2,2,7-trimethylguanosine (TMG) cap formation about go-ontology

[ValWood]

@pgaudet how do I add a comment? I added the comment above, but I had to remove it because of some problem

:: ERROR: ascii-check: Line: def: "Catalysis of two successive methyl transfer reactions from AdoMet to the N-2 atom of guanosine, thereby converting 7-methylguanosine in an RNA cap to 2,2,7 trimethylguanosine." [PMID:11983179, PMID:18775984] {comment="A 2,2,7-trimethylguanosine (TMG) cap is found on many RNA polymerase II transscribed small noncoding RNAs including small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and telomerase RNA. It is also found on nematode mRNAs that undergo trans-splicing of a 5′-capped leader sequence"}

[ValWood]

I checked with expert and
m7G as normal (cap 0) and then tgs1 converts that to 2,2,7 tri-methylG on snRNA (and sno)

so I will change the function-like term
7-methylguanosine cap hypermethylation (GO:0036261)
into 2,2,7-trimethylguanosine (TMG) cap formation

(this will make it a little broader because it can then be used to describe all of the capping steps for a TMG cap

@pgaudet is that OK?

[pgaudet]

@pgaudet how do I add a comment? I

It looked liked you added the comment to the definition
You add the comment by clicking the top right + sign next to Annotations,

select 'rdfs comment' and type = string

[pgaudet]

so I will change the function-like term
7-methylguanosine cap hypermethylation (GO:0036261)
into 2,2,7-trimethylguanosine (TMG) cap formation
@pgaudet is that OK?

Could you present your plan at the next ontology call (Feb 12th).

What I did for the methylstranferases was to organize by substrate (tRNA, rRNA, etc), rather than by modification. It seemed more useful for classifications of biological processes.
But I dont know how you're planning to organize the branch.

[ValWood]

What I did for the methylstranferases was to organize by substrate (tRNA, rRNA, etc), rather than by modification. It seemed more useful for classifications of biological processes. But I dont know how you're planning to organize the branch.

This is a pathway/process I'm trying to describe, not a simple modification (it's usually 4-7 steps on most RNAs, slightly different depending on the RNA). I'm planning to organize by substrate (that is important so that it can be grouped with the relevant transcriptional unit see #26931
Right now I'm only addressing pol II co-trancriptional processing.

, but some pathways have more than one substrate so it's tricky.
In, the RNA capping pathway the first 3 enzymes in are shared (between mRNA/snoRNA/snRNA and some ncRNA) , then there are specific modifications for the specific caps.

This is the TGM cap which is specific for snoRNA/snRNA (but also awkwardly telomerase and some C. elegans mRNA transgenes)

At present it is not possible to completely annotate most cap pathways because the RNA specific enzymes are not described in GO. (for example the first 3 shared MF steps specify mRNA and there is no equivalent term for sno/snRNA even though they use the same enzyme) ........I need to check about what to do there.

[pgaudet]

I was asking because I dont see a substrate in the term label you mentioned above ' 2,2,7-trimethylguanosine (TMG) cap formation'; was the plan for this to cover all types of RNAs? Or is this supposed to be a grouping class?

[ValWood]

This was the tricky part hence the comment:
"A 2,2,7-trimethylguanosine (TMG) cap is found on many RNA polymerase II transcribed small noncoding RNAs including small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and telomerase RNA. It is also found on nematode mRNAs that undergo trans-splicing of a 5′-capped leader sequence.

Down the line we probably need to add
snoRNA trimethylguanosine (TMG) cap formation
snRNA trimethylguanosine (TMG) cap formation
as necessary (even though they use the same enzymes)
but first I want to remove the modification-type terms in BP and ensure all of the existing terms correctly labelled and positioned in the ontology (and to check if the specific terms are necessary before adding). I also wanted to ensure the these terms didn't get swept away in the modification clean up, and it's easier to repurpose these when I see what they are for rather than figure it all out again.

I can't currently make it more specifically either "snRNA" or "snoRNA" because it has been used for annotation both caps.

[ValWood]

I won't do this
rename 7-methylguanosine cap hypermethylation (GO:0036261)
into 2,2,7-trimethylguanosine (TMG) cap formation
synonym 2,2,7-trimethylguanosine sno/snRNA capping
the existing term describes the activity rather than the process (this term can then also be used for the previous steps too)
and will be a more appropriate sibling to
7-methylguanosine mRNA capping GO:0006370

I'll obsolete create new terms because the def is quite different, and we will need specific terms