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...

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 ...

Excited to read this! @andersshansen.bsky.social @nicholas-aboreden.bsky.social

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

APEX-seq maps transcriptome-wide subcellular RNA localization in living cells Nature Protocols - This Protocol describes the transcriptome-wide labeling of RNAs in a particular subcellular compartment using proximity biotinylation by localized APEX2 enzyme and subsequent...

Excited to share our @natprot.nature.com paper on using RNA proximity labeling to map subcellular RNA transcriptomes. We’ve been working in this area for a while and wanted to create a resource paper to guide the uninitiated reader. rdcu.be/fblvI

Welcome, Tony Hyman!

EMBL welcomes its new Director General, Tony Hyman, as he takes up the mandate of leading EMBL's six sites.

www.embl.org/news/embl-an...

Amazing work from @asmitajha.bsky.social et al on fast super-res imaging:

Fluorogenic speed-optimized DNA-PAINT probes enable super-resolution imaging of whole cells
www.biorxiv.org/content/10.6...

Genetic influences on haematopoiesis Nature Reviews Genetics - Haematopoiesis is a classic process for understanding the genetic basis of human health and disease. In this Review, Poeschla and Sankaran discuss this history and more...

🚨🧬🩸 Delighted to have this @naturerevgenet.bsky.social review w/ Michael Poeschla published today - Genetic Influences on #hematopoiesis: rdcu.be/e9vlD

Ever wondered how a eukaryotic transcription factor finds its specific DNA motif in the vast genome? In this preprint, we directly measured the dynamics of this search process in living cells, revealing a cooperative mechanism mediated by disordered regions. 1/10 doi.org/10.64898/202...

Kinetic Proofreading - PubMed Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theor …

My friend has written on this topic as it is very dear to his heart pubmed.ncbi.nlm.nih.gov/35363508/

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!

How do pairs of DNA loci - such as enhancers and promoters - find each other inside the nucleus? 🤔

Most models assume the random forces driving locus motion are independent in space

New preprint by
@janniharju.bsky.social: this assumption fails in living cells 🧵

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

🧵 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...

Recently out: “Uniform dynamics of cohesin-mediated loop extrusion in living human cells”. In this study led by brilliant former PhD student Thomas Sabaté we use live cell microscopy and polymer simulations to characterize how DNA loops and TADs form in human cells by cohesin-driven extrusion. (1/4)

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...

I had a lot of fun putting this together with @suminkim.bsky.social and @andersshansen.bsky.social! Glad to have had the chance to work on it!

Happy to share our new review on Polycomb-mediated 3D chromatin interactions! Thanks to @mileshuseyin.bsky.social and @andersshansen.bsky.social for great discussions throughout the process :)

Thanks also to @lucagiorgetti.bsky.social and @djost-physbiol.bsky.social for the invitation and for putting together a very interesting themed issue - the other reviews in the issue can be found here
www.sciencedirect.com/special-issu...

Excited to share @suminkim.bsky.social and @mileshuseyin.bsky.social 's new Current Opinion review on how Polycomb complexes mediate 3D genome interactions including mechanistic models and potential roles in gene regulation:
www.sciencedirect.com/science/arti...

Come on join us! We are searching for the next technical associate to join our lab ~Summer 2026.

This could be a great position for someone who is graduating this spring and is looking for 2 more years of research experience before starting their PhD:
careers.peopleclick.com/careerscp/cl...

🚨Preprint alert🚨 How does chromatin “architecture” form at CTCF sites? Our new preprint with @voslab.org and @andersshansen.bsky.social shows CTCF dimerization promotes nucleosome oligomerization on chromatin. tinyurl.com/CTCF-nucleos...

This was a serendipitous finding with so many involved (👀 @voslab.org and @andersshansen.bsky.social). Especially proud of Farnung Lab contributors @mosorio91.bsky.social (on the job market) and PhD candidate Alex Stone. Biochemistry, structural biology, and cell-based assays (Micro-C!!!).

Happy to share part of my postdoctoral work at the @lucas.farnunglab.com lab. Great collaboration with @voslab.org and @andersshansen.bsky.social. “Structural basis for CTCF-mediated chromatin organization” www.biorxiv.org/content/10.6...

🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...

Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation Somatic mutations that increase the fitness of hematopoietic stem cells (HSCs) drive their expansion in clonal hematopoiesis (CH) and predispose individuals to blood cancers. Population variation in t...

New @science.org today
Discovery of a genomic variant that protects against blood cancer by reducing risk of CHIP (blood stem cell mutation clones, common with aging)
@bloodgenes.bsky.social
@kharaslab.bsky.social
science.org/doi/10.1126/...

Dynamics of microcompartment formation at the mitosis-to-G1 transition Nature Structural & Molecular Biology - Goel et al. produce high-resolution three-dimensional genome structure mapping from mitosis to G1 phase to show unseen interactions between enhancers and...

We co-submitted this article with the work of @andersshansen.bsky.social , @irate-physicist.bsky.social , and authors, who characterize similar cre microcompartments : rdcu.be/eWK1u

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm Nature Cell Biology - Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through...

Happy to share that my postdoc work with @jobdekker.bsky.social is out!
rdcu.be/eWHD2

We characterize interphase chromatin folding programs with distinct modes of mitotic inheritance and identify the chromosome-intrinsic capacity to form a microcompartment of active CREs during mitotic exit.

Happy #FluorescenceFriday! Meet our CCCTC-binding factor cell line and plasmid. It illuminates a binding site involved in transcription and is available for just the cost of shipping!

📦 @coriellinstitute.bsky.social and @addgene.bsky.social

Dynamics of microcompartment formation at the mitosis-to-G1 transition - Nature Structural & Molecular Biology Goel et al. produce high-resolution three-dimensional genome structure mapping from mitosis to G1 phase to show unseen interactions between enhancers and promoters in prometaphase. Polymer modeling in...

Be sure to also check out the great paper from @andersshansen.bsky.social and colleagues where they discover microcompartments on mitotic chromosomes using Region Capture Micro-C. Exciting times for those interested in chromosome conformation during cell division!
www.nature.com/articles/s41...

Inheriting chromosome conformation - Nature Cell Biology Chromosomes unfold and refold each time cells divide. A study by Schooley et al. demonstrates that chromosome-intrinsic and cytoplasmic factors uniquely contribute to interphase chromosome structure, with new possibilities for how gene expression programs are passed from mother cells to daughter cells.

Excited to share a News & Views highlighting a new, excellent paper from @jobdekker.bsky.social and @allanaschooley.bsky.social!
www.nature.com/articles/s41...