Daan Noordermeer lab

Happy to share scHiCAR, an ultra-high throughout (millions of cells), low cost (5 cents/cell including NGS), and trimodal platform for integrated single-cell level analysis of mRNA, open chromatin, and 5-kb resolution looping with ground-truth data the same individual cell.

Very excited to see this published - thanks to @djost-physbiol.bsky.social & all co-authors for the fantastic work!

🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...

🚨Preprint alert🚨 How does chromatin “architecture” form at CTCF sites? Our new preprint with @voslab.org and @andersshansen.bsky.social shows CTCF dimerization promotes nucleosome oligomerization on chromatin. tinyurl.com/CTCF-nucleos...

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm - The EMBO Journal Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in ...

How do compartmentalization & loop extrusion organize eukaryotic genomes beyond classical model organisms?
Hi-C analysis of silkworm chromosomes by Drinnenberg, Muller, Mirny et al reveals new combination of these mechanisms, and a new, secluded “S” compartment
link.springer.com/article/10.1...

Thank you Max, I’ll transmit the message 😃

That looked like an excellent visit!

New paper from the Feil lab! congratulations🍾👏

Great thread below ⤵️

@agencerecherche.bsky.social @frm-officiel.bsky.social Thank you for your support

@cnrs.fr @cnrsbiologie.bsky.social @cnrsoccitanieest.bsky.social @umontpellier.bsky.social @biolum-montpellier.bsky.social
#epigenetics

This has been an exciting collab with (all non-BS): Yui Imaizumi in Robert Feil’s lab (@igmm-montpel.bsky.social ), Francois Charon and Benoit Moindrot from @i2bcparissaclay.bsky.social and Jean-Charles Cadoret (@ijmonod.bsky.social) and others. Thanks to @agencerecherche.bsky.social for funding.

How about 3D organization? Correlations emerge at larger scale, but our high-res allelic data has poor overlap, both for timing and for boundaries between repli domains and TADs. At imprinted domains, regulators that desynchronize replication timing also uncouple links with genome organization (4/n)

(2) perturbing lncRNA expression on the early chromosome delays replication, but further away. Methylation and lncRNA expression thus provide means to locally override the intrinsic replication program (3/n)

Imprinted domains can replicate asynchronously, making them excellent study objects. High-res allelic Capture Repli-seq reveals unexpected outcomes: (1) removal of DNA methylation from the tiny Imprinting Control Region on the late replicating chromosome advances replication over 100s of kbs (2/n)

🔔 New paper alert 🔔 www.nature.com/articles/s41...
Some regions in the genome replicate early and some late, but the why and how remain poorly understood. DNA replication and 3D genome organization appear linked, raising the question if one may regulate the other? (1/n)

Bravo Anne and colleagues!

Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41...

Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)

What a nice start of the year!

Postdocs at Center for Gene Expression in Department of Cellular and Molecular Medicine - Copenhagen, Hovedstaden (DK) job with University of Copenhagen | 12849488 We are looking for 2 or more highly motivated postdocs interested in ribosome biology, 3D chromatin organisation, or regulation of protein turnove...

We are looking for a Postdoc at the Center for Gene Expression in Copenhagen. Deadline for applications is the 11th of January. If you are interested in 3D chromatin, SMC complexes, and super-resolution microscopy, join us. www.nature.com/naturecareer...

This story is absolutely wild. Did you know that avocados change sex over the course of a day? And that it's controlled by a single ancient balanced polymorphism? This is flat our crazy

😃

Great to see this out Agnese. It’s a very interesting mechanism. Congratulations to all authors!

Thank you Vicky. We’re looking forward to an exciting 5 years ahead of us!

very tumblr: gaygothur: At this point, every round mammal is a hamster to me. cantanopeshitthatwastaken: coconut gaygothur: I think we both have different definitions of what mammal is but I can't say I disagree with you. oregonnukesailor: has hair. give milk

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

now revised and journal accepted at www.science.org/doi/10.1126/...

🧵👇

It’s been an immense pleasure to present and discuss our work on genome organization and genomic imprinting with the Canadian community at the CEEHRC Epigenetics meeting #CanEpi25 in beautiful Banff. Immensely grateful to the trainee committee for their kind invitation

📢 Open Call! The Max Perutz Labs invite applications for a Tenure-Track Professorship in Genome Biology. We are particularly interested in researchers investigating the molecular and biophysical mechanisms underlying genome function and regulation. More details ➡️ tinyurl.com/3t7vvdct

I am very proud to announce that our team has received an ERC synergy grant from @erc.europa.eu. A wonderful recognition of a truly collaborative effort with friends (Julius Lukes, Leos Valasek and Mark Osborn). Excited to begin this journey at @i2bcparissaclay.bsky.social @cnrs.fr

Our latest paper has just been published in Cell!

doi.org/10.1016/j.ce...

We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

We’re pleased to share our new bioRxiv preprint:
“The Pre-clinical Animal Network (PCAN)...t”
www.biorxiv.org/content/10.1...

#PraderWilliSyndrome #MouseGenetics #Phenotyping #FPWR #TranslationalResearch #OpenScience #DigitalTwin #IMPC #INFRAFRONTIER #MRC #RareDisease

Characterization of induced cohesin loop extrusion trajectories in living cells Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...

The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!

If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!

rdcu.be/eLiT5

Enhancer-promoter compatibility is mediated by the promoter-proximal region Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...

What is a promoter? And how does it work?

We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters

www.biorxiv.org/content/10.1...