Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one? Check our latest preprint, led by @mmasoura.bsky.social, to find out! www.biorxiv.org/content/10.1...

Various hypotheses suggested that specificity might have to do with 3D genome organization, the sequence of the core promoter, etc... We now provide evidence that the answer instead lies upstream of the core promoter, in the promoter-proximal region!

To reach this conclusion, we first had to study an enhancer in great detail. We did this using the E3 enhancer of twist in Drosophila melanogaster embryos. E3 was previously characterized as a mesodermal enhancer driving the expression of the twist gene during early embryogenesis.

However, to our surprise, we realized that in reporter assays, the activity of E3 is actually much more complex! The enhancer seemed to be active in tissues and stages when twist is not expressed, including non-mesodermal tissues!

In fact, we realized that E3 is a pleiotropic enhancer that is driving the expression of at least 3 other genes, each expressed in a very different spatio-temporal context.

If E3 can drive such complex expression, how is each target gene expressed only in a very specific spatio-temporal window then?? We discovered that the answer does not lie in the sequence of the enhancer or in its ability to form enhancer-promoter loops.

Instead, we found that the promoter-proximal region of each target gene plays a critical role. Indeed, the ability of a reporter gene to respond to E3's input varies drastically depending on the promoter.

Importantly, this promoter-proximal region does not drive enhancer activity on its own. It only seems to restrict the input of the enhancer. We therefore called it a "gatekeeper".

Altogether, we believe that these promoter-proximal gatekeepers belong to an emerging class of non-canonical regulatory elements that, together with facilitators and other similar elements, can modulate enhancer activity without acting as enhancers themselves.

Finally, we believe that these elements are not unique to the E3 enhancer or to Drosophila as beautiful work from @blanka-majchrzycka.bsky.social in @danielibrahim.bsky.social lab arrives to similar conclusions at the mouse Sox9 locus. www.biorxiv.org/content/10.1...

To finish, I would like to acknowledge all the members of the lab who made this work possible, in particular @mmasoura.bsky.social, soon to be graduating and on the job market!