XBP1 unconventional splicing

[gocentral]

Following on from SF:11485:

We have two sibling terms (GO:0070055 and GO:0030969) that are both being used to annotate IRE1: an endonuclease that cleaves Hac1 mRNA (in yeast) or XBP1 mRNA in worm, fly and mammals, during the unfolded protein response:

mRNA splicing, via endonucleolytic cleavage and ligation ; GO:0070054 —[partof]HAC1-type intron splice site recognition and cleavage ; GO:0070055 —[isa]UFP-specific transcription factor mRNA processing involved in endoplasmic reticulum unfolded protein response ; GO:0030969

IRE1-mediated unfolded protein response ; GO:0036498 —[partof]UFP-specific transcription factor mRNA processing involved in endoplasmic reticulum unfolded protein response ; GO:0030969

The definition of GO:0070055 is narrower since it doesn’t cover the ligation steps (see PMID:21924241 for discussion of the ligation reactions). I think the terms should be renamed and definitions tweaked to move them to be a parent-child relationship instead (current annotations will remain correct):

NEW STRUCTURE AND RENAMES:

mRNA splicing, via endonucleolytic cleavage and ligation ; GO:0070054 —[isa]mRNA splicing via endonucleolytic cleavage and ligation involved in unfolded protein response ; GO:0030969 ——[partof]mRNA cleavage involved in unconventional mRNA splicing in unfolded protein response ; GO:0070055

mRNA cleavage involved in mRNA processing ; GO:0098787 —[isa]mRNA cleavage involved in unconventional mRNA splicing in unfolded protein response ; GO:0070055

[Term] id: GO:0070055 name: HAC1-type intron splice site recognition and cleavage namespace: biological_process def: "The process in which the tertiary structure of a HAC1 type intron is recognized, and the endonucleolytic cleavage of the RNA at both the 5' and 3' splice sites occurs." [GOC:krc, GOC:mah, PMID:10357823]

[Term] id: GO:0070055 name: mRNA cleavage involved in unconventional mRNA splicing in unfolded protein response namespace: biological_process def: “The endonucleolytic cleavage of a mRNA containing an HAC1-type intron at the 5’ and 3’ splice sites.” [GOC:krc, GOC:mah, GOC:bf, PMID:10357823]

New synonyms for GO:0030969: non-spliceosomal mRNA splicing in the unfolded protein response pathway [10357823] spliceosome-independent UFP-specific transcription factor mRNA processing [GOC:dph] unconventional mRNA splicing during UPR IRE1-mediated XBP-1 mRNA splicing Ire1p-mediated HAC-1 mRNA splicing Also add PMID: 21924241 to the definition DBXref.

Let me know if you have better (e.g. shorter) name suggestions- if not, I’ll go ahead and implement these changes.

Thanks!

Reported by: rebeccafoulger

Original Ticket: geneontology/ontology-requests/11782

[gocentral]

You should also add 'HAC1-type intron splice site recognition and cleavage' as a synonym for GO:0070055. You were probably going to but I wanted to make sure.

Additional synonym for GO:0030969

unconventional mRNA splicing in unfolded protein response

Should the other synonym be

unconventional mRNA splicing during UPR

or

unconventional mRNA splicing in UPR

?

Original comment by: tberardini

[gocentral]

• assigned_to: RFoulger

Original comment by: tberardini

[gocentral]

• status: open --> closed-fixed

Original comment by: rebeccafoulger

[gocentral]

Thanks Tanya!

I've made sure to add 'HAC1-type intron splice site recognition and cleavage' as a synonym for GO:0070055.

And for GO:0030969, I made the synonym 'unconventional mRNA splicing involved in UPR'

The new names are: mRNA splicing via endonucleolytic cleavage and ligation involved in unfolded protein response ; GO:0030969 mRNA endonucleolytic cleavage involved in unfolded protein response ; GO:0070055

Original comment by: rebeccafoulger