Ozren Bogdanovic

Combinatorial BMP4 and activin direct the choice between alternate routes to endoderm in a stem cell model of human gastrulation Inge et al. show that human endoderm originates from two converging developmental routes with distinct dynamics and efficiencies yet similar developmental potential. Combinatorial activin and BMP4 sig...

So exciting to see this in print! Ever wondered how embryonic cells know what (fate) to become during early development? In particular when they might see different signaling cues? We investigated this!

And a lovely cover from Zoe Ruiz and @oliveringe.bsky.social!

www.cell.com/developmenta...

👏👏Congrats @fany-real.bsky.social for the EMBO YIP. Brilliant!!!

🐟Meet the DANIO-ReCODE team!🐟
This week: Martina Sevo and Prof Blaz Zupan from University of Ljubljana

Martina´s research focuses on conversational AI for exploring complex data in tissue regeneration research

📢Stay tuned! #DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social

Extreme autotomy and whole-body regeneration in photosynthetic sea slugs Autotomy, the voluntary shedding of a body part, is common among animals. Mitoh and Yusa report an extreme case of autotomy with the shedding of the main body, including the whole heart, and subsequen...

Photosynthetic sea slugs can decapitate themselves & regenerate whole body from the detached head (without the heart or guts), while the shed body do not regenerate. The process takes ~2-3 weeks. A new model for regeneration?

From: www.cell.com/current-biol...

Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.

Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9

piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....

🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)

🐟Meet the DANIO-ReCODE team!🐟
This week:Parth Bhatia and Prof @ferencmueller.bsky.social from @unibirmingham.bsky.social

Parth´s research focuses on the annotation,characterisation and dynamics of cis-regulatory elements (CREs) in telencephalon injury

📢Stay tuned! #DANIO #MSCA @obog.bsky.social

Mechanisms of DNMT3A–3L-mediated de novo DNA methylation on chromatin - Nature Structural & Molecular Biology Yan et al. use cryo-EM to obtain structures that reveal how DNMT3A2 and DNMT3L cooperate to read histone signals and bind chromatin, illustrating a mechanism that controls DNA methylation and shapes e...

Some hardcore mechanism, for the aficionados (from Peter Jones @vai.org and Ting-Hai Xu @slu-official.bsky.social labs) @natsmb.nature.com www.nature.com/articles/s41...

#CABDseminars

"Rewriting Cell Identity Through TET2 Chromatin Profiling and DNA Methylation Editing" by José Luis Sardina @jlsardinalab.bsky.social, @carrerasijc.bsky.social

🗓️ November 7th
⏰ 12 pm
📍sala Grado, edificio 25 (biblioteca UPO) ‼️

Hosted by @obog.bsky.social

YouTube video by John Rawls Zebrafish in the wild

Part 6: For decades, the zebrafish has helped scientists unlock the mysteries of genetics, development, & disease. But the fish that power most discoveries have spent generations inside lab tanks. This video captures footage of zebrafish in their natural environment in Nepal.
youtu.be/cCZhZpPALqw

Two back-to-back stories on mitosis led by my incredible postdoc @krunovuk.bsky.social at @institutrb.bsky.social, in which we challenge the gliding model of CENP-E-driven chromosome congression! Today in @natcomms.nature.com
doi.org/10.1038/s414...
doi.org/10.1038/s414...

Thanks for the great collaboration!!

💥 Another fruitful collaboration!

Along with @obog.bsky.social & Juan Tena’s teams we provide a multiomics study of zebrafish spermatogenesis
🐟#meiosis

👇
www.embopress.org/doi/full/10....

A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation | Molecular Systems Biology imageimageA multiomics study of zebrafish spermatogenesis integrating scRNA-seq, scATAC-seq, and base-resolution DNA methylomes defines the chromatin and transcriptional states of germ cells, revealing the regulatory dynamics of this continuous ...

www.embopress.org/doi/full/10....

Thanks Max!!

A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation | Molecular Systems Biology imageimageA multiomics study of zebrafish spermatogenesis integrating scRNA-seq, scATAC-seq, and base-resolution DNA methylomes defines the chromatin and transcriptional states of germ cells, revealin...

Now out in @molsystbiol.org www.embopress.org/doi/full/10....

Bogdanovic Lab

We’re looking for a Research Assistant / Lab Manager to join the 🧬 Developmental Epigenomics lab at the Andalusian Centre for Developmental Biology (CABD, Seville 🇪🇸)!
🐟 Work with zebrafish, CRISPR–Cas9, and genomics technologies
💫 3-year fully funded position
Details 👉 www.bogdanoviclab.org

🐟Meet the DANIO-ReCODE team!🐟
This week: Dario González and Dr Csilla Várnai from @unibirmingham.bsky.social

Dario studies the annotation, characterisation, and conservation of 3D chromatin topology in telencephalon injury

📢Stay tuned!
#DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social

Embryonic signatures of intergenerational epigenetic inheritance across paternal environments and genetic backgrounds | The EMBO Journal imageimagePaternal environmental exposures have been linked with modulation of phenotype and disease risk in offspring via largely unclear mechanisms. This study employs in vitro fertilization and sin...

❓Can a father’s environmental exposures before conception influence their offspring?

We systematically tackled this - identifying effects of paternal age, environment and genetics on early embryos - as well as confounding influences

www.embopress.org/doi/full/10....

Epigenetic relay: Polycomb-directed DNA methylation in mammalian development In mammals, repression of germline-specific gene expression is essential for preserving somatic cell identity and preventing disease. Germline gene silencing is often dependent on the presence of prom...

Very excited to share an excellent review from @teresa-urli.bsky.social, published one week before her PhD defense! We did a deep dive into the fascinating biology of the variant Polycomb complex, PRC1.6 (1/5) journals.plos.org/plosgenetics...

Non-CG DNA methylation in animal genomes Nature Genetics - This Review discusses noncanonical DNA methylation (mCH) in animal genomes and highlights the remaining need to clarify whether mCH represents a conserved regulatory layer or a...

Very happy to have contributed to this review on "non-CG" #methylation in animals now out in @natgenet.nature.com. Working again with @obog.bsky.social and Tirsa is always a pleasure. We think this not so well studied form of methylation should be more widely considered, please read: rdcu.be/eFAEk

@jenncoughlan.bsky.social @alexdemendoza.bsky.social @obog.bsky.social @planktomancer.bsky.social @zrlewis.bsky.social

Many people were essential, I can only tag a handful here! @caseywdunn.bsky.social @stevehaddock.bsky.social @colinjanthony.bsky.social @rebeccarhelm.bsky.social @catmunro.bsky.social @amandine-oceano.bsky.social @scientifikita.bsky.social @guillermodelia.bsky.social & Yale Peabody Museum

Physalia megalista, a cnidiran with a gas filled float, raised sail, and long blue tentacles hanging below. Image credit: Dalila Destanović

Excited to share our study on sailing siphonophores, AKA bluebottles or man-o'-war! 🌊 we received hundreds of samples from scientists around the world, part of a huge effort to sequence genomes and test for multiple species 🧬 out today in @currentbiology.bsky.social doi.org/10.1016/j.cu... 🦑🧪📌

Cholangiocytes contribute to hepatocyte regeneration after partial liver injury during growth spurt in zebrafish - Nature Communications During partial liver injury in growing zebrafish, cholangiocytes regenerate hepatocytes through transdifferentiation, revealing a stage-specific regeneration mechanism regulated by mTORC1 signaling.

🚨 Just out in Nature Communications:
Cholangiocytes contribute to hepatocyte regeneration after partial #liver #injury during growth in #zebrafish
We challenge old assumptions on liver regeneration!
🔗 nature.com/articles/s41...
🧵(1/8)

EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!

Sequence-alignment is not the best way to detect conserved cis-regulatory elements?
Tobi Zehnder from Vingron-Lab developed #IPP a synteny based algorithm with @ferencmueller.bsky.social, @borislenhard.bsky.social& @da-bar.bsky.social
We used it to find conserved enhancers with diverged sequences

Boromir Meme: One does not simply select the longest ORF

I am super excited to announce the first (brief) pre-print purely from my group:

Start right to end right: authentic open reading frame selection matters

www.biorxiv.org/content/10.1...

This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!

The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila The pioneer factor Zelda activates a specific set of developmental and structural genes to end tissue regeneration.

So excited that our latest work is out! We have been working to understand how damaged tissue exits regeneration and returns to normal gene expression, and found a major role for the pioneer transcription factor Zelda in flies. Kudos to @anishbose.bsky.social @keatonschuster.bsky.social et al!