clr4 (Cryptic loci regulator 4 / Kmt1) — S. pombe — Curation Notes

UniProt: O60016 (CLR4_SCHPO). PomBase SPBC428.08c. 490 aa. Synonym kmt1.
EC 2.1.1.355 (H3K9 trimethyl), 2.1.1.366 (H3K9me2), 2.1.1.367 (H3K9 monomethyl), plus protein-lysine activities.

Core identity

Clr4 is the SOLE histone H3 lysine 9 (H3K9) methyltransferase of fission yeast and the catalytic
subunit of the CLRC (Clr4 methyltransferase complex). It is the homolog of metazoan SUV39H1/2 and
Drosophila Su(var)3-9. Domain architecture: N-terminal chromodomain (8–69), disordered linker,
pre-SET (258–325), SET (328–452), post-SET (473–489).

• PMID:11283354
• PMID:10949293
• PMID:24449894
• PMID:34524082

Catalytic activity / methylation states

Catalyzes H3K9 mono-, di-, and trimethylation. Also methylates non-histone substrates (Mlo3 and
others) — "protein-lysine N-methyltransferase activity".
- PMID:28143796
- PMID:28143796

Reader/writer (chromodomain)

The chromodomain reads H3K9me; together with the SET writer it gives a read-write feedback that
spreads/maintains heterochromatin.
- PMID:18345014
- PMID:31165882

CLRC complex (E3 ligase / methyltransferase)

Clr4 + Rik1 + Cul4(Pcu4) + Raf1/Dos1 + Raf2/Dos2 + Rbx1/Pip1; resembles a CRL4 cullin-RING ligase.
Preferred ub substrate is H3K14 (H3K14ub), which stimulates Clr4 H3K9 methylation.
- PMID:16127433
- PMID:16024659
- PMID:31468675
- PMID:34524082
- PMID:34010645

Autoregulation (automethylation)

An internal autoregulatory loop autoinhibits the SET pocket; automethylation of Lys455 switches it on.
- PMID:30051891
- IDR also regulates activity: PMID:40923761

Biological processes (silencing / heterochromatin)

H3K9me recruits Swi6/HP1 -> silencing at centromeres, telomeres, mating-type locus, rDNA.
- Mating-type silencing: PMID:8001791
- Pericentric/silencing via RNAi self-enforcing loop: PMID:15615848
- Co-transcriptional gene silencing / RNA turnover: PMID:17512405 (Clr4 IMP for GO:0033562)
- Facultative heterochromatin islands at meiotic genes: PMID:22144463
- Subtelomeric: [PMID:24240238 deletion of shelterin restores pericentric heterochromatin in RNAi mutants — Clr4 IMP for subtelomeric formation] ; PMID:32269268
- siRNA processing/antisense suppression via Mlo3: PMID:21436456

Localization

Nucleus; active in pericentric, mating-type, subtelomeric heterochromatin. SPB localization from a
single high-throughput GFP study (16823372) — weak/likely non-core; nucleus is the functional site.
- [PMID:16823372 global GFP localization study] ; [PMID:18345014 ClrC components distributed throughout heterochromatic domains]

DNA/RNA/nucleosome binding

PMID:22727667 is actually about the Chp1 chromodomain, not Clr4 — the dsDNA/ssDNA/ssRNA binding IDA
annotations attributed to clr4 from this paper look mis-attributed/over-annotated (paper title and
abstract concern Chp1). Treat with caution. Nucleosome binding (31165882) is genuine and core-relevant.
ssRNA binding ARBA IEA is generic.

Stc1 interaction (GO:0005515 IPI, PMID:20211136)

Stc1 links RNAi (Ago1) to CLRC; bridges RITS to Clr4 complex. Adapter/recruitment interaction.
- PMID:20211136

Summary of action plan

• Core MF: histone H3K9 methyltransferase (mono/di/tri) — ACCEPT specific terms; generalize generic
  "methyltransferase activity" and "histone methyltransferase activity".
• Core MF: H3K9me reader / chromodomain (GO:0062072) — ACCEPT.
• Core BP: heterochromatin formation at pericentric, subtelomeric, mating-type; RNAi-related — ACCEPT/KEEP.
• protein binding (GO:0005515) bare terms — replace/mark; capture as complex membership / adapter.
• DNA binding IEA, ssRNA IEA, zinc IEA — keep_as_non_core / accept low-value structural.
• SPB localization — KEEP_AS_NON_CORE (single HTP study).
• 22727667 DNA/RNA binding IDA — likely mis-attributed (paper is about Chp1) -> MARK_AS_OVER_ANNOTATED / UNDECIDED.