Interesting finding that rats have a disproportionate expansion of deep cortical layers when compared to other mammalian species - an output of extended duration in deep-layer neurogenesis, mediated by prolonged canonical WNT activity - link.springer.com/article/10.1...

Interspecific diversity in the neuronal composition of the mammalian cortex arises from heterochrony in neurogenesis - The EMBO Journal

Mammals share a laminar cerebral cortex, with excitatory neuron subtypes organized in distinct layers. Although this framework is conserved, subtype balance varies markedly between species due to larg...

link.springer.com

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

nature.com

#DBfeature A tribute to Gail R Martin, mouse geneticist and mentor extraordinaire (April 12, 1944 - Feb 9, 2026) By Alexandra Joyner doi.org/10.1016/j.ydbio.2026.05.007

Maybe they can just join up the extensive network of potholes we already have 👀

Phil Rodgers@philrodgers.co.uk · 2w ago

BBC #FoI request reveals that options for mass rapid transit (MRT) in Cambridge include "converting Mill Road, Histon Road, Milton Road, Newmarket Road, and parts of Hills Road and Trumpington Road, to one-way to enable implementation of MRT lanes" www.bbc.co.uk/news/article...

🐙 Octopuses appear to have evolved a ribosomal innovation that increases protein translation fidelity. *suggests that evolution can tune core components of the proteostasis machinery, extending adaptation beyond gene regulation www.biorxiv.org/content/10.6...

Evolution of a core ribosomal innovation in octopus

Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations in other steps of the central dogma. Octopuses exhibit complex nervous systems and soph...

biorxiv.org

How does an embryo generate the right cells in the right place? Delighted to share our latest findings on how neural crest cells acquire vagal or trunk identities Spoiler alert: The timing & combination of CDXs preconfigures cell identity & distinct HOX states www.biorxiv.org/content/10.6...

Temporally distinct CDX programmes preconfigure vagal and trunk neural crest

Neural crest cells (NCCs) are progenitor cells vital in establishing the head, heart, gut and peripheral nervous system of vertebrate embryos. Disruptions to NCC development underlie neurocristopathie...

biorxiv.org

Delighted that our story on chromatin architecture inside human cells is now published — the last chapter of my PhD. It was a pleasure working with @sergiocruzleon.bsky.social, @johannesbetz.bsky.social, and everyone involved. #teamtomo www.nature.com/articles/s41...

Molecular architecture of heterochromatin at the nuclear periphery of primary human cells - Nature Communications

The 3D organisation of chromatin inside a human cell is still not fully resolved. Here the authors reveal that in situ cryo-ET resolves individual nucleosomes and predicts DNA linkers, thus showing th...

nature.com

Max Planck Institute of Biophysics@mpibp.bsky.social · 3w ago

How do 2 meters of DNA fit inside a nucleus you can barely see? 🧬 Our new study mapped individual nucleosomes inside human cells.

New preprint from the group, comparing CRISPRko and CRISPRi via a Perturb-seq readout: www.biorxiv.org/content/10.6...

Direct comparison of CRISPR knockout and interference with Perturb-seq

CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are two workhorse technologies for loss-of-function studies, yet direct comparisons between the two are scant relative to their widespread ...

biorxiv.org

Excited to share our new preprint led by Fred and me in collaboration with the archaeal community! We found that the molecular foundation of histone-based chromatin has pre-eukaryotic roots in Asgard archaea. (1/4) #ArchaeaSky www.biorxiv.org/content/10.6...

Emergence of histone-based chromatin complexity in Asgard archaea

The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the e...

biorxiv.org

25 years ago, we implicated rare variants of the FOXP2 gene in a severe speech disorder. I’ve spent much time stressing that FOXP2, while interesting, is not the mythical “gene for language”. Weirdly, on occasion I also need to explain why it’s not “proof of aliens”. Full disclosure in this 🧵. 1/n 🧪

Does every enhancer work with every promoter? With @jengreitz.bsky.social and Will Greenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 www.biorxiv.org/content/10.6...

Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers

Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac...

biorxiv.org

It is out 😍 check it out!! Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. @cschwayer.bsky.social @silviabarbiero.bsky.social @davidbrueckner.bsky.social @ehannezo.bsky.social www.cell.com/cell/fulltex...

Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning

During regeneration, tissues must translate transient cellular variability into stable spatial organization. Tissue architecture generates a density-dependent window of heterogeneity in the mechanosen...

cell.com

I am on paternity leave but I need to talk about this work by the @andersshansen.bsky.social lab that was published @natsmb.nature.com. The authors provide absolute quantification of chromatin loops across the genome. www.nature.com/articles/s41... Putting actual numbers in E-P, P-P and all loops!

Genome-wide absolute quantification of chromatin looping - Nature Structural & Molecular Biology

By calibrating Micro-C against live-imaging data in mouse embryonic stem cells, Jusuf et al. quantified 65,929 chromatin loops genome-wide, finding that most loops form pairwise interactions with an a...

nature.com

Led by @jamesdmanton.bsky.social & Jacob Lamb @mrclmb.ac.uk, take a look at this cool new approach to image cleared whole-mount tissues with LSFM! Great to have participated in it, even if it was Ksena Longrin, a great postdoc in my lab, who did our contribution. www.biorxiv.org/content/10.6...

Index-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolution

We present cleared-tissue direct-view oblique plane microscopy (CtDvOPM), which enables optically sectioned subcellular resolution imaging of centimetre-scale tissues at high throughput over the full ...

biorxiv.org

Never too many 💪

🍁 Alex Smith 🍁@alexsmithants.bsky.social · last mo.

🧪🧵 🪰 🐜🪲🐞🦗🐛🦋🪳🦟 How many species of insect are there?  A seemingly simple question, but one that has been 'bugging' scientists for years.  Our work out today suggests that there are millions more than we had previously expected.  doi.org/10.1073/pnas... @gdfcf.bsky.social

Terrific resource, now on @biorxivpreprint.bsky.social: The Vertebrate Genomes Project Phase I: A global reference genome resource 🧪🧬 www.biorxiv.org/content/10.6...

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all ve...

biorxiv.org

Our late Neandertal paper is officially out! 💀❤️🧬 www.nature.com/articles/s41... It was years in the making, a tremendous feat spearheaded by our PhD student Alba Bossoms Mesa and co-led by @janetk.bsky.social and @benmpeter.bsky.social

In what may be one of Earth’s craziest forms of mimicry, researchers in 2023 reported a species of rove beetle that grows a termite puppet on its back to fool real termites into feeding it. Learn more during #InsectWeek: https://scim.ag/4mM2aS9

Such a nice use of a synthetic promoter + cis-regulatory element system to actually ask the fundamental questions about gene regulation in 3D! Also love how the caveats of each method are accounted for by combining them. Thoroughly enjoyed reading this.

Anders Sejr Hansen@andersshansen.bsky.social · last mo.

(3/n) We engineering a synthetic 339 kb E-P pair in 'vacant' region - Vary E-P dist - +/- CTCF at E and P - See nice dot in RCMC maps - Can track E-P 3D distance and nascent RNA from 2Hz to 6+ hours using Super-Res Live Cell Imaging - Txn strictly dependent on E. - New DNA fluor label: synBsr1 (!)

(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...

If you want to get a glimpse of how long range sequencing has revolutionized our view of the human genome, unveiling the true complexity of copy number variation between individuals and using spinal muscular atrophy as an example of the clinical impact, this is for you! 🧪

Ewout Groen@ewout.bsky.social · 2mo ago

Very excited to share our new review on the complexity of SMA genetics, now online @cp-trendsgenetics.bsky.social! General interest in complex genetics? Want to know more about long-read sequencing? Segmental duplications? ✅✅✅ Have a look! www.cell.com/trends/genet...

Whole genome duplications over 450 million years ago enabled the emergence of different kinds of brain cells 🧠 These cellular innovations are shared across vertebrates - from primitive fish to mammals - and form the basis of the sophisticated brains seen today 👇

Ancient genome duplications laid the foundations of complex brains

bit.ly

Our latest: Minimal essential requirements for neural tube self-organisation How does a single cell give rise to a tissue with the right cell types in the right proportions? We deconstruct and rebuild a self-organising tissue from first principles A thread🧵 www.biorxiv.org/content/10.6...

Minimal essential requirements for neural tube self-organisation

The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from p...

biorxiv.org

What can 70,000+ human and chimpanzee regulatory elements tell us about skeletal evolution? A new study in @genomebiolevol.bsky.social uncovered genomic differences linked to skeletal development using a massively parallel reporter assay. We're glad our ATx® could support! 🔗 https://bit.ly/3PV2naf

In Vitro Massively Parallel Screening of Human Regulatory Elements Involved in Postcranial Skeletal Development for Differential Activity Compared to Chimpanzee

Abstract. Every element of the human skeleton exhibits some differences in comparison to our closest living relatives, chimpanzees. Many of these skeletal

academic.oup.com

Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation. https://scim.ag/4nTQ3nq

'We primarily do comparative analysis using human stem cells/organoids and genetically modified mouse models, with some minor use of frog models. We use this approach because, for developmental anomalies, it is impossible to assess true function without in vivo models' @karenjliu.bsky.social

Why in vivo models of disease remain indispensable

Summary: The call to arms for alternatives to model organisms of disease will fail without ongoing integration with – and validation against – complex animal models and support from the animal modelli...

journals.biologists.com

Bilaterian BMP signaling gradients suggest an ancestral anti-neural role. Study of #cnidarians shows that #BMP signalling promotes neurogenesis; its "anti-neural" function is a side effect of its role in the DV axis @paulknabl.bsky.social @genikhovich.bsky.social @plosbiology.org 🧪 plos.io/4dJHoiR

If you are interested in the mechanisms linking variants in histone modifying enzymes to Autism Spectrum Disorder phenotypes, have a read! New from @bassonlab.bsky.social 🧠 congrats to @lperezsisques.bsky.social and everyone else! www.science.org/doi/10.1126/...

Autism-like phenotypes and increased NMDAR2D expression in mice with KDM5B histone lysine demethylase deficiency

Inhibitors targeting NMDA receptors may represent viable therapies for KDM5B neurodevelopmental disorders.

science.org

This is red shanked douc langur.

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.