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Ed Banigan

@irate-physicist.bsky.social
197 followers 307 following 60 posts

biophysicist

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Reposted by Ed Banigan
Anton Goloborodko @golobor.bsky.social · 03/09/2026
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
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Alex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 14/07/2026
Four hours left. Do it. Two or three paragraphs of your own text are enough.
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Ed Banigan @irate-physicist.bsky.social · 12/07/2026
waited until nearly the last minute, but I joined 250k+ others and submitted a comment on the disastrous OMB proposal for rule changes to federal funding of science. used the great thread/articles quoted below. comment here: www.federalregister.gov/documents/20...
federalregister.gov
Regulation for Federal Financial Assistance
The Office of Management and Budget (OMB) proposes to revise the Guidance for Federal Financial Assistance to improve government- wide policies and requirements related to the management of grants, co...
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Reposted by Ed Banigan
Anders Sejr Hansen @andersshansen.bsky.social · 22/06/2026
(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...
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Jacquelyn Gill @jacquelyngill.bsky.social · 29/05/2026
🧵 Public science in the US has taken some heavy hits over the last year, but the White House OMB is proposing a series of changes that will result in a TKO for science as we know it unless we fight back. Here's what's happening, and why it matters. 1/n
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Alex Wild @alexwild.bsky.social · 30/05/2026
tl,dr; Scientists no longer allowed to use federal funding to publish, attend meetings, or talk to the public. They cannot collaborate internationally. Grants can be cancelled for any reason, at any time, political appointees have a final say over what gets funded, and who gets funded.
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Aykut Erbas, Ph.D. @erbash.bsky.social · 20/05/2026
Lamina-associated domains are mostly repressive, yet some genes “escape” and get transcribed. We explored this tunneling-like mechanism using polymer physics: chromatin adsorption+peripheral compaction may largely exclude proteins interacting with active chromatin. www.biorxiv.org/content/10.6...
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
4/ Our key realization: not all enhancer-promoter physical interactions are functionally equal. Enhancer-promoter communication appears exquisitely sensitive to direct physical bridges - not just mere physical proximity. 🌉
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
6/ The dynamics of cohesin bridges directly emerges from the biophysics of loop extrusion and are very different from how enhancer and promoter loci would diffuse when not bridged. @timothyfoldes.bsky.social modeled bridging dynamics and the expected effect on transcription
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇
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Ranjith Padinhateeri @ranjithpa.bsky.social · 08/05/2026
Our new preprint: Chromatin at ~10–100 kb scales behaves very differently from standard polymer expectations. DNA-PAINT data reveal broad fluctuations and sharp local bends. Our study suggests emergent active forces at these scales and quantifies the nature and strength of this activity
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Anton Goloborodko @golobor.bsky.social · 06/05/2026
how does loop extrusion and chromatid cohesion interact in interphase? Find out in our latest collaboration with Gerlich lab | | | vvv
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Reposted by Ed Banigan
Anders Sejr Hansen @andersshansen.bsky.social · 05/05/2026
(1/n) Super excited to share that our preprint is out today in @natsmb.nature.com with a new name "Integrated MINFLUX tracking reveals two distinct chromatin dynamics classes across cell types" and more than 2x more data: www.nature.com/articles/s41... See also MIT News news.mit.edu/2026/how-chr...
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Ed Banigan @irate-physicist.bsky.social · 29/04/2026
also see this related paper by Shah, Tortora et al. @elphegenoralab.bsky.social @gfudenberg.bsky.social published in the same issue: Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption bsky.app/profile/elph...
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Ed Banigan @irate-physicist.bsky.social · 29/04/2026
Paper published! PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes -PDS5 facilitate NIPBL dissociation from cohesin, stopping loop extrusion -Extrusion governs chrm compartmentalization by competing w/polymer relaxation authors.elsevier.com/sd/article/S...
cell.com
PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes
PDS5 proteins regulate genome organization by halting cohesin-mediated loop extrusion. Wutz et al. show that PDS5 promotes NIPBL dissociation from cohesin, enabling CTCF boundary formation and proper ...
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Aurele Piazza @aurelepiazza.bsky.social · 23/03/2026
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!
nature.com
Condensin accelerates long-range intra-chromosomal interactions - Nature Communications
Long‑range chromosome encounters in cells are hard to quantify. Here, the authors induce artificial contacts in yeast and show that intra‑chromosomal interactions form faster than inter‑chromosomal on...
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 17/03/2026
Inter-lamin interactions control meshwork topologyin a polymer-gel model of nuclear lamina www.biorxiv.org/content/10.64898/20…
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Daniel Jost - Physical Biology of Chromatin group @djost-physbiol.bsky.social · 23/02/2026
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...
journals.aps.org
Active loop extrusion modulates the mechanical response of chromatin under tension
Chromosomes are complex biopolymers folded into dynamic loops via a loop-extrusion process and may experience various mechanical forces in vivo. We develop a force-dependent model of chromatin loop ex...
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Ed Banigan @irate-physicist.bsky.social · 12/02/2026
Our paper is out in this week's Soft Matter! @softmatter.rsc.org pubs.rsc.org/en/content/a...
pubs.rsc.org
Differential crosslinking and contractile motors drive nuclear chromatin compaction - Soft Matter (RSC Publishing) DOI:10.1039/D5SM00812C
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Nick Adams @nickadams-phd.bsky.social · 10/02/2026
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...
cell.com
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...
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Reposted by Ed Banigan
Aleksandra Galitsyna @agalicina.bsky.social · 09/02/2026
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/...
science.org
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.
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Reposted by Ed Banigan
Job Dekker @jobdekker.bsky.social · 03/02/2026
Terrific paper on a new chromosomal compartment where extensive loop extrusion isolates domains from other such domains
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Ed Banigan @irate-physicist.bsky.social · 06/02/2026
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...
link.springer.com
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 ...
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Reposted by Ed Banigan
The EMBO Journal @embojournal.org · 03/02/2026
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...
link.springer.com
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 ...
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Reposted by Ed Banigan
Progressive Mass @progressivemass.bsky.social · 04/02/2026
Healey is the only Democratic governor with a 287(g) agreement. Tell her: De-ICE Mass. #mapoli actionnetwork.org/letters/tell...
actionnetwork.org
Tell Gov. Healey: No Collaboration with ICE
Governor Maura Healey is the ONLY Democratic governor in New England to have a 287(g) collaboration agreement with ICE. This means our tax dollars are being used to provide free labor for ICE. We sa...
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Reposted by Ed Banigan
Allana Schooley @allanaschooley.bsky.social · 29/12/2025
Check out the News & Views by @kyleeagen.bsky.social : www.nature.com/articles/s41...
nature.com
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, ...
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Reposted by Ed Banigan
Allana Schooley @allanaschooley.bsky.social · 29/12/2025
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
rdcu.be
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...
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Reposted by Ed Banigan
Allana Schooley @allanaschooley.bsky.social · 29/12/2025
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.
rdcu.be
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...
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Reposted by Ed Banigan
Daniel Jost - Physical Biology of Chromatin group @djost-physbiol.bsky.social · 23/12/2025
🚨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...
link.springer.com
Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes - Genome Biology
Genome Biology - Although significant progress has been made in our understanding of DNA replication and spatial chromosome organization in eukaryotes, how they interplay remains elusive. In...
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Reposted by Ed Banigan
Kyle Eagen @kyleeagen.bsky.social · 23/12/2025
Excited to share a News & Views highlighting a new, excellent paper from @jobdekker.bsky.social and @allanaschooley.bsky.social! www.nature.com/articles/s41...
nature.com
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.
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Job Dekker @jobdekker.bsky.social · 22/12/2025
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...
nature.com
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.
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Aykut Erbas, Ph.D. @erbash.bsky.social · 16/12/2025
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...
pubs.rsc.org
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Ed Banigan @irate-physicist.bsky.social · 15/12/2025
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
December 2025 Cover of NSMB. "Mitotic chromatin microcompartments." Image is colorful tents scattered across a snowy mountainside.
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Alberto Marin @albertomarin.bsky.social · 04/12/2025
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/...
science.org
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...
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Anders Sejr Hansen @andersshansen.bsky.social · 20/10/2025
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 👇
nature.com
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...
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dimitristypas.bsky.social @dimitristypas.bsky.social · 20/10/2025
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...
nature.com
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...
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Nature Structural & Molecular Biology @natsmb.nature.com · 18/10/2025
ICYMI: New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
go.nature.com
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.
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Ed Banigan @irate-physicist.bsky.social · 18/10/2025
Me with family at local No Kings. I’m holding a sign that says “no kings, quacks, camps” with pictures of Trump, rfk, ice
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Elzo de Wit lab @ NKI @dewitlab.bsky.social · 16/10/2025
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
rdcu.be
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,...
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Ed Banigan @irate-physicist.bsky.social · 17/10/2025
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!
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.
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Ed Banigan @irate-physicist.bsky.social · 17/10/2025
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
nature.com
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...
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Nature Structural & Molecular Biology @natsmb.nature.com · 17/10/2025
New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
go.nature.com
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.
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Ed Banigan @irate-physicist.bsky.social · 01/10/2025
thanks! reading your paper (I see now accepted, congrats) really inspired the approach that made sense of the physics for me
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Ed Banigan @irate-physicist.bsky.social · 03/09/2025
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!
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Ed Banigan @irate-physicist.bsky.social · 03/09/2025
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...
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Ed Banigan @irate-physicist.bsky.social · 03/09/2025
I also want to point out another interesting and relevant recent preprint by @elphegenoralab.bsky.social and @gfudenberg.bsky.social
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Ed Banigan @irate-physicist.bsky.social · 03/09/2025
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
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Ed Banigan @irate-physicist.bsky.social · 03/09/2025
Summary -PDS5 facilitates NIPBL dissociation from cohesin by invading NIPBL binding site -PDS5 strengthns CTCF boundaries by limiting NIPBL-cohesin life -PDS5 lowers avg extrusion speed/depletion ups processivity -Compartmentalization governed by competition of extrusion &polymer relaxation dynamics
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Ed Banigan @irate-physicist.bsky.social · 03/09/2025
Can PDS5 therefore strengthen CTCF boundaries by limiting NIPBL-cohesin processivity (=speed x residence time)? Hi-C in cells depleted of PDS5 & now partially of NIPBL recover some of CTCF boundaries (+ also compartments)
Hi-C contact maps in control, PDS5AB-depleted, and PDS5AB+partial NIPBL -depleted cells.
Top 87 Mb window maps show checkerboard (compartments) in control, but not PDS5A/B depletion. Some recovery of compartments with partial depletion of NIPBL + PDS5 depletion.
Bottom 10 Mb window maps show corner peaks and TADs, diminished/lost in PDS5AB depletion, partially recovered with co-depletion of NIPBL
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Ed Banigan @irate-physicist.bsky.social · 03/09/2025
To understand this Iain did 3-color single-molecule expts w/loop-extruding NIPBL-cohesin. PDS5+NIPBL could colocalize on cohesin leading to NIPBL unbinding! Loops often released but sometimes shrunk & NIPBL returned. So PDS5 slows loop growth + speeds NIPBL unbinding by facilitated dissociation!
Images of single-molecule expts with DNA tethered at two ends with fluorescent DNA, NIPBL, and PDS5 (+cohesin in solution, not tagged)
Left: While NIPBL is on DNA, DNA fluorescence locally accumulates indicating an extruded loop. After some time, PDS5A briefly colocalizes. Shortly later NIPBL unbinds and loop is lost/released. PDS5A subsequently unbinds.
Middle: Similar sequence with PDS5B
Right: DNA loop growth with NIPBL localization on DNA, interrupted by stalling of growth when PDS5A intermittently binds and unbinds. After some time a PDS5A event occurs prior to NIPBL loss. The loop is lost, but NIPBL rebinds while PDS5A remains present and the loop begins to grow again after PDS5A unbinds
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