🚨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...

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/...

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

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#FluorescenceFriday

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...

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

See this recent paper by @andersshansen.bsky.social that discovers similar microcompartmentalization during mitotic exit: www.nature.com/articles/s41...

And also see this nice News and Views by @kyleeagen.bsky.social www.nature.com/articles/s41...

Congrats to @allanaschooley.bsky.social et al. @jobdekker.bsky.social on this beautiful paper, using a very elegant experimental system, to discover a chromosome intrinsic 3D genome folding program and microcompartmentalization of CREs at mitotic exit:

Excellent @activemotifusa.bsky.social epigenetics podcast w @andersshansen.bsky.social It’s interesting, while going through specific projects and lines of questioning, the conversation acts as a nice reflection of the state of our field (fields?) Lots of ideas! open.spotify.com/episode/19Nd...

An MIT lab director was killed in a shooting at his home in Brookline, Massachusetts Monday night, the school confirmed. No one is in custody, Brookline police deputy superintendent said.

Our (Viraat Goel, @andersshansen.bsky.social et al) paper Dynamics of microcompartment formation during the M-to-G1 transition is in this month's @natsmb.nature.com -- thanks to NSMB editors and staff for the cover space and art! www.nature.com/nsmb/volumes... See quoted posts for quick summary

An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost! www.biorxiv.org/content/10.6...

Absolutely fantastic Epigenetics and Genomics session on the latest frontiers of enhancer biology by @andersshansen.bsky.social, Martin Rivas and Mira Kassouf at the @ash.hematology.org annual meeting. Chaired by Megan McNerney.

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇

Wonderful to see the beautiful preprint from Sabate et al now published - TADs are also dynamic structures in human cells, with remarkably similar parameters between mESCs and HCT116 cells www.nature.com/articles/s41...

In this episode we talked with @andersshansen.bsky.social from MIT about his work on the impact of 3D genome structures on gene expression and advanced techniques like Region Capture Micro-C for mapping genome organisation. #podcast #epigenetics Listen here: activemotif.com/podcasts-and...

From an accidental discovery of hidden biology to a new framework to understanding and diagnosing rare disease. Thrilled to share the most recent work from our lab and the amazing Jimmy Ly. wi.mit.edu/news/alterna...

🧬🔬🦠🧫🧪@science.org Escherichia coli with a 57-codon genetic code | Science www.science.org/doi/10.1126/...

Thanks also very much to Anne Trafton from MIT News for writing a nice article about the findings: news.mit.edu/2025/surpris...

Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41... Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon Brief thread 👇

Very happy that this insightful story by @andersshansen.bsky.social is out @natsmb.nature.com, www.nature.com/articles/s41.... A nice press release explaining the progress also from the home institute @mitdeptofbe.bsky.social here: news.mit.edu/2025/surpris...

Excited to share our paper on dynamics of microcompartments during M-to-G1 is now published in @natsmb.nature.com www.nature.com/articles/s41... Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from @andersshansen.bsky.social lab) on transcriptional spiking

Check out Shdema's preprint that uses high-res Micro-C to delineate 3D genome structure in three tomato species highlighting both activating and repressive loops and the independence of looping and insulation in tomato: www.biorxiv.org/content/10.1...

What is a promoter? And how does it work? We very happy to share our latest work trying to understand enhancer-promoter compatibility. I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters www.biorxiv.org/content/10.1...

Neat trick if you polycolonal ab's suck. Incubate them with fixed cells with a KO of your protein of interest, then spin. Protocol here: www.med.upenn.edu/markslab/ass... I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands) #WesternBlot #cellsky

Happy #FluorescenceFriday! Our #CellLineOfTheWeek is SMC (structural maintenance of chromosomes) protein 1A! 🧬🛠️ Our cell lines & plasmids are available for just the cost of shipping to reduce the barriers to scientific discovery. 📦 Dist. by @coriellinstitute.bsky.social & @addgene.bsky.social

Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK. Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD

Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance. The regulation of most proteins is dominated by different regulatory mechanisms across cell types. Gratifyingly, this complex regulation defines simple rules ⬇️ www.biorxiv.org/content/10.1...

New cures feel sudden, but the seeds were planted decades ago by basic scientists. Which seeds will turn into cures? Unpredictable looking forward, a straight line looking back. 🧪🧬 🧵

It's also nice to see a very rigorous and careful approach to analyzing interactions in live-cell imaging data subject to noise. Direct simple thresholding of such data will inevitably give artefactual numbers.

Really enjoyed reading the new @lucagiorgetti.bsky.social lab preprint that makes the case that not all E-P interactions are created equal - it is the subset of long-lived extrusion-mediated E-P interactions that are most transcriptionally important: www.biorxiv.org/content/10.1...

That was >40 years ago! So many of John's papers still read incredibly prescient to this day. Fun fact, John is still around and scheduled to give his faculty talk to my department this Wednesday.

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first? I know of earlier single-locus papers (1982). www.sciencedirect.com/science/arti...

Jamie Drayton and I were fortunate to contribute some RCMC analyses to this beautiful paper from Eder, Moene...van Steensel that systematically maps the relationship between enhancer location and gene expression (and nice to see RCMC predict expression in Fig 2H-I): www.science.org/doi/10.1126/...

Excited to share another new preprint from our lab in which we developed a cluster-based phasing strategy using long read nano-NOMe-seq data to link distinct CTCF binding states—captured at the single molecule level—to the transcriptional status of genes: biorxiv.org/content/10.1...

Speaker Spotlight: Don’t miss @Anders_S_Hansen from MIT as he unpacks the secrets of distal gene regulation in space and time! Learn how enhancers find and activate their target genes—revealing new insights into the selectivity and dynamics of gene control. Reserve your seat:

Very interesting new @wbickmor.bsky.social commentary on the mechanistic mystery that is very distal enhancer-promoter interactions www.nature.com/articles/s41...

New preprint! Graduate student Océane Marescal leverages quiescence - proliferative hibernation - to reveal unexpected dynamics for “constitutively”-localized centromere proteins. To understand the logic of cell division, you need to consider non-dividing cells. www.biorxiv.org/content/10.1...

This is a fantastic review

Excited to share our preprint w/Gordana Wutz, Iain Davidson, Leonid Mirny, Jan-Michael Peters www.biorxiv.org/content/10.1... Evidence that PDS5A/B limits NIPBL-cohesin life w/effects on CTCF boundaries & chrm compartments, +mechanisms of compartment-extrusion interplay & cohesin regulation by PDS5

Final version of Bingbing Duan’s main thesis work is out now now in Nature Communications @natureportfolio.nature.com www.nature.com/articles/s41... I’m so pleased with this study that we’ve been working on for so long #epistasis #transcription #geneexpression 1/

Fine structural organization of the interphase nucleus in some mammalian cells, Monneron & Bernard, 1969 Gotta love these classic papers about nuclear architecture. In hindsight, all that we understand and discover today was already contained in their images. www.sciencedirect.com/science/arti...

(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen! Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org! doi.org/10.1073/pnas... 👇🧵

Congratulations to Masahiro Nagano on his new paper on STAG3-cohesin. STAG3-cohesin has a much shorter residence time which leads to altered 3D genome organization and STAG3-cohesin is important for male germ cell differentiation. www.nature.com/articles/s41...

Today, I would like to honor the memory of Roger Y. Tsien, who died on August 24, 2016. His legacy lives with all who use his technologies, including calcium sensors, fluorescent proteins, the acetoxymethyl (AM) ester, & many more! #FluorescenceFriday www.nature.com/articles/nme...