I'm wondering if anyone could help me with a genetics problem.

 

I know that for RNA Polymerase II genes - you have a promoter, on which forms the preinitiation complex (PIC). As part of this apparatus, you have general transcription factors (GTFs) necessary for basal transcription in vitro. Things like TFIID, TFIIB, etc.

 

But for efficient transcription in vivo, you need activators and co-activators, yeah? Activators bind to enhancers way upstream (or downstream!), which then bind to co-activators which can either (i) associate with the PIC directly, like certain TAFs and mediator OR (ii) remodel the chromatin to make things slide along easily.

 

What I've just described is a model system. But can anyone think of any real examples of this? Something with clinical correlations would be awesome. I.e. if someone could point out an Activator & Co-activator for a certain eukaryotic virus which both associates with the PIC and/or remodels chromatin, that would be superb. Or perhaps some physiological process.

 

It would be great to have a solid example which covers all the points of this model description of gene activator.

 

Much appreciated.

First, not all genes require an activator for transcription. Sometimes it just enhances the transcription rate. Most viral systems, for instance, do not rely on positive regulation via activators, but rather on strong promoters plus negative regulation via repressors.

That being said there are a number of viruses known that express transcriptional activators. These, however, do not necessarily bind to the DNA (and thus e.g. promote closed complexes), but can actually induce transcription by starting a signaling cascade. An example that I read recently is the X protein from HBV. Or they hijack transcriptional activators (or repressors) from the host, to couple their replication to the cellular state of their host.

The first example I think of is the bacteriophage lambda, about which a fair amount is known.