Change label 'genetic imprinting' -> 'genomic imprinting'

pgaudet commented 3 years ago

@ValWood confirmed with Prof Olaf Nielsen from U of Coppenhagen - there is no difference between 'genomic imprinting' and 'genetic imprinting'.

However in PubMed there are 8000 results with ''genomic imprinting' and 200 with 'genetic imprinting' , so I will swap the label on these terms:

GO:0071514 genetic imprinting
GO:0071515 genetic imprinting at mating-type locus
GO:0006349 regulation of gene expression by genetic imprinting
GO:2000653 regulation of genetic imprinting
GO:0060819 inactivation of X chromosome by genetic imprinting

pgaudet commented 2 years ago

@colinlog @ValWood @RLovering @hattrill

Can I move 'genomic (genetic) imprinting' under regulation of gene expression, epigenetic

It's currently under

GO:0006139 nucleobase-containing compound metabolic process
GO:0060255 regulation of macromolecule metabolic process

ValWood commented 2 years ago

That works for me.

pgaudet commented 2 years ago

Actually I don't understand the difference between

GO:0071514 genetic imprinting: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules by a mechanism that is mediated by DNA, is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.

and GO:0006349 regulation of gene expression by genetic 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.

ValWood commented 2 years ago

Me neither.

Both definitions are unsuitable. "passed through the paternal or the maternal germline" is too specific for yeast imprinting (in yeast it is part of mating-type switching) https://pubmed.ncbi.nlm.nih.gov/10408447/

pgaudet commented 2 years ago

How about this as a logical definition for 'genomic imprinting at mating-type locus'

'genomic imprinting' and 'occurs in' some 'mating-type region heterochromatin'

pgaudet commented 2 years ago

GO:0006349 regulation of gene expression by genetic imprinting

[x] Change def to

"An epigenetic mechanism of regulation of gene expression in which epigenetic modifications (imprints) are established during gametogenesis. For a given gene to show parentally biased expression, the imprint are established exclusively in one of the two parental genomes, thus generating an asymmetry between the maternal and paternal alleles."

pgaudet commented 2 years ago

genomic imprinting

[x] move under 'heterochromatin assembly'
[x] Change def to "The establishment of epigenetic modifications (imprints) during gametogenesis, leading to an asymmetry in the heterochromatin between the maternal and paternal alleles, hence to differential expression of the corresponding alleles. This asymmetry results from the different epigenetic pathways acting in maternal and paternal gametes."

pgaudet commented 2 years ago

@ValWood

[x] GO:0071516 establishment of imprinting at mating-type locus has no annotations; can I merge into GO:0071515 genetic imprinting at mating-type locus?
[ ] GO:0071517 maintenance of imprinting at mating-type locus has no annotations either; do you want to keep ?

PMID:14765111 suggests that establishment and maintanance exist; but they have not been annotated.

I have moved the GO:0071515 genetic imprinting at mating-type locus under 'heterochromatin assembly', because it's a completely different mechanism (with the endonuclease) than the mammalian/plant pathway, with DNA methylation and other chromatin modifications.

I also changed the label to 'mating-type locus imprinting'

OK ?

ValWood commented 2 years ago

GO:0071516 establishment of imprinting at mating-type locus has no annotations; can I merge into GO:0071515 genetic imprinting at mating-type locus? GO:0071517 maintenance of imprinting at mating-type locus has no annotations either; do you want to keep ?

you can merge both -but I think there is some confusion here:

I have moved the GO:0071515 genetic imprinting at mating-type locus under 'heterochromatin assembly',

Unless I have this completely wrong (I never annotated this area), but mating-type switching isn't part of heterochromatin assembly.

The heterochromatin silences the non expressed mating cassette. But the mating-type switching isn't part of the heterochromatin assembly. It is the process that switches (replaces) the gene sequence that is expressed in the active locus from the silenced/donor locus by some recombination event (a little bit like VDJ recombination). This item does not currently have any relationship to heterochromatin assembly, and I don't think it should, but I would need to do a lot of reading to remember exactly how it happens. @Antonialock might be able to comment/confirm but she is away until the New Year.

colinlog commented 2 years ago

Mating type switching in S.c. is driven by endonuclease HO cleavage followed by gene conversion. This is a form of (non-reciprocal) DNA recombination, hereby the genetic information in one of the two silent mating type loci on chromosome III are used to change the DNA at the expressed mating type locus on that sae chromosome. The silent copies are assembled into heterochomatin. The active locus is euchromatin, bearing all the hallmarks of an expressed gene, always. " Imprinting " has not been used as word in this context as it usually refers to gender-specific methylation patterns in the gametes (sperm or egg) of eutherians (mammals, marsupials) that influence (epigenetically) the expression of autosomal chromosome genes that are expressed in a parent-of-origin-specific fashion i the devloping embryo and placenta, in hat has been term a 'war of sexes' whereby the mother must protect itself from a too voracious embryo.

I am not sure botu mating type switching in S. pombe ...

On Fri, Dec 17, 2021 at 12:02 PM Val Wood @.***> wrote:

GO:0071516 establishment of imprinting at mating-type locus has no annotations; can I merge into GO:0071515 genetic imprinting at mating-type locus? GO:0071517 maintenance of imprinting at mating-type locus has no annotations either; do you want to keep ?

you can merge both -but I think there is some confusion here:

I have moved the GO:0071515 genetic imprinting at mating-type locus under 'heterochromatin assembly',

Unless I have this completely wrong (I never annotated this area), but mating-type switching isn't part of heterochromatin assembly.

The heterochromatin silences the non expressed mating cassette. But the mating-type switching isn't part of the heterochromatin assembly. It is the process that switches (replaces) the gene sequence that is expressed in the active locus from the silenced/donor locus by some recombination event (a little bit like VDJ recombination). This item does not currently have any relationship to heterochromatin assembly, and I don't think it should, but I would need to do a lot of reading to remember exactly how it happens. @Antonialock https://github.com/Antonialock might be able to comment/confirm but she is away until the New Year.

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pgaudet commented 2 years ago

There are still 2 open questions here:

For GO:0071515 mating-type locus imprinting, it sounds like heterochromatin assembly is OK here?
Merge these two into their parent 'GO:0071515 mating-type locus imprinting' ? Only the parent has annotations
- GO:0071516 establishment of imprinting at mating-type locus
- GO:0071517 maintenance of imprinting at mating-type locus

@ValWood @Antonialock @srengel

ValWood commented 2 years ago

I don't think imprinting is part of heterochromatin assembly, I would say Imprinting is part of 'mating-type switching' and related to heterochromatin assembly in some way (upstream?) but not part of it. I previously tended to ignore this bit of biology because @Antonialock was our in-house expert. She explained it to me about 100 times ;)

pgaudet commented 2 years ago

[x] Changed subclasses GO:0071515 mating-type locus imprinting -intersection_of: GO:0031507 ! heterochromatin assembly -intersection_of: occurs_in GO:0031934 ! mating-type region heterochromatin +is_a: GO:0022413 ! reproductive process in single-celled organism
[ ] obsolete
GO:0071516 establishment of imprinting at mating-type locus
- GO:0071517 maintenance of imprinting at mating-type locus
replace by GO:0071515 mating-type locus imprinting

pgaudet commented 2 years ago

Dear all,

The proposal has been made to obsolete

GO:0071516 establishment of imprinting at mating-type locus
GO:0071517 maintenance of imprinting at mating-type locus

The reason for obsoletion is that these represent molecular functions that play a role in imprinting at mating-type locus (establishment is done by an endonuclease, the maintenance by a inhibitor of DNA repair). There are no annotations or mappings to these terms; these terms are no in any subsets.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/22217

Thanks, Pascale

geneontology / go-ontology

Change label 'genetic imprinting' -> 'genomic imprinting' #22217