pole cell formation - Githubissues

Moved from: [ 1325781 ] term name changes - development terms https://sourceforge.net/tracker/index.php? func=detail&aid=1325781&group_id=36855&atid=440764

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This term was flagged up by Chris's obol parser as being wrong:

GO:0007279 pole cell formation

Comments:

This can become a cell development term. A new formation chld term can be made. Standard defs can be applied.

Jen

2)I would agree, the stand def would apply (I assume you mean standard 'development' definition). However, 'pole cell development ; O:0007277' already exists, but I see no reason why they cannot be merged.

Russ

3)Comments form Becky:

Hi Jen,

Looking at the definitions, the problem I can see with merging pole cell formation and pole cell development is that:

in the definition of cell development is the phrase: Cell development DOES NOT INCLUDE the steps involved in committing a cell to a specific fate

However, I've thought of pole cell formation as including the determination steps (based on the blue book I think). Therefore it wouldn't be analagous to pole cell development (which is just a catch-all at the moment based on its position in the tree).

would probably be worth asking Russ what he takes 'pole cell formation' to encompass.... ie is it just the cellularization bit, or is it the cell determination bit too? Or whether the cell determination comes later.

then we can work out what to do with these terms.

does that help any?. Hope I haven't just confused the matter.

Becky

4) I've written to Russ to ask for his thoughts.

Jen

5) More from Becky:

...also if pole cell formation and development are merged, we'd still need to find another home for 'pole cell determination' cos it cant stay under pole cell development, given the definition of pole cell development.

6) pole cell differentiation GO:new --<pole cell fate commitment ; GO:new ----<pole cell fate specification ; GO:new ----<pole cell fate determination; GO:0007278 --<pole cell development ; GO:0007277 ----<pole cell morphogenesis ; GO:new ------<pole cell formation ; GO:0007279 ----<pole cell migration ; GO:0007280

david

7) There seem to be a few problems with the 'pole cell x' terms, at least from a Drosophila point of view (are pole cells insect specific?). Most of the problem is with 'pole plasm' vs 'pole cell'. To explain, let me first give a brief summarize germ cell formation in Drosophila (from PMID:15268881 and others):

The Drosophila embryo begins development as a syncytium. Early in development a number of cytoplasmic determinants (RNAs, proteins) accumulate at the posterior end if the embryo forming the pole plasm. The nuclei in the pole plasm are the first to cellularize. Upon cellularization these cells ARE the pole cells because pole plasm forms their cytoplasm. They are transcriptionally silent and therefore cannot 'develop' or 'differentiate' beyond their formation. These pole cells will eventually form the germ cells.

Because pole cells are fully developed at the moment they are formed it would seem that 'pole cell formation ; GO:0007279' and 'pole cell development ; GO:0007277' are completely synonymous. The definition of one entirely encompasses the definition of the other.

Merging these terms should be no problem. The problem is where to put them. The shouldn't be any where under 'cell differentiation ; GO:0030154' because this term has in it definition: 'The process whereby relatively unspecialized cells...acquire specialized structural and/or functional features that characterize the cells...'. There is no 'relatively unspecialized cell' that differentiates/develops into a pole cell. Perhaps they could live under 'cellularization ; GO:0007349'? If so part the definition of this term should be changed from 'each nucleus' to 'a nucleus'.

Of course, I now realize that 'cellularization ; GO:0007349' is a child of 'cell differentiation ; GO:0030154'!!

The other big problem is with term 'pole cell fate determination ; GO:0007278' which has in its definition: 'Process by which a cell becomes capable of differentiating autonomously into a pole cell...' Again, pole cells are pole cells from their genesis, there are no cells that can be fated to become pole cells.

I would suggest: 1) obsolete 'pole cell fate determination ; GO:0007278' and make a new term 'pole plasm formation; go:new' with the suggestion that annotations to 'GO:0007278' be checked and likely migrated to 'pole plasm formation; go:new' (I've had a quick look at the FlyBase annotations, this change would be an improvement).

The dag structure could be.

cellularization ; GO:0007349 --[i] pole cell formation ; GO:0007279 (merged with pole cell development ; GO:00072770) ----[p] pole plasm formation; go:new

(although I don't know where 'cellularization ; GO:0007349' should live)

And maybe:

germ cell development ; GO:0007281 --[p] pole cell formation ; GO:0007279 ----[p] pole plasm formation; go:new

(but I think there's a tpv in there...)

One more thing: The recent literature seems to prefer the name 'primordial germ cells' to 'pole cells' and 'germ plasm' to 'pole plasm'. These names should at least be in symonyms...

Russ

8) Hi Russ,

C. elegans also have P cells, but they are generated during the first few divisions of the embryo. They are thought of in the same context as pole cells. In fact, I think that any germ line cells that are sequestered during early embryogenesis are thought of in this way.

There is a relatively unspecialized cell that gives rise to pole cells in drosophila. It is the fertilized egg. It gives rise to lots of other cells too. Pole cells are also determined in drosophila. Where the poles cells form is where pole plasm exists. Some of the original experiments with determinants had to do with pole plasm. The pole plasm represents the "determinants" for these cells. The gene products in pole plasm that make the decision to form pole cells would be involved in pole cell fate determination. The drosophila embryo is special beacuse commitment of cell fates begins in the syncytial blastoderm, but the molecules that are set up along the axes of the embryo are still involved in cell fate commitment once cellularization takes place. That is why mutations like ftz and the others are so interesting.

Making pole cell development synonymous with pole cell formation depends on whether the migration of pole cells during embryogenesis would be part of their development. I would argue that this is part of their normal development, but I would also accept that once the migration phase begins these cells become germ cells outright and this process is part of germ cell development. This would require us to make a distinction between pole cells and germ cells. I'm not sure this would be a good idea.

Also, we have to consider the P-cell lineage in C. elegans with this. In C. elegans, "determinants" are segregated to the posterior end of the embryo and during the initial cleavages of the embryo, these determinants are sequested into the cells that will become the germ cells.

I think the structure proposed below will work for both Drosophila and C. elegans with perhaps very specific children to describe the processes in flies and worms. I also think if pole cell formation were an is_a cellularization we would be o.k.

David

9) >There is a relatively unspecialized cell that gives rise to >pole cells in drosophila. It is the fertilized egg.

If you consider a syncytial blastoderm to be 'A' cell. In the context of cell differentiation I don't think that it is. But, you are correct, the syncytial blastoderm does give rise to the pole cells. But you also, quite correctly, state:

>It gives >rise to lots of other cells too.

And that is exactly the problem. I do not see anywhere in the definition of 'cell differentiation', either expressly stated or implied, that would allow the process of a SINGLE cell (e.g. syncytium) giving rise to MULTIPLE cell types to be considered 'cell differentiation'.

The process that forms pole cells in Drosophila is 'cellularization' NOT differentiation. These are distinct Processes. The difference between these processes is reflected in the structure of GO. Cellularization is NOT a child of cellular differentation in GO. They do not share any children, and they reside in quite separate locations in the ontology.

Pole cells are also >determined in drosophila. Where the poles cells form is >where pole plasm exists. Some of the original experiments >with determinants had to do with pole plasm. The pole plasm >represents the "determinants" for these cells.

This I know, it's why I suggested the new term 'pole plasm formation'.

>The gene >products in pole plasm that make the decision to form pole >cells would be involved in pole cell fate determination.

I disagree, the definition of x cell fate determination has 'Process by which a (i.e. one) cell becomes capable of differentiating autonomously into a (i.e. one) x cell'. But a syncytial blastoderm doesn't differnetiate into 'A' pole cell, it 'cellularizes' to form several pole cells. And 'lots of other cells too'.

>The >drosophila embryo is special beacuse commitment of cell >fates begins in the syncytial blastoderm, but the molecules >that are set up along the axes of the embryo are still >involved in cell fate commitment once cellularization takes >place. That is why mutations like ftz and the others are so >interesting.

>Making pole cell development synonymous with pole cell >formation depends on whether the migration of pole cells >during embryogenesis would be part of their development. I >would argue that this is part of their normal development, >but I would also accept that once the migration phase begins >these cells become germ cells outright and this process is >part of germ cell development.

I don't see any were else in GO where 'x cell migration' is part_of 'x cell development'. There's no reason why 'pole cell migration' should be any different.

>This would require us to make >a distinction between pole cells and germ cells. I'm not >sure this would be a good idea.

This distinction is already well established in the literature.

>Also, we have to consider the P-cell lineage in C. elegans >with this. In C. elegans, "determinants" are segregated to >the posterior end of the embryo and during the initial >cleavages of the embryo, these determinants are sequested >into the cells that will become the germ cells.

They seem to be distinct processes. I've noticed that the literature often makes a point of the fact the germ cell formation varies considerably between organisms. Perhaps we should have sensu terms?

>I think the structure proposed below will work for both >Drosophila and C. elegans with perhaps very specific >children to describe the processes in flies and worms. I >also think if pole cell formation were an is_a >cellularization we would be o.k.

11)

Russ,

I think that we are being much to rigid in interpreting the definition of differentiation being only one cell to another. The key part of differentitation is the end point, not the beginning. Lots of cells can give rise to more than one cell type, depending on the signals they receive and what gets partitioned where. In worms and other mosaic organisms, each early cell division results in different daughter cells as the cells divide. The determination often takes place prior to cell division. In worms the first division of the zygote gives rise to two cells,P and AB, and the determination step occurs before cell division. This is also the case in more regulative embryos. In sea urchin embryos division of the bottom tier of cells in the 8-cell embryo gives rise to four macromeres and four micromeres. Micromeres then carry out some very important functions in the embryo. I think that not allowing for the idea that determination can occur before cell division would be a great disservice to the community. I think these cells are determined, it is just that the process occurs before cellularization/cell division.

I do agree that there should be a term describing pole plasm formation, but it should be related to the determination of pole cells. That's where organisms really begin to differ in how they segregate determinants.

Can't cellularization of pole cells be a child of both their development/morphogenesis and cellularization? I think this is a special case. It seems that in any case of cellularizationof a specific cell type, that process would be part of the morphogenesis of that cell.

I'm not against making sensu terms. I try to do it only as a last resort so we can keep commonalities together. Maybe in this case, the split needs to be made at a higher level.

David

12) Hi, just in response to:

>there should be a term describing pole plasm formation,

we have in process already: pole plasm assembly ; GO:0007315 --%pole plasm assembly (sensu Insecta) ; GO:0048113

so these should get the synonym 'pole plasm formation', and extra relationships to link the sensu Insecta one at least to the pole cell terms.

Becky

13) To my mind, having a cell is a prerequisite for cell fate determination and cell differentiation. How can a cell differentiate if that cell does not yet exist? It's clear that cell fate determinants are present in the pole plasm, and and in the portion of the cytoplasm that is incorporated into one of the daughter cells following asymmetric cell division. But the asymmetric distribution of these components before cell division or cellularization is NOT part of cell fate determination. They do nothing to determine the fate if a cell until after the cell has been formed.

The function of a signaling molecule is dependent on it being secreted at the right time and the right place, should we don't consider the components of the secretory pathway to be part of cell cell signaling?

14) Russ,

I can sort of see where you are coming from, but I really don't think it is how things work. Fate is often determined before cell division. The Par mutants in worms are a good example. If they are mutant, then the cells do not adopt the correct fates in the early embryo. I would say that the Par genes are involved in the specifiacation of cell fate. Perhaps we should let a worm person weigh in on this.

David

15) Hello,

I don't think I was suggesting (I certainly didn't intend to) that the determinants that are incorporated into a cell during asymmetric cell division or cellularization should not be considered part of that cell's fate determination. These components should be annotated with the cell fate determination term, if such a term exists.

However, I do not think the process of making these determinants or moving them to a sub-cellular location within the precursor cell (e.g. pole plams assembly) should be considered part of the cell fate determination of one, or some, of the daughter cells. Nor do I think the process of cellularization or asymmetric cell division should be considered part of cell differentation of the daughter call.

Russ

16)

"Nor do I think the process of cellularization or asymmetric cell division should be considered part of cell differentation of the daughter call."

I'm with you on the asymmetric division. I think if we considered cell division in general to be part of the morphogenesis of any cell, we would run into real trouble. I am on the fence with the cellularization. I guess it depends on in this special case whether one would consider it part of the morphogenesis of these cells.

For the other issue, let's let other folks weigh in. If I'm interpreting the discussion coerrectly it comes down to whether or not having the right things in the right place in an embryo to make the right cells there is a part of fate commitment. In my mind this is the difference between specification and determination. But, I would be willing to change if other think not.

David

17) Hi--

Here are some thoughts from a worm person trying to weigh in on this:

From Russ:

"However, I do not think the process of making these determinants or moving them to a sub-cellular location within the precursor cell (e.g. pole plams assembly) should be considered part of the cell fate determination of one, or some, of the daughter cells."

In WormBase, we've annotated genes like the par genes to the term: asymmetric protein localization during cell fate commitment. The par genes do not encode determinants, but by being asymmetrically localized themselves, direct the asymmetric localization of determinants. The par-dependent process that localizes determinants begins in the zygote, before the daughter cells are born. If this process fails, then daughter cell fate determination is abnormal. I think that in the early C. elegans embryo, the ideas of asymmetric protein localization and cell fate determination are inextricably linked and that's why it has made sense to us to annotate to the term, asymmetric protein localization during cell fate commitment.

Russ, do I understand correctly that you would prefer this term not be a child of cell fate commitment and that genes like the par genes be annotated to asymmetric protein localization without the connection to cell fate commitment?

--Kimberly

18) PMID: 14597570 has a nice review of primordial germ cells across several species if anyone is interested in the biology here.

It seems to me that there is no such thing as "pole cell fate determination" or "pole cell fate commitment"...at least not as we have defined this in GO. Pole cells, or Primordial Germ Cells do not appear to be generated through the standard mechanisms of cell face specification and determination. I think gene products involved in the generation of pole cells would be annotated to "pole cell formation" or "pole cell development".

While we are at this...I concur with Russ that 'Primordial germ cell" should be a synonym where "pole cell" is used.

-Doug

19)

Sorry...gonna have to back peddal a bit on this.

PMID: 15666347

1) Seems to clearly discuss the specification of PGCs from PGC precursor cells in mice 2) Indicates that PGCs can be generated from pluripotent ES cells 3) Indicates that PGCs are restricted in their lineage...ie they can only produce gametes

Perhaps there are two slightly different processes going on here. One, the concept of preformation, where the PGCs are formed by segregating germ plasm, and a different more 'standard' cell fate commitment process that involved cell-cell interactions and extracellular cues. Perhaps these two modes of PGC formation need different GO terms?

-Doug

20)

Hi Doug,

I certainly think that there are two processes going on here. In one, fate is decided by what you contain (flies and worms) and in the other fate is decided by where you are (mice). I thik this is the classic difference between regulative mechanisms of cell fate commitment and mosaic mechanisms of cell fate commitment. It also gets at the breakdown of cell fate commitment into two steps, specification and determination. I don't think this is necessarily restricted to germ cells. In mosaic animals, determination occurs because the cells contain or don't contatin "determinants" that dictate their fate. However, even in worms, fates are not determined by entirely mosiac mechanisms.

In animals, germ cells are special beasts and they are segregated early from the somatic cells, so in some cases the determination of germ cells occurs very early with the segregation of the germ plasm in the fertilized egg. Move the germ plasm and you make germ cells somewhere else. In plants germ cells are not segregated.

David

21) I suppose that if the germ plasm segregates, resulting in the production of PGCs whose fate is unchanged by moving that germ plasm to a new location, then the determinants in that germ plasm are in fact involved in cell fate determination. In fact...their name "determinants" implis that, no? I guess the crux of the issue then is if we can agree that the genes that make these determinants are involved in the process of "pole cell determination" (aka "primordial germ cell determination"), just as other factors are that are involved in 'regulative' mechanisms?

Are the various genes involved in "pole cell fate committment" regardless of how you get there...or do these two mechanisms demand different GO terms like "regulative pole cell fate commitment" and "preformative pole cell fate commitment"??

22)

I won't comment on these cell terms specifically but would like to point out that the issue of "formation" came up during the discussion on organogenesis and we decided to make formation a part of morphogenesis, in particular with respect to the initial generation of form.

David

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/3433":https://sourceforge.net/p/geneontology/ontology-requests/3433

geneontology / go-ontology

pole cell formation #3418