It was a fantastic exploration during my PhD, a new method, with new struggles. I had an amazing team of Artem and Aleksander to deal with all of them. Also my first experience of project supervision, it was hard but extremely cool. And thanks to @mardzix.bsky.social and Pepe for all the support!

Have you ever wondered how chromatin states shape developmental trajectories? In our preprint, we address this question using single-cell nanoCUT&Tag, a method developed by Marek Bartosovic @mardzix.bsky.social, which simultaneously profiles active H3K27ac and repressive H3K27me3 in the same nucleus

(1/14) Excited to share our new preprint: ArChIPelago — classic ML on top of multiple PWMs improves genomic TFBS prediction. shorturl.at/jnxDA Builds on our MEX paper (Vorontsov et al., 2025). w/ @pensarata.bsky.social @vorontsovie.bsky.social @sevamakeev.bsky.social @halfacrocodile.bsky.social

Fascinating work on enigmatic octopuses with my wife’s @tatiana-atpase.bsky.social MD simulations! Huge congrats to the lab, where she makes her PhD @eriklindahl.bsky.social, and the collaborators lead the project @nbellono.bsky.social!

Male octopuses use a specialized arm that acts as both a sensory and reproductive organ to navigate the female’s mantle, locate oviducts, and transfer sperm. These findings reveal how sensory systems shape reproductive behavior and drive speciation. Learn more in Science: https://scim.ag/4dYMtFq

If you know a graduating undergraduate looking for the chance to spend 1-2 years in a lab before graduate school, we're hiring! Our lab explores morphogenesis, defining how the cell adhesion & cytoskeletal machinery work together to allow cells to change shape & move tarheels.live/peiferlab/ 1/n RT

Evdokimova, A. A., Kolesnikova, T. D., Mazina, M. Y., ...., Vorobyeva, N. E. (2025). Transcriptional induction by ecdysone in Drosophila salivary glands involves an increase in chromatin accessibility and acetylation. Nucleic Acids Res, 53(7) pmc.ncbi.nlm.nih.gov/articles/PMC...

I am very happy (and a bit scared) to present to you what we have been working on over the last 4 years. This manuscript is exactly what I dreamt of when I started the lab and I could not be happier and prouder of the outcome!

1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.

Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social. www.nature.com/articles/s41...

Thrilled to share that I’ll be joining @imbmainz.bsky.social in February 2026 to start my own group! We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology. PhD positions available!

Kicked off a series on #Drosophila TE discovery and naming. The first post covers elements that predate the term "mobile element", and more. artemilin.dev/posts/te_nam...

🧬Postdoc position alert! 🚨 We're hiring a postoc in Computational Modeling of Epigenetic Inheritance at the Hubrecht Institute (Alexander van Oudenaarden, Utrecht 🇳🇱) & Danish Cancer Institute (Anja Groth, Copenhagen 🇩🇰). Come work in our collaberative team of top scientists shorturl.at/avBBy

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...

The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field? That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience A 🧵 1/n

To be or not to be 🤴💀: read how hamlet orchestrates the assembly of adult male reproductive system in #Drosophila in a new paper from our colleagues! Led by Huazhen Wang, a PhD student in Qi Dai group, the study explores how this protein mediates the fusion of testis and supportive gonadal tissue

Happy to announce a new preprint from my lab looking in to the establishment of polycomb domains in early fly development and contributions from pioneer factors Zelda and GAGA-factor.

How did life begin & why does it matter? A new ASM report, supported by the Gordon and Betty Moore Foundation, explores the origins of microbial life & how understanding it can help tackle some of humanity’s biggest questions around climate, biotech & more. Press release➡️ asm.org/press-releas...

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

The amazing projects wait for curious minds! From fly genetics to transcriptional kinetics, from whole-embryo single-cell atlases to the charming chromatin microscopy! Welcoming at @stockholm-uni.bsky.social #epigenetics #chromatin #DevBio

We currently have a call for support that has gone out to European labs, to support FlyBase-UK. We are asking our colleagues from labs in the US and other countries to wait for a similar call to them that will go out in the near future, to support the US sites. We thank you for your patience.

Very interesting! I liked James's comment "We should probably think of decision making as a dynamical process rather than an event. And relate to this to dev bio concepts such as competence, specification and commitment." I wonder how it would look like if applied to scATAC/scCUT&Tag data. Fuzzier?

Excited to share our new paper in @cp-molcell.bsky.social Molecular Cell: "Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation" — the big part of my PhD! www.cell.com/molecular-ce...

The superb conference in EMBL Epigenetics&Chromatin is over. Fantastic talks, a lot of incredible research in the poster section. I was glad to present two of my PhD projects: catalytic and non-catalytic function of CBP/p300 in development, and single-cell epigenetic landscapes of Drosophila embryo.

Attending the EMBL conference on Chromatin and epigenetics www.embl.org/about/info/c... ?? Check out posters 184 and 185 by SCENTINEL partners Mattias Mannervik and Sergei Pirogov, cbp/p300 unexpected function! Just accepted! doi.org/10.1101/2024...

I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...

Read the paper here! www.biorxiv.org/content/10.1... Congrats to Janith and the rest of the lab @petermaccc.bsky.social, and thanks to collaborators Shabih Shakeel @wehi-research.bsky.social, @benparkerlab.bsky.social and @burrlab.bsky.social, and ongoing support from @snowmedical.bsky.social (6/6)

Last day to apply to a PhD position in my lab - comparative epigenomic project focusing on development nad evolution of the human brain. Apply below 👇

Our recent paper reports extremely long-range (up to 5.1 Mb 😲) regulation of certain genes in fly neurons and provides new insights into how they form (see short thread below 👇). genesdev.cshlp.org/gca?gca=gene...

Thrilled to see my postdoc work at Adelman Lab @hms-bcmp.bsky.social on Integrator(INT) now out @cp-cell.bsky.social. We found that INT deficiency allows immature+unlicensed RNAPII to precociously enter genes. This immature RNAPII can transcribe short genes but terminates prematurely in long genes:

Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!! www.science.org/doi/10.1126/... A short clip describing the key results: www.youtube.com/watch?v=pmvO...

The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...

I could not be more excited to have our lab's first story online where we report our discovery that HDACs ~reverse~ their activity to ADD acyl groups to lysine! We found this for our favorite ketone body, BHB, but this pathway controls other lysine modifications too!🧵 www.nature.com/articles/s41...

Kseniia Petrova, a Russian scientist at Harvard Medical School, was detained at Logan Airport after returning from France and sent to an ICE detention in Louisiana, The Insider reports. A big critic of Putin and the war in Ukraine, she may now be deported to Russia.

So, is it compaction or decompaction? Here is a notable alternative hypothesis: "Our data suggest that the process of..loop extrusion per se is not required for enhancer function..Rather, it is the chromatin compaction brought about by loop extrusion that may be the important factor to consider."

Excited to share this story from the “Chromatin Dream Team” in the @arnausebe.bsky.social lab on chromatin evo across eukaryotes! 12 histone mark profiles from 12 species, including rhizarians, discobans, and cryptomonads. Read on to see what we found! www.biorxiv.org/content/10.1... 1/n

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇

Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?

1/ H3K27me3 mimicry has repeatedly emerged through evolution, but what's the physiological relevance? We show that JARID2 and PALI1 mimic H3K27me3 to antagonise PRC2 in vivo and restrict the spread of Polycomb domains. 🧵 www.biorxiv.org/content/10.1...

Together with @smandrup.bsky.social and Minna Kaikkonen we are happy to announce the 3rd Edition of the EMBO Workshop on #Enhancers and #Enhanceropathies. This time we will meet during the beautiful Danish summer (June 16-21). Book the dates and register soon!!! meetings.embo.org/event/25-enh...

𝐇𝐨𝐰 𝐝𝐨 𝐜𝐞𝐥𝐥𝐬 𝐫𝐞𝐦𝐞𝐦𝐛𝐞𝐫 𝐰𝐡𝐨 𝐭𝐡𝐞𝐲 𝐚𝐫𝐞 𝐚𝐟𝐭𝐞𝐫 𝐃𝐍𝐀 𝐫𝐞𝐩𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧? Our new study “Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability” is out in 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘈𝘥𝘷𝘢𝘯𝘤𝘦𝘴. Led by @lleonie.bsky.social @biranalva.bsky.social 🧵 More below👇

Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that: 1) active histone mods occur independently of transcription 2) transcription coordinates histone deacetylation at active promoters www.science.org/doi/10.1126/...

🧬 1/ Heterochromatin protein 1 (HP1) still surprises us after all these years: It simply sticks to chromatin when pericentric heterochromatin domains – the chromocenters – are activated in mouse fibroblasts and acts as a local rather than global repressor. New preprint: doi.org/10.1101/2024...

It's challenging to uncouple Pol II expression and Pol II activity (Pol II activity creates Pol II expression, & vice versa) but we managed! We did many things, but the most notable is that we suppressed lethality caused by loss of Pol II by giving cells a non-functional form of Pol II! (4/n)

We wrote an opinion article inspired by the recent exciting reports on the sequence determinants of TSS selection + old observations on TFs activation domains. More posts on this soon! Q-rich activation domains: flexible ‘rulers’ for transcription start site selection? www.cell.com/trends/genet...

🔖New paper from the lab! 'Evolution of 3D Chromatin Folding' | Annual Reviews - go.shr.lc/3B60kZF

And our new preprint! "Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture", biorxiv (2024). Led by Yohsuke T Fukai, in collaboration with Kurumizaka lab (U Tokyo) and Umehara lab (RIKEN BDR). www.biorxiv.org/content/10.1...

Our recent study in Cell Metabolism provides compelling evidence that chromatin accessibility and transcription factor network remodeling in aging reflect the predictable degrading effects of a mechanism initially driving organismal maturation. Link: doi.org/10.1016/j.cmet.2024.06.006 Thread 🧵👇1/9