cec-10 (ZK973.2, Q9N4L7) curation notes

Status of literature

Automated deep research (falcon) failed in this environment (authentication), so no
-deep-research-*.md file exists. These notes are a manual literature search via PubMed.
PubMed search for "cec-10" OR ZK973.2 returned no hits (2026-10-19). No publication
characterises cec-10 directly. The UniProt entry is unreviewed (TrEMBL) and the only
reference it cites is the genome paper PMID:9851916.
Expression: Bgee summary in UniProt
["Expressed in germ line (C elegans) and 4 other cell types or tissues."].

N-terminal chromodomain, residues 49-110 [UniProt Q9N4L7 "FT DOMAIN 49..110"; PROSITE PS50013, SMART SM00298].
One ankyrin repeat, 520-552 (PROSITE PS50088), in an ankyrin superfamily region 451-589.
Long disordered regions (1-47, 116-135, 141-381, 814-865).
No KilA-N / APSES DNA-binding domain (see cec-10-bioinformatics/RESULTS.md).
PANTHER PTHR43828 ("ASPARAGINASE" in the PANTHER OBO; InterPro calls it "Cell Cycle
Transcription Regulator" / IPR051642 "SWI6-like"), subfamily SF3, named
"CHROMO DOMAIN-CONTAINING PROTEIN". Per the InterPro entries list in
interpro/panther/PTHR43828/PTHR43828-entries.csv, SF3 also contains budding yeast Swi6
(P09959) and fission yeast Cdc10 (P01129), the non-DNA-binding subunits of SBF/MBF.

PTN000917496 is a PANTHER ancestral node in PTHR43828, seeded by fission-yeast MBF
subunits (Res2 SPAC22F3.09c, Cdc10 SPBC336.12c, Res1 SPBC725.16) and budding-yeast
Swi4 (S000000913), Mbp1 (S000002214) and Swi6 (S000004172), plus Candida and Aspergillus
members. cec-10 descends from it because the PTHR43828 HMM matches across residues
17-793, probably through the ankyrin region and what lies around it.
Pairwise alignment to the six yeast seeds is weak: Z 1.9-5.5 against shuffles, 23-32%
identity, mostly over low-complexity stretches. The DNA-binding seeds' KilA-N/APSES
domain has no counterpart in cec-10
[file:worm/cec-10/cec-10-bioinformatics/RESULTS.md].
SBF/MBF DNA-binding subunits are fungal-specific, derived from a viral KilA-N protein
PMID:27162172;
animals use E2F PMID:27162172.
Conclusion: the PAINT IBD is placed at a node deep enough to take in a sporadic
metazoan ankyrin/chromodomain lineage. That lineage cannot form an MBF complex, since
animals have no MBF DNA-binding subunit. In IBA_REVIEW terms this is PROPAGATION_BAD with
LINEAGE_OR_TAXON_MISMATCH (node too deep). Wei et al. 2020
PMID:32470107 flagged GO:0030907 and GO:0033309 for this protein. The flag holds.
The InterPro API lists 48 metazoan PTHR43828 proteins (cnidarians, molluscs, an
annelid, a priapulid, insects); cec-10 is the only Caenorhabditis member. A few
coral/octopus entries are named "MBP1"/"SWI4-like" and may carry KilA-N domains
(not checked). That would be a separate question.

CEC-4 is a C. elegans chromodomain protein that binds methylated H3K9 and anchors
heterochromatin at the nuclear periphery PMID:26607792. No such data exist for CEC-10. Shared
"CEC" nomenclature reflects the chromodomain only. It does not show that CEC-10 binds
H3K9me.

All MBF/SBF-derived IBA rows (MBF complex, contributes_to RNAPII cis-regulatory DNA
binding, DNA-binding activator activity, positive regulation of RNAPII transcription,
G1/S transition) are removed.
Cytoplasm IBA (donor: budding-yeast Swi6, which shuttles) marked as over-annotated.
Nucleus (ARBA IEA) accepted as plausible for a chromodomain protein, without evidence
of any specific function.
No core function can be stated honestly. The knowledge gaps are recorded in the review.