Gerlich Lab

Our latest paper is out in @embojournal.org! Chromatin compaction is a hallmark of apoptosis, but the mechanism & function of this process was unclear. We show apoptotic compaction is required to prevent fragmented DNA from spreading beyond the dying cell, and is driven by histone deacetylation.

To understand how histone deacetylation drives compaction in apoptosis & living cells, we used synthetic nanobodies to direct charge to the nucleosome surface. Our charged nanobodies drove compaction & decompaction in cells, showing nucleosome electrostatics alone can determine chromatin density.

Recess time at IMP–IMBA @impvienna.bsky.social @imbavienna.bsky.social ! ✨ Yesterday, Daniel @danielgerlich.bsky.social took the stage to present some of the latest work from the Gerlich Lab. Always a great opportunity to hear exciting science from across both institutes.

Congratulations to Neos @neoscruz.bsky.social on placing 3rd last week at Falling Walls Lab Vienna 2026! 🎉 In his pitch, “Breaking the Wall of RNA’s Hidden Shape,” he showed how his PhD work lets us visualize the shapes of individual mRNA molecules inside cells.

Our paper is out in The EMBO Journal @embojournal.org! 🎉 We show how replicated chromosomes can maintain sister chromatid cohesion while still allowing dynamic loop folding within nested hierarchy of TADs. Check it out below 👇 1/2

That’s a wrap on this year’s Chromatin Consortium in Woods Hole! 🧬 The @danielgerlich.bsky.social , @rcollepardo.bsky.social , @vram142.bsky.social, Gibson, and Rosen labs came together to exchange ideas, run experiments, and explore chromatin organisation from different angles. 1/4

The consortium was also about community: BBQs, sushi nights, and plenty of time together outside the lab 🍣🔥. Huge thanks to the Isenberg family for supporting the consortium, both this year and over the years. 3/4

That’s a wrap on this year’s Chromatin Consortium in Woods Hole! 🧬 The @danielgerlich.bsky.social , @rcollepardo.bsky.social , @vram142.bsky.social, Gibson, and Rosen labs came together to exchange ideas, run experiments, and explore chromatin organisation from different angles. 1/4

The Gerlich lab recently attended the International Symposium on Chromosome Dynamics: from Structure to Cellular Function in Awaji, Japan 🇯🇵 A really nice chance to share our work, exchange ideas, and catch up with the chromosome dynamics community. 1/3

Daniel @danielgerlich.bsky.social presented Caelan’s work in a talk titled “An electrostatic repulsion model of centromere organization,” highlighting how electrostatic repulsion helps position centromeres at the chromosome surface during mitosis. 2/3

Congratulations to Max @mfdspicer.bsky.social on completing his PhD! 🎉 Yesterday, he successfully defended his thesis, “Electrostatic control of apoptotic chromatin compaction.” The lab is very proud of you, Max! 👏 1/2

Max’s work showed that histone tail deacetylation drives chromatin compaction during apoptosis, helping prevent DNA release into apoptotic extracellular vesicles. This work was also a collaboration with @rcollepardo.bsky.social and the Rosen labs. More in our thread here: 2/2

New preprint out!🧬 How do cells keep replicated sister chromatids linked for DNA repair while folding 3D loops for gene expression? Extrusion folds DNA but separates sisters, while cohesion connects them, risking mutual interference. How do they coexist?🧵👇 🔗 doi.org/10.64898/2026.05.02.722390 1/6

Huge congratulations to co-first authors Zsuzsanna Takacs and Dmitry Mylarshchikov @dmitrymyl.bsky.social, and to Sofia Kolesnikova, Christoph Langer @cchlanger.bsky.social, Anton Goloborodko @golobor.bsky.social, and Daniel Gerlich @danielgerlich.bsky.social! 👏 5/6

New preprint out!🧬 How do cells keep replicated sister chromatids linked for DNA repair while folding 3D loops for gene expression? Extrusion folds DNA but separates sisters, while cohesion connects them, risking mutual interference. How do they coexist?🧵👇 🔗 doi.org/10.64898/2026.05.02.722390 1/6

This creates a nested hierarchy: top-level boundaries act as discrete "cohesion zones" linking sisters for repair, while smaller, nested domains loop independently for gene regulation. 3/6

New preprint out!🧬 How do cells keep replicated sister chromatids linked for DNA repair while folding 3D loops for gene expression? Extrusion folds DNA but separates sisters, while cohesion connects them, risking mutual interference. How do they coexist?🧵👇 🔗 doi.org/10.64898/2026.05.02.722390 1/6

Congratulations to Caelan on completing their PhD! 🎉 Last week, they defended their thesis, “Unravelling the Surface Localisation of Centromeres on Vertebrate Chromosomes in Mitosis.” The lab is very proud of you, Caelan! 👏 1/2

Caelan’s work is also part of a recent preprint from a collaboration between the Rosen, Redding, Collepardo-Guevara, and Gerlich labs, showing that electrostatic repulsion positions centromeres at the chromosome surface during mitosis. More in our thread here: 2/2

Last week, the Gerlich lab went to Prein an der Rax for a writing retreat, or as we liked to call it, a “storython” ✍️🏔️ Led by Iain Patten, it was a chance to step away from day-to-day experiments and focus on building clearer, more coherent stories around our research. 1/4

The retreat included group discussions, focused thinking and writing time, amazing food, evenings by the bonfire, and a beautiful setting surrounded by nature 🌿🐦 A really nice mix of science, reflection, and time together. 3/4

Last week, the Gerlich lab went to Prein an der Rax for a writing retreat, or as we liked to call it, a “storython” ✍️🏔️ Led by Iain Patten, it was a chance to step away from day-to-day experiments and focus on building clearer, more coherent stories around our research. 1/4

1/New preprint just dropped! 🔥🔥 We investigate how the genome is destroyed in apoptotic cells in a way that prevents DNA fragments from spreading beyond the dying cell 🧬⚰ Done here at @imbavienna.bsky.social & in the super @rcollepardo.bsky.social & Rosen labs: www.biorxiv.org/content/10.6...

9/Our results show apoptotic chromatin compaction, driven by histone deacetylation, sequesters DNA fragments produced during genome destruction. Synthetic perturbations suggest charge alone is enough to induce compaction, which may help us to better understand and alter chromatin in living cells

1/New preprint just dropped! 🔥🔥 We investigate how the genome is destroyed in apoptotic cells in a way that prevents DNA fragments from spreading beyond the dying cell 🧬⚰ Done here at @imbavienna.bsky.social & in the super @rcollepardo.bsky.social & Rosen labs: www.biorxiv.org/content/10.6...

7/Expression of the positively charged nanobody in live cells caused chromatin hypercompaction, while the negatively charged nanobody induced a homogenous phenotype reminiscent of HDAC inhibition. In vitro & in silico, nanobody addition alone caused similar changes in chromatin structure

1/New preprint just dropped! 🔥🔥 We investigate how the genome is destroyed in apoptotic cells in a way that prevents DNA fragments from spreading beyond the dying cell 🧬⚰ Done here at @imbavienna.bsky.social & in the super @rcollepardo.bsky.social & Rosen labs: www.biorxiv.org/content/10.6...

5/We wondered if compaction might also prevent DNA from entering apoptotic extracellular vesicles, which are shed from the plasma membrane of the dying cell. ApoEVs are usually devoid of DNA, but became filled with chromatin fragments when we inhibited histone deacetylation

1/New preprint just dropped! 🔥🔥 We investigate how the genome is destroyed in apoptotic cells in a way that prevents DNA fragments from spreading beyond the dying cell 🧬⚰ Done here at @imbavienna.bsky.social & in the super @rcollepardo.bsky.social & Rosen labs: www.biorxiv.org/content/10.6...

3/Chromatin is compacted in apoptosis, might this sequester fragments? Histone deacetylation, which drives compaction in living cells, has been observed in apoptosis, but a role in apoptotic compaction was unknown. We inhibited apoptotic deacetylation which resulted in drastic chromatin decompaction

1/New preprint just dropped! 🔥🔥 We investigate how the genome is destroyed in apoptotic cells in a way that prevents DNA fragments from spreading beyond the dying cell 🧬⚰ Done here at @imbavienna.bsky.social & in the super @rcollepardo.bsky.social & Rosen labs: www.biorxiv.org/content/10.6...