Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication. www.biorxiv.org/content/10.1... A🧵👇

Cecilia Payne-Gaposchkin ✨ figured out what stars are made of ✨ when she was just 25. 🔭🧪 Her PhD thesis basically established the Harvard astro department — at a time when Harvard didn't officially allow woman students. I wrote this little profile to mark the 100th anniversary of her thesis:

🔥 New episode of the Night Science Podcast with Akiko Iwasaki @virusesimmunity.bsky.social Yale & HHMI professor, and one of Time Magazine’s 100 most influential people in 2024! Akiko explains how leading large collaborations requires managing expectations, not micromanaging the research.

🔥A really interesting new episode of the Night Science Podcast came out today! Akiko Iwasaki talks about the art of creativity management & how a discovery is like a gem hidden inside a hairball. nightscience.buzzsprout.com/1744020/epis... @virusesimmunity.bsky.social @nightsciencepod.bsky.social

Check out @cassyni.bsky.social seminar Mechanisms of cellular plasticity presented by @itaiyanai.bsky.social Great talk about how cells evade chemo with stepwise reprogramming of their transcriptional repertoire -fascinating, and profound implications for therapy! cassyni.com/events/ApfsK...

✨Exciting news: the main story of my PhD is out in Science! Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation. 📖 Read the full story here: www.science.org/doi/10.1126/...

New preprint is up, led by former postdoc Braulio Bonilla. We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C. www.biorxiv.org/content/10.1...

When the cell needs to respond to the environment: A chromatin-splicing love affair

Interested in cellular plasticity? Come to my live virtual talk at the Night Science Seminar Series! Free register here: cassyni.com/events/ApfsK...

Engineered histones reshape chromatin in human cells https://www.biorxiv.org/content/10.1101/2025.09.10.674980v1

Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)

🔥 New episode of the Night Science Podcast! We talk with the leaders of Google's AI Co-Scientist project, Alan Karthikesalingam and Vivek Natarajan, about how their system evolved parts of human hypothesis generation while also diverging in fascinating ways.

Spotify: open.spotify.com/episode/0cTb... Apple: podcasts.apple.com/us/podcast/n...

'Both competition and cooperation' – that is an underlying principle of how Google designed its "AI co-scientist" platform to generate ideas and think like a scientist. We talk with the leaders of this project on the latest episode of the Night Science Podcast. @nightsciencepod.bsky.social

Peptide-RNA photo-crosslinks with tunable RNA chain map protein-RNA interfaces https://www.biorxiv.org/content/10.1101/2025.09.05.674461v1

🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬 Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...

"In our view, it [hexanediol] should thus be avoided and not be used as evidence for the formation of an assembly via phase separation or the fluid-like nature of a condensate in vitro or in vivo." doi.org/10.1038/s414...

We’re back! Registration is NOW OPEN for the 6th Annual Meeting on Advances in Nuclear Topology & 3D Chromatin Architecture in Cancer. Don’t miss insights from leading experts in the field. Join us online on Nov 25, 2025—register for free: bit.ly/chromatin-2025 #chromatin2025

out today: my labmate Shubham developed a super clever new technique to profile TF-DNA interactions with unprecedented resolution of low-affinity binding sites, revealing patterns in how these sites are organized in the genome to modulate TF occupancy: www.nature.com/articles/s41...

This was a fun message to receive ☺️ ‘I thought you may be interested to know this - I got my girlfriend a poster of your “it takes two” Nature correspondence for our first anniversary and it is now up on our wall!’ (Posted with permission)

Have you heard about the Night Science Podcast, where we talk about the actual creative process of doing science? We explore this with discussions with brilliant scientists & also philosophers and artists, to figure out the tricks of the creative scientific trade. podcasts.apple.com/us/podcast/n...

I am excited to share that I will join the Friedrich Miescher Institute @fmiscience.bsky.social in Basel as a group leader, starting my lab in March 2026 🎉 We will explore cell fate regulation during organogenesis, with a focus on how cell elimination underlies the emergence of functional tissues.

The genetic architecture of the human bZIP family https://www.biorxiv.org/content/10.1101/2025.08.21.671354v1

An overlooked aspect of becoming a scientist is realizing that you have a particular brand; a unique approach, an attraction to a certain kind of problem and a set of connections that you like to make. Uri calls it finding your internal tuning fork. podcasts.apple.com/us/podcast/n...

I’m excited to highlight our latest paper, just published in Cell 🎉 We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression. 1/n 🧪 www.cell.com/cell/fulltex...

Why would anyone want to be a scientist? There are the pleasures of: 1. Having the initial idea or insight, 2. Watching the idea develop into new experiments or a new model, and 3. Telling others. Martin A. Schwartz Check out also his Night Science podcast episode: podcasts.apple.com/us/podcast/7...

New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...

Synthetic genomic dissection of enhancer context sensitivity and synergy https://www.biorxiv.org/content/10.1101/2025.08.13.669251v1

Can #creativity be learnt? A Nature Careers feature on Night Science featuring our Founders @itaiyanai.bsky.social and @martinlercher.bsky.social investigates this issue at the heart of #NightScience www.nature.com/articles/d41...

Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts https://www.biorxiv.org/content/10.1101/2025.08.08.669284v1

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

Excited to share that my first-author publication from my PhD on the interplay of p53 with cofactors on chromatin is now online in Molecular Cell @cp-molcell.bsky.social : www.cell.com/molecular-ce... Nucleosomes filter cofactor access to p53 - USP7 can bind whereas E6AP-E6 fails to form a complex.

Dive into the step-by-step choreography of transcription-coupled DNA repair. In our new review published in Nature Cell Biology, we explore what we know and what’s next in this exciting field of research! www.nature.com/articles/s41...

Delighted to have our preprint led by @lvchosen1.bsky.social up: Genetic variation reveals a homeotic long noncoding RNA that modulates human hematopoietic stem cells biorxiv.org/content/10.1... 🧵 below ...

Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit! tinyurl.com/ydn6e3ac

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model https://www.biorxiv.org/content/10.1101/2025.06.25.661532v1

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u A short thread follows 1/n

How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u

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

In the nucleus, many intrinsically disordered proteins (IDPs) form condensates. What IDP sequence features drive this behavior? We developed CondenSeq, a high-throughput approach to measure nuclear condensate formation, and applied it to ~14,000 IDPs to find out! rdcu.be/eq975

Awesome paper alert! Learn about spectrum of chromatin condensate morphologies due to elastocapillary effects (no, liquids do not need to be spherical!), from amazing duo @dnamystrom.bsky.social & Hongbo Zhao, w/ important contributions from co-authors Jorine Eeftens, Mikko Haataja, Andrej Kosmrlj.

If heterochromatin is really a liquid-like condensate, why is it not spherical? We investigated whether mechanical interactions between a condensate and a fiber network can explain the variety of morphologies seen in phase-separated nuclear compartments www.biorxiv.org/content/10.1...

A high-affinity split-HaloTag for live-cell protein labeling https://www.biorxiv.org/content/10.1101/2025.06.15.659771v1

Capture C identifies promoter interacting sequences. MPRA tests sequences for regulatory activity. Here, we combined them both to test sequences with their target promoter. Amazing work by @colinearnould.bsky.social, Pia Keukeleire, Martin Kircher and many others. www.biorxiv.org/content/10.1...

90% of doing science is being open to new ideas.

🔥 New episode of the Night Science podcast! The brilliant Eve Marder, professor at Brandeis University, talks with us about how "Recipe Science" ruins creativity. Apple: podcasts.apple.com/us/podcast/n... Spotify: open.spotify.com/episode/4mSv...

A protein-DNA surface hydrogel mechanically protects the cell nucleus https://www.biorxiv.org/content/10.1101/2025.05.21.655270v1

Many people are busy doing recipe science.. If you ask a grad student what they need to do to get a paper, they'll tell you this & this, & they'll know that 2 years before the project is done. And I'm thinking, what's wrong with this picture? Eve Marder, on @nightsciencepod.bsky.social

🚨Our new paper is online🚨 We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics www.cell.com/cell/fulltex...

PSA: We just finished processing nearly all public ATAC-seq datasets from SRA (about 22,000 datasets). (Not?) Surprisingly, we had to throw-out nearly ~50% because they were low-quality (low signal-to-noise, duplicate rate, etc.). Check quality before analysis (TSS-enrichment is not sufficient!).