Our International Developmental Mechanics Zoom Seminar Series returns this fall! Interested in sharing your research with an international community? Sign up to speak at an upcoming session: sites.google.com/view/devmech... #DevBio #Mechanobiology #Morphogenesis

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/

Jesse Engreitz@jengreitz.bsky.social · 2y ago

Introducing scE2G: a new model to link enhancers to target genes using single-cell data. Excited that scE2G will enable building enhancer maps in hundreds of cell types in the human body! Wonderful collaboration with @randersson.bsky.social @613weilin.bsky.social @mayayayas.bsky.social Thread👇

A huge congratulations to Zheng and the entire Guo lab for this beautiful story! Very cool mechanism! www.nature.com/articles/s41...

Intestinal stem cells count self-renewal divisions to switch multipotency - Nature

In Drosophila, cell fate switching in adult intestinal stem cells is determined through an epigenetic mechanism in which these cells count divisions, switching from producing enterocytes to producing ...

nature.com

Finally out - our work on high throughput design and characterization of disordered protein sequences 🪱🪱🪱. A long time collaboration with BFFs @alexholehouse.bsky.social and @remenecker.bsky.social, with experimental work led by @trevorbrandt.bsky.social and @karaehunt.bsky.social.

Rational design of disordered proteins for sequence–function investigation - Nature

GOOSE enables the design and testing of thousands of disordered protein region sequences to reveal distinct sequence-to-function relationships.

nature.com

Excited to share a new preprint from the lab, by @andrewmatheson.bsky.social and team, where we dive into the superpower of newts: plasticity! www.biorxiv.org/content/10.6... Like many good projects, this started with a serendipitous observation... 🧵1/5

4D Nucleome special issue of Science, featuring our paper "Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease–linked transcription factor", led by Zoe Grant in my lab and Zhuzhen Kuang in Katie Pollard's lab @gladstoneinst.bsky.social www.science.org/toc/science/...

Our new paper is out in @nature.com! We uncovered how a naked mole-rat queen 👑 controls an entire colony: a natural contraceptive scent that suppresses reproduction in other females! A remarkable mammalian parallel to bees and ants! 🐝🐜 @garyrlewin.bsky.social youtu.be/enfv3zJrWKM?...

Naked mole-rats are ruled by a queen: this chemical puts her in power

YouTube video by nature video

youtu.be

Please RP! Excited to share our new preprint: “Single-cell chromatin tracing reveals multimodal molecular programs during memory formation” We built a single-cell multiomic atlas of aversive learning and used it to trace memory-linked molecular programs. doi.org/10.64898/202...

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...

Identifying critical lysines in mammalian histone H3 with high-throughput CRISPR prime editing - Nature Genetics

This study uses a precise and efficient clustered regularly interspaced short palindromic repeats (CRISPR) prime editing system to substitute lysine residues in histone H3, individually or in combinat...

nature.com

I had an (honestly) really fun time writing up an "In Preprints" piece on the two fantastic studies from @grandlab.bsky.social and @schubelerlab.bsky.social. Check it out here. I have also put the original threads from the authors below. journals.biologists.com/dev/article/...

In preprints – housekeeping the housekeeping genes

The term ‘housekeeping gene’ evokes a sense of banality. These are the boring genes that hum in the background, impervious to cell state or stress. For a developmental biologist captivated by the impa...

journals.biologists.com

Better late than never... an update on the recent work from the lab. First of all, the Foundation: @astridd93.bsky.social phenomenal paper on the evolution of layering in the cerebral cortex 🧵1/7 www.biorxiv.org/content/10.1...

Our new #preprint has: ✅ A KRAB Zinc Finger (the SCAN domain-containing kind) ✅ #transposon sequences (the SINE kind) ✅ #epigenetic regulation (the #enhancer kind) ✅ lineage specification (the neural kind) ❌ and NO heterochromatin! All by PhD student Daniel Moore 🚀 www.biorxiv.org/content/10.1...

The KRAB-Zinc Finger protein ZKSCAN3 represses enhancers via embedded retrotransposons

Gene cis -regulatory sequences are increasingly recognised as containing “domesticated” transposable elements that impact their function. The KRAB Zinc Finger Protein (KZFP) family of transcription fa...

biorxiv.org

🔥 Published today, and just in time for summer conferences, here are your guidelines for presenting badly www.nature.com/articles/s41... rdcu.be/fqa92

Gloves are off! TODAY WE RELEASE THE 1% A list of the year’s very best papers 👇 (see thread)

(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...

Very nicely done Radiolab episode featuring @emilyjacobs.bsky.social and team’s work. Check it out! radiolab.org/podcast/this...

This is Your Brain on Hormones

We don’t have hormones, hormones have us.

radiolab.org

Researchers recorded from single neurons across frontotemporal cortex in 8 awake individuals during natural speech. They show how activities of collections of cells can capture syntactic & semantic properties of words, & also dynamically incorporate sentence context to encode combinatorial info. 🗣️🧠🧪

Mapping the neuronal building blocks of human language with language models - Nature

Wide-scale recordings reveal neurons in the human brain that encode fundamental components of language such as the grammatical relationships between words, their parts of speech and the...

nature.com

🧬 🧪Our RNA velocity benchmark is out in PLOS Comp Biol We tested 5 methods on mouse & zebrafish data. They often disagree (just 1/100 driver genes shared 😬). A hypothesis tool, not ground truth. Open access 👉 doi.org/10.1371/jour... Led by the brilliant Sarah Ancheta (not on bsky)

New preprint from our lab on bioRxiv: “Stoichiometric transcription factor partnerships control GABAergic neuron fate allocation” www.biorxiv.org/content/10.6... A great collaboration with @annrosebright.bsky.social, Connor Lynch, @chr-mayer.bsky.social, and many others.

Stoichiometric transcription factor partnerships control GABAergic neuron fate allocation

Combinatorial transcription factor (TF) codes specify neuronal fates, yet how quantitative differences in interacting TFs shape these decisions remains unresolved. We address this in the developing ba...

biorxiv.org

#Science #Biologie  🦇 « L’évolution des mécanismes du développement » 🖥️ Les vidéos du colloque organisé par le Pr @denisduboule.bsky.social, titulaire de la chaire #Évolution du développement et des #génomes, sont disponibles ! 👉 https://tinyurl.com/39p4h5pn

Sun et al, 2026. NuRD-enabled CTCF-TET crosstalk orchestrates epigenome reprogramming and genome architecture www.cell.com/molecular-ce...

Bumble bees can apparently play with balls, count, recognize faces, & perceive rhythm. A new study out today in @science.org argues they can also solve novel tasks spontaneously without explicit training, challenging the idea that such cognitive skills are exclusive to large-brained vertebrates.😲🐝🧪👇

Spontaneous problem-solving in bumble bees

Problem-solving using novel solutions without explicit training is often considered a hallmark of cognitive flexibility. We investigated whether bumble bees (Bombus terrestris) could solve a novel obj...

science.org

Exciting breakthrough technology from the lab, now live in @cellcellpress.bsky.social ! Instead of cutting the genome where proteins bind (e.g., Cut&Tag), D&D-seq scars the DNA with a deaminase, allowing single cell genome mapping of TFs and chromatin remodellers!

Single Cell Genomics Day: A (Virtual) Practical Workshop. June 12, 2026, organized by @nygenome.org's Rahul Satija Free, livestreamed, no registration.

Out now in Science! Our study challenges long-standing assumptions about transcription factor specificity in eukaryotes. Novel single-molecule measurements of TF behavior in living cells reveal an independence of locus-specific binding from DNA sequence recognition.🧵 www.science.org/doi/10.1126/...

Unstructured transcription factor interactions enable emergent specificity

How intrinsically disordered regions (IDRs) shape chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We used proximity-assisted photoactivation (PAPA), a single...

science.org

Single-cell proteomics illuminated new mechanisms of mammalian development. We found that spatially polarized protein distributions and intracellular protein gradients emerge during the earliest stages of mammalian embryogenesis and bias subsequent cell fate decisions. www.cell.com/cell/fulltex...

This a very important, and extremely well-executed study from Ralph Grand’s group @uniheidelberg.bsky.social. Congrats to all the authors! www.biorxiv.org/content/10.6...

Smell is topographically organized after all. A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain: Cell www.cell.com/cell/fulltex...

A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain

Dorsoventral epithelial position induces graded expression of a transcriptional program that maps each of the 1,100 olfactory sensory neuron subtypes to stereotyped spatial distributions in the epithe...

cell.com

Can we control cells by forcing TFs to collaborate? Interested? Read our preprint! An awesome collaboration with @cgersbach.bsky.social, @igvfconsortium.bsky.social, Christian McRoberts Amador, @rachel-savage.bsky.social: www.biorxiv.org/content/10.6... 🧵