More questions! If Sox9 has so many long-range enhancers - Can core promoters alone be activated without #promoter-proximal-region-proximalenhancer-cis-regulatory-element?
So we tested only core promoters in our assay

FACT3: No - core promoters alone are not activated by Sox9 long-range enhancers

We then wondered: Can any other promoter be activated?

So we generated a library of 18 promoters from various genes and measured if they're activated in NPCs.

FACT2: Full promoters show differential activity in NPCs. So there is enhancer-promoter specificity in mammals!!!

Blanka developed Promoter-RMCE, an elaborate method to exchange the Sox9 FULL promoter with libraries of other promoters in mESCs. Sox9 is OFF in mESCs but ON in NPCs. So... Are truncated Sox9 promoters activated by long-range enhancers?

FACT1: Sox9 needs its proximal region to be activated in NPCs

What is a promoter and how does it work? Let’s dive in!

We wanted to understand why most promoters have some sort of cis-regulatory element (a.k.a. promoter-proximal region a.k.a. proximal enhancer) directly upstream of the core promoter.

Sequence-alignment is not the best way to detect conserved cis-regulatory elements?
Tobi Zehnder from Vingron-Lab developed #IPP a synteny based algorithm with @ferencmueller.bsky.social, @borislenhard.bsky.social& @da-bar.bsky.social
We used it to find conserved enhancers with diverged sequences

Paper - accepted
PhD student - graduated

Congratulations Dr. Mikie Phan! You've done great

It's been a good month.

#proudPI