meiosis, mitosis and the cell cycle

[gocentral]

Several things:

- the defs of the terms under meiosis are uninformative and could do with improvement.

- is 'entry into meiosis ; GO:0042061' really an example of regulation of meiosis?

- according to the def of meiosis, DNA replication occurs some time during meiosis I; however, as far as I can see, there are no DNA replication terms under 'meiosis'.

- what's the difference between DNA amplification and DNA endoreplication?

- 'premeiotic DNA synthesis' appears as a part of 'DNA replication', which is in turn a part of 'S phase of mitotic cell cycle'. Is the DNA synthesis covered by this term premeiotic in the sense that it occurs during mitosis, rather than during meiosis?

- is 'S-specific transcription in mitotic cell cycle ; GO:0000115' supposed to mean 'S-phase-specific transcription during mitotic cell cycle'?

- 'meiotic mismatch repair ; GO:0000710' looks like a subclass of 'mismatch repair ; GO:0006298' - is this correct?

- anyone know what the somewhat vague term 'DNA replication and chromosome cycle ; GO:0000067' is supposed to mean?

- 'cellular DNA uptake ; GO:0009290' is under 'DNA metabolism' and has the child 'DNA fragmentation'. If 'cellular DNA uptake' means what I think it does (DNA uptake into a cell), then I think it needs to be moved to the 'transport' node. 'DNA fragmentation' to me doesn't sound like a subclass of 'cellular DNA uptake', and I think it would be better suited to 'DNA catabolism'.

It looks like we may need to split DNA replication into meiotic and mitotic flavours to resolve some of the problems above.

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/1650":https://sourceforge.net/p/geneontology/ontology-requests/1650

[gocentral]

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> - what's the difference between DNA amplification and DNA > endoreplication?

I'm not sure there is a genuine difference in the concept; best to ask others. But I do think the two phrases get used in slightly different contexts, such that 'endoreplication' (or 'endoreduplication') carries overtones of more of the genome being replicated (e.g. polytene chromosomes). 'DNA amplification' seems to crop up when a smaller subset of the genome is copied, such as when sequences are amplified in response to presence of a drug because they encoding some product that confers resistance.

It may well be OK to merge these terms, though ... unless DNA amplification is broader ... it might be relevant to bacteria, in which case the difference between amplification and endoreplication is the cell cycle regulation aspect of the latter.

> - 'premeiotic DNA synthesis' appears as a part of 'DNA replication', > which is in turn a part of 'S phase of mitotic cell cycle'. Is the DNA > synthesis covered by this term premeiotic in the sense that it > occurs during mitosis, rather than during meiosis?

DNA synthesis never occurs during mitosis; I assume the 'premeiotic' refers to the fact that the synthesis takes place prior to (wait for it) meiosis rather than mitosis.

The problem would appear to be the parentage of 'DNA replication'; the generic DNA replication and DNA-dependent DNA replication terms shouldn't be under S phase at all, since the latter is quite irrelevant to bacteria.

> - is 'S-specific transcription in mitotic cell cycle ; GO:0000115' > supposed to mean 'S-phase-specific transcription during mitotic > cell cycle'?

probably

> - anyone know what the somewhat vague term 'DNA replication > and chromosome cycle ; GO:0000067' is supposed to mean?

Well, sort of ... I can tell you where I got it: from the chapter on the S. cerevisiae cell cycle in the CSHL Press all-you-could-possibly-want-to-know- about-yeast three-volume set (when the SGD site is back among the living I'll look up the real citation).

The phrase, which I shamelessly cribbed straight out of the book, seems to refer to 'What Happens to DNA during the Cell Cycle' from a very S. cerevisiae-centric point of view, and covers both DNA replication and the regulation thereof, and chromosome dynamics.

I haven't looked at this stuff in ages. It's a scary place. Believe it or not, the cell cycle stuff used to be even worse than it is now.

m :P

Original comment by: mah11

[gocentral]

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"- according to the def of meiosis, DNA replication occurs some time during meiosis I; however, as far as I can see, there are no DNA replication terms under 'meiosis'."

No - we would need to add 'DNA replication during meiosis', 'DNA replication during mitosis' children to be complete. Ah

• just read to the end and that's what you suggest - good idea!

"- what's the difference between DNA amplification and DNA endoreplication?"

'DNA endoreplication' is a perfectly good process, that occurs in e.g. Drosophila, while I think 'DNA amplification' basically means PCR, which we don't want. It's also used when talking about cancer cells, which we also don't want. It has two annotations, both for the same protein, which is involved in DNA replication. So I'd obsolete 'DNA amplification' .

Original comment by: jl242

[gocentral]

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>> "- what's the difference between DNA amplification and DNA >> endoreplication?" > > 'DNA endoreplication' is a perfectly good process, that > occurs in e.g. Drosophila, while I think 'DNA amplification' > basically means PCR, which we don't want. It's also used > when talking about cancer cells, which we also don't want.

True, but it is also used to refer to the entirely normal process of making copies of certain genes (e.g. insect chorion genes; e.g. pmid:10541550).

> It has two annotations, both for the same protein, which is > involved in DNA replication. So I'd obsolete 'DNA > amplification' .

I don't think we should make 'DNA amplification' obsolete. I'm not sure whether it's effectively a synonym for 'DNA endoreplication' (i.e. merge), or
covers more, but either way there's a valid concept in there somewhere.

Since my earlier comment I've dug a tiny bit more, and found a few more bits consistent with the possibility that endoreplication = most or all of the genome and amplification = a few genes. It could do with more literature hunting to conficm, tho.

m

Original comment by: mah11

[gocentral]

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Copying from Midori's previous comment: "The problem would appear to be the parentage of 'DNA replication'; the generic DNA replication and DNA-dependent DNA replication terms shouldn't be under S phase at all, since the latter is quite irrelevant to bacteria."

I agree with this. The specific cell cycle phases in the process ontology can violate all sorts of true paths since many processes can't be binned nicely into a specific time frame, such as SPB duplication and separation cycles for yeast.

"premeiotic DNA synthesis" (GO:0006279) is the meiotic equivalent to DNA replication during regular mitotic growth. It's just the preferred terminology in the field. Many of the same gene products involved in mitotic DNA replication are also used for meiotic DNA replication.

RE: "meiotic mismatch repair" - yes and no. mismatch repair during meiosis has been implicated in processes broader than just fixing mismatched base pairs. So does that mean if "meiotic mismatch repair" becomes a child of "mismatch repair", we need to fix the definition of "mismatch repair"? And possibly the definition of "meiotic mismatch repair" ....

Original comment by: eurie

[gocentral]

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- I'm going to remove 'DNA replication' from 'S phase of mitotic cell cycle' to remove all the TPVs that this placement is generating. It'll now have the parents 'DNA replication and cell cycle' and 'DNA metabolism'. I will also add two specific children, meiotic and mitotic DNA replication, just for good measure.

- 'premeiotic DNA synthesis' will be OK once 'DNA replication' has been moved; should it be given a cell cycle parent term, though, and if so, what should it be? Presumably not meiosis if it is premeiotic.

- 'DNA amplification' seems to be a sticky issue. Dorland's Med Dict has the following def for gene amplification: 'a process by which the number of copies of a gene is increased in certain cells because extra copies of DNA are made in response to certain signals of cell development or of stress from the environment. In humans this process is seen most often in malignant cells.'. Dorlands and the other two medical dictionaries in onelook.com speak of endoreduplication in terms of entire chromosomes. I think that we should keep 'DNA amplification' with a def derived from the text above.

- I'll change the name of GO:0000115 to 'S-phase-specific...'.

Original comment by: girlwithglasses

[gocentral]

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I guess that 'premeiotic DNA synthesis' is equivalent to 'meiotic DNA replication'; is there a similar phrase used for 'mitotic DNA replication'? I couldn't really find anything on PubMed (a meagre 13 hits for 'premitotic DNA synthesis').

Original comment by: girlwithglasses

[gocentral]

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> I guess that 'premeiotic DNA synthesis' is equivalent to 'meiotic DNA > replication'

I think so.

> is there a similar phrase used for 'mitotic DNA replication'?

I don't think so -- at least, I've never heard one.

Original comment by: mah11

[gocentral]

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See also SF:934796 for proposed DNA replication defs.

Original comment by: girlwithglasses

[gocentral]

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All the problems here have either been resolved or will be resolved once the new cell cycle node comes into action.

Original comment by: girlwithglasses

[gocentral]

• assigned_to: nobody --> girlwithglasses
• status: open --> closed-works-for-me

Original comment by: girlwithglasses