GO:0016440/GO:0006342

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I think these are conceptually the same, chromatin silencig occurs via methylation leading to the formation of heterochromatin,

also chromtin silencing has no siblings....

GO:0016440 transcriptional gene silencing Gene inactivation (silencing) at the level of transcription, usually associated with methylation of gene promoter region and DnaseI insensitivity.

GO:0006342 chromatin silencing Repression of transcription by conversion of large regions of DNA into an inaccessible state often called heterochromatin.

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/1161":https://sourceforge.net/p/geneontology/ontology-requests/1161

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In a review of silencing in cerevisiae (pmid 12676793) there's no mention of DNA methylation being part of the silencing mechanism, so the def of 16440 might actually be a bit too specific (tho it does say 'usually' not 'always'). But a merge still seems reasonable, since silencing does involve some change in chromatin structure.

Possible def for merged term: Complete inactivation of transcription of a gene or genes by formation of an altered chromatin structure, such as the compacted state called heterochromatin.

Will email the list to get the transcription group to look at this item.

Original comment by: mah11

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• labels: --> Other term-related request

Original comment by: mah11

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Hi,

Just a quick note to say that I'll take a look more carefully.

My initial thought though was actually that the parentage should be reversed, not to merge them, that 'chromatin silencing' could represent any sort of silencing for any region, while 'transcriptional gene silencing' is a subset dealing only with transcriptional silencing of genes.

I also really don't like the def of 'transcriptional gene silencing' because I think it may have been written from a very mammalian -specific perspective. I'm not aware of silencing by DNA- methylation in yeast.

Anyway, I'll take a look.

-Karen

Original comment by: krchristie

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yes reversing the parentage would work

the children of chromatin silencing are chromatin silencing at centromere chromatin silencing at ribosomal DNA (rDNA) chromatin silencing at silent mating-type cassettes

transcriptional gene silencing would be equivalen t to chromatin silecing at genes.

would chromatin silencing at ribosomal DNA (rDNA) then be a child of this?

methylation correlates with transcriptional activation in pombe but not in cerevisiae. Perhaps the definition could be changed to 'usually associated with histone modification'

Original comment by: ValWood

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I see another potential problenm with the parentage of chromatin silencing

GO:0016568 : chromatin modification GO:0016582 : non-covalent chromatin modification GO:0006338 : chromatin modeling GO:0006342 : chromatin silencing

what do chromtin modification (undef) and non-covalent chromatin modification (undef) refer to?

it doesn't look as if though they should be parents of chromatin modelling ( ah this is going to be renamed chromatin remodelling) so some of this may overlap with the other SF entry.

anyway 'chromatin remodelling' isn't a chromatin modification, or a non-covalent chromatin modification

i'll have a look what i put on the other SF entry before I get too confused.....

Original comment by: ValWood

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found it... see SF 831157. these should probably be treated as 1 item as they are related

Original comment by: ValWood

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Good idea Val to combine these two. Since there is only one follow-up comment on your other item, I'm going to copy the text of that one into here and close the other one (SF 831157)

thanks,

-Karen

text of Item 831157 inserted here to combine these two items about chromatin into 1:

0006346 methylation dependent chromatin silencing

add additional parentage 0006342 chromatin silencing

also are covalent chromatin modification and non covalent chromatin modification meaningful in the sense they are being used ?

It looks as though chromatin modification here actually means chromatin remodelling.....it has the child chromatin modelling (a.k.a. remodelling)....which isn't really a chromatin 'modification'

methylation dependent chromatin silencing should also be a part of isa part of chromatin remodelling.

thanks

Val

Date: 2003-10-27 09:44 Sender: val_wood Logged In: YES user_id=516865

chromatin modeling (a.k.a. remodeling) has child terms to represent its involvement in transcriptional silencing events, but not recombination replication and repair. ....I'll come back to this.....

Original comment by: krchristie

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Original comment by: krchristie

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ah I lost this one...jen has already merged chromatin silencing and transcriptional gene silencing but does she know about this item...I'm still not sure whether it should be a merge or

chromatin silencing --transcriptional gene silencing

tha above may be preferable because there are certainly some differences in the mechanisms of silencing at different regions...proably safest to have them like this and merge later if necessary

Maybe Robin would only refer to centromeric silencing as transcriptional gene silencing because his assay for centromeric silencing involved putting a protein coding sequence in the centromeric region and seeing if it was expressed....a curator may want to make the distinction to this level though

Original comment by: ValWood

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this entry is duplicate with 908374, although there are possibly some bits of this item which need ciopying over.

Original comment by: ValWood

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can this one be closed?

val

Original comment by: ValWood

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• assigned_to: kchris --> nobody

Original comment by: krchristie

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sorry, I thought I'd already unclaimed this when I was on maternity leave, but apparently not, the SourceForge site was really slow from home, so I guess I didn't quite finish unclaiming items

-Karen

Original comment by: krchristie

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Hmm, looks to me as though everything in this item is either done or also covered in SF 907476, so we could close. Karen, OK with you?

m

Original comment by: mah11

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sounds reasonable to me Midori, though I think Jodi is more up-to-date on this subject than I am, so I forwarded her the SF email and asked her to take a look as well.

-Karen

Original comment by: krchristie

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Yes, I'd agree that this one can be closed.

Jodi

Original comment by: jodih

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OK, closing now.

m

Original comment by: mah11

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• status: open --> closed-fixed

Original comment by: mah11

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• milestone: --> PomBase

Original comment by: mah11