parentage

[gocentral]

Hi,

I'm no expert on chromatin silencing, and wondered whether GO:0031936 (negative regulation of chromatin silencing) should be a child of GO:0006345 (loss of chromatin silencing)? so that the negative regulation of negative regulation of transcription becomes a positive regulation of transcription? :)

Chris

Reported by: c_tissier

Original Ticket: "geneontology/ontology-requests/4114":https://sourceforge.net/p/geneontology/ontology-requests/4114

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I think there are two issues here. One is whether there should be a relationship between GO:0031936 (negative regulation of chromatin silencing) and GO:0006345 (loss of chromatin silencing); it seems to me there should, but I'm not enough of an expert to know which should be the parent and which should be the child (or if they should be merged).

The other is the odd-looking relationships that result from negative regulation of chromatin silencing being a type of regulation of chromatin silencing (GO:0031935), which in turn is part_of chromatin silencing (GO:0006342). The relationship GO:0031936 is_a GO:0031935 is accurate, so it wouldn't make sense to remove it; the real problem is that the relationship between GO:0031935 and GO:0006342 should be 'regulates', not 'part_of'. When we're able to use the 'regulates' relationship, structures like this one will make a lot more sense.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=473890 Originator: NO

Maybe this question should be merged into Val's item, which is already titled 'chromatin silencing' so that these related questions can all be dealt with together.

[ 1708213 ] chromatin silencing https://sourceforge.net/tracker/index.php?func=detail&aid=1708213&group\_id=36855&atid=440764

-Karen

Original comment by: krchristie

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Tanya - I'm assigning this to you & David because (a) it has to do with regulation; and (b) it seems a lot more tractable now that we have the lovely 'regulates' relationships than before.

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> tairtb

Original comment by: mah11

[gocentral]

Logged In: YES user_id=579762 Originator: NO

After reviewing this long dormant item, here are the changes we've made:

made loss of chromatin silencing is_a negative regulation of chromatin silencing

removed is_a link between 'loss of chromatin silencing' and 'chromatin remodeling' because 'negative regulation of chromatin silencing' relates to that term already

removed is_a link between loss of chromatin silencing and positive regulation of gene expression, epigenetic and created new is_a link between negative regulation of chromatin silencing and positive regulation of gene expression, epigenetic instead

created new is_a link between chromatin silencing and heterochromatin formation, based on definition of chromatin silencing

removed link between pos reg of transcription, DNA-dependent and loss of chromatin silencing

created new is-a link between neg reg of chromatin silencing and pos reg of transcription, DNA-dependent

Original comment by: tberardini

[gocentral]

• status: open --> closed-accepted

Original comment by: tberardini