RR6: Mechanisms of transcriptional activation/initiation Flashcards
What’s the difference between mammalian and bacterial expression vectors?
Mammalian expression vectors need to have different elements to drive the expression of the genes, like promoters, it’s more complex because the expression is more complex than in bacteria.
What is the Mediator?
It’s a big multisubunit protein complex.
Interacts with RNA pol2.
Interacts with DNA-binding transcriptional activators.
Up to 31 subunits.
3 major domains: head, middle, tail.
Can get through vast sections of chromatin to enhance transcriptional activation.
It acts as a bridge between transcription factors bound to enhancer regions and RNA polymerase II at the promoter region of a gene.
Acts like glue inside of a chromatin loop.
Makes sure that RNA pol 2 is at the right place to carry out the transcription reaction.
How can the Mediator pass through vast sections of chromatin?
With associations between general transcription factors, TAFs, transcription factor activation domains bound to enhancers, and promoter-proximal activators on specific Mediator subunits.
To what do the transcription activation factors bound to enhancers go on the Mediator?
To the Head of the Mediator.
To what do the promoter-proximal activators bind to the Mediator?
To the Tail of the Mediator.
Does transcription happen in a linear manner?
No, the Mediator acts like a bridge. It helps create the loops that happen during transcription where it brings elements closer together.
When is the mediator first involved in the reaction?
During the pre-initiation. It brings everything together. But it’s still important during the rest of transcription.
What makes a gene highly transcribed?
More RNA is produced from that given gene.
What’s a shadow enhancer?
It’s a strong enhancer in the Snail gene.
TRUE OR FALSE? Transcriptional efficiency is associated with increases burst frequency.
TRUE! Transcription works through bursts. The better the enhancer, the higher the burst frequency. The higher the burst frequency, the more efficient the transcription.
What is a burst and how does it happen?
It’s a random process when a cell transcription activity happens through bursts of activity and non-activity. For example, to initiate transcription, all of the necessary factors would get together, form a condensate and then dissociate. That would cause a burst.
What are P-Granules?
They are droplets of liquid (liquid-liquid condensates) found in every organism. They don’t mix. Condensates are important for the transcription reaction.
How did we find out about P-granules?
In C elegans and in Drosophila. They move to the posterior end of the embryo before cell division. And the posterior will eventually give rise to the germ line.
Why are droplets so important?
Because they form places where proteins, that would normally come together, can congregate so they maintain their functions with those proteins.
The formation of these condensates (droplets) is largely dependent on what?
On the concentration of macromolecules, like DNA, RNA, proteins, etc.
And on the valency of the constituents, like electrostatic interactions that really promote the formation, or the post-translational modifications (like phosphorylation), or the intrinsically disordered proteins.
