Ed Banigan

Our work on the interplay between loop extrusion and chromatin mechanics is finally out in @physrevresearch.bsky.social . Congrats @hosseinsalari.bsky.social for the hard work ! 👏
journals.aps.org/prresearch/a...

Our paper is out in this week's Soft Matter! @softmatter.rsc.org
pubs.rsc.org/en/content/a...

Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells Powerful interferon (IFN)-I-producing capacity distinguishes plasmacytoid dendritic cells (pDCs) from related innate cells. Adams et al. find that, during pDC development, the locus encoding IFN-I gen...

Why are pDCs so good at producing type I interferons? We set out to address this long unanswered question in our @cp-immunity.bsky.social study. A great collaboration between the Reizis Lab @NYU @uchicagocoi.bsky.social and @agalicina.bsky.social & Leonid Mirny @MIT 1/
www.cell.com/immunity/ful...

Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells Chromatin-organizing cohesin complex cooperates with transcription factor IRF8 to enable the functionality of dendritic cells in vivo.

One of the first in vivo demonstrations that cohesin loss in non-dividing cells can hit hard physiologically, impairing immune function of dendritic cells in mouse. Out in Science Immunology, major contributors: @nickadams-phd.bsky.social, Boris Reizis, Leonid Mirny www.science.org/doi/10.1126/...

Terrific paper on a new chromosomal
compartment where extensive loop
extrusion isolates domains from
other such domains

Our paper on the intriguing pattern of compartmentalization newly observed in silkworm now published w/ EMBO Journal @embojournal.org, congratulations @emily-nav.bsky.social and collaborators!
link.springer.com/article/10.1...

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm - The EMBO Journal Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in ...

How do compartmentalization & loop extrusion organize eukaryotic genomes beyond classical model organisms?
Hi-C analysis of silkworm chromosomes by Drinnenberg, Muller, Mirny et al reveals new combination of these mechanisms, and a new, secluded “S” compartment
link.springer.com/article/10.1...

Healey is the only Democratic governor with a 287(g) agreement.

Tell her: De-ICE Mass.

#mapoli

actionnetwork.org/letters/tell...

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, ...

Check out the News & Views by @kyleeagen.bsky.social : www.nature.com/articles/s41...

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.

🚨Our work on the impact of DNA replication on 3D genome is out in Genome Biology: replication-dependent loop extrusion by sister-forks, wave of replication, no evidence for large-scale replication factory. Great collab with @aurelepiazza.bsky.social. More here: link.springer.com/article/10.1...

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...

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 the cytoplasm.

Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!

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

New publication from our lab! Can semiflexible polymers (lamin fibers, dsDNA, actin, etc) alter the shape of elastic shells or lipid vesicles? Indeed, the nematic/random ordering of these polymers on the surface could tune their shapes.
Read more on: pubs.rsc.org/en/content/a...

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

Cohesin drives chromatin scanning during the RAD51-mediated homology search Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...

Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n
www.science.org/doi/10.1126/...

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 👇

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...

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...

Dynamics of microcompartment formation at the mitosis-to-G1 transition Nature Structural & Molecular Biology, Published online: 17 October 2025; doi:10.1038/s41594-025-01687-2Goel 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 indicates the interactions are facilitated by chromosome compaction.

ICYMI: New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition

Me with family at local No Kings. I’m holding a sign that says “no kings, quacks, camps” with pictures of Trump, rfk, ice

Characterization of induced cohesin loop extrusion trajectories in living cells Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...

The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!

If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!

rdcu.be/eLiT5

Panel B. Top left: Pol II ChIP at 88 TSSs across M-to-G1 transition, showing varied behavior, but clear spiking of some genes. Bottom left: First principal component of time series shows spike in ana/telophase Right: Colored stackup, sorted on PC1 at each time point showing normalized Pol II ChIP. prometa is very low ChIP across all genes (all blue). 33 spiking genes have high Pol II ChIP in ana/telo & associated with larger PC1 (red on top); small/negative PC1 associated with low/no ChIP signal (bluer on bottom). Less correlation in G1 (blue,red,white scattered across genes sorted by PC1). Panel D four plots from left to right: 1. Mean microcomp. loop strength of TSSs vs. time point. Spikes in ana/telophase, more dramatically for transcriptionally spiking TSSs 2. Scatter plot of Mean loop strengths in ana/telo vs. mid g1 showing stronger interactions in A/T 3. microcomp. strengths of PP loops vs time for spiking promoter pairs, 1 spiking 1 not, and non-spiking pairs. Txn spike associated with stronger microcomp interaciton spike 4. Same as 3 except for EP and EE pairs.

Previous experiments observed a transient spike in transcription of a subset of genes during ana/telophase. We now observe that these spiking genes are associated with microcompartments that peak in interactions during ana/telo, suggesting a 3D-genome-based mechanism for this transcriptional spike!

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

Dynamics of microcompartment formation at the mitosis-to-G1 transition Nature Structural & Molecular Biology, Published online: 17 October 2025; doi:10.1038/s41594-025-01687-2Goel 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 indicates the interactions are facilitated by chromosome compaction.

New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition

thanks! reading your paper (I see now accepted, congrats) really inspired the approach that made sense of the physics for me

I didn’t really complete the thought earlier: these papers point toward some of the key principles governing compartmentalization-extrusion interplay and are definitely worth reading!

Postscript: for a long time I was very confused about the PDS5-WAPL depletion expts+sims & how extrusion alters compartments. I was fortunate to eventually stumble across @ranjithpa.bsky.social‬'s preprint www.biorxiv.org/content/10.1... & later this by Chan/Rubinstein www.pnas.org/doi/abs/10.1...

I also want to point out another interesting and relevant recent preprint by @elphegenoralab.bsky.social and @gfudenberg.bsky.social

Thanks to our other co-authors who had essential contributions: Ryotaro Kawasumi, Roman Stocsits, Wen Tang, Kota Nagasaka, Lorenzo Costantino, Ralf Jansen, Kouji Hirota, Dana Branzei