C. elegans P granules

Reviewing GO annotations for 19 genes of a germline RNA-protein condensate

AI Gene Review · projects/CAEEL_P_GRANULES · 2026

Bottom line

  • P granules are liquid-like germline condensates built on PGL and MEG scaffolds and GLH helicases, loaded with Piwi/Argonaute small-RNA machinery.
  • We reviewed every GO annotation on 19 genes: 393 rows, 274 ACCEPT, 20 MODIFY, 14 REMOVE, 39 NEW.
  • Existing annotation is sparse, so the review mostly adds: condensate scaffold activity, P granule assembly, Z granule. Removals target propagated nuclear and catalytic rows.

Why P granules

  • Among the first cellular condensates shown to behave as liquids (Brangwynne et al. 2009).
  • Essential for fertility and for transgenerational small-RNA silencing.
  • Most components are worm-specific, so there is little to propagate from other species.
  • Test: can GO describe phase-separation scaffolds and condensate membership without falling back on protein binding?

Where the 19 genes act

Actions per gene

What was added

Term Genes (NEW)
GO:0140693 molecular condensate scaffold activity meg-3, meg-4 (IDA), meg-2 (IGI), deps-1 (NAS), pgl-2 (IC)
GO:1903863 P granule assembly glh-1, glh-4, deps-1 (IMP); meg-1, meg-2 (IGI); pgl-3 (IDA)
GO:0060293 germ plasm meg-3, meg-4 (IDA)
GO:0120279 Z granule; GO:0043186 P granule znfx-1 (IDA)
GO:0010526 transposable element silencing wago-1, mut-16 (IMP)

What was removed

Gene Term Evidence Why
wago-1 RNA endonuclease activity IBA WAGO Argonautes lack the catalytic tetrad
znfx-1 nucleus; chromosome; nuclear RdRP complex IEA/IBA Z granule is cytoplasmic, perinuclear
glh-1 nucleus IBA perinuclear granule, not nuclear
glh-4 maturation of SSU-rRNA IBA propagated from DEAD-box relatives
car-1 spliceosomal complex; RNA splicing IEA atypical Sm domain; acts in mRNA regulation

Reasons paraphrased from review.reason in genes/worm/<gene>/<gene>-ai-review.yaml.

Status and next steps

  • ✅ 19/19 gene reviews complete.
  • ✅ csr-1 re-fetched under its correct accession (H2KZD5) in 2026; the page's older "wrong gene" note is out of date.
  • ⬜ Fold in reviews that exist outside the project: glh-2, mex-6, rde-2, wago-4.
  • ⬜ Not yet reviewed: prg-2, npp-10, par-1, pab-1.

Read more: projects/CAEEL_P_GRANULES.md · genes/worm/<gene>/