ntrs/tpv/ontology changes: mRNA decay related

[gocentral]

Hi,

This is a rather huge item in the most part related to the BP branch under GO:956 'nuclear-transcribed mRNA catabolic process'.

A) Please broaden the definition of 'Ski complex' GO:55087 from "heterotrimeric" to "heteromeric". PMID:18042677 shows that in S. cerevisiae, this complex is actually heterotetrameric.

B) There is a tvp for 'exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay' GO:43928.

Based on the definition, it should not be a part_of child of GO:290 'deadenylation-dependent decapping of nuclear-transcribed mRNA' but an is_a child of GO:288 'nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay'. If a separate term is needed for the exonucleolytic cleavage of the cap, then a new one should be created, but I think that this term should stay as defined to describe the decay of the transcript body.

C) Please broaden the definition of 'nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay' GO:288. The definition explicitly states that decapping as one of the ordered steps of this process, but 3'-5' nonsense mediated decay, a child term being requested below, does not require decapping but is deadenylation dependent.

new proposed definition: A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.

D) I would like to request 4 new terms:

1. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay (exact synonyms: 3'-5' NMD; 3'-5' nonsense-mediated decay; 3'-5' nonsense-mediated mRNA decay; plus any other appropriate synonyms as needed related to catabolism/breakdown). [This process is decapping INdependent and adenylation dependent.]

reference: PMID:12881429

definition: The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction.

2. nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay (exact synonyms: 5'-3' NMD; 5'-3' nonsense-mediated decay; 5'-3' nonsense-mediated mRNA decay; plus any other appropriate synonyms as needed related to catabolism/breakdown): [This process is decapping dependent and adeynylation INdependent.]

reference: PMID: 18554525 (review)

definition: The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 5' end is not protected by a 5'-cap; degradation proceeds in the 5' to 3' direction.'

3. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-independent decay

definition: The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear- transcribed mRNA that occurs when the ends are not protected by the 5'-cap.

4. Nuclear-transcribed mRNA catabolic process, non-stop decay (exact synonyms: non-stop mRNA decay; nonstop decay; nonstop mRNA decay)

reference: PMID: 11910110

definition: The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.

nuclear-transcribed mRNA catabolic process GO:956 .nuclear-transcribed mRNA catabolic process, nonsense-mediated decay GO:184 ..3'-5' NMD GO:new1 ..5'-3' NMD GO:new2 .nuclear-transcribed mRNA catabolic process, exonucleolytic GO:291 ..nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' GO:34427 ...3'-5' NMD GO:new1 ..nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' GO:34428 ...5'-3' NMD GO:new2 ..exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay GO:43928 ...3'-5' NMD GO:new1 ..exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-independent decay GO:new3 ...5'-3' NMD GO:new2 .nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay GO:288 ..exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay GO:43928 ...3'-5' NMD GO:new1 .nuclear-transcribed mRNA catabolic process, deadenylation-independent decay GO:31086 ..exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-independent decay GO:new3 ...5'-3' NMD GO:new2 .nuclear-transcribed mRNA catabolic process, non-stop decay GO:new4

Thanks! -Julie

Reported by: juliep

Original Ticket: "geneontology/ontology-requests/5884":https://sourceforge.net/p/geneontology/ontology-requests/5884

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Just wanted to add that I will probably also need some new mRNA catabolic process terms for some catabolic processes that occur in the nucleus. Looking over the existing terms, most of these are for degradation of mRNAs in the cytoplasm. I will need some terms for quality control/surveillance processes that occur in the nucleus to degrade incompletely or improperly formed mRNAs. I can add them to this item, when I know what to ask for.

-Karen

Original comment by: krchristie

[gocentral]

Hi,

Sorry, I copy/pasted the wrong reference for 3'-5' NMD (D1 above). It should be PMID:12769863.

-Julie

Original comment by: juliep

[gocentral]

added nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay GO:0070478 nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay GO:0070479 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-independent decay GO:0070480 nuclear-transcribed mRNA catabolic process, non-stop decay GO:0070481

I also did everything else as requested, except that I made GO:0043928 part_of GO:0000288, not is_a --- GO:43928 represents the exonucleolytic part of the whole GO:288 process, where decapping and tail shortening are the other parts.

m

p.s. leaving open for Karen's additions

Original comment by: mah11

[gocentral]

• milestone: --> SGD

Original comment by: mah11

[gocentral]

Thanks Midori!

re: GO:43928 yes yes, you are absolutely right. I didn't think about that. =)

-Julie

Original comment by: juliep

[gocentral]

Hi,

I've started to think I have a reasonable idea what we'll need, but since there's already a lot that was done in this item, and there is another open item related to the part I need:

[ 2549961 ] ? about GO:0043633 - modification-dependent RNA catabolic pr https://sourceforge.net/tracker/index.php?func=detail&aid=2549961&group\_id=36855&atid=440764

I think I'll close this item, and put the info for what I'd like to do into the other item, since it's all specifically about child terms of "GO:0043633 - modification-dependent RNA catabolic process". I think I'll probably rename this term, rather than merge it and create some new child terms. Let me know if you'd rather have me open a separate item for the new terms, rather than just put in this existing one.

I assume closing this item, and using the other one that also already exists, works for you Midori, since I know you like getting SF items closed, and if not, I'm sure you'll reopen it ;)

thanks,

-Karen

Original comment by: krchristie

[gocentral]

• status: open --> closed

Original comment by: krchristie

[gocentral]

SF item handling is fine with me, since it makes sense to you.

m

(and yes, I do like closing items :) )

Original comment by: mah11

[gocentral]

• status: closed --> closed-accepted

Original comment by: mah11