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ianakim.bsky.social
Iana V. Kim
@ianakim.bsky.social
330 followers 500 following 29 posts
Postdoctoral researcher in the Sebe-Pedros and Marti-Renom Labs at CRG. Transposable elements enthusiast, passionate about piRNAs, 3D genomes, and Star Trek 🖖
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · 3h
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.
philipcball.bsky.social
Philip Ball @philipcball.bsky.social · 10h
I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
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Reposted by Iana V. Kim
arnausebe.bsky.social
Arnau Sebé-Pedrós @arnausebe.bsky.social · 5h
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.
philipcball.bsky.social
Philip Ball @philipcball.bsky.social · 10h
I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
5 21
Reposted by Iana V. Kim
rafeeque.com
Rafeeque Mavoor @rafeeque.com · May 13
🧵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.

Save and share the post!
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Reposted by Iana V. Kim
ferdix.bsky.social
Ferdinand Marlétaz @ferdix.bsky.social · Aug 13
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
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 ...
www.nature.com
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Reposted by Iana V. Kim
seanamontgomery.bsky.social
Sean Montgomery @seanamontgomery.bsky.social · Jun 13
Updating my intro slides with this fantastic figure now! (And maybe I'll add an extra dashed line for my beloved bryophytes)
strassert.bsky.social
Jürgen Strassert @strassert.bsky.social · Jun 13
Happy to have contributed to this great article: #Protist genomics: key to understanding eukaryotic evolution. Congrats Alexandra Schoenle et al. #ProtistsOnSky
authors.elsevier.com/sd/article/S...
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Reposted by Iana V. Kim
danielibrahim.bsky.social
Daniel Ibrahim @danielibrahim.bsky.social · May 27
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...
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...
rdcu.be
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Reposted by Iana V. Kim
kazu-maeshima.bsky.social
Kazuhiro Maeshima @kazu-maeshima.bsky.social · Mar 29
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
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 11
Thank you so much, Lorenza :)
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 9
Thank you, Joe :)
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 8
Thank you, Isabel!
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
Thank you very much, Thibaut!
ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
Thank you, Paula :)
ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
thank you, Juan!
ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
thanks a lot, Claus! :)
ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
thank you, Dima!
ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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?
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
This is our (current/tentative) model for the early evolution of animal chromatin architecture.
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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:
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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.
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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 (?).
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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.
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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.
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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.
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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).
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
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.
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