gocentral
commented
16 years ago Logged In: YES user_id=473890 Originator: NO
Hmmm, to me it seems that the role of Sre1 is in usage of an alternate transcription start site. Many, if not most, genes have multiple start sites and there are many well characterized examples where regulation of start site usage has regulatory consequences. In taking a look at the current process ontology, I don't see any terms for anything relating to regulation of transcription start site usage. I think we definitely need to represent this in GO, perhaps like this:
- regulation of transcription ; GO:0045449 -- regulation of transcription start site selection ; GO:new
Named like that, it seems hard to make child pos and neg terms, since named like this it could be inclusive of cases where usage of one start site goes up while another goes down, so maybe there are better names for the new term, maybe this:
-- regulation of alternate transcription start site selection ; GO:new
With this name, one is definitely designating a 'normal' versus 'alternate' start site, but it would be easier to make pos and neg child terms, since it would be clear that the pos or neg reg was for usage of the alternate start site.
You've also requested a ntr for 'neg reg of gene exp'. Regarding terms with direct relationships to pos and neg regulation of gene expression, I'm not completely sure whether this is warranted, but thinking it through with the possible alternate txn start site term, it might come out like this:
- regulation of gene expression ; GO:0010468 -- negative regulation of gene expression ; GO:new -- negative regulation of gene expression by regulation of alternate transcription start site selection ; GO:new
I'm not completely sure if this is a good way to go. Sometimes alternate start site selection produces a different product, rather than something as simple as up or down reg.
-Karen
P.S. At the moment, I'm not really sure whether the new term should have any additional relationships to either "transcription initiation" or to "transcriptional preinitiation complex assembly", but that could be added later, if appropriate.
Original comment by: krchristie
How would we deal with this one? I don't know where to start!
It is a regulation of protein expression via upregulation of a translationally silent transcript.
Would it be silly to have a term like:
ntr: negative regulation of gene expression by positive regulation of gene-specific transcription (OR sterol regulatory element binding protein target gene-specific transcription )
as a child of both
GO:0043193 positive regulation of gene-specific transcription or even GO:0035104 positive regulation of sterol regulatory element binding protein target gene transcription
and
ntr: negative regulation of gene expression
Abstract Eukaryotic cells respond to changes in environmental oxygen supply by increasing transcription and subsequent translation of gene products required for adaptation to low oxygen. In fission yeast, the ortholog of mammalian sterol regulatory element binding protein (SREBP), called Sre1, activates low-oxygen gene expression and is essential for anaerobic growth. Previous studies in multiple organisms indicate that SREBP transcription factors function as positive regulators of gene expression by increasing transcription. Here, we describe a unique mechanism by which activation of Sre1-dependent transcription downregulates protein expression under low oxygen. Paradoxically, Sre1 inhibits expression of tco1(+) gene product by activating its transcription. Under low oxygen, Sre1 directs transcription of tco1(+) from an alternate, upstream promoter and inhibits expression of the normoxic tco1(+) transcript. The resulting low-oxygen transcript contains an additional 751 nt in the 5' untranslated region that is predicted to form a stable, complex secondary structure. Interestingly, polysome profile experiments revealed that this new longer transcript is translationally silent, leading to a decrease in Tco1 protein expression under low oxygen. Together, these results describe a new mechanism for oxygen-dependent control of gene expression and provide an example of negative regulation of protein expression by an SREBP homolog.
PMID: 18276645 Nucleic Acids Res. 2008 Apr;36(6):2024-31. Epub 2008 Feb 14.
Reported by: ValWood
Original Ticket: "geneontology/ontology-requests/5014":https://sourceforge.net/p/geneontology/ontology-requests/5014