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... 🧵

De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion - Nature Genetics The authors deplete the cohesin activator NIPBL during the mitosis-to-G1-phase transition. They observe that structural loop formation is impaired proportionally to loop length, while gene activation ...

De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion
www.nature.com/articles/s41...

Our bat–mouse limb paper is now on bioRxiv!
🦇www.biorxiv.org/content/10.64898/2026.04...

This was a collaborative effort across the @nadavahituv.bsky.social Nicola Illing, Dorit Hockman, Guy Kelman, Tommy Kaplan labs and my lab at @washugenetics.bsky.social

Excited to host Evgeny Kvon (UC Irvine) @evgenykvon.bsky.social at IQB on March 30 (Mon)! Everyone is welcome, including non-IQB members. Hope to see you there!!

来週3/30月曜に、UC IrvineのEvgeny Kvonさんのセミナーを開催します！定量研外からの参加もウェルカムですので、是非ご参加ください！！

🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...

Incredibly proud to share our new preprint, lead by the Incomparable Rithika Sankar.
Here we temporally dissect the role of FACT in mES cells, finding that FACT loss drives progressive deterioration of chromatin architecture, leading to transcriptional collapse.
www.biorxiv.org/content/10.6...

Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila Identification of ZAD-ZnF genes as key regulators of genome organization during Drosophila embryogenesis.

Diving into evolutionary biology! What is the origin of the most abundant class of insect transcription factors, ZAD-ZnFs? We suggest that they evolved from ancestral insulator-binding proteins that control 3D genome topology.

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

Transposable element–gene chimera cartography, origination and role in enhancing transcriptome plasticity Nature Structural & Molecular Biology, Published online: 25 February 2026; doi:10.1038/s41594-026-01757-zLeveraging long-read RNA sequencing and multiomics analyses, Cheon and Alvstad et al. systematically map transposable element (TE)-derived isoforms across species and cell states, revealing RNA quality control mechanisms regulating TE–gene chimeras that shape transcriptome plasticity.

New online: Transposable element–gene chimera cartography, origination and role in enhancing transcriptome plasticity

Exited to share Current Opinion review on how chromatin hubs involving multiple enhancers and promoters are formed, and their potential roles in gene regulation: www.sciencedirect.com/science/arti...

Very sad news. Gail Martin (1944-2026) was a figure in developmental biology. She pioneered the field of ES cells.
A great colleague, a friend and a lovely person.

Interested in transcriptional regulation, enhancers and 3D genome folding?

In this new study we wondered about the role of cohesin loading at enhancers for long-range transcriptional control

www.biorxiv.org/content/10.6...

detailed 🧵👇

New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes “multi-way regulatory hubs” in early Drosophila embryos.
www.biorxiv.org/content/10.6...

Neil H. Shubin has been elected as the next NAS President! A leading evolutionary biologist and science communicator, Shubin will succeed Marcia McNutt on July 1. The Academy also named Cherry Murray as International Secretary and elected new councilors. Read more: www.nasonline.org/news/2026_pr...

Join us this week for the next exciting VGZT session! 🎉

🗓️ Thursday, February 5th
⏰ 9:30 PST / 12:30 EST / 17:30 UTC / 17:30 GMT / 18:30 CET

Our speakers are
👉 Evgeny Kvon (@evgenykvon.bsky.social)
👉 Silas Boye Nissen (on X: @SilasBoyeNissen)

See you on Thursday! 👋

excellent thread

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...

📣 I'm excited to share our latest preprint!

We adapt and characterise a neurosphere-based CNCC differentiation protocol, and demonstrate utility for quantitative phenotyping and craniofacial disease modelling! 🧫

Read about Array-CNCC here:
www.biorxiv.org/content/10.6...

@uoe-igc.bsky.social

Sonic hedgehog is not a limb morphogen but acts as a trigger to specify all digits in mice Limb patterning by Sonic hedgehog (Shh), via either graded spatial or temporal signal integration, is a paradigm for “morphogen” function, yet how Shh…

Finally had a chance to read this beautiful paper from Susan Mackem's lab. It's interesting that even well-established paradigms, like Sonic Hedgehog's role as a traditional morphogen in limb development, can be proven wrong over time.
www.sciencedirect.com/science/arti...

And it's out indeed! Huge congrats to @josanesousa.bsky.social, @gabrielalima19.bsky.social, @perezlouise.bsky.social & Hannah Schof! A true tour-de-force that highlights how emerging model systems can shed new light on long-standing macro-evolutionary questions. Go #axolotl, #polypterus #zebrafish!

A table of funding for fiscal year 2025 and proposed for fiscal year 2026 by institute and center.

Now for the money...

Overall, the budget is essentially flat.

The biggest winner is NINDS with a 5.9% increase. The biggest losers are NIEHS and NIDDK.

4/5

SEC. 224. In making Federal financial assistance, the provisions relating to indirect costs in part 75 of title 45, Code of Federal Regulations, including with respect to the approval of deviations from negotiated rates, shall continue to apply to the National Institutes of Health to the same extent and in the same manner as such provisions were applied in the third quarter of fiscal year 2017.

I am still going through the materials, but it seems to be mostly good news.

The language in the bill about indirect costs following the historical process seems very strong.

2/5

Our work on #RegulatoryTrajectories is out today in Nat. Comms: www.nature.com/articles/s41...
Led by @raquelrouco.bsky.social, this study establishes a new framework to study how enhancer landscapes act sequentially at developmental loci and are silenced to shape gene expression patterns. (1/n)

Gratitutde to all NIH study section participants who are participating in rescheduled meetings now and in January. Thank you for your service and thanks also to the hard working NIH staff who are making these happen. 🥰🧪

Now out: The new ENCODE registry of candidate cis-regulatory elements (🐭/👶)

Major consortium effort, led by @moorejille.bsky.social - stay tuned for her "meme-torial"

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

@berkeleylab.lbl.gov @biosci.lbl.gov

Finally out! We studied the retinas of the longest-living vertebrate, the Greenland shark, and found that the retinas remain remarkably healthy in animals around 150 years old. What is the mechanism? It may be a highly efficient DNA repair system. Enjoy!
www.nature.com/articles/s41...

I have always been fascinated by transcriptional activators that display intrinsic specificity towards some but not other promoter types as this implies alternative mechanisms! Hcfc1 directly bridges TFs to TFIID to overcome a CGI-specific rate-limiting step and activate CGI transcription. (2/2)

Activator-promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID Transcription from CpG island (CGI) promoters controls the expression of two-thirds of mammalian genes, yet despite their prevalence, it remains unknown whether CGI-specific co-activators with intrins...

Activator-promoter compatibility in mammals - Hcfc1 is a key and intrinsically CGI-promoter-specific co-activator that cannot activate non-CGI promoters. Lead by @nemcko.bsky.social & Kevin Sabath in collab. with @plaschkalab.bsky.social @impvienna.bsky.social www.biorxiv.org/content/10.6... (1/2)

Join @stirlingchurchman.bsky.social,
@moffittlab.bsky.social, @saramostafavi.bsky.social, me and all speakers for the 2026 CSHL meeting Systems Biology: Global Regulation of Gene Expression, March 11-14. Abstract deadline January 9! More infos and registration at meetings.cshl.edu/meetings.asp...

Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)