EM structures of SWI/SNF on a nucleosome.

What a review looks like

CHD1 review page: nucleus accepted; the IBA histone binding row kept as non-core, since CHD1 engages nucleosomes mainly through DNA.

Status and next steps

  • ✅ Reviewed: genes/yeast/{SPT16,POB3,CHD1,SWI1}/
  • ⬜ 22 genes with no folder: MRX + SAE2, RAD51/52/54/55/57, RAD9, CHK1, DUN1, MSH2/MSH6/MLH1/PMS1, RAD3, REV3, RNR1-4.
  • Checklist is deduplicated; checkpoint and repair labels now reflect yeast RAD9, CHK1, RAD3 and REV3 biology.

Read more: projects/YEAST_DNA_REPAIR_CHROMATIN.md