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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Review branch GO:0070920 regulation of production of small RNA involved in gene silencing by RNA #19303

Closed pgaudet closed 2 years ago

pgaudet commented 4 years ago

@RLovering @ValWood

ValWood commented 4 years ago

I haven't used this term.

but I'm wondering why it isn't MF part_of regulation of gene silencing by (mi)RNA -the production of the si/mi RNA are the individual well-characterised steps in the pathway (performed by argonaut dicer etc).

(@pgaudet note that this term is not part of 'chromatin silencing, the ones we were looking at)

pgaudet commented 2 years ago

(ie, current hierarchy: is_a regulation of pre-miRNA processing is_a regulation of production of miRNAs involved in gene silencing by miRNA

pgaudet commented 2 years ago

Annotations are here: https://docs.google.com/spreadsheets/d/1Pm_-HYbAC1Sp4Xewm0GvcHTUPGWgVbIxvOXNxq1Kbbg/edit#gid=0

pgaudet commented 2 years ago

The proposal is to obsolete:

'regulation of production of small RNA involved in gene silencing by RNA'

miRNA 'regulation of production of miRNAs involved in gene silencing by miRNA' 'negative regulation of production of miRNAs involved in gene silencing by miRNA' 'positive regulation of production of miRNAs involved in gene silencing by miRNA' -> miRNA are produced by transcription of DNA -> these should be annotated to 'transcription' or processing, or simply 'gene silencing by miRNA' when the data is not direct enough ,

siRNA GO:0030422 production of siRNA involved in RNA interference GO:0070919 production of siRNA involved in gene silencing by small RNA' GO:0010267 production of ta-siRNAs involved in RNA interference' -> siRNAs are produced by transcription of RNA, so we need a new term, 'siRNA transcription', child of 'GO:0001172 transcription, RNA-templated' -> some annotations could go to this new term, or to some siRNA processing, or 'gene silencing' or 'RNA interference' when the data is not direct enough

'regulation of production of siRNA involved in gene silencing by small RNA' 'regulation of production of siRNA involved in RNA interference' 'negative regulation of production of siRNA involved in RNA interference' 'positive regulation of production of siRNA involved in RNA interference' -> likewise these should be 'regulation of siRNA transcription'

pgaudet commented 2 years ago

Actions - from discussion with @colinlog

pgaudet commented 2 years ago

+[Term] +id: GO:0140745 +name: siRNA transcription +namespace: biological_process +def: "The transcription of a small interfering RNA from an RNA template." [PMID:23001036] +is_a: GO:0001172 ! transcription, RNA-templated +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/19303 xsd:anyURI +created_by: pg +creation_date: 2021-12-13T13:08:09Z + +[Term] +id: GO:0140746 +name: siRNA catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of small interfering RNA transcripts (siRNAs)." [PMID:25928405] +intersection_of: GO:0009056 ! catabolic process +intersection_of: has_primary_input SO:0000646 ! siRNA +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/19303 xsd:anyURI +created_by: pg +creation_date: 2021-12-13T13:11:22Z

pgaudet commented 2 years ago
pgaudet commented 2 years ago

'production of small RNA involved in gene silencing by RNA' -> small RNA processing 'production of lsiRNA involved in RNA interference' -> lsi RNA processing 'production of miRNAs involved in gene silencing by miRNA' -> mi RNA processing 'production of siRNA involved in gene silencing by small RNA' -> si RNA processing 'production of siRNA involved in RNA interference' merge into 'si RNA processing ' above 'production of ta-siRNAs involved in RNA interference' -> ta-siRNA processing

ValWood commented 2 years ago

I don't think the merge of 'production' into 'processing' is a generally safe assumption.

In none Metazoans, annotations to this term also include RNA-directed RNA polymerase. e.g. https://www.pombase.org/gene/SPAC6F12.09 This isn't processing, but it is production (I don't mind removing production terms, but the merge is not safe).

ValWood commented 2 years ago

+id: GO:0140745 +name: siRNA transcription

This term seems to combine different processes. In pombe siRNA is produced by "RNA-directed RNA polymerase" in which case the process is equivalent to a molecular function. This might not be the case for other species though. What do you expect to see annotated to this term?

pgaudet commented 2 years ago

GO:0140745 +name: siRNA transcription

Indeed it was for the polymerase, similar to any transcription - isn't it?

ValWood commented 2 years ago

Is it useful for modelling to describe this as 'transcription' though? (it is really part of negative regulation of gene expression). Transcription is really about "information content" and could refer strictly to transcribing 'genes'.

siRNAs are expressed as part of "siRNA dependent gene silencing" but this is just a single step. I don't see the advantage of a term to describe the expression of the siRNA as a process.

It seems that "RNA-directed RNA polymerase" part_of "siRNA-dependent facultative heterochromatin assembly" or similar would be sufficient. It is a single step in the nucleation of heterochromatin formation, and connecting in this pathway to the other components of siRNA generation (dicer, argonaut etc) we really don't need to say anything about 'transcription' explicitly.

This would make the ontology much cleaner, since then "positive regulation of transcription" would not be simultaneously be a positive and negative regulation of gene expression in different contexts.

Although as you know, I think transcription should be represented by pathways (Pol I,II and III) rather than by molecule type, which can be described by inputs using SO terms or database identifiers to describe the transcribed entities. The pathways align more closely with other processes (for example transcription by polymerase I is always causally upstream of ribosome biogenesis , transcription from pol II is always causally upstream of tRNA metabolism (although it is also upstream of other processes).

So I don't see the advantage of annotating "RNA-directed RNA polymerase" to a "transcription" bin, because it is not connected in any way to canonical transcription. In fact, adding this to the transcription 'bin' will make enrichment worse for "transcription of hereditary information".

ValWood commented 2 years ago

This parentage seems problematic for centromeric heterochromatin assembly where the siRNAs aren't always part of "gene expression". This is a more general issue though, probably only the "transcription associated" heterochromatin terms should be under transcription (i.e. GO:0045815 | epigenetic maintenance of chromatin in transcription-competent conformation AND co-transcriptional chromatin reassembly (GO:0140673)

GO:0010467 gene expression

pgaudet commented 2 years ago

Annotations are here: https://docs.google.com/spreadsheets/d/1Pm_-HYbAC1Sp4Xewm0GvcHTUPGWgVbIxvOXNxq1Kbbg/edit#gid=0

pgaudet commented 2 years ago

I opened an annotation ticket for the review of annotations, see https://github.com/geneontology/go-annotation/issues/4168

I will close this - @ValWood I think the centromeric heterochromatin is unrelated, please open a new ticket if you want changes to that term.

Thanks, Pascale