This is our (current/tentative) model for the early evolution of animal chromatin architecture.

Finally, in unicellulars, chromatin architecture is “passively” defined by active/repressive chromatin states, without evidence of sequence elements or specific factor binding. See for example co-segregating repressive domains in Sphaeroforma, highly enriched in TEs:

In sponges we do not identify loops, despite the existence of distal enhancers. We hypothesize this could be explained by the relative proximity (<10Kb) of these enhancers to the closest TSS. What we do observe are prominent chromatin jets/fountains, as also recently described in other species.

In the cnidarian Nematostella, we observe multiple enhancer-promoter loops, including some very distal ones (1Mb). Interestingly, here loops show a characteristic one-sided stripe, which may suggest active extrusion (?).

In placozoans, we observed promoter-promoter hubs, highly conserved across two distantly related species.
Not all genes participate in these hubs, only those containing a sequence motif found in TIR sequences of a Mutator DNA transposon, with highly conserved insertions across all placozoans.

What proteins are involved in forming these loops? CTCF is absent in non-bilaterians. Using chromatin proteomics and DAP-seq, we identified two ctenophore-specific zf-C2H2 proteins that we called Ctenophore Tethering Element Proteins, which also cannot bind methylated sites.

The most unexpected finding is the presence of chromatin loops genome-wide in ctenophores, cnidarians and placozoans. Nothing in unicellular holozoans. See an example of the beautiful regulatory landscapes in Mnemiopsis, with thousands of loops connecting enhancers and promoters.

To interpret these maps we first generated new, chromosome-scale assemblies for Capsaspora, Mnemiopsis and Ephydatia, reassembled pre-existing scaffolds for others species, and profiled diverse linear epigenomic marks (hPTMs, accessibility, methylation).

To reconstruct the evolutionary history of animal regulatory genomes, we used Micro-C to explore 3D genomes across 7 lineages (9 species in total!) spanning the origin of Metazoa.

Such an inspiring discussion on how to disseminate science. It's all about making your research seen, heard and felt! Huge thanks to the panel members #CRGBIpostdocs @crg.eu @babrahaminst.bsky.social