really impressive scaling feat! i’m jealous of it. very neat assay, wonderful acronym. i’m all for it though lit refs could be better and are 5 x1kb fragments really a mammalian locus?

Jay Shendure@jshendure.bsky.social · 6d ago

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

Obviously a strong supporter of this type of tool, but troubled by the literature review. No reference to @chribue.bsky.social work on combinatorial enhancers, and our EXTRA-seq -> kilobase-scale E-P landscapes in a native locus (no minP). Same principle, just ONT.

Jay Shendure@jshendure.bsky.social · 6d ago

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

I am very excited to share the work of my PhD with @eddaschulz.bsky.social, now on BioRxiv! 🎉 🧵⬇️ (1/9) How does the transcription↔️chromatin crosstalk ensure monoallelic expression?

bioRxivpreprint@biorxivpreprint.bsky.social · last wk.

Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome https://www.biorxiv.org/content/10.64898/2026.07.22.737064v1

40 individuals with the clinical picture of FOXG1 syndrome and a completely intact FOXG1 gene. So what’s going wrong then? Our new paper in @natcomms.nature.com traces the answer to a stretch of non-coding DNA 665 kb away from the gene. (1/7)

The STRAIGHT-IN (Dual) kit is now available via @addgene.bsky.social! 🧬 A complete 24-plasmid toolkit for installing up to two orthogonal CLYBL landing pads, DASIT-based enrichment without FACS, and efficient large DNA integration in human cells. Link: www.addgene.org/kits/gallowa... 🧵

When I was writing this piece about the Ocean Cleanup, I had a surreal experience: They assured me that they only kill invasive species, and sent me a published paper to demonstrate that. But the paper said the opposite! I wonder how many journalists just took their word for it and didn't check?

Why The Ocean Cleanup Hasn’t Solved the Plastic Pollution Crisis • The Revelator

Global problems are rarely solved by one person or invention. The Ocean Cleanup didn’t work, for the reasons experts said it wouldn’t. What can we learn from this?

therevelator.org

Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:

Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics

Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...

doi.org

Luca Giorgetti lab @FMI@lucagiorgetti.bsky.social · last yr.

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

really good take from Aydan! I‘m also quite disturbed by the whole 1% marketing gag. masterful click-baiting as expected from oded (worked for me). but it kind of feels like a right out of a Black Mirror episode. As if it wouldn’t lead to a new glorification of articles ranked well by an AI.

Aydan Bulut-Karslioglu@bulutkarslioglu.bsky.social · last mo.

I have been thinking since yesterday about why I find the 1% thing so, so disturbing. It's a visceral reaction of 'just no', which goes beyond the general yuck towards the enshittification of/via AI. I have finally put my finger on it: it is the feeling you get when

The cooling system was installed by the village AC technician, Thermodynamix 😊

Standplaats Kraków could really use some cash!@standplaatskrk.pl · last mo.

1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...

22/n On a personal note, I’ll soon start an independent research group in the Genome Biology Unit at EMBL Heidelberg. If you enjoy this type of work and want to engineer genomes at the largest scale, please reach out! jonas-koeppel.github.io/koeppellab/ www.embl.org/groups/koepp...

Join is in Budapest in October! For the 6th time, all things epigenetics, gene and genome regulation and more. A fantastic opportunity to present, to talk to speakers and colleagues in a friendly, informal setting at a great location. Please note, travel grant deadline will expire soon.

We are over the moon! 🎈 Dr. Marieke Oudelaar joins the MPI-IE as a new #MaxPlanck Director, heading the newly established Department of Genome Biology She studies how the 3D folding of DNA controls gene expression – more details below ⬇️ Welcome to #Freiburg, @mariekeoudelaar.bsky.social!

Marieke Oudelaar becomes new Director at MPI-IE in Freiburg

ie-freiburg.mpg.de

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

Alexis Verger 🧬🧫🧪@alexis-verger.cpesr.fr · 3mo ago

#RIP Pierre Chambon (1931-2026) 1963 PARP 1970 RNA Pol II 1975 Nucleosome 1977 Split genes 1980 Promoter 1983 enhancer 1986 Nuclear receptor

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 💐

And more plasmids for using STRAIGHT-IN Dual from the Galloway Lab here: www.addgene.org/browse/artic...

In 2015, the Los Angeles SPCA gave their annual National Hero Dog award to a tabby cat named Tara. Yes, you read that right, a cat was given a dog award.

⭕️ The STRAIGHT-IN dual plasmids are now available on Addgene! 🧬 @addgene.bsky.social A full STRAIGHT-IN kit with 20+ plasmids, including everything needed to set up and run the platform, is coming soon 🔥 Stay tuned 🚀

Addgene@addgene.bsky.social · 3mo ago

Need a solution for multi-transgene integration? Check out the STRAIGHT-IN Dual platform! Thanks to the Galloway and Davis Labs for sharing the plasmids: www.addgene.org/browse/artic...

Excellent opportunity @mrc-lms.bsky.social for a human physiologist to start their own group. Deadline 4th May. Core funding, excellent package. Please repost! lms.mrc.ac.uk/work/vacanci...

Programme Leader Track - MRC Laboratory of Medical Sciences

lms.mrc.ac.uk

Happy to share our review of the past, recent, and future applications of synthetic genomics in studying the 3D functional organization of chromosomes, a set of approaches that are gaining momentum! www.sciencedirect.com/science/arti...

Synthetic chromosomes for 3D functional genomics: from principles to AI-guided design

The role of genome 3D organization for fundamental chromatin processes, such as long-range promoter-activator regulatory interactions, remains ambiguo…

sciencedirect.com

A new study shows how different regulatory genetic elements control when a key developmental gene is active in the body. The findings could explain subtle differences seen in patients with congenital limb malformations, for which the underlying disease mechanisms often remain unknown.

Waves of regulation control an important developmental gene

In a new study published in Genes & Development, research led by Dr Lila Allou at the MRC Laboratory of Medical Sciences (LMS) in London and Professor Stefan Mundlos at the Max Planck Institute for Mo...

lms.mrc.ac.uk

Just look at this graph (Fig 5A,B from Koeber et al). Amazing. Congratulations to the Pollard lab and all authors. www.nature.com/articles/s41...

Die Bundesregierung will geheimhalten, wo sie neue fossile Infrastruktur in Deutschland plant. Wir schaffen Transparenz und zeigen, wo neue Kraftwerke, Bohrungen, Pipelines und Flüssiggas-Terminals entstehen sollen – und wie ihr dagegen aktiv werden könnt: fragdenstaat.de/aktionen/cli...

Meilenstein in der Neurochirurgie: Neue Methode ermöglicht personalisierte Präzisionschirurgie bei Hirntumoren Forschende des Universitätsklinikums Schleswig-Holstein (UKSH), Campus Kiel, der Christian-Albrechts-Universität zu Kiel (CAU) un... weiterlesen

Harvey Yang and I were fortunate to contribute polymer simulations to this paper from @nicholas-aboreden.bsky.social Zhao... Zhang, Blobel showing that most CRE loops can form de novo after mitosis without loop extrusion www.nature.com/articles/s41...

Meet people @mpi-cbg.de and their younger selves! At MPI-CBG, 500 curiousity-driven individuals, from over 50 countries & from the most diverse backgrounds, explore fundamental molecular and cellular processes underlying the formation of organs and organisms and their healthy maintenance. #thisiswho

New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...

Want to know how histone marks regulate your favorite gene? Go single molecule with ChromSMF: integrated measure of chromatin accessibility and histone marks + DNA methylation, TF footprints and genotype for free! Very proud of @mpalamin.bsky.social ! @embl.org

Michela Palamin@mpalamin.bsky.social · 4mo ago

ChromSMF preprint is out!🚀 tinyurl.com/ChromSMF We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting! In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬 What does this unlock? ⬇️

ChromSMF preprint is out!🚀 tinyurl.com/ChromSMF We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting! In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬 What does this unlock? ⬇️

🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders? In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸 🔗 www.science.org/doi/10.1126/... #EvoDevo