Anders Sejr Hansen

Extra kudos and thanks to all the staff at NIH and NSF and other federal funding agencies for working extra hard in very small windows of opportunity to get grants reviewed and funds released before the attention-addled federal policies change again (on an hourly basis).

Contrasting photographs of the night-time skylines of Manhattan (left) and Nijmegen (right), with matching genome-wide association plots underneath each.

Not sure who came up with "Manhattan Plot", but in 2014 I coined the alternative term "Nijmegen Plot" (inspired by the Dutch town where I live) to describe underwhelming results from our earliest genome-wide association scans of language/reading traits.

Exited to share our recent work on viral cis-regulatory elements in collaboration with @tewhey.bsky.social!
We identified >2000 CREs across the genomes of 27 human-infecting dsDNA viruses from the Herpesvirus, Adenovirus, Papillomavirus, and Polyomavirus families.
www.biorxiv.org/content/10.1...
1/8

Beyond excited to share our #NewPaper in @cellcellpress.bsky.social! Inflamed environments acidify intracellular #pH. BRD4 senses this via transcriptional condensates, tuning #macrophage responses to match demand and consequences of #inflammation authors.elsevier.com/sd/article/S...

The PCP method for pairwise and multi-way 3D genome mapping is a very original and elegant alternative to the pairwise proximity ligation methods:

This seems like a really important paper comparing chromosome tracing methods, demonstrating that classical denaturing DNA-FISH and chromosome tracing leads to substantial distortion of 3D genome structure, likely due to the high-temperatures involved (70-90C):
www.nature.com/articles/s41...

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...

Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to @olimpiabompadre.bsky.social, to Marie Kmita's lab, and to all the co-authors. www.nature.com/articles/s41...

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/

Our new preprint 🧬🔗 www.biorxiv.org/content/10.1...
BRD4-NUT forms liquid-like condensates that locally constrain nucleosomes via BRD4-mediated crosslinking— physical control of #chromatin by #LLPS transcription condensates. @semeigazin.bsky.social @katsuminami.bsky.social @masaashimazoe.bsky.social

A very comprehensive review of single molecule tracking:

A little belated posting, but we (Emily Navarrete, Leonid Mirny, me) have an updated preprint in collaboration the Ines Drinnenberg, Héloïse Muller, José Gil Jr, + others on the strange and striking compartmentalization of silkworm chromatin: www.biorxiv.org/content/10.1...

Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition Using mouse pluripotent stem cells, Nosaka et al. created an ovarian somatic cell (OSC)-free system to induce an abundant number of oocyte-like cells at diplotene arrest, followed by their growth into...

Sorcery. That's my only explanation for Mitinori Saitou's research program www.cell.com/developmenta...

I very much look forward to @andersshansen.bsky.social's talk on 'Spatiotemporal Mechanisms of Distal Gene Regulation by Enhancers' in @enhancedgenomics.bsky.social seminar series 'The 3D Regulatory Genome'.
📅 July 3rd 2025 (tomorrow!)
⏰ 4pm GMT
Pleaase join us and register at: lnkd.in/eeRnyjC5

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec

(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators: doi.org/10.1093/nar/.... A Bluetorial🧵:

How to represent genomes in 3D?

In this paper (and video), we propose Geometric Diagrams of Genomes (GDG)—a visual grammar that aims at emulating the effect ribbon diagrams (Richardson et al 1981) had in protein structural biology. Time will tell.😅

👉🏼 genomebiology.biomedcentral.com/articles/10....

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

Wissenschaftliche*r Mitarbeiter*in/ Postdoc (m/f/d) Chromatin ist nicht unbeweglich. Es handelt sich um ein hochdynamisches Material, dessen 3D-Struktur zentrale genomische Prozesse – von der Transkription bis zur DNA-Reparatur – steuert. Doch wie verhält sich Chromatin als Material – als Flüssigkeit, Feststoff oder viskoelastisches Gel –, um diese Funktionen in lebenden Zellen auszuführen? Ohne eine Antwort auf diese Frage können wir nicht vollständig verstehen, wie Chromatin bei Krankheiten gestört wird.

Postdoc🚨!

Come join our HFSP team to uncover how chromatin moves in cells and what this means for genome function! Great opportunity to combine single-cell genomics, live imaging and polymer physics in the unique mammalian retina with @andersshansen.bsky.social, Davide Michieletto & Sandra Tenreiro

EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!

Huge shout out to the creative team that produced this beautiful video capturing our teaching efforts at the intersection of mechanics and biology! Learn more about our work to integrate hands-on experiences in biomechanics and mechanobiology for students at MIT:
www.youtube.com/watch?v=tult...

We're thrilled to continue our deep dive into how chromatin mechanics govern how our genomes function with our A-team @andersshansen.bsky.social @Davide Michieletto, and @Sandra Tenreiro.

A huge thanks to the @dfg.de and @hfspo.bsky.social for supporting us.

Stay tuned! PhDs/Postdocs coming soon!

Great to see this published @genesdev.bsky.social. Evidence that enhancers can activate a bystander gene in an adjacent TAD, and that cohesin facilitates this. @uoe-igc.bsky.social.
pubmed.ncbi.nlm.nih.gov/40436628/

Such a cool approach:

Congratulations to Dr. Viraat Goel and Dr. Domenic Narducci @domenicnarducci.bsky.social , both new PhDs in Biological Engineering from the lab 🎉

Guided nuclear exploration increases CTCF target search efficiency - Nature Chemical Biology Single-particle tracking and mathematical modeling methods reveal the searching mechanism of CTCF for its cognate sites on DNA. An RNA-binding region in CTCF mediates its trapping in small zones and i...

Looks extremely interesting. Can't wait to read in full. Do you know if the IDR of Msn2 also affects the average sliding length?

BTW, for another ZF-IDR protein, CTCF, we also see that an IDR-like RNA-Binding-Region increases the kON rate without affecting kOFF www.nature.com/articles/s41...

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...

Congratulations to @suminkim.bsky.social on joining the Leading Edge Fellows Program 🎉

Our new paper is out@ScienceAdvances👇
www.science.org/doi/10.1126/...
🧬Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live human cells.
🔍 @katsuminami.bsky.social et al. have developed a chromatin behavior atlas within the nucleus. 1/2

Years ago, @arnausebe.bsky.social gave talk that prompted us to discuss on #3DGenomics and #Evolution. I offered we could help. Next, @ianakim.bsky.social came to the rescue 😁.

The results are out today at Nature, including support from @encent.bsky.social.

Iana explains what she did here 👇🏻🎉👏🏻 👏🏻👏🏻

Very happy to share the peer-reviewed version of our paper in which we study the formation and function of pair-wise and multi-way enhancer-promoter interactions in gene regulation (see thread below): www.nature.com/articles/s41...