Closed hattrill closed 6 months ago
hattrill
commented
6 months ago examples for proteins to annotate: Spocd1(Mus musculus)SPOC domain-containing protein 1 (UniProtKB:B1ASB6) Dnmt3a(Mus musculus)DNA (cytosine-5)-methyltransferase 3A (UniProtKB:P0DOY1)
pgaudet
commented
6 months ago +[Term] +id: GO:0141176 +name: gene silencing by piRNA-directed DNA methylation +namespace: biological_process +def: "A small RNA-based gene silencing process in which Piwi-associated RNAs (piRNAs) guide de novo DNA methylation. This results in a heterochromatin assembly, a chromatin conformation that is refractory to transcription." [PMID:32674113, PMID:38359823] +is_a: GO:0140966 ! piRNA-mediated heterochromatin formation +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27238" xsd:anyURI +created_by: pg +creation_date: 2024-03-11T13:47:09Z +
The current definition for silencing by RNA-directed DNA methylation GO:0080188 is for an siRNA-guided process: "A small RNA-based gene silencing process in which small interfering RNAs (siRNAs) guide DNA methylation to the siRNA-generating genomic loci and other loci that are homologous to the siRNAs for de novo DNA methylation....."
piRNAs can also mediate DNA methylation https://pubmed.ncbi.nlm.nih.gov/33419460/ but with different factors.
So, think we need separate terms for piRNA-mediated process and update the existing terms to make them explict for siRNA-guided processes
1.
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Suggested new term label: gene silencing by piRNA-directed DNA methylation
Definition (free text) A small RNA-based gene silencing process in which Piwi-associated RNAs (piRNAs) guide de novo DNA methylation. This results in a heterochromatin assembly, a chromatin conformation that is refractory to transcription.
Reference, in format PMID:####### PMID:32674113, PMID:38359823
Parent term(s)
is_a GO:0140966 piRNA-mediated heterochromatin formation
Synonyms (please specify, EXACT, BROAD, NARROW or RELATED) EXACT piRNA-directed de novo DNA methylation
3.
Suggested new term label: retrotransposon silencing by piRNA-directed DNA methylation
Definition (free text) A retrotransposon silencing process in which Piwi-associated RNAs (piRNAs) guide de novo DNA methylation. This results in a heterochromatin assembly, a chromatin conformation that is refractory to transcription.
Reference, in format PMID:####### PMID:32674113, PMID:38359823
Parent term(s)
is_a GO:0141006 piRNA-mediated retrotransposon silencing by heterochromatin formation
is_a gene silencing by piRNA-directed DNA methylation (new)
Synonyms (please specify, EXACT, BROAD, NARROW or RELATED) EXACT piRNA-directed de novo retrotransposon DNA methylation