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...
Not intended! I didn’t remember 😅 But I’m also now thinking about this a lot
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!
Amazing story! It’s so interesting to know whether these “redeployed” TFs bind to a new gene set just because of a present landscape of accessibility, or TFs themselves spliced in different isoforms (as in the recent talk of M.Harrison about Zld in neuroblasts that bind to a novel motif)
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...
Having your paper for our JC ;-)
Phew! Oxygen is for above 5000, bru. But pics are pretty pretty
🧬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.
It seems both mechanisms involved. We see piRNA pathway, and apparently it gets piRNAs directly from ribosomal locus (www.biorxiv.org/content/10.1...). And we also see a mysterious regulation at the promoter (pubmed.ncbi.nlm.nih.gov/35037046/). So interesting how much it’s conserved!
Great idea and amazing to see R2 doing its job very well! I studied before how rRNA gene copies with R2 get inactivated in insects. Is it possible that rDNA can be sensitive to the R2-mediated intrusions as well? And after some generations start switching off them?
Report cover page
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...
A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.
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?
PRO-seq measures nascent transcription with high precision. Degradation of CBP leads to a decrease in Pol II occupancy on promoters, which means the affected initiation step. Oppositely, catalytically inactive CBP leads to enriched Pol II on promoters of downregulated genes, which implies a defect in the pause-release step into productive elongation.
Using PRO-seq and CUT&Tag, we found that CBP activates zygotic genes in two steps:
- It helps recruit RNA Pol II to promoters without requiring catalytic activity.
- Its catalytic acetyltransferase function then triggers pause release.
Loss of catalytic (acetyltransferase) activity of CBP impedes gastrulation, both by optogenetic CBP inactivation (blue-light switches off CBP fused to CRY2) and by point mutation in the HAT domain.
CBP can often be found at the Zld-bound sites. When Zld is removed, CBP is also gone there.
We show that transcription factor Zelda is required for CBP recruitment, but CBP is dispensable for Zelda pioneer factor function. Instead, CBP catalytic activity is essential for zygotic genome activation and successful gastrulation.
This was a fantastic collaboration with the Melissa Harrison lab @harrisonflylab.bsky.social, where we use powerful Drosophila tools: optogenetic inactivation, full CBP degradation (DeGrad), and classic catalytic-dead mutants, to investigate the mechanism of gene activation during development.
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 CBP project will be out in Molecular Cell very soon—don’t miss it if you're into ZGA, transcription regulation, and histone acetyltransferases! The second project is a great collaboration with @mardzix.bsky.social and part of the @scentinel.bsky.social consortium #epigenetics #chromatin #devbio
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.
