Arnaud Krebs

your starter pack for Single Molecule Genomics! Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa

🧬 Mark your calendars! Our EMBO Workshop "Chromatin evolution from molecules to genomes" is coming to St Feliu de Guíxols (Spain), 4–7 Oct 2027 🌊 Amazing programme! #EMBOchromatinEvo meetings.embo.org/event/27-chromatin-evo Register early!

New preprint from Dodonova lab 🔔! Capturing multiple states by cryo-EM❄️, we show for the first time how archaeal RNA Polymerase engages a nucleosome and forms direct contacts with histones! 🧬 Great work by Gabriele & a fantastic collaboration with Dina Grohmann! 🧵 www.biorxiv.org/content/10.6...

When a scientific revolution happens on your doorstep. Simply spectacular.

We are recruiting! Wet&Dry either combined or separate. If you are excited about gene regulation, new methods in genomics and AI-based interpretation! Talk to us!

Pierre Chambon was one of the driving architects of modern molecular biology, whose scientific vision transformed the understanding of gene regulation in eukaryotic cells. His passing in May 2026 represents the loss of an extraordinary scientist. www.nature.com/articles/s41...

🎉Excited to share the latest paper from my lab, where we developed a new framework to investigate DNA methylation at single-molecule resolution using @oxfordnanopore.bsky.social (ONT) long read sequencing. Work spearheaded by a very talented student Young Jun Kim. www.biorxiv.org/content/10.6... 1/n

Everything you wanted to know about single-molecule epigenomics but were too afraid to ask! Wonderful to co-write (h/t ENORMOUS lift by @arnaudkr.bsky.social) this primer on our nascent field. Also, a 💯 example of wonderful colleagues building something *together*, not in competition =)

🧫 We’re hiring a staff/research scientist to develop new experimental approaches that capture cell state dynamics. Join us in Heidelberg, details + application here: embl.wd103.myworkdayjobs.com/EMBL/job/Hei... Closes September 30th

EMBL QBMM is back this year with an outstanding line-up! Plenty of talks will be selected from submitted abstracts, with emphasis on junior scientists and representation across diverse fields. The abstract deadline is the end of this week, so don’t miss out! www.embl.org/about/info/c...

Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)

🚨Happy to share that the first part of my PhD is out on @cp-devcell.bsky.social! This has been an exciting project in the lab of @eileen-furlong.bsky.social @embl.org, studying the regulation of Pol II pausing across embryogenesis and its impact on gene expression dynamics. tinyurl.com/5n88ykk7

A triptych of reviews on the transcription cycle @natrevmcb.nature.com 1️⃣ Initiation Chen & Xu 2️⃣ Elongation @camimoso.bsky.social @isaacfianu.bsky.social @adelmanlab.bsky.social 3️⃣ Termination Song et al. www.nature.com/articles/s41... www.nature.com/articles/s41... www.nature.com/articles/s41...

Is activation of multiple enhancers and promoters coordinated? Short answer is yes. Check full story from @mathias-boulanger.bsky.social @kasitc.bsky.social leveraging long read single molecule sequencing to address this. @embl.org www.cell.com/molecular-ce...

Inferring transcription factor activity: use ATAC-seq, reporter assays, or both? link.springer.com/article/10.1...

Exciting news! We've just moved into the brand new Livsvitenskapsbygningen (Life Science Building) in Oslo, with the whole @ncmbm.bsky.social! Incredible space, great views, and so many opportunities for collaboration ahead. 🧬🏢 @uio.no #LifeScience #Oslo #LVB

Very much looking forward to this! Join us!

Sign up now for the EMBO meeting 'quantitative biology to molecular mechanisms'. Fantastic speaker lineup and plenty of speakers slots selected from abstracts. Submit your abstract before Sept 11!

This is an outstanding meeting across fields. The lineup is amazing this year. Do not miss it.

Finally, many thanks to the EMBL communication team for their beautiful piece www.embl.org/news/science...

And into our companion computational method paper for details on FootprintCharter doi.org/10.1093/bioi...

Dive into the revised paper for a deeper validation of our F1 and SOX2 dTAG perturbations, as well as a brand-new combinatorial TF motif deletion mCHIRA experiment.

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

Check out our new review about SAGA (Spt-Ada-Gcn5 acetyltransferase) and ATAC (Ada Two-A Containing) coactivator complexes in EMBO. doi.org/10.1038/s443.... We dissect the functions of SAGA and ATAC, which are crucial for understanding regulation by these complexes as targets in precision oncology.

Read this article, get excited, and come to the Epigenome Editing symposium! Marianne Rots, Charlie Gersbach, and Angelo Lombardo (all featured in the piece) will be there in person!! Registration only 50€, talks from abstracts, plus Paris 😜 @natureportfolio.nature.com www.nature.com/articles/d41...

Latest from @arnaudkr.bsky.social on TF cooperation at enhancers, liked the combination of single-molecule footprinting at ectopic vs endogenous loci in mESCs. Curious if the cumulative activation frequency model holds for other less proliferative/plastic cell types? www.nature.com/articles/s41...

'Gene regulation, one molecule at a time' is coming back in July 17! Book your calendars and stay tuned!

One of my favorite meetings. Many slots for abstract selected talks! Friendly to junior scientist - apply!

I am starting my lab at the University of Geneva next January! Incredibly excited to soon be joining the MOCEL department as an Asst. Professor. The lab will use evolutionary cell biology to study chromosomes, centromeres & speciation 🧬🔬🌱 Intrigued, want to join or collaborate? 🔗 helsenlab.org

In memory of Pierre Chambon (1931–2026): a visionary pioneer of modern molecular biology by Hinrich Gronemeyer in @embojournal.org link.springer.com/article/10.1...

Interesting. Full deletion of all introns in yeast was actually my project in the Staley lab, *20 years ago*. I actually found a bunch of phenotypes. We did this in collaboration with the Guthrie lab. www.cell.com/cell/abstrac...

1/ Very excited to share the first publication from my lab! In this work, we developed an efficient strategy to precisely mutate mammalian histone genes in their native genomic context using CRISPR prime editing: www.nature.com/articles/s41...

First preprint stemming from a fantastic collaboration with @hanhtkvu.bsky.social Shared PhD student and BIF fellow @gvaidya.bsky.social led this tour de force - check it out ! How does temperature affect whole-organism cellular trajectories?

Super excited that the first preprint from the lab is out! Led by an amazing student, Gaurav @gvaidya.bsky.social, jointly supervised with @mwdorr.bsky.social.

Frank Grosveld has been a giant in the field of long-range gene regulation. Inspirational to me and I am sure for many others. Rest in peace.

First pre-print from the lab, a collaborative effort led by Jess Bourn @bournsupremacy.bsky.social, a fantastic PhD in my group. We resolve a key problem in development + evolution: how do we quantify heterochrony and link temporal variation to phenotype? www.biorxiv.org/content/10.6...

Pressure works. Three days ago, I joined lawmakers pressuring the White House to stop its plan to dismantle a $368 million ocean monitoring system that is CRITICAL to understanding climate change and marine ecosystems, including right here off the coast of Oregon. Today, Trump backed down.

Excited to share our new preprint! 🧬❄️ by brilliant @mdreimann.bsky.social and great collaborators! Using cryo-ET&EM, we reveal archaeal chromatin in a near-native state: variable-beads-on-a-string fibers shaped by growth phase and histone composition #ArchaeaSky www.biorxiv.org/content/10.6...

"So ... so I said ... why not sign your treaty here, at Versailles?"

JIT 4 summer, the latest preprint from our lab, brilliantly led by @kaitezhang.bsky.social w/ support from Collepardo lab (@juliamaristany.bsky.social / @janhuemar.bsky.social). www.biorxiv.org/content/10.6... describes a new single-molecule epigenomic method, & discoveries it enables ... (1/n)

This will be cool! Featuring Valentina presenting her PhD work in my lab.

🚨Preprint Drop🚨 We are very pleased to release our study on DNA methylation dynamics at enhancers during ESC differentiation! This work was led by Marlet Morales-Franco and Priscillia Lhoumaud 🧵(1/13) www.biorxiv.org/content/10.6...

Thrilled to share the updated video of my paper in Nature with Maciej (under supervision of @simonemattei.bsky.social & @jomaalab.bsky.social) Proud to use Cryo-ET to uncover how hibernation factors are key to translation restart! To model PTMs in situ and render animations fulfilled my PhD dream!🥹🎉

Out today - structure of the human HIRA histone chaperone complex bound to nucleosomes. Ever wondered how nucleosomes are assembled in the wake of transcription? It takes a 'hulk of a protein complex'. Work by the amazing Wei Tian weetian558.bsky.social. www.biorxiv.org/content/10.6... 🧵

Sad news - he certainly was a towering figure with many influential discoveries - see below. Why he was never awarded the 'big' prize is truly baffling, but his many contributions to science will be remembered much longer than any prize. Thank you @alexis-verger.cpesr.fr for putting this together.

An historical figure of the transcription field has gone. Founder of @igbmc.bsky.social where I started my career. A great enabler as well.

Pierre Chambon was a great scientist. And a good man too. He alone opposed to leading British embryologists during the evaluation of a case of scientific misconduct more than 40 years ago, to defend young scientists against an establishment to which he belonged. An unforgettable lesson. RIP Pierre 💐

Excited to share our new study on CpG islands (CGIs) regulation by transcription factors (TFs)! CGIs drive most transcription initiation with unclear regulation. We find that chromatin-opening TFs are key players—following a surprisingly simple rule. 🧵 www.biorxiv.org/content/10.6... 1/9

Excited to share our first story led by @martinacapriati.bsky.social! How do cells control the expression of viability genes? We find that single transcription factors can drive both chromatin opening and gene activation from densely co-bound CpG island promoters, including at essential genes