imprinting at the mating type locus (sensu Fungi)

[gocentral]

imprinting at the mating type locus (sensu Fungi) PMID: 11030618

would this be appropriate?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/1070":https://sourceforge.net/p/geneontology/ontology-requests/1070

[gocentral]

Logged In: YES user_id=436423

It depends - is there something about it that really distinguishes it from any other imprinting process? (In other words, could you just annotate to 'imprinting' GO:0006349?)

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

Hmm, dunno, This includes (possibly ) single strand break, conversion to DS break, induced recombination event which leads to mating type switching. I have no idea what processes or groups of processes are involved in other types of imprinting. ....

I'll just annotate to imprinting for now.

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423

oh, in that case how about mating-type switching/recombination ; GO:0007533 ?

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

yep.

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423

Val, can we close this one?

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

I was going to say yes, but thinking about it I still think it would be easier for curators not to miss appropriate terms if 'imprinting at the mating type locus (sensu Fungi)' was a child of both imprinting GO:0006349?) and mating-type switching/recombination ; GO:0007533

As further justification, I don't know much about imprinting, but I know it can occurs by other molecular mechanisms ie methylation in higher euk. In fact the phenomenon may have arisen independently a number of times so it may occur by a variety of molecular mechanisms ? the yeast version appears to be a sufficiently different process.

what do you think?

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423

OK as long as we can come up with a definition that distinguishes 'imprinting at the mating type locus (sensu Fungi)' from 'mating-type switching/recombination'. Any thoughts?

Another possibility would be to add a synonym (exact or 'related term' flavor).

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

O.K back to this one......

I actually don't like the term 'mating-type switching/recombination' ...the recombination bit doesn't seem to make sense...the gene conversion is the recombination event and this has a parent 'mitotic recombination' so recombination as part of this term seems to be redundant?

It seems that mating-type switching can be broken down into

imprinting and the recombination event (gene conversion)...at least in S. pombe there are 2 groups of mutants which are epistatic.

A proposed resolution would then be mating-type switching --GONEW imprinting at the mating type locus --0007534 gene conversion at the mating type locus (note term name change because mat in S. pombe MAT in S. cerevisiae)

GONEW imprinting at the mating type locus def. The formation and maintenence of a double strand break which forms the initial step in mating-type switching

would have the additional parent 'imprinting GO:0006349

would this work?

see chapter 9 of the fission yeast handbook and PMID: 14663140

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=516865

there may be a problem here though...

I just saw that has the child term GO:0000729 DNA double-strand break processing The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang.

is a part of gene conversion at the MAT locus, but this isn't always true so it looks like a TPV?

The position of the existing terms looks wrong, because the definition of gene conversion at MAT locus is The conversion of the mating-type locus from one allele to another resulting from the recombinational repair of a site-specific double-strand break at the mating-type locus

"gene conversion at MAT locus, DNA double-strand break formation" is a child of this process?

this term is analogous to the term I proposed below as imprinting at the mating type locus, so maybe a merge of both of these concepts would be more informative.

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=451873

Yep - that is a tpv Val, in fact, there's a whole load of them under that node, 'strand invasion', 'heteroduplex formation', 'DNA recombinase assembly' etc. I might have a go at sorting this lot out...

Original comment by: jl242

[gocentral]

• milestone: --> 224410
• assigned_to: nobody --> jl242

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Okay, how about this:

Term name changes:

gene conversion at MAT locus (GO:0007534) -> gene conversion at the mating type locus

gene conversion at MAT locus, DNA double-strand break formation (GO:0000728) -> DNA double-strand break formation during gene conversion at mating type locus

gene conversion at MAT locus, DNA repair synthesis (GO:0000734) -> DNA repair synthesis during gene conversion at mating type locus

DNA catabolism, exonucleolytic ; GO:0000738 ---%DNA double-strand break processing ; GO:0000729 ------%DNA double-strand break processing during gene conversion at mating type locus ; GO:new ------%DNA double-strand break processing during double-strand break repair via synthesis-dependent strand annealing ; GO:new

mating-type determination ; GO:0007531 ---%mating-type switching ; GO:0007533 ------%gene conversion at mating type locus ; GO:0007534 ---------<DNA double-strand break processing during gene conversion at mating type locus ; GO:new ---------<DNA recombinase assembly during gene conversion at mating type locus ; GO:new ---------<heteroduplex formation during gene conversion at mating type locus ; GO:new ---------<strand displacement during gene conversion at mating type locus ; GO:new ---------<strand invasion during gene conversion at mating type locus ; GO:new ---<imprinting at the mating type locus ; GO:new % imprinting ; GO:0006349

DNA recombination ; GO:0006310 ---<DNA recombinase assembly ; GO:0000730 ------%DNA recombinase assembly during double-strand break repair via synthesis-dependent strand annealing ; GO:new ------%DNA recombinase assembly during gene conversion at mating type locus ; GO:new ---<heteroduplex formation ; GO:0030491 ------%heteroduplex formation during double-strand break repair via synthesis-dependent strand annealing ; GO:new ------%heteroduplex formation during gene conversion at mating type locus ; GO:new ---<strand displacement ; GO:0000732 ------%strand displacement during double-strand break repair via synthesis-dependent strand annealing ; GO:new ------%strand displacement during gene conversion at mating type locus ; GO:new ---<strand invasion ; GO:0042148 ------%strand invasion during double-strand break repair via synthesis-dependent strand annealing ; GO:new ------%strand invasion during gene conversion at mating type locus ; GO:new

imprinting at the mating type locus ; GO:new definition: The formation and maintenence of a double strand break which forms the initial step in mating-type switching.

Would that be okay?

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Hi Val - we've just figured out that 'imprinting' in pombe is very similar to something called 'donor preference' in cerevisae (GO:0007535). If we could think of something to re-name this term to, we could have both 'imprinting (sensu Fungi)' and 'donor preference' as synonyms, and use the same term. Any ideas what we could call it?

Original comment by: jl242

[gocentral]

Logged In: YES user_id=554670

Hi,

I'm responsible for creating these TPV's. sorry for not being so careful and being too cerevisiae-specific! ack!

I wonder if we should remove the "mating-type switching/ recombination" (GO:0007533) term because not all mating-type switchings are equivalent with recombination. And this would free up the tree to allow non-recombination mating-type switching events to be placed as children...

And I put "donor preference" as a part_of child of "gene conversion".

1. obsolete following terms: a. "mating-type switching/recombination" (GO:0007533) b. "activation of recombination (HML)" (GO:0007536) --> terms would be annotated to the new "regulation" term below c. "inactivation of recombination (HML)" (GO:0007537) --> terms would be annotated to the new "regulation" term below

2. new tree

mating-type determination (GO:7531) ---% gene conversion at the mating type locus (GO:0007534) ------ < [all current child terms] - but I still to make sure they're all organism safe ------ < donor preference (GO:0007536) ------ < regulation of gene conversion at the mating type locus GO:NEW ---% [future non gene conversion based mating-type determination processes]

I'm still reading up to see if the child terms of "gene conversion" are all still valid and true. more to come....

eurie

Original comment by: eurie

[gocentral]

Logged In: YES user_id=554670

oh yeah, Mike mentioned that Bernard Dujon gave a talk at last year's yeast meeting in Sweden about mating type switching in different types of fungi. I'm trying to see if he's published it but if I can't find it, I'll drop him a note.

eurie

Original comment by: eurie

[gocentral]

Logged In: YES user_id=451873

Hi Eurie - that looks fine to me - the only thing I'd say is that the equivalent process to 'donor preference' in Pombe is 'imprinting' (confusingly). So I wonder whether we could come up with another name that we could use to refer to the processes in both species?

I'll still fix those paths as outlined below - I'll wait to hear from you about the children of 'gene conversion at the mating type locus' first though.

Original comment by: jl242

[gocentral]

Logged In: YES user_id=554670

I'm not quite sure if "donor preference" in Spombe is "imprinting". I'm getting the impression that imprinting is referring to how double strand breaks are being formed at the pombe mating type locus. It doesn't seem like there is an endonuclease involved (like the HO endonuclease that is invovled in double strand break formation in cerevisiae).

I dunno, I'm swimming up to ears in mating type switching in other fungi so I might be misinterpreting something. But this is what I'm reading: PMID: 14765111.

Also, PMID: 14745027 has a overview of the potential different aspects of mating type switching in a major group of fungi. Scerevisiae has silent mating type cassettes and an HO. Others have the same. But some have silent mating type cassettes only. I've sent email to Dujon to see if there is anything known about the molecular mechanism of different matying type systems.

Original comment by: eurie

[gocentral]

Logged In: YES user_id=516865

I don't think imprinting at the mating type locus and donor preference are analogous

quoting from PMID 11265754

"The switching pattern is programmed by an imprinting event which restricts mat1 gene conversion to only one of the two sister cells, leading to asymmetric cell division. ..... The nicked DNA is stable throughout the cell cycle. The features of the nick fulfil all the requirements for the `epigenetic', site and strand-specific chromosome modification at the mat1 locus, providing strong evidence that an SSB can initiate mitotic and meiotic gene conversion during replication.

The imprint is the ss nick and the process of imprinting is the events leading up to (and including) the formation of the double strand break. Significantly there is biochemical evidence for the imprinting process in the absence of the identification of the genes involved in the imprinting (likely to include an as yet unidentified endonuclease in S. pombe ), so this SF request may have been a bit premature. However, i usually make the requests when I see the need as they usually take a while to filter through ;)

I wanted this to be a child also of GO:0006349 imprinting

Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself.

(perhaps this def needs tweaking for fungal imprinting?)

I envisaged the term I am proposing as a parent of 'gene conversion at the mating-type locus DNA double-strand break formation' or perhaps a merging of the 2 concepts (i.e the DS break is an imprint). Would this make sense for other fungi?

Also,

do the current proposals involve obsoleting mating-type switching/recombination?

Possibly the term should be renamed to mating-type switching, but should be retained as a child of mating type determination, because mating-type switching is a specific part of mating type determination (for instance you wouldn't annotate the mating pheromones or their receprotrs etc. to mating-type switching but you would annotate them to mating-type determination).

Again I know v. little about these processes but if any of this seems incorrect we can contact Benoit Arcangioli for clarification

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423

oops, that was me dragging donor preference in, cos I got confused about which aspects of mating type switching are relevant. very sorry about that!!

But there are some legitimate concerns about 'imprinting' as used in the pombe context -- it looks like it doesn't affect gene expression directly, and therefore doesn't fit the definition of the existing 'imprinting' term (GO:0006349), even if we were to remove the mention of maternal & paternal germline. Instead, the pombe imprint is closely connected with DNA replication -- its formation depends on the direction of replication (e.g. PMID:11226610), and its presence affects replication elongation. We might need sensu terms, and a generic imprinting parent that's not under regulaton of gene expression. Arg.

It looks like we'll also have to be careful how we define the term for pombe imprinting -- PMID:15059961 suggests that the imprint is not a break in vivo, but is one or two RNA residues stuck into the DNA. If they're right, we can't put anything about a break in the def.

it just keeps getting more complicated :P m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

Oh crikey. I hadn't noticed that imprinting was directly under 'regulation of gene expression epigenetic'...but doesn't this indirectly affect expression by controlling which gene is in the expressed locus...or is that stretching it a bit?

Are there any other examples of epegenetic mechanisms which don't affect expression directly, which would require a rearrangement of this term?

I don't mind if we sit on this one for a while as i'm not desperate for the term to annotate to. We can bear this entry in mind if any other imprinting related items crop up, and I can extend this entry with any new info that becomes available.....It was probably a bit premature anyway. I only made the entry because I read the paper (so long ago I have forgotton its content) and couldn't really do anything with it annotation wise except make sure the necessary terms were in place.

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=451873

Eurie's taking over this item...

Original comment by: jl242

[gocentral]

• assigned_to: jl242 --> eurie

Original comment by: jl242

[gocentral]

Logged In: YES user_id=516865

this can probably be closed? val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423

up to you & Eurie (tho I'm never sorry to see 'em close ...)

I now think a generic parent for the existing 'imprinting' term and imprinting in the S. pombe sense would be silly ... it's just that two communities have happened on the same word for two very different phenomena.

The pombe process is a casne of regulation of mating type switching, so maybe that would be a good term to add.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

yes please to the new term

val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423

added regulation of mating type switching GO:0031494 negative regulation of mating type switching GO:0031495 positive regulation of mating type switching GO:0031496

will that do? m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

I think that will be fine. I'm still not sure about the 'imprinting' bit but if I need to i'll return to this when I know more about it....which won't be soon!

val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423

OK, I'll close this for now.

m

Original comment by: mah11

[gocentral]

• status: open --> closed-later

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11