query term, loss of chromatin silencing q for SGD

gocentral commented 17 years ago

I spotted this term, but I'm not really sure what it means

loss of chromatin silencing

The process leading to expression of genes that are typically not expressed due to silencing by regulatory proteins.

It looks like a sort of 'regulation of chromatin silencing'

At least, it should have a relationship to

chromatin silencing.

It looks like its the opposite of :

maintenance of chromatin silencing The maintenance of chromatin in a transciptionally silent heterochromatin state.

its child term is also odd... loss of chromatin silencing during replicative cell aging

I'm not sure this really is a process but something which occurs due to accumulated mutations as a cell ages

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/3799":https://sourceforge.net/p/geneontology/ontology-requests/3799

gocentral commented 17 years ago

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Hi Val,

I'll get someone from SGD to take a look.

thanks,

-Karen

Original comment by: krchristie

gocentral commented 17 years ago

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Hi Val,

The phrase "loss of chromatin silencing" or "loss of transcriptional silencing" is used in the yeast literature to describe what happens when the SIR protein complex is redistributed from regions that are silenced (like telomeres) to the nucleolus. The redistribution leads to loss of transcriptional repression at a site. Maybe it's too jargony a term for GO? I guess it could be merged with 'negative regulation of chromatin silencing'. (But that may be confusing to people because loss of silencing actually results in transcription of the silenced gene, so negative regulation of silencing leads to activation of transcription--and positive regulation leads to repression of transcription at the silenced locus).

I don't know...since GO contains all those 'regulation of silencing' terms, as child terms of 'chromatin silencing', there must have been a feeling that we didn't have that biology covered by the 'loss of' terms.

I think 'loss of chromatin silencing during replicatvie cell aging' is a process, based on papers like:

PMID: 9150138 Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S. cerevisiae.

Let me know what you think about merging 'loss of chromatin silencing' with 'negative regulation of chromatin silencing' and I can ask other SGDers to weigh in. We'd then have to change 'loss of chromatin silencing during replicatvie cell aging' to 'negative regulation of chromatin silencing during replicative cell aging'.

Jodi

Original comment by: jodih

gocentral commented 17 years ago

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Perhaps it is OK and just needs moving to under chromatin silencing. We have a chromatin expert here in the pombe microarray group. I'll check with him over the next couple of days.

Val

Original comment by: ValWood

gocentral commented 17 years ago

assigned_to: nobody --> kchris

Original comment by: mah11