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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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OBSOLETE: [cap-dependent translational initiation] #22348

Open ValWood opened 2 years ago

ValWood commented 2 years ago

has 5 annotations. 2 are NOTS?

Isn't this just normal translation initiation?

ValWood commented 2 years ago

Actually maybe there are more annotations. PomBAse has an annotation to this term https://www.pombase.org/term/GO:0002191 but it isn't visible in AmiGO.....

ValWood commented 2 years ago

There are 32 evidence used in manual assertion in GOA so there appears to be an issue with the AmiGO loading?

https://www.ebi.ac.uk/QuickGO/annotations?goUsage=descendants&goUsageRelationships=is_a,part_of,occurs_in&goId=GO:0002191&evidenceCode=ECO:0000352&evidenceCodeUsage=descendants

@pgaudet @kltm @suzialeksander

ValWood commented 1 year ago

@pgaudet do you agree? merge or obsoletion?

pgaudet commented 1 year ago

Obsolete with replaced by - this is now our procedure.

We also need to obsolete the regulation children

I think we should also obsolete the other grouping terms of the 'cap-independent' sibling:

Thanks, Pascale

ValWood commented 1 year ago

I'm not sure if we want to obsolete all of these but there is definitely a problem.

Screenshot 2023-03-09 at 17 04 57

  1. The GO:0110019 IRES-dependent translational initiation of circular RNA seems to be a viral process, so it isn't "cytoplasmic translation"

  2. The CAP-independent translation does exist, but it seems to be part of the translational stress response making different translational start sites. So it's some sort of regulation of translation in response to stress.

  3. We don't need cap-dependent terms, that's normal translation, but maybe we should keep the GO:0002192 biological_process IRES-dependent translational initiation but as a translational response to stress?

ValWood commented 1 year ago

QuickGO basket: GO:0110019 biological_process IRES-dependent translational initiation of circular RNA GO:0110017 biological_process cap-independent translational initiation of linear mRNA GO:0110018 biological_process cap-independent translational initiation of circular RNA GO:0075522 biological_process IRES-dependent viral translational initiation GO:0002190 biological_process cap-independent translational initiation GO:0002191 biological_process cap-dependent translational initiation GO:0002192 biological_process IRES-dependent translational initiation of linear mRNA GO:1903674 biological_process regulation of cap-dependent translational initiation GO:1903675 biological_process negative regulation of cap-dependent translational initiation GO:1903678 biological_process negative regulation of cap-independent translational initiation GO:1903679 biological_process positive regulation of cap-independent translational initiation GO:1903676 biological_process positive regulation of cap-dependent translational initiation GO:1903677 biological_process regulation of cap-independent translational initiation

ValWood commented 1 year ago

GO:0110019 IRES-dependent translational initiation of circular RNA (0 annotations, misplaced, obsolete) GO:0110018 cap-independent translational initiation of circular RNA (0 annotations, misplaced, obsolete)

GO:0075522 IRES-dependent viral translational initiation (17 EXP annotation 14 human, 2 drosophila, 2 viral should this term move under viral process and challenge the other annotations should they move to GO:0002192 ?)

GO:1903674 regulation of cap-dependent translational initiation (0 direct) GO:1903676 positive regulation of cap-dependent translational initiation (1 annotation from NCK1 from PMID:11959995, I'm not sure this is physiologically relevant)

GO:0002192 IRES-dependent translational initiation of linear mRNA (3EXP a human, 1 mouse, 1 drosophila) GO:0110017 cap-independent translational initiation of linear mRNA (has no direct annotations, parent of GO:0002192) These 2 could merge?

GO:0002190 cap-independent translational initiation (1 annotation [human RBM4] GO:1903678 negative regulation of cap-independent translational initiation (0 annotations) GO:1903679 positive regulation of cap-independent translational initiation (3 EXP human METTL3 , NCK1, YTHDF2) GO:1903677 regulation of cap-independent translational initiation (0 direct)

CAP DEPENDENT TERMS (this is canonical translation) GO:0002191 cap-dependent translational initiation (6 annotations , 2 NOTs (Flybase, 3 complex portal, 2 uniProt) GO:1903675 negative regulation of cap-dependent translational initiation (0 annotations , obsolete)

ValWood commented 1 year ago

Also IRIS does not see to be "cap-independent".....

PMID: 34873729 As an alternative mechanism for cap-dependent (m7GpppN) translation, internal ribosome entry site (IRES)-dependent translation has been observed in the 5' untranslated regions (5' UTR)

(added later, I now think this means 'alternative method to .....')

ValWood commented 1 year ago

Here is an example where and IRS results in a translated form which does not localize to the nucleus (normal location) https://pubmed.ncbi.nlm.nih.gov/31397627/ It isn't clear is the cytosolic version is functionally relevant. But in this case it seem that the Internal Ribosome entry site IRS is a mechanism of translational regulation (alternative translation via IRES) , but is isn't a different type of initiation. I don't know how we model this. ....

pgaudet commented 1 year ago

GO:0110019 IRES-dependent translational initiation of circular RNA seems to be a viral process,

Is it? Paper cited mention CircRNAs, which are eukaryotic, see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5387669/

Circular RNAs (circRNAs) in animals are a large class of particularly stable RNAs produced by circularization of specific exons

ValWood commented 1 year ago

I looked last night and found a few papers, but I couldn't find a single one which demonstrated that these circularized translation products are functional if translated. I also found a reviews bot none really appear to say these are functional and question the reliability of the assays https://pubmed.ncbi.nlm.nih.gov/27853833/ https://pubmed.ncbi.nlm.nih.gov/20576611/ and others

I think we should probably get rid of the cap-dependant/independant axis of classification, and collapse down the IRES-dependent to the minimum number of terms as a "translational stress response"

ValWood commented 1 year ago

I also asked my boss for input, translation is his area of expertise.