add synonym GO:0006342 chromatin silencing

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+ heterochromatin formation

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/1479":https://sourceforge.net/p/geneontology/ontology-requests/1479

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Done.

Original comment by: jl242

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• assigned_to: nobody --> jl242
• milestone: --> 224410
• status: open --> closed-accepted

Original comment by: jl242

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yes I don't know why I added this.

but is there a term which could be used for heterochromatin formation ?

perhaps a new term could be added here

0006325 establishment and or maintenence of choromatin architecture --GONEW heterochromatin formation

the other related term chromatin assembly/disassembly appears from its children to refer to nucleosome assembly rather than the topological changes which occur during heterochromatin formation

also heterochromatin formation would have GO:0006338 chromatin remodeling as a parent

Original comment by: ValWood

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• status: closed-accepted --> open-accepted

Original comment by: jenclark

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Hi Val - am I missing something here? Why isn't heterochromatin formation a type of 'chromatin silencing'?

Original comment by: jl242

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according to Michael, (see the thread about this synonym) in drosophilla not all heterochromatin is transcriptionally inactive .......although I thought about it later and I don't understand how its physically possible to have transcription from heterochromatin ....

Original comment by: ValWood

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Oh right. Could be this he means:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list\_uids=7813435&dopt=Abstract

Original comment by: jl242

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I only read the abstract but isn't this saying

'paradoxical finding that GAGA factor'

ie not acting as a transcriptional acrivator but acting as a transcriptional repressor ie

'transcriptional regulator can associate with specific DNA sequences in a fully condensed mitotic chromosome'

...it doesn't say and activates transcription. I think this is pretty standard, that some DNA binding factors (often typical thought of as transcriptions) bind and maintain silent heterochromatin.

for instance the fungal binuclear zinc finger is usually a TF but one of them is involved in maintaining centoromere sequence in S. cerevisiae.....

Original comment by: ValWood

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Oh yeah - that's true.

Original comment by: jl242

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Hi Val - I just checked the archive, and he says that the Y chromosome in Drosophila is heterochromatic, yet it is still transcriptionally active in some cell types. I found this paper:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list\_uids=1465096

which seems to confirm this (sort of). So I guess we need to rethink...

Original comment by: jl242

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Actually, what you suggest below would be fine then. Maybe we could have a child term:

transcriptionally inactive heterochromatin formation

which could go under 'heterochromatin formation' and 'chromatin silencing'?

Original comment by: jl242

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hmm, still not sure. Again I haven't read the papers (type first, read later) but from a quick scan of google top hits it seems as though the lampbrush loops are small locally unfolded regions of chromosomes which are generally condensed.

for example http://www.uni-duesseldorf.de/MathNat/Genetik/buneman.html

to me the structure of heterochromatin makes it physically impossible for transcription to take place because the complementary strands cannot separate. This necessarily requires a disruption of the heterochromatin.?? this may be a simplistic view....I work on a simple organism

Original comment by: ValWood

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I think we need to find an expert in chromatin structure - do you know any?!

Original comment by: jl242

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I can ask Robin Allshire. Perhaps should ask Michael to recommend a drosophila expert.

Original comment by: ValWood

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en route to looking up something else, I saw a review that might help: Annu. Rev. Genet. 1995 pp 577-605, PMID:

Original comment by: mah11

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Any word from Robin Val?

Original comment by: jl242

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I have just mailed Robin about somthing vaguly related. I'll do this one when he responds. its on my list. v

Original comment by: ValWood

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GO:0006342 now has heterochromatin formation as a non-exact synonym (which is probably as good a solution as we're going to come up with). So can we close this?

Original comment by: mah11

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I think so...I'm sure it will be revisited :)

Original comment by: ValWood

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I think this can be closed.

although I just came across this review:

Transcriptional interference - a crash course. Shearwin KE, Callen BP, Egan JB. School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia 5005.

The term 'transcriptional interference' (TI) is widely used but poorly defined in theliterature. There are a variety of methods by which one can interfere with the process or the product of transcription but the term TI usually refers to the direct negative impact of one transcriptional activity on a second transcriptional activity in cis. Two recent studies, one examining Saccharomyces cerevisiae and the other Escherichia coli, clearly show TI at one promoter caused by the arrival of a transcribing complex initiating at a distant promoter. TI is potentially widespread throughout biology; therefore, it is timely to assess exactly its nature, significance and operative mechanisms. In this article, we will address the following questions: what is TI, how important and widespread is it, how does it work and where should we focus our future research efforts?

PMID: 15922833 which may be useful, and would trancriptional interference /TI be an appriopriate synonym for chromatin silencing?

Original comment by: ValWood

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• status: open-accepted --> closed-accepted

Original comment by: mah11

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Sounds like TI doesn't fit the def of chromatin silencing at all -- TI is more transient and doesn't involve .heterochromatin

So I'll close this; open a new one if it turns out we need a term for transcriptional interference.

Original comment by: mah11

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• labels: --> Other term-related request

Original comment by: mah11

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• milestone: 224410 --> PomBase

Original comment by: mah11