Synthetic chromosomes for 3D functional genomics: from principles to AI-guided design The role of genome 3D organization for fundamental chromatin processes, such as long-range promoter-activator regulatory interactions, remains ambiguo…

Happy to share our review of the past, recent, and future applications of synthetic genomics in studying the 3D functional organization of chromosomes, a set of approaches that are gaining momentum!

www.sciencedirect.com/science/arti...

Our H1 paper is out #ScienceAdvances:
www.science.org/doi/10.1126/...
@masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in live cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/

Mosaic gastruloids reveal a temporal restriction for developmental cell competition - Nature Cell Biology Frenster et al. utilize mosaic mouse gastruloids as a model of cell fitness and competition, identifying a temporal window between primed pluripotency and early gastrulation during which cell competit...

🥳 I am happy to share our latest manuscript published in @natcellbio.nature.com We use #Gastruloids to study #CellCompetition during early mammalian development and find not only that this is highly pronounced in our system but also tightly restricted in time. (1/12) www.nature.com/articles/s41...

Please check out our newest work on fluorogenic speed imager probes, in which we combine the strengths of speed-optimized imagers and fluorogenic imagers.

#SuperResolution #DNAPAINT #microscopy

www.biorxiv.org/content/10.6...

Delighted to share the lab's latest led by superstar Janith and funded by @snowmedical.bsky.social.
What happens when embryonic factors are reawakened in cancers? We uncovered how DPPA2/4 amplify chromatin states in non-small cell lung cancer 🧬🔬🧪
genesdev.cshlp.org/content/earl...
Tutorial 👇 (1/8)

At #EMBLTranscript, experts will share breakthroughs across the full spectrum of #transcription – from cis-regulatory function and long-range regulation to 3D looping, basal transcriptional machinery, #chromatin modifications, #epigenetic inheritance, and more 🧬

Join us: s.embl.org/trm26-01-bl

New preprint from our lab... We applied our hopping technology to relocate CTCF binding sites to thousands of alternative positions in the Sox2 locus: www.biorxiv.org/content/10.6...

Interallelic cis-regulatory dominance promotes robustness and evolutionary innovation www.biorxiv.org/content/10.64898/2026.03...

🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...

How do pairs of DNA loci - such as enhancers and promoters - find each other inside the nucleus? 🤔

Most models assume the random forces driving locus motion are independent in space

New preprint by
@janniharju.bsky.social: this assumption fails in living cells 🧵

www.biorxiv.org/content/10.6...

Very happy to have contributed to this mastodon of a paper by Yinan @yinanwan.bsky.social. Whole-mount spatial transcriptomics in zebrafish y'all 🐟🧪

Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...

Very happy to see this out. 👏 @yinanwan.bsky.social
Bogdan Bintu and team.
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...

Ever wondered how a eukaryotic transcription factor finds its specific DNA motif in the vast genome? In this preprint, we directly measured the dynamics of this search process in living cells, revealing a cooperative mechanism mediated by disordered regions. 1/10 doi.org/10.64898/202...

I started Awesome Life Science Resources: a curated list of resources on work culture, career, and communication for life scientists. Built for PhD students, postdocs, and PIs.

Check it out:
github.com/jjfroehlich/...

Accessory subunits of PRC2 mimic H3K27me3 to restrict the spread of Polycomb domains Some proteins mimic the repressive mark H3K27me3, but the physiological relevance of this phenomenon was unclear. Agius et al. show that the PRC2 subunits JARID2 and PALI1 mimic H3K27me3 to antagonize...

1/ 🧵 In our new paper, we show that JARID2 and PALI1 mimic H3K27me3 to antagonise PRC2. www.cell.com/molecular-ce...

Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila Identification of ZAD-ZnF genes as key regulators of genome organization during Drosophila embryogenesis.

Diving into evolutionary biology! What is the origin of the most abundant class of insect transcription factors, ZAD-ZnFs? We suggest that they evolved from ancestral insulator-binding proteins that control 3D genome topology.

www.science.org/doi/10.1126/...

Post-replicative chromatin accessibility predicts cell fate change Knudsen and colleagues use repli-ATAC-seq to compare replicated and unreplicated chromatin in two models of cell identity change. They find that lineage-specific elements are accessible earlier in rep...

DNA replication globally disrupts the epigenome. But does this create a chromatin-access opportunity for TF binding to facilitate cell identity change? Now 𝐫𝐞𝐩𝐥𝐢-𝐀𝐓𝐀𝐂-𝐬𝐞𝐪 shows 𝘥𝘦 𝘯𝘰𝘷𝘰 chromatin opening & TF binding occurs specifically post-replication, in cellular differentiation & reprogramming!

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here:

journals.biologists.com/dev/article/...

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.

Excited to share this work done during my PhD here in Vienna!

We show how chromatin compaction prevents the release of fragmented DNA in apoptosis, and use new tools to study the mechanism of compaction itself.

See our summary/"bluetorial" below & our preprint here: www.biorxiv.org/content/10.6...

New paper alert from the group!! 🚨: DNA flexibility tips the balance between stability and plasticity in nucleosomes

One of the works from my PhD, co-led alongside @nachper.bsky.social, is finally out! Work from @rcollepardo.bsky.social & @janhuemar.bsky.social
⬇️
www.biorxiv.org/content/10.6...
⬆️

Excited to share @suminkim.bsky.social and @mileshuseyin.bsky.social 's new Current Opinion review on how Polycomb complexes mediate 3D genome interactions including mechanistic models and potential roles in gene regulation:
www.sciencedirect.com/science/arti...

We are delighted to launch the (free!) registration for our 5th AICC symposium, hosted this year in @ucddublin.bsky.social on May 27th.

If you are interested in chromatin, gene regulation or the nucleus please join us!

allirelandchromatinconsortium.ie/annual-meeti...

Looking forward to it!

Know a promising undergrad who wants more time before applying to grad school? Pitt has a funded postbac program for students from underrepresented groups.

This year, my lab will consider applications for solo supervision or to be co-supervised by @mehrgol.bsky.social!

App deadline is March 15!

Interested in transcriptional regulation, enhancers and 3D genome folding?

In this new study we wondered about the role of cohesin loading at enhancers for long-range transcriptional control

www.biorxiv.org/content/10.6...

detailed 🧵👇

Please join Andreas Ladurner and me for the GRC Chromatin Structure and Function conference to be held near Barcelona Spain from May 31-June 5! We accepting abstracts for posters and talks. The meeting is preceded by an awesome GRS. Learn more in our video below and apply www.grc.org/chromatin-st...

Want to interpret DNA sequence-to-function models to understand the underlying molecular mechanisms? Then this is a must read!

DOT1L provides transcriptional memory through PRC1.1 antagonism - Nature Cell Biology Neville, Ferguson et al. show that non-canonical Polycomb repressive complex 1.1-mediated gene silencing is antagonized by DOT1L and is required for the therapeutic efficacy of Menin and DOT1L inhibit...

www.nature.com/articles/s41...

happy i could be a part of this paper from the Gilan lab out now. Along with many other things, it provides strong evidence of chromatin memory for gene activation, and suggests that DOT1L is the missing link balancing the fast and slow arms of the MLL/Polycomb axis

Terrific paper on a new chromosomal
compartment where extensive loop
extrusion isolates domains from
other such domains