changes to ncRNA gene silencing terms

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From https://pubmed.ncbi.nlm.nih.gov/33419460/

change silencing by RNA-directed DNA methylation -> gene silencing by siRNA-directed DNA methylation change retrotransposon silencing by RNA-directed DNA methylation -> retrotransposon silencing by siRNA-directed DNA methylation

and make new terms:

gene silencing by piRNA-directed DNA methylation (is_a GO:0140966) 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. Ref:PMID:32674113, PMID:38359823

synonym:piRNA-directed de novo DNA methylation

retrotransposon silencing by piRNA-directed DNA methylation (is_a GO:0141006) 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.

Ref:PMID:32674113, PMID:38359823

synonym: piRNA-directed de novo retrotransposonDNA methylation

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lncRNA activities: HOTAIR forms a triple-helix formating activity with DNA, how should this be described: base-pairing triple-helix forming activity ref: Detection of RNA–DNA binding sites in long noncoding RNAs PMID: 30698727

OR Term to describe: an RNA which binds a chromosomal DNA position to recruit proteins: chromatin DNA-protein adaptor activity? protein-base-pairing dsDNA adaptor activity?

The formation of a DNA:DNA:RNA triplex is a mechanism of interaction that is common to many chromatin-bound lncRNAs, such as Meg3, PARTICLE, HOTAIR, and KHPS1

PMID: 35412350 another example of a triple helix "The formation of a DNA:DNA:RNA triplex is a mechanism of interaction that is common to many chromatin-bound lncRNAs, such as Meg3, PARTICLE, HOTAIR, and KHPS1"

Should it be dsDNA-binding-chromatin adaptor activity?

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+[Term] +id: GO:0160164 +name: negative regulation of chromatin loopin +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of chromatin looping." [PMID:34856126] +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0140588 ! chromatin looping

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Good review on TE silencing:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9998948/

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+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

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