Thanks! Obvsly, I have many thoughts on that. I think enhancer-reporters tell you a lot about what expr. the enhancer might be driving, but that could be quite different from what it does endogenously.
And pairing the same enhancer with different core promoters in vivo - could be another story 😉

My new lab at the @molgen.mpg.de will be following up on some of the nuclear organization aspects of ecDNA so please do reach out if this is of interest :)

This project started when I was a postdoc in @stemundi.bsky.social lab and supported all the way. Thanks also to @molgen.mpg.de and @bihatcharite.bsky.social for an inspiring work environment

@blanka-majchrzycka.bsky.social did an absolutely amazing job!! created everything from scratch, set up #RMCE with the fantastic help from @arnaudkr.bsky.social and saw this thing through.
She'll be looking for a #postdoc position very soon. I'd ask her if I were you!!!

you must check out @yghavi.bsky.social and @mmasoura.bsky.social's story, who found a similar mechanism in Drosophila. it's so cool if two works align!!

www.biorxiv.org/content/10.1...

even more results in the #preprint!

Our interpretation (TL;DR)
We think that the promoter-proximal cis-regulatory element acts like a #facilitator that helps to filter and relay long-range enhancer activity to the core promoter!

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.