Molecular mechanisms driving transcriptional initiation (1)

How does transcription occur?

Not in a linear manner

What makes the different elements of gene replication (enhancers) interact with each other if it’s folded?

The mediator complex

What are the different parts of the mediator complex?

Head, Middle and Tail

Head+Tail are…

DNA binding mediators

What is the structure in blue on the picture?

dsDNA

What are the circles in the picture?

RNA Pol II

What are the lines with smaller circles on them?

RNA+ribosomes

What is a highly transcribed gene?

A gene that shows high frequency bursts

Transcript used to prove the bursts theory

Singular gene that has sequence elements that give rise to specific RNA structures (stem loops, hairpins)

How will the structures be recognized?

By specific RNA binding proteins fused to GFP

Sna Pr

Gene in Drosophila for gastrulation

Enhancer for Sna

sna shadow

Does the position of sna shadow affect transcription?

Yes: in the 3' position, transcription is weaker

How was it proved that frequency was the only factor that had a correlation with transcription?

When a weaker enhancer was introduced at the 3’ end, the amplitude of the bursts were the same while frequency was notably weaker.

What structures were studied to understand P-granule migration?

C elegans embryo

Solubility of RNA, macromolecules in the embryo

Anterior: soluble/diffused

Posterior: not soluble= droplet/liquid-liquid condensate formation

What explains the formation of those condensates?

Linker domains that are intrinsically disordered regions (IDR)

Factors that control liq-liq. condensate formation (2)

1. Concentration of macromolecules (cofactors too)

2. Valency (electrostatic interactions, post-translational modifications, IDR (AA sequence))

Dynamic kissing model

Observable phenomenon that proves that frequency is important for eukaryotic transcription

Enhancer RNA is thought to…

Act as the initial glue (factor #1) for the formation of the condensate until there’s too much of it (threshold)+mediator action and starts to repel (=dissolution)