Anders Sejr Hansen

(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...

🚨Preprint from our lab🚨 How and when did TADs emerge during evolution? 🐁🐟🪰 HINT: the diversification of CTCF regulation and functions enabled new mechanisms of 3D chromatin folding 🧬 With Liene Astica & @rdacemel.bsky.social Link: www.biorxiv.org/content/10.6... Bluetorial 1/15👇

Check out our new preprint led by @mileshuseyin.bsky.social unexpectedly discovering Polycomb 3D interactions that persist without cPRC1. Also look out for Miles who is on the faculty job market!

Happy to share our new preprint! We find that PHC proteins help drive Polycomb-mediated 3D chromatin interactions, but some interaction strength remains independent of canonical PRC1. Really comprehensive work by @mileshuseyin.bsky.social. I had a lot of fun working on the imaging side :)

Great to see this work @mileshuseyin.bsky.social out. Enjoyed seeing some of the data when he visited our lab, looking forward to digging in the details

Very interesting historical perspective on cohesin and its role in transcriptional regulation: link.springer.com/article/10.1...

Have you ever looked at a gene in IGV or a genome browser and wondered “What are all those (ATAC-seq/H3K27ac/CTCF ChIP-seq/…) peaks doing?” 🤔 I’m thrilled to share that we developed a new technology called Swap-seq to answer that exact question. Swap-seq: www.biorxiv.org/content/10.6...

Excited that our work on Microfluidics-Enhanced 3D DNA-Based Points Accumulation for Imaging in Nanoscale Topography has been published in ACS Applied Materials & Interfaces. doi.org/10.1021/acsa... @pubs.acs.org #microscopy #nanoscale

Very interesting paper. These <10kb "protrusions" remind me, albeit at a different length scale, of the "looping out" of active regions from chromosome territories. www.sciencedirect.com/science/arti...

CpG islands are fascinating both from molecular mechanism point of view and in terms of evolutionary conservation in the context of elevated mutation rate of CpG dinucleotides in mammalian genomes. Lots of new insights from cool technical and theoretical advances from @robklose.bsky.social + lab.

Very nice new paper from Paggi, Long, Zhang using physical modeling of RCMC data to reconstruct physical structures of euchromatin at the nucleosome scale: Euchromatin forms condensed domains and E-P interactions largely occur on the surface! www.nature.com/articles/s41...

Happy Stanislav Petrov Day He passed in 2017. As Encyclopedia Britannica puts it, “He is survived by his two children, two grandchildren, and the entire human race.” If you don't know his story, please take 3 minutes now to learn it. @gchalliance.bsky.social @docsforclimate.bsky.social

The 4DN Center for 3D Structure and Physics of the Genome proudly presents: "Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation". www.biorxiv.org/content/10.6...

. @matteomazzocca.bsky.social and I were fortunate to contribute single molecule imaging of chromatin dynamics to this beautiful study from K Alimenti and M Blower on SAF-A/HNRNPU:

Enhancer–promoter proximity predicts transcriptional competence but not transcriptional output in the Drosophila brain arxiv.org/pdf/2609.03058

"we found that human sister chromatids are consistently misaligned in the 5′→3′ direction of inherited DNA strands." www.science.org/doi/epdf/10....

Very thankful to the @valleefoundation.bsky.social for supporting our work with a 2026 Vallee Scholar Award: thevalleefoundation.org/news/vallee-...

Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...

We always knew you couldn't trust these antibody data sheets, but the extent to which it is essentially industry practice to manipulate data is truly shocking

Glad to share that my preprint "ID2 secures cDC1 specification by antagonizing E proteins at a pleiotropic Zeb2 enhancer" is out today in Nature Immunology. This represents another major piece of my PhD work. www.nature.com/articles/s41... Original preprint thread: bsky.app/profile/feiy...

Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n

‼️🚨Out now in Molecular Cell - Our latest study 𝐫𝐞𝐯𝐞𝐚𝐥𝐢𝐧𝐠 𝐧𝐞𝐰 𝐢𝐧𝐬𝐢𝐠𝐡𝐭𝐬 𝐢𝐧𝐭𝐨 𝐅𝐀𝐂𝐓 𝐟𝐮𝐧𝐜𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐭𝐡𝐞 𝐢𝐦𝐩𝐨𝐫𝐭𝐚𝐧𝐜𝐞 𝐨𝐟 𝐧𝐮𝐜𝐥𝐞𝐨𝐬𝐨𝐦𝐞 𝐨𝐫𝐠𝐚𝐧𝐢𝐬𝐚𝐭𝐢𝐨𝐧 𝐟𝐨𝐫 𝟑𝐝 𝐠𝐞𝐧𝐨𝐦𝐞 𝐦𝐚𝐢𝐧𝐭𝐞𝐧𝐚𝐧𝐜𝐞: tinyurl.com/2xctvx38. It was a pleasure to lead this collaborative effort alongside @nilskrietenstein.bsky.social More in🧵below 🪡

Exciting news for personalized mRNA cancer vaccines, especially if the phase 3 effect size matches the phase 2 trial (49% reduced death or recurrence), although we have to wait for the official numbers arstechnica.com/health/2026/...

we sometimes do bootcamps or workshops over the summer as a lab. Last week we did our microscopy bootcamp: everyone in the lab built a fluorescence microscope :)

Really interesting new paper from Krietenstein and Groth labs showing that FACT depletion has a dramatic effect on microcompartments leading to aberrant microcompartment (AMC) formation through loss of ordered nucleosomes: www.cell.com/molecular-ce...

Happy to share our last work on mitotic bookmarking where we describe a new role for extensively studied TFs. Heroic effort by first author Inma over many years. genesdev.cshlp.org/content/earl...

Amazing physical chemical analysis of chromosome condensation and decondensation from Andrew Beel, PJ Mattei, and Roger Kornberg. I was tickled to see some expressions that I am used to from Roger's writing in the paper www.science.org/doi/10.1126/...

Multi-way Micro-C to go beyond pair-wise interactions:

Nucleosomes and IDRs suppress promiscuous GCN4 binding on minichromosomes www.nature.com/articles/s41...

How many TFs to you need to open chromatin at enhancers? Very excited to see this one out! Check out the augmented version with combinatorial motif mutant libraries in Figure 5! Very proud of @guidobarzaghi.bsky.social @valentinabaderna.bsky.social @embl.org

It was an honor to write this remembrance of Susumu Tonegawa (1939–2026) -- a scientist whose discoveries transformed biology and whose lab shaped generations of neuroscientists. I hope this piece captures even a small part of his remarkable legacy. www.nature.com/articles/s41...

New paper from my group at @mitkochinstitute.bsky.social, MIT IMES, and MIT Biology! I am thrilled to share that our paper describing scAmp, a new method for analyzing extrachromosomal DNA amplifications at single-cell resolution, has been published in @natcomms.nature.com. Thread below 👇

@science.org Generative design of bacteriophages with genome language models | Science www.science.org/doi/10.1126/...

Very happy to see this story finally out in @natbiotech.nature.com: www.nature.com/articles/s41... Fantastic collaboration with @lancasterlab.bsky.social on how to identify and ‘fix’ differentiation-compromised human pluripotent stem cells. @babrahaminst.bsky.social @mrclmb.ac.uk 🧵 below

We just submitted a manuscript to biorxiv. Keep in mind that this hasn't been peer reviewed yet but is submitted to PNAS for peer review. Our lab has closed so it will be the 2nd to last paper we publish. Data for one final paper will be written up in my retirement www.biorxiv.org/content/10.6...

Happy to share my first preprint! We looked at how the 3D genome changes during red blood cell differentiation, especially at erythroid CREs. It was fun to work on this collab with many wonderful people from the @andersshansen.bsky.social and @bloodgenes.bsky.social labs esp. Chun-Jie.

Very happy to see this story finally out (link in comments)! We used low-input Capture Hi-C to profile promoter-anchored chromosomal interactions in Type 3 innate lymphoid cells (ILC3s) - rare tissue-resident lymphocytes that lack antigen receptors and regulate barrier immunity.

Update: scE2G is now online at Nature Genetics! Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well nature.com/articles/s41588-026-02695-8 1/

Our new study shows a CHD-family remodeler can nucleate and spread H3K9 methylation de novo, inverting the canonical hierarchy between writers and remodelers. www.biorxiv.org/content/10.6...