possible obsoletion of mitotic/meiotic transcription terms

[gocentral]

I found some more odd transcription terms suggest obsoletion

1# regulation of transcription during mitosis (I doubt we mean 'mitosis" as in nuclear division more likely this means regulation of tanscription during mitotic cell cycle) PomBase 11 (query the ace2 ones)

2# negative regulation of transcription during mitosis SGD 6 PomBase 6 Flybase 2

3# positive regulation of transcription during mitosis PomBase 3

For these we would be happy to capture by adding an extension to the transcription terms to capture the relevant phase.

ALSO

positive regulation of transcription on exit from mitosis ; GO:0007072 is under this term..... I'm not sure that it should be (what does "on exit?" mean?) does it mean after M-phase?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/10399

[gocentral]

The 'regulation of transcription during mitosis' terms appear to have a long history:

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045897#term=history

Renaming happened way after the term was created, getting rid of the dreaded 'comma' in the original term name.

For GO:0007072, the term is similarly long-lived:

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007072#term=history

Perhaps the histories jog your memory?

Original comment by: tberardini

[gocentral]

• assigned_to: Tanya Berardini

Original comment by: tberardini

[gocentral]

Not really ;)

I think that we just didn't think about these so much when we used them previously.

I don't think these mean during "mitosis" the process of nuclear division though, I still think they mean "during the mitotic cell cycle" and we were using "mitosis" to distinguish from "meiosis".

This is supported by the fact that some of the annotated genes operate at G1/s.

Original comment by: ValWood

[gocentral]

I've just looked at this issue again. For 'regulation of transcription during mitosis,' we've got 42 experimental evidence annotations to this term or children. There are more IEA/ISS annotations as well.

PomBase (30) SGD (8) FB (2) MGI (1) UniProtKB (1)

It looks like everyone except FlyBase could capture the 'during' bit using col16. I'll bring this up during editors' SF call tomorrow and may send out an obsoletion email tomorrow if they agree.

Original comment by: tberardini

[gocentral]

There was agreement on the SF call this morning that 'regulation of transcription during mitosis' and its children should be obsoleted. I'll work up the obsoletion email and send it around.

Original comment by: tberardini

[gocentral]

• labels: --> Term obsoletion

Original comment by: tberardini

[gocentral]

Val - As it usually happens, I found more stuff while getting the obsoletion email together. There are also terms for 'regulation of transcription during meiosis.' Should these suffer a similar fate?

Experimental annotations: PomBase (16) SGD (13) FB (3) MGI (1) RGD (1)

Original comment by: tberardini

[gocentral]

All terms affected: regulation of transcription during mitosis positive regulation of transcription during mitosis negative regulation of transcription during mitosis regulation of transcription from RNA polymerase I promoter, mitotic positive regulation of transcription from RNA polymerase I promoter during mitosis negative regulation of transcription from RNA polymerase I promoter during mitosis regulation of transcription from RNA polymerase II promoter, mitotic positive regulation of transcription from RNA polymerase I promoter during mitosis negative regulation of transcription from RNA polymerase I promoter during mitosis regulation of transcription from RNA polymerase I promoter, mitotic positive regulation of transcription from RNA polymerase I promoter during mitosis negative regulation of transcription from RNA polymerase I promoter during mitosis positive regulation of transcription on exit from mitosis positive regulation of transcription on exit from mitosis, from RNA polymerase I promoter positive regulation of transcription on exit from mitosis, from RNA polymerase II promoter positive regulation of transcription on exit from mitosis, from RNA polymerase III promoter regulation of transcription during meiosis positive regulation of transcription during meiosis negative regulation of transcription during meiosis regulation of transcription from RNA polymerase II promoter during meiosis regulation of transcription from RNA polymerase II promoter during meiosis negative regulation of transcription from RNA polymerase II promoter during meiosis *positive regulation of transcription from RNA polymerase II promoter during meiosis

Original comment by: tberardini

[gocentral]

I've updated the PomBase annotations.

cheers, m

Original comment by: mah11

[gocentral]

Hi Val - Can you respond wrt my earlier question about 'regulation of transcription during meiosis'?

---

Val - As it usually happens, I found more stuff while getting the obsoletion email together. There are also terms for 'regulation of transcription during meiosis.' Should these suffer a similar fate?

Experimental annotations: PomBase (16) SGD (13) FB (3) MGI (1) RGD (1)

Original comment by: tberardini

[gocentral]

Sorry missed this one . Well most of the PomBase annotations look a bit wonky (I think this was problaby me) and the ones which are 'correct' I think should be "regulation of transcription during meiotic cell cycle" rather than 'meiosis' so yes, I would say obsoletion is safer...

We need the term "regulation of transcription during meiotic cell cycle" instead.

I can see how the problem arose too... meiosis is currently defined as "A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle. A meiotic cell cycle is the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations."

most of this def needs to move up to "meiotic cell cycle"

It should be more equivalent to the "mitosis" def A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.

(and refer to nuclear division) I think this is one of the outstanding tasks from the cell cycle workshop...

I'll transfer this part to the outstanding cell cycle ticket...

Maybe should double check with SGD as they have the 2nd most annotaions to this term...I'll ask

Val

Original comment by: ValWood

[gocentral]

Also, terms like this should go under the replacement term regulation of transcription involved in mitotic cell cycle : GO:0000083 regulation of transcription involved in G1/S transition of mitotic cell cycle (although I guess the reasoner will find these)

Original comment by: ValWood

[gocentral]

I've just fixed some annotations to GO:0007070 and GO:0046022 that escaped my previous dragnet. But I took care of the meiosis ones last month, so they shouldn't still be cropping up anywhere ...

Original comment by: mah11

[gocentral]

I think SGD are OK with this. Val

Original comment by: ValWood

[gocentral]

I transferred the part about the meiosis definition to a new ticket https://sourceforge.net/p/geneontology/ontology-requests/10678/

Can we go ahead with the obsoletion notice for this?

Thanks

Val

Original comment by: ValWood

[gocentral]

• Priority: 5 --> 8

Original comment by: ValWood

[gocentral]

I'll get back to working on the obsoletion email. The longest bit is gathering info on the annotations (and not getting sidetracked by other ontology issues that pop up). Thanks for your patience, Val.

Original comment by: tberardini

[gocentral]

Hi Tanya, I only commented on it because it came up in the list with the cell-cycle label that Jane and I were trying to clear yesterday. Which is odd, as it does not have a "cell cycle" label, I don't get SF..... Anyway, no particular hurry...

Original comment by: ValWood

[gocentral]

• Group: None --> PomBase

Original comment by: ValWood

[ValWood]

I think this one is pending obsoletion notice and migration of existing to the "regulation of transcription during mitotic/meiotic cell cycle"

[tberardini]

@ValWood : I dug into the history a bit. It looks like the terms for the meiosis regulation tsc terms were transformed from 'regulation of transcription, meiotic' to 'regulation of transcription during meiosis' to 'regulation of transcription involved in meiotic cell cycle' all while retaining the same id. (done in 2015)

Example:

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051037#term=history

What if we just do the same for the mitosis terms?

Convert all 'during mitosis' (or , mitotic) to 'involved in mitotic cell cycle?

regulation of transcription during mitosis positive regulation of transcription during mitosis negative regulation of transcription during mitosis regulation of transcription from RNA polymerase I promoter, mitotic positive regulation of transcription from RNA polymerase I promoter during mitosis negative regulation of transcription from RNA polymerase I promoter during mitosis regulation of transcription from RNA polymerase II promoter, mitotic positive regulation of transcription from RNA polymerase I promoter during mitosis negative regulation of transcription from RNA polymerase I promoter during mitosis regulation of transcription from RNA polymerase I promoter, mitotic positive regulation of transcription from RNA polymerase I promoter during mitosis negative regulation of transcription from RNA polymerase I promoter during mitosis

What about these? Are they good as is?

positive regulation of transcription on exit from mitosis positive regulation of transcription on exit from mitosis, from RNA polymerase I promoter positive regulation of transcription on exit from mitosis, from RNA polymerase II promoter positive regulation of transcription on exit from mitosis, from RNA polymerase III promoter

[ValWood]

Hi Tanya,

I don't think we can do that. These really are "during". So this is more about the distinction between "mitotic nuclear division" and "mitotic cell cycle"

All these transcription terms mean is that the transcription occurs during the mitotic cell cycle. In known cases where they are involved, a term already exists http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000083#term=ancchart this term could have the "involved in" parent you suggest. But, the other annotations to the existing "during" terms are not involved in cell cycle regulation.

For example, the genes transcribed can include every cellular process which occurs during the mitotic cell cycle.

I don't know about "positive regulation of transcription on exit from mitosis" (exit from mitosis is not a well defined process, and I'm still not convinced that it isn't really a transition, rather than a process)...I hope to follow up on this at some point when I move onto cytokinesis (Need to finish chromosome segregation first) so maybe these terms can hang around for a while longer.

[ValWood]

positive regulation of transcription on exit from mitosis only has 3 annotations. it wont do any harm . However the confusion in the other terms between

during mitosis = GO:0007067 mitotic nuclear division and (incorrect)

and during GO:0000278 mitotic cell cycle (correct)

Longer term "during" terms can be made consistently with annotation extensions, so potentially longer term these can all go....

[ValWood]

Actually I think you can make these terms 'regulation of transcription involved in mitotic cell cycle'

but I would not automatically merge the old term unless the annotations are checked individually (I think the other ones were)

[tberardini]

Val - there are no 'involved in mitotic cell cycle' terms to merge into. There are only the existing 'during mitosis' and ',mitotic' terms. If renaming is fine, that makes the job a WHOLE LOT easier.

[ValWood]

No this was the problem.

The phrase "during mitosis" appears to be used as shorthand for "during mitotic cell cycle" in the same way that "during meiosis" was used as shorthand for "during meiotic cell cycle"

The scan of the annotations validated this, because it is used for transcription which occurs "during the mitotic cell cycle" but which is NOT "during mitosis"

Clearer?

There are 2 solutions i) change all terms and logical definitions to "during mitotic/meiotic cell cycle" not "during meiosis/mitosis" or ii) obsoletion (probably better as the terms are not really required)

this problem all comes back to these ticket: https://github.com/geneontology/go-ontology/issues/10864 https://github.com/geneontology/go-ontology/issues/10690

[tberardini]

Ok. I'll write up an obsoletion email for these terms:

regulation of transcription during mitosis positive regulation of transcription during mitosis negative regulation of transcription during mitosis regulation of transcription from RNA polymerase I promoter, mitotic positive regulation of transcription from RNA polymerase I promoter during mitosis negative regulation of transcription from RNA polymerase I promoter during mitosis regulation of transcription from RNA polymerase II promoter, mitotic positive regulation of transcription from RNA polymerase II promoter during mitosis negative regulation of transcription from RNA polymerase II promoter during mitosis regulation of transcription from RNA polymerase III promoter, mitotic positive regulation of transcription from RNA polymerase III promoter during mitosis negative regulation of transcription from RNA polymerase III promoter during mitosis

[ValWood]

I thought they had already been cleared for obsoletion. But I guess there are more terms now. I see what you mean. You could change all to

"during mitotic cell cycle", which is broader.

[tberardini]

Yes, I started with just the root term but when I went to look at annotations, I saw the raft of children terms and that's kind of where it stalled.

This is the spread of annotations to 'regulation of transcription during mitosis' and children

[tberardini]

If looking at only experimental annotations:

[ValWood]

I would change to the "mitotic cell cycle" for now, which is how the terms have been used. At some future date we might want to visit the value of "precompostition" of these transcription "during" terms

[tberardini]

I would change to the "mitotic cell cycle" for now,

To be absolutely clear, this means changing '% regulation of transcription % during mitosis' or 'regulation of transcription from RNA polymerase [I or II] promoter, mitotic' to '%regulation of transcription % involved in mitotic cell cycle' and 'regulation of transcription from RNA polymerase [I or II] promoter involved in mitotic cell cycle'.

Final answer?

[ValWood]

Nearly;)

All should still be "during" not "involved in" (these are different) All should be during "mitotic cell cycle", not during "mitosis"

[tberardini]

Ok, restating:

• [x] '% regulation of transcription % during mitosis' change to '%regulation of transcription % during mitotic cell cycle'
• [x] 'regulation of transcription from RNA polymerase [I or II or III] promoter, mitotic' change to 'regulation of transcription from RNA polymerase [I or II or III] promoter during mitotic cell cycle'.

[ValWood]

Yes, sorry for the confusion!

[tberardini]

OK, done and done.