Congratulations to @jasoncasler.bsky.social (and @lllackner.bsky.social lab)! Jason’s article was judged by our Editors to be the best article published in @jcellsci.bsky.social last year and earns him a £1000 prize 🏆

We have an exciting new story out at @science.org's Science Immunology! It is all about using #AAV-mediated cytokine delivery to change the lung environment. We can boost #lung #Tregs or delivery anti-inflammatory #cytokines, preventing fatal respiratory collapse

www.science.org/doi/10.1126/...

Heritability of intrinsic human life span is about 50% when confounding factors are addressed How heritable is human life span? If genetic heritability is high, longevity genes can reveal aging mechanisms and inform medicine and public health. However, current estimates of heritability are low...

The role of genetics in longevity: 50% heritability - huge potential to look into genetics and mechanisms of longevity

Nice work from @urialonlab.bsky.social ‘s lab

www.science.org/doi/10.1126/...

This @anshulkundaje.bsky.social, Kyle Fahr and William Greenleaf paper is finally out, we've been following it for a while in its preprint form, phenomenal work.

www.nature.com/articles/s41...

We are so excited to see our work out in @nature.com! We present a multi-omic single-cell atlas of 12 organs in human fetal development, explore the enhancer landscape, use deep learning to infer rules of transcription factor activity, and interpret non-coding variants in complex traits: #GeneReg 🧬🖥️

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…

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...

Happy to share our new preprint on non-coding genetic variation in the human brain and Parkinson's disease. Great team effort with @alexanrna.bsky.social, @juliedeman.bsky.social, Koen Theunis, and all co-authors, supervised by @steinaerts.bsky.social and @jdemeul.bsky.social.
Thread below:

New paper in Genes & Dev: we dissected how Sox2 — a key pluripotency TF — is regulated by a distal enhancer cluster (SCR) 100 kb away. The results challenge simple models of cohesin-mediated loop extrusion of gene regulation. genesdev.cshlp.org/content/earl... 🧵

See also the concordant and related papers from

@tessapopay.bsky.social @jesserdixon.bsky.social
www.nature.com/articles/s41...

UkJin Lee @efapostolou29.bsky.social
www.nature.com/articles/s41...

@karissalhansen.bsky.social @elphegenoralab.bsky.social
www.science.org/doi/epdf/10....

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...

In Memoriam: Professor Greg Hannon (1964–2026) - Cancer Research UK Cambridge Institute Greg was already a world-renowned scientist when appointed Director, and for the community, he was a visionary leader, a cherished mentor, and a singular force of nature whose influence shaped the research landscape.

Very upsetting to hear the sad news of Greg Hannon’s passing. I always enjoyed our far too few conversations we had over the years. He had an interesting and insightful perspective on any science being discussed. He will be missed. www.cruk.cam.ac.uk/news/in-memo...

Latest from Shendure & Qiu labs (@cxqiu.bsky.social)
)! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).

First first-author paper out! 🎉

We show that the classically repressive mark H3K27me3 can be linked to active transcription through a newly identified reader complex 🤯

Really grateful to everyone involved in this project during my PhD!

Thread below 👇

A H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium - Genome Biology Background The ability to deposit histone H3K27-trimethyl (me3) marks is essential for transcriptional repression by Polycomb Repressive Complex 2 (PRC2). This is largely attributed to Polycomb repres...

Our latest publication is now out at Genome Biology!
link.springer.com/article/10.1...

We uncover a unique association between a H3K27me3 reader complex and active transcription.
A thread with our key findings: (1/8)

#TEsky #Polycomb #transcription #smallRNAs

In addition to the cool findings, this paper is worth reading if only for the clear experimental logic and elegantly executed assays. A very nice teaching example 👏

Our H1 paper is out #ScienceAdvances:
www.science.org/doi/10.1126/...
@masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in live cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/

Image of a planarian, from Wiki.

Do you do a PhD on Chromatin in this cool critter?

Work with @jordisolana.bsky.social @seanflynn.bsky.social, Magda Strauss and myself @lsiexeter.bsky.social on developing #singlecell #chromatin analyses to better understand pluripotency #planarians.
www.exeter.ac.uk/research/ins...

Undaria pinnatifida gametophyte

Our work on chromatin evolution in brown algae is now published in @natecoevo.nature.com! We show that developmentally complex brown algae evolved without epigenetic silencing pathways long thought universal, underscoring why non-model lineages are important to study. www.nature.com/articles/s41...

📢📢 join us for this edition of the “Quantitative biology to molecular mechanisms” EMBO workshop

Gene regulation, cell dynamics & systems biology

17th - 20th November

More info: s.embl.org/omx26-01-bl

Epigenetic memory of colitis promotes tumour growth - Nature Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...

A little late to Bluesky but my postdoc work w/ @jbuenrostro.bsky.social now out in @nature.com
"Epigenetic memory of colitis promotes tumour growth"
www.nature.com/articles/s41...

We wanted to understand how transient inflammation can create an increase in cancer risk, even after full recovery 🧵

Distinctive DNA sequence features define epigenetic longevity of inflammatory memory Tissues harbor memories of inflammation, which heighten sensitivity to diverse future assaults. Whether and how these adaptations are sustained through time and cell division remain poorly understood....

I am very pleased with our latest paper showing that cells can remember past injury for a long time! Here a simple interpretable AI was used as a discovery tool to pinpoint the DNA code and biological mechanism. Big foundation models failed. www.science.org/doi/10.1126/...

We then introduced an oncogenic mutation.

What we saw was striking: cells with prior inflammatory memory formed larger tumors, effectively lowering the threshold for transformation.

Same mutation, different outcome depending on the cell’s past experiences.

Epigenetic memory of colitis promotes tumour growth - Nature Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...

It’s well known that inflammation increases cancer risk, but how?

The answer: the epigenome "remembers" inflammation and primes stem cells for cancer.

Here is our paper: nature.com/articles/s41...
And a special shoutout to the lead author
@snaga13.bsky.social

A 🧵

Supercoiling not only brings DNA to life (and makes it dance) but also changes how key proteins such as #CRISPR interact with it. Thanks @qmsmith.bsky.social for the brilliant collaboration, Sylvia for developing an amazing new #imageanalysis pipeline & @eddierollins.bsky.social for beautiful #AFM.

Delighted to see our work now published at the EMBO Journal! Check also this concomitant paper by the Bai and Mirny labs with an orthogonal approach that aligns well with our measurements www.nature.com/articles/s41... Great system to study how SMCs facilitate/regulate target search in chromatin!

Just finished reading this lovely paper by @zbobo2.bsky.social , @teamgogl.bsky.social , Gilles Travé, and collaborators, describing a new technique for quantifying transcription factor:DNA binding without protein purification. A short reader's summary follows.

🔥 How does CTCF shape enhancer–promoter communication?

In our new preprint, we systematically test how the position and orientation of CTCF binding sites (CBSs) influence gene regulation at the mouse Sox2 locus.

🧪 full paper can be found here: 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

Trust me--read this. You'll be glad you did. and thank you Dr. Bennet for writing it. 🧪

Kinetic proofreading as a mechanism for transcriptional specificity: www.biorxiv.org/content/10.6...
Very nice follow up to their review from last year genesdev.cshlp.org/content/39/1...
Non-equilibrium models may be key to understanding specificity in transcriptional regulation!