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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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query: nucleolus organization #10746

Closed gocentral closed 3 years ago

gocentral commented 10 years ago

Is this really a "process" or is it only a phenotype that is a consequence of problems with rRNA processing/ ribosome biogenesis?

The gene products annotated to it (only ~24 experimental appear to be defects in these processes).

If it is a 'good' term, should it have things like: protein localization to nucleolar rDNA repeats recombination within rDNA repeats replication fork processing at rDNA locus rDNA condensation be children?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/10559

gocentral commented 10 years ago

Original comment by: jl242

gocentral commented 10 years ago

Original comment by: tberardini

gocentral commented 10 years ago

Hi Val,

This is certainly a process - a phenotype would be when it is defective. Also, we need to keep ribosome biogenesis separate (see prokaryotes). I agree about adding more children though: "protein localization to nucleolar rDNA repeats " should be a part. The others I will need to look into further. Can you suggest some papers?

Cheers, David

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Hi Val,

I've added 'protein localization to nucleolar rDNA repeats' and rDNA condensation parts. The latter is justified I think because the 'condensin complex' that results is part of the nucleolus, at least for some part of the cell cycle (http://www.ncbi.nlm.nih.gov/pubmed/10811823)

I'm still not convinced of the other two:

replication fork processing at rDNA locus: . (i) Probably occurs in prokaryotes - replication forks certainly process through rDNA in prokaryotes. Def of this term makes clear that the meaning is more specific that implied by the name: "The process in which a DNA replication fork that has stalled at the rDNA replication fork barrier (RFB) is repaired and replication is restarted." I couldn't find any refs specifically on an rDNA RFB in prokaryotes, but Transcription-Replication Collisions (which is what the rDNA RFB is) do occur in bacteria see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC544003/. . (ii) This process is quite peripheral to organising the nucleolus - or at least only indirectly necessary for it (no replication => no new nucleolus).

recombination within rDNA repeats: . Couldn't find papers on this occurring in prokaryotes, but seems rash to exclude that it could, as recombination does occur at other repeats in prokaryotes (http://www.pnas.org/content/98/15/8319.full.pdf)

Cheers, David

Original comment by: dosumis

gocentral commented 10 years ago

Original comment by: dosumis

ValWood commented 3 years ago

reopening. I'm still not really sure that "nucleolus organization" should be a process. Any time it is used it is just the phenotypic consequence of disorganization of the rDNA. I don't know any gene that actually 'organizes' the nucleolus. It isn't even a independent structure really, it's nuclear region where the rDNA is located?

ValWood commented 3 years ago

I am asking this becasue I don't use this term, but now I have a mapping for dnt1

GO:0007000 nucleolus organization IBA with S000003612 , PTN002000197 , S000001718

(a protein involved in rDNA heterochromatin assembly)

ValWood commented 3 years ago

Older papers talk about nucleogenesis an d the nucleolus appearing, newer papers only talk about chromatin organization of rDNA. Does nucleogenesis inlude anything else? Otherwise we would have 2 ways to say the same thing.

(Note that nucleolus organization still only has 36 EXP annotations)

pgaudet commented 3 years ago

I see 18 direct EXP annotations, by the following groups:

(5) FlyBase (4) SGD (3) MGI (3) TAIR (3) UniProt

Annotations are here: https://docs.google.com/spreadsheets/d/1I5Ef-7xFELHwVQC3a5wgjP0Fh0wSoNeq8xP9opybdMk/edit#gid=0

What do you think @hattrill @srengel @hdrabkin @tberardini @ccasalsc

Thanks, Pascale

hdrabkin commented 3 years ago

The nucleolus is a recognizable structure; its assembly/appearance would be organization; there must be things that cause it to form; I think the term is real.

ccasalsc commented 3 years ago

Hi, I had a look on the annotation in which I've used this term, and in the article's discussion the authors say : ' We therefore propose that the primary role of USP36 is to regulate the transcription and processing of rRNA by deubiquitylating various proteins involved in these processes, and the aberrant nucleolar structure in its absence is secondary to deficient ribosome biogenesis. ' So, I don't really know if you should keep the term or not but in my case I think will remove it and keep the term 'regulation of rRNA processing'. Best

ValWood commented 3 years ago
  1. nucleolus organization has children GO:0007576 ucleolar fragmentation The cell aging process that results in the nucleolus breaking down into fragments. PMID:9271578

I don't know how the nucleolus can 'break into fragments.'This proba bly means fragmentation of nucleolar DNA?

GO:0000183 rDNA heterochromatin assembly

ukemi commented 3 years ago

I would suggest looking into the plant literature as well. ping @tberardini

ValWood commented 3 years ago

The other children are GO:0034503 protein localization to nucleolar rDNA repeats and GO:0017126 nucleologenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells.

so maybe it is OK. I can't figure out what could be organized other than chromatin though (at least in yeast)?

ValWood commented 3 years ago

If it is kept it should be a parent of GO:0000183 rDNA heterochromatin assembly

ValWood commented 3 years ago

I have just never seen anything which "actively" organizes the nucleolus.

There are 36 EXP annotations. all IMP. Of course if you bugger up ribosome biogenesis or rDNA heterochromatin organization you bugger up the nucleolar organization, but this is just a consequence of stuffing up another process. Is the organization a 'spontaneous consequence' of the rDNA heterochromatin organization?

There is one (more) IDA, mouse, I will take a look at that one.

ValWood commented 3 years ago

I guess the 'nucleolar organization covers various processes like rDNA synthsis

We suggest that fundamental differences in molecular organization of rDNA synthesis and postranscriptional processes between cycling somatic and pre-implantation embryonic cells may be in selective transport of transcription and/or processing-complexes of proteins to the nucleolar organizer regions (NOR). Mol. Reprod. Dev. 59:277-284, 2001.

Let's move GO:0000183 rDNA heterochromatin assembly under here and close this for now.

It would be good to make "nucleolar organization" not for direct annotation to get the required specificity in case things need to be pulled apart later (and also most of the descendant processes will have additional parentage).

ValWood commented 3 years ago

@hdrabkin MGI pages give an error from QuickGO.

hdrabkin commented 3 years ago

@ValWood ; which pages (paste link here) so I can inform

ValWood commented 3 years ago

@hdrabkin with/from links https://www.ebi.ac.uk/QuickGO/annotations?goUsage=descendants&goUsageRelationships=is_a,part_of,occurs_in&goId=GO:0007000&evidenceCode=ECO:0000269&evidenceCodeUsage=descendants&taxonId=10090&taxonUsage=descendants

ValWood commented 3 years ago

I just found another lost relative

GO:1990700 nucleolar chromatin organization

Currently not related to "nucleolar organization" OR "GO:0000183 rDNA heterochromatin assembly"

hdrabkin commented 3 years ago

@ValWood You mean from the alleles in the with/from field. These are valid alleles; you should check your parser it loads 'http://www.informatics.jax.org/accession/MGI' but no allele (http://www.informatics.jax.org/accession/MGI:2445464 Also note: MGI:2445464 is the allele id MGI:MGI:2445464 is not

ValWood commented 3 years ago

It's the links from QuickGO, nothing to do with any parser of mine:

https://www.ebi.ac.uk/QuickGO/annotations?goUsage=descendants&goUsageRelationships=is_a,part_of,occurs_in&goId=GO:0007000&evidenceCode=ECO:0000269&evidenceCodeUsage=descendants&taxonId=10090&taxonUsage=descendants

is presumably using information in the GO files?

hdrabkin commented 3 years ago

Do any of its pages with MGI alleles work do you know? I'd contact quickgo;

ValWood commented 3 years ago

I have no idea. They haven't been working for a while (I noticed it last week but was too busy to report it). I don't mind, can just Google but I thought MGI might like to get it fixed.

tberardini commented 3 years ago

I updated the TAIR annotations, those gps had other annotations to more relevant processes (telomere maintanance for example) and the nucleolus related ones were really just downstream phenotypes.

ValWood commented 3 years ago

This seems to be an example of nucleolus organization that isn't rDNA organization: https://www.pombase.org/reference/PMID:33176152 so maybe close this (although 'nuclolar organization'could maybe 'not for direct annotation'?)

hattrill commented 3 years ago

I think that I would rather leave it available for direct annotation - better to be vague than wrong here. Some proteins are clearly organising at some level - recruitment, etc, but difficult to draw an exact cause and effect.

Should GO:1990700 'nucleolar chromatin organization' be under this term?

ValWood commented 3 years ago

Should GO:1990700 'nucleolar chromatin organization' be under this term?

I think so....