#11782 XBP1 unconventional splicing

[RFoulger]

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!

[Tanya Berardini]

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

?

[RFoulger]

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