Iana V. Kim

Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.

An expanded registry of candidate cis-regulatory elements - Nature The existing ENCODE registry of candidate human and mouse cis-regulatory elements is expanded with the addition of new ENCODE data, integrating new functional data as well as new cell and tissue types.

Nature research paper: An expanded registry of candidate cis-regulatory elements

go.nature.com/4pAbARf

Huge congrats, Dr. Alberti 🎉!

Check out this beautiful work from our lab and discover how some corals adapted to live without symbionts 🪸https://www.nature.com/articles/s41586-025-09623-6 !!! Huge congratulations to Shani Levy and @xgrau.bsky.social. It was a privilege for me to contribute to your project 🙏

Congratulations, Alex 👏👏👏

Really grateful to see our work featured by @quantamagazine.bsky.social in this piece on the evolution of genome regulation. Huge thanks to @philipcball.bsky.social for such a beautifully written article.

A thoughtful and beautifully written @quantamagazine.bsky.social article about genome regulatory innovation at the origin of animals. Featuring some of our work and highlighting key open questions. Thanks to @philipcball.bsky.social for this fantastic piece.

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!

These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.

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The genomic origin of the unique chaetognath body plan - Nature Genomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem ...

After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41...
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1

Updating my intro slides with this fantastic figure now! (And maybe I'll add an extra dashed line for my beloved bryophytes)

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...

Our new paper is out@ScienceAdvances👇
www.science.org/doi/10.1126/...
🧬Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live human cells.
🔍 @katsuminami.bsky.social et al. have developed a chromatin behavior atlas within the nucleus. 1/2

Thank you so much, Lorenza :)

Thank you, Joe :)

Thank you, Isabel!

Thank you very much, Thibaut!

Thank you, Paula :)

thank you, Juan!

thanks a lot, Claus! :)

thank you, Dima!

There’s much more to explore in the paper—so dive in! It also opens exciting questions for future research: What is the role (if any) of loop extrusion in the formation of these structures? Are these loops dynamic across development/cell types? When did insulating sequence elements evolved?

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.