new term request:maintenance of G0 arrested cells

[gocentral]

def: The maintenance of a cell in the G0 quiescent (non dividing) state. Cells are usually in pre-replicative and accompanied by a shut down of protein biosynthesis

child of cellular developmental process GO:0048869?

See PMID: 17535257

I'm not sure about the parentage but it seems the best one?

but maybe we need a 'grouping term' for G0 related processes.

We already have a term G0 to G1 transition GO:0045023

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4669":https://sourceforge.net/p/geneontology/ontology-requests/4669

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correction ntr: establishment and maintenance of G0 arrested cells --ntr: maintenance of G0 arrested cells --ntr:establishment of G0 arrested cells/ synonym: G1/G0 transition

Original comment by: ValWood

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• summary: new term request:maintenence of G0 arrested cells --> new term request:maintenance of G0 arrested cells

Original comment by: ValWood

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--ntr:establishment of G0 arrested cells/ synonym: G1/G0 transition ----ntr:establishment of G0 arrested cells in response to nitrogen starvation / synonym: G1/G0 transition in response to nitrogen starvation /synonym nitrogen-starvation arrest

(I think we also need this term if not all GO arrest is in response to nitrogen starvations as it seems to be in fungi?)

and this would need to be a child of respone to nitorgen starvation

Original comment by: ValWood

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the final term I suggested sounds like it is equivalent to GO:0030996 cell cycle arrest in response to nitrogen starvation?

Original comment by: ValWood

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Oh, no it won't be equivalent as the arrest will either result in transition to GO, or if cell of the oposite mating tyope are p[resent, to mieosis/sporulation

Original comment by: ValWood

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OK, before I actually work on these, I'm gonna whinge about the term names: I really don't like "G0 arrested cells" because it sounds like the process involves/requires a population of cells, when in fact a single cell can enter G0.

Could we use something like establishment/maintenance/etc "of G0" or "of quiescence" (with synonyms all over the place)?

Also, GO:0045023 (G0->G1) has a path to cell cycle process. Is it correct that the terms for entering G0 (which one could think of as exiting from the cell cycle) and staying in G0 don't?

maybe we could chat about this some time next week ...

Original comment by: mah11

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I agree with the suggestion to name the term using 'quiesence' also, consider 'stationary-phase' in some 'related synonym capacity

I think the cell cycle part might be OK... David and Tanya convinced me recently that they were. If you think of them of being a 'cell cycle process' (i.e negative regulation of), but not being a 'regulation of cell cycle' (which is defined in terms of progression 'through' the cell cycle...actually that doesn't make sense does it?

maybe need to think about this some more. Can meet up any time next week.

Original comment by: ValWood

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Shall we chat about this at some point? I'd like to get the annotations done as its a paper thet the author mailed me about to annotate.

v

Original comment by: ValWood

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Oh yeah, we meant to! This week is out, obviously, because of the beer festival (and the entirely-too-much-to-do today) but next week is only as busy as usual. I'm working from home monday (28th); any other day should be ok. mail me ...

m

Original comment by: mah11

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OK will mail you Tuesday, V

Original comment by: ValWood

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Proposed new terms in OBO stanza format (IDs are temporary so ignore):

[Term] id: newGO:0100101 name: G1 to G0 transition namespace: biological_process def: "A process by which progression through the cell cycle is halted during G1 phase, whereupon the cell enters a specialized resting state known as G0 or quiescensce." [GOC:mah, ISBN:0815316194] synonym: "cell cycle quiescence" RELATED [] synonym: "G1/G0 transition" EXACT [] synonym: "stationary phase" RELATED [] is_a: GO:0007050 ! cell cycle arrest

[Term] id: newGO:0100102 name: G1 to G0 transition involved in cell differentiation namespace: biological_process def: "A process by which progression through the cell cycle is halted during G1 phase, whereupon the cell enters G0 phase, in the context of cell differentiation." [GOC:mah, ISBN:0815316194] synonym: "G1/G0 transition involved in cell differentiation" EXACT [] is_a: newGO:0100101 ! G1 to G0 transition relationship: part_of GO:0030154 ! cell differentiation

[Term] id: newGO:0100103 name: regulation of G0 to G1 transition namespace: biological_process def: "A cell cycle process that modulates the rate or extent of the transition from the G0 quiescent state to the G1 phase." [GOC:mah] is_a: GO:0051726 ! regulation of cell cycle relationship: part_of GO:0045023 ! G0 to G1 transition

[Term] id: newGO:0100104 name: negative regulation of G0 to G1 transition namespace: biological_process def: "A cell cycle process that stops, prevents, or reduces the rate or extent of the transition from the G0 quiescent state to the G1 phase." [GOC:mah] synonym: "maintenance of G0 phase" EXACT [] is_a: GO:0045786 ! negative regulation of cell cycle is_a: newGO:0100103 ! regulation of G0 to G1 transition

[Term] id: newGO:0100105 name: positive regulation of G0 to G1 transition namespace: biological_process def: "A cell cycle process that activates or increases the rate or extent of the transition from the G0 quiescent state to the G1 phase." [GOC:mah] is_a: GO:0045787 ! positive regulation of cell cycle is_a: newGO:0100103 ! regulation of G0 to G1 transition

Original comment by: mah11

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Hi Midori,

Comments from Tanya and I are interspersed. > Hi, > > Val - these are the terms we were talking about; I'll also paste them into the SF item. > > David & Tanya - can you check whether the proposed definitions parents look reasonable from a regulation POV? Or if you can suggest improvements, cool. > > If you plop these into any of the GO OBO files, they should show up in the right places in OBO-Edit. > > cheers, > m > > [Term] > id: newGO:0100101 > name: G1 to G0 transition > namespace: biological_process > def: "A process by which progression through the cell cycle is halted during G1 phase, whereupon the cell enters a specialized resting state known as G0 or quiescensce." [GOC:mah, ISBN:0815316194] quiescence? > synonym: "cell cycle quiescence" RELATED [] > synonym: "G1/G0 transition" EXACT [] > synonym: "stationary phase" RELATED [] > is_a: GO:0007050 ! cell cycle arrest > > Question: do we need regulation terms for the above? If so, what parents (since negative regulation of new1 = pos reg of cell cycle and vice versa)? Defs? If there are gene products that control (regulate) the transition and are separate from the machinery that carries out the transition, then we need the regulation terms. > > [Term] > id: newGO:0100102 > name: G1 to G0 transition involved in cell differentiation > namespace: biological_process > def: "A process by which progression through the cell cycle is halted during G1 phase, whereupon the cell enters G0 phase, in the context of cell differentiation." [GOC:mah, ISBN:0815316194] > synonym: "G1/G0 transition involved in cell differentiation" EXACT [] > is_a: newGO:0100101 ! G1 to G0 transition > relationship: part_of GO:0030154 ! cell differentiation > > Comment: This term could be an is_a parent of GO:0021883, cell cycle arrest of committed forebrain neuronal progenitor cell. Presumably quite a few other cell differentiation types could also have cell cycle arrest part_of children. Is cell differentiation the best parent, or cell development? I'm not sure about this. The cell cycle arrest in these cells is a key step in their differentiation program. It is coupled to their migratory and fate specifications. I'm not sure we care about the G1 to G0 transition per se. I'm not even sure it goes to a real G0. I think sometimes these cells arrest and migrate, then divide again to give rise to a glial cell and a neuron. > > [Term] > id: newGO:0100103 > name: regulation of G0 to G1 transition > namespace: biological_process > def: "A cell cycle process that modulates the rate or extent of the transition from the G0 quiescent state to the G1 phase." [GOC:mah] > is_a: GO:0051726 ! regulation of cell cycle > relationship: part_of GO:0045023 ! G0 to G1 transition If there are gene products that control (regulate) the transition and are separate from the machinery that carries out the transition, then we need the regulation terms. The parentage looks fine. > > [Term] > id: newGO:0100104 > name: negative regulation of G0 to G1 transition > namespace: biological_process > def: "A cell cycle process that stops, prevents, or reduces the rate or extent of the transition from the G0 quiescent state to the G1 phase." [GOC:mah] > synonym: "maintenance of G0 phase" EXACT [] > is_a: GO:0045786 ! negative regulation of cell cycle > is_a: newGO:0100103 ! regulation of G0 to G1 transition

If there are gene products that control (regulate) the transition and are separate from the machinery that carries out the transition, then we need the regulation terms. The parentage looks fine. > > [Term] > id: newGO:0100105 > name: positive regulation of G0 to G1 transition > namespace: biological_process > def: "A cell cycle process that activates or increases the rate or extent of the transition from the G0 quiescent state to the G1 phase." [GOC:mah] > is_a: GO:0045787 ! positive regulation of cell cycle > is_a: newGO:0100103 ! regulation of G0 to G1 transition > If there are gene products that control (regulate) the transition and are separate from the machinery that carries out the transition, then we need the regulation terms. The parentage looks fine.

David & Tanya

Original comment by: ukemi

[gocentral]

• labels: --> New term request
• assigned_to: nobody --> gomidori
• milestone: --> 224410

Original comment by: mah11

[gocentral]

I've added the terms as originally proposed; actual IDs are: G1 to G0 transition GO:0070314 G1 to G0 transition involved in cell differentiation GO:0070315 regulation of G0 to G1 transition GO:0070316 negative regulation of G0 to G1 transition GO:0070317 positive regulation of G0 to G1 transition GO:0070318

If you need terms for regulation of G1-to-G0, open a new SF item. I'm closing this one!

m

p.s. I have not changed the definition of 'cell cycle arrest' (arrest isn't always G1 -- e.g. oocytes).

Original comment by: mah11

[gocentral]

• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

What about the original term, maintenance of G0 arrested cells can I have this one?

val

Original comment by: ValWood

[gocentral]

sounds like it would probably be 'negative regulation of G0 to G1 transition' ... can add a synonym

Original comment by: mah11

[gocentral]

• status: closed-accepted --> open-accepted

Original comment by: mah11

[gocentral]

Of course, can you add as a synonym then I won't be confused next time

val

Original comment by: ValWood

[gocentral]

synonym 'maintenance of G0 arrest' added to GO:0070317

Original comment by: mah11

[gocentral]

• status: open-accepted --> closed-accepted

Original comment by: mah11

[gocentral]

I'm still not sure this is what I want. I think the maintenance of cells in G0 is slightly different from negative regulation of G0 to G1 transition this is more about maintaining viability in the G0 state, rather than the negative regulation of the G0-G1 transition. See the example in the paper I am now curating PMID:19197239 (I would also want to use this terms here)

Granted the scenario is rather artificial, and the transition to G1 would be affected, but what I want to capture with these (and the previous) is the ability to survive in G0. They seem subtly different.

Original comment by: ValWood

[gocentral]

OK, I understand what you mean now. But I don't think "the ability to survive in G0" corresponds to a GO process.

We had a somewhat similar question arise years ago (late 2001!), when Erich Schwarz wanted to add terms for 'adult survival' and 'larval survival' because of lethal RNAi phenotypes in C. elegans. We didn't add those terms because Michael A and I agreed that it was really phenotype information, and didn't correspond to a specific identifiable process.

I think the same applies here: the cells are dying in G0 as a downstream effect of some problem, in this case apparently accumulating DNA damage. So Tdp1 seems to have some role in coping with oxidative DNA damage that occurs in G0; I'm not sure they know enough to say whether it's involved in detection, repair, etc. I also don't know what's special about G0 -- whether more oxidative damage occurs then, or if the mechanisms for dealing with it differ.

Original comment by: mah11

[gocentral]

OK this makes sense, and the same applies to my others. THere are phenotypes.

Thanks

VAl

Original comment by: ValWood

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11