We observed that while gene activity groups cell type functionally, whereas CREs and regulatory seqs group them ontogenetically. E.g. mesenteric and tentacle retractor muscles, a dev convergence described by @alisongcole.bsky.social and @ulrichtechnau.bsky.social.

www.nature.com/articles/s41...

With this TF-motif collection, we defined important TF in every cell type (expressed and with high motif accessibility) and we predicted TF-CRE regulatory links. In the example, the predicted cnidocyte GRN.

A major challenge was inferring TF binding motifs. We first derived multispecies motif archetypes from known and de novo motifs, then assigned archetypes to TFs by combining phylogenetic analysis (@zolotarg.bsky.social) with correlations between TF expression and motif accessibility.

Then, we used different sequence models to predict CRE activty. With the crucial help of @steinaerts.bsky.social and @lukasmahieu.bsky.social, who introduced us to the world of DL sequence models. In this example, top motif grammars defining cnidocyte CREs:

We map cell type-specific accessible regulatory landscapes in adult and gastrula stages, identifying over 112,000 candidate cis-regulatory elements (CREs), representing different types of promoters and non-promoter elements.

Finally, comparisons with other cnidarian atlases show specific adaptations in Oculina, pointing to an evolutionary shift toward increased capacity for heterotrophic feeding, a dual hetero/symbiotrophic feeding strategy that may underpin Oculina resilience to extreme conditions.

We also reconstruct the evolution of the algal-hosting cell type gene expression program (see @xgrau.bsky.social's beautiful summary figure below!)

Comparing naturally aposymbiotic to symbiotic Oculina colonies showed an increase in (putative) phagocytic immune-like cells and a dowregulation of diverse metabolic pathways in the gastrodermis.

Building on our 2021 Stylophora cell (www.sciencedirect.com/science/arti...), we now provide new atlases for Oculina and Acropora millepora
and reveal remarkable conservation of cell type programs across 250+ million years of stony coral evolution.

The Oculina genome shows high macrosyntenic conservation across corals. Remarkably high gene counts are explained by species-specific expansions driven by tandem duplications and, using single-cell data, we can explore the functional fate of these frequent duplicates:

We are happy to share our latest work in @nature.com . We study the genomic and cellular basis of facultative symbiosis in Oculina patagonica - a Mediterranean coral remarkable for its ability to survive long periods without algal symbionts. Led by Shani Levy and @xgrau.bsky.social
rdcu.be/eLbaZ

These discussions started in Barcelona in 2023, and BCA is now taking its first steps thanks to the support of the @moorefound.bsky.social. This is just the very beginning - reach out and get involved: biodiversitycellatlas.org

Understanding evolution, decoding genome regulation, predicting gene function, biomonitoring, and much more.

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...

We are looking for a student to continue our work on chromatin evolution:
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...

The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes.

More info: recruitment.crg.eu/content/jobs...

In keeping with tradition - here Cris receiving the lab porró from @aelek.bsky.social and celebrating in style. Congratulations Cris!

Today @crisnava.bsky.social succesfully defended her thesis on eukaryotic chromatin evolution, the second PhD in the lab.
Many thanks to the committee members Nick Irwin, Nacho Maeso and Sara Sdelci @sdelcilab.bsky.social!

We offer three new positions to join BCA Phase 0:
1. A full-stack developer to work on the BCA database with @ebi.embl.org
2. A senior research technician to develop sc methods
3. A bioinformatician to analyze new atlases with @sangerinstitute.bsky.social

Details below.

Please, share and repost.