Join us in person or online for the 24th edition of the Gene Regulation Workshop at Uni Lausanne on Sept 1st, with an again fantastic group of speakers 🥳
Edouard Bertrand
Antonio Giraldez
Phillip Grote @phillipgrote.bsky.social
Susan Mango
Danny Nedialkova
Lucia Strader @luciastrader.bsky.social‬

Lola-I was, however, only required to form a single meta-domain. This highlights a dichotomy between factors like Lola-I, which may control neuronal fate largely independently of inter-TAD interactions, and structural proteins like Cp190, which may enable ultra-long range gene regulation.

We developed an unbiased proteomics approach (inspired by Baldi..Becker 2018) to identify proteins bound to meta-loop anchors. This identified a specific isoform of the axon guidance protein Longitudinals lacking (Lola-I) as enriched at several meta-loop anchors, in our pull-downs and in vivo.

Many meta-loop anchors coincide with TAD boundaries. We found that a major determinant of TAD boundary formation in flies (called Cp190) is required to form a large fraction of meta-loops, including CTCF-dependent meta-loops.

How do meta-loops form?
Most meta-domains contain 2 or more meta-loops, with some of these forming earlier during neurogenesis than the other(s) in the same meta-domain.
We found that in many meta-domains, specific meta-loops (often the earlier forming ones) nucleate others.

1 meta-domain we studied contains a meta-loop connecting promoters of Glutamate receptors 1A and 1B. Disrupting the meta-domain uncoupled their co-transcription (similar to Levo..Levine 2022 for intra-TAD loops connecting paralogous gene promoters).

We recently showed that in fly neurons, specific pairs of TADs megabases apart specifically come together to form meta-domains (Mohana et al. 2023).
Within meta-domains, meta-loops connect accessible chromatin peaks present at promoters of specific neuronal genes or in non-coding intergenic DNA.

We highlighted new research from the past two years on examples of long-range gene regulation - within large TADs, across TADs, and across chromosomes - comparing mechanisms in flies and mammals 🪰❤️🐁.

www.sciencedirect.com/science/arti...

Exciting findings using insulator-seq are:
Not all insulator-binding protein sites act as enhancer-blockers.
Not all TAD boundaries act as enhancer-blockers.
Both a CTCF motif and its surrounding sequence context are essential for enhancer-blocking.

(2) The insulator activity of CTCF binding sites depends on an intact CTCF motif.

Here’s some proof that insulator-seq works:
(1) It identifies biologically meaningful insulators in genomic DNA (both known and novel).

Anastasiia Tonelli in the lab established insulator-seq - a massively parallel reporter assay for enhancer-blockers in Drosophila cells