TPV: mei2 nuclear dot, parentage fix

[gocentral]

The Mei2 nuclear do has a parent "nucleoplasm"

It is in fact chromosome/chromatin associated.

Can this be changed?

Thanks

Val

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0033620#term=ancchart

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/10628

[gocentral]

Argh - another can of worms I'm afraid!

I'm happy to take 'Mei2 nuclear dot' out from under 'nuclear body' and place it under 'nuclear chromosome part' (and add something from the abstract of PMID: 12808043 to make the location more explicit). But another child of 'nuclear body' should be moved likewise:

'histone locus body' (A nuclear body associated with the histone gene locus that is thought to contain all of the factors necessary for histone mRNA transcription and pre-mRNA processing. In Drosophila, U7 snRNP is located in the histone locus body rather than the distinct Cajal body.)

All other children of 'nuclear body' look ok to me under the 'nucleoplasm' parentage, but would you mind taking a look too please? (Some are found in mammals, I know...)

Then up to 'nucleoplasm part'... ("Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus.") It's got many children, and several of them are associated with DNA:

• DNA replication preinitiation complex (it's a protein-DNA complex)
• the histone-related complexes: they are made of proteins, but the histones are wrapped up in DNA... ...and several others I suspect. Maybe we should ask Karen and/or David Hill. Also, several terms have Midori's initials.

Let me know if you have/can gather any feedback, and I'll set to clean up. Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• labels: --> Other term-related request
• Description has changed:

Diff:

--- old
+++ new
@@ -1,4 +1,3 @@
-
 The Mei2 nuclear do has a parent "nucleoplasm"

 It is in fact chromosome/chromatin associated.

• assigned_to: Paola Roncaglia

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

I agree. I had a look though the list, I spotted Mmi1 focus. It is possible this is actually the same thing as the Mei2 dot.....(it is possible that there are mitotic meiotic differences to account for) I will check further on this.

I don't think we use any of the other terms so I am unsure on these.

Nuclear body is a bit of a placeholder "Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins."

I suspect this term could be obsoleted once the child componet terms are sufficiently defined to be able to place them properly under more appropriate complex terms....

VAl

Original comment by: ValWood

[gocentral]

I think nuclear body, and possibly some of the child terms should be obsoleted. Is the nuclear body grouping term required? The terms which are valid could just be children of nucleoplasm, with the relevant protein complex parentage.

One of the problems with the existing terms, is that because you don't really know the organisation or components of the structure, we could end up with multiple terms representing the same components.

"Mei2 dot" is a ribonucleo-protein complex. It is just that it is referred to as the "Mei2 dot" because it was first identified as a 'dot' on chromosome 2. So it should have GO:0030529 ribonucleoprotein complex parent. We could rename it as "Mei2 nuclear dot complex" to make this clearer....

Original comment by: ValWood

[gocentral]

"Mei2 dot" and MMi1 nuclear focus are different (I can see this from defs now). Although Mei2 dot complex contains mmi1 during meiosis, "mmi1 nuclear focus" is a larger 'processing body' for the catabolism of meiosis specific transcripts during the mitotic cell cycle.

I would be happy for "mmi1 nuclear focus" to be defined as a "complex" (its just that we don't know the binding partners of mmi1 yet....)

Perhaps, if you keep "nuclear body" it should not be allowed for direct annotation (should be annotated only to nucleoplasm)

v

Original comment by: ValWood

[gocentral]

Hi Val,

As a first pass at cleaning up the 'nuclear body' node, I've taken GO:0033620 'Mei2 nuclear dot' and GO:1990251 'Mmi1 nuclear focus' out from under 'nuclear body'. But I've given them both a related synonym for 'nuclear body' as this grouping term is used in the literature. Here are the diff:

[Term] id: GO:0033620 -name: Mei2 nuclear dot +name: Mei2 nuclear dot complex namespace: cellular_component -def: "A nuclear body that forms during meiotic prophase in a fixed position in the horsetail nucleus; contains Mei2 and meiRNA. May play a role in the progression of meiosis I." [PMID:12808043] +def: "A ribonucleoprotein complex that forms during meiotic prophase in a fixed position in the horsetail nucleus; contains Mei2 and meiRNA. May play a role in the progression of meiosis I." [GOC:vw, PMID:12808043] synonym: "Mei2 dot" EXACT [] -is_a: GO:0016604 ! nuclear body +synonym: "Mei2 nuclear dot" BROAD [] +synonym: "nuclear body" RELATED [] +is_a: GO:0030529 ! ribonucleoprotein complex +relationship: part_of GO:0005634 ! nucleus

[Term] id: GO:1990251 -name: Mmi1 nuclear focus +name: Mmi1 nuclear focus complex namespace: cellular_component -def: "An nuclear body that forms during vegetative growth and is involved in the selective degradation of meiosis-specific transcripts. Contains at least Mmi1, or an ortholog of." [GOC:al, PMID:16823445, PMID:23980030] +def: "A protein complex that forms during vegetative growth and is involved in the selective degradation of meiosis-specific transcripts. Contains at least Mmi1, or an ortholog of." [GOC:al, GOC:vw, PMID:16823445, PMID:23980030] subset: termgenie_unvetted -is_a: GO:0016604 ! nuclear body +synonym: "Mmi1 nuclear focus" BROAD [] +synonym: "nuclear body" RELATED [] is_a: GO:0043234 ! protein complex relationship: part_of GO:0005634 ! nucleus created_by: al

More soon... Thanks Paola

Original comment by: paolaroncaglia

[gocentral]

• Group: None --> PomBase

Original comment by: ValWood

[gocentral]

• status: open --> open-accepted

Original comment by: paolaroncaglia

[gocentral]

• labels: Other term-related request --> Other term-related request, mini-project

Original comment by: paolaroncaglia

[ValWood]

Looks OK to me?