Review: GO:0036260 RNA capping and descendants

[ValWood]

Please provide as much information as you can:

• GO term ID and Label

GO:0036260 RNA capping and descendants

• Reason for deprecation Put an x in the appropriate box:

  • [ ] The reason for obsoletion is that this term represents a molecular function.

• "Replace by" term (ID and label)

If all annotations can safely be moved to that term

move to GO:0006396 RNA processing

• "Consider" term(s) (ID and label) Suggestions for reannotation (also check that appropriate MF term is annotated)

• Are there annotations to this term?

• How many EXP:

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)

• Is this term in a subset? (check the AmiGO page for that term)

• Any other information

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Checklist for ontology editor

Check term usage and metadata in Protégé

• [ ] check term usage in the ontology
• [ ] check internal mappings: RHEA, EC, MetaCyc
• [ ] check subset usage
• [ ] check taxon constraints

Check annotations

• [ ] create Annotation Review spreadsheet
• • Annotation Review template: https://docs.google.com/spreadsheets/d/1izV3q1jnq_Ybg5MJ53O_b5BCTkGtjl_Fi-cOg3-7eBE/edit#gid=0
• • Instructions: https://wiki.geneontology.org/Annotation_Review_Request
• [ ] create annotation review ticket: https://github.com/geneontology/go-annotation/issues/new?assignees=&labels=annotation+review&template=annotation-review-for-obsoletion.md&title=Review+annotations+to+%5BINSERT+GO+TERM%5D
• [ ] find external mappings (via IEAS), include in obsoletion notice
• [ ] tag curators in Annotation Review ticket. Responsible annotator for each group: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Notification

• [ ] create obsoletion announcement
• [ ] announce to GO friends (go-friends@mailman.stanford.edu)
• [ ] paste the text in the ontology ticket

[ValWood]

@sjm41 @pgaudet does this sound OK for these processes, should be captured as MF + appropriate RNA processing term?

[sjm41]

Not sure. "GO:0036260 RNA capping" is defined as "The sequence of enzymatic reactions by which a cap structure is added to the 5' end of nascent RNA polymerase transcripts. Examples of RNA capping include 7-methyl-G caps found on all RNA polymerase II transcripts and nucleotide-containing cofactor caps, such as NAD(H) or FAD, found on bacterial trancripts." The "sequence of enzymatic reactions" bit suggest this is a bona fide process term?

But I agree that the specific child terms look like MFs.

[ValWood]

OK I will keep RNA capping and deal with the children. So is capping a multispet process? (I haven't looked at this in detail yet)

[sjm41]

So is capping a multispet process? (I haven't looked at this in detail yet)

Right. That's what the current def says, and here's a quote from PMID: 27317694 ("mRNA capping: biological functions and applications"):

Nuclear RNA capping Capping is the first modification made to RNA polymerase II-transcribed RNA and takes place co-transcriptionally in the nucleus as soon as the first 25–30 nts are incorporated into the nascent transcript. Three enzymatic activities are required to generate the cap 0 structure, namely, RNA triphosphatase (TPase), RNA guanylyltransferase (GTase) and guanine-N7 methyltransferase (guanine-N7 MTase. Each of these enzyme activities carries out an essential step in the conversion of the 5′ triphosphate of nascent RNA to the cap 0 structure.

[ValWood]

So clearly capping isn't single step.

I just removed the child GO:0034471 ncRNA 5'-end processing which was wrong (ncRNA 5'-end processing is broader) here https://github.com/geneontology/go-ontology/issues/26208

Now there will be 2 children or RNA capping GO:0036261 7-methylguanosine cap hypermethylation Hypermethylation of the 7-(mono)methylguanosine (m(7)G) cap structure at the 2' position of the guanosine residue to convert a mono-methylated cap to a 2,2,7-trimethylguanosine cap structure. This type of cap modification occurs on small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) and is dependent on prior guanine-N7 methylation. PMID:11983179 PMID:18775984

and GO:0009452 7-methylguanosine RNA capping The sequence of enzymatic reactions by which the 5' cap structure, an inverted 7-methylguanosine linked via a 5'-5' triphosphate bridge (m7G(5')ppp(5')X) to the first transcribed residue, is added to a nascent transcript.

Q The first one GO:0036261 7-methylguanosine cap hypermethylation should probably be described as a MF term (@pgaudet @sjm41 do you agree)?

Q GO:0009452 7-methylguanosine RNA capping is clearly a process, it describes a sequence of reactions. BUT if GO:0036261 7-methylguanosine cap hypermethylation was obsoleted there would then be only one child of RNA capping. What should the siblings be?

ACTIONS

• [ ] make GO:0036260 RNA capping a descendent of GO:0000966 RNA 5'-end processing

[pgaudet]

Covered by other tickets