Ed Banigan
@irate-physicist.bsky.social
📤 170
📥 294
📝 55
biophysicist
pinned post!
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
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10 days ago
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Daniel Jost - Physical Biology of Chromatin group
2 days ago
🚨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...
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Kyle Eagen
3 days ago
Excited to share a News & Views highlighting a new, excellent paper from
@jobdekker.bsky.social
and
@allanaschooley.bsky.social
!
www.nature.com/articles/s41...
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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.
https://www.nature.com/articles/s41556-025-01851-2
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Job Dekker
3 days ago
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...
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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.
https://www.nature.com/articles/s41556-025-01828-1
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Aykut Erbas
9 days ago
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...
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https://pubs.rsc.org/en/content/articlehtml/2026/sm/d5sm00899a
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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
add a skeleton here at some point
10 days ago
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Alberto Marin
21 days ago
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/...
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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...
https://www.science.org/doi/10.1126/science.adw1928
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Anders Sejr Hansen
2 months ago
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 👇
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2 months ago
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...
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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...
https://www.nature.com/articles/s41594-025-01687-2
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Nature Structural & Molecular Biology
2 months ago
ICYMI: New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
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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.
https://go.nature.com/4n5YpWT
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2 months ago
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Elzo de Wit lab @ NKI
2 months ago
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
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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,...
https://rdcu.be/eLiT5
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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
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2 months ago
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Nature Structural & Molecular Biology
2 months ago
New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
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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.
https://go.nature.com/4n5YpWT
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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
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PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes
Cohesin-NIPBL complexes extrude genomic DNA into loops that are constrained by CTCF boundaries. This process has important regulatory functions and weakens the separation between euchromatic and heter...
https://www.biorxiv.org/content/10.1101/2025.08.30.673243
4 months ago
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Elphege Nora Lab at UCSF
4 months ago
Excitingly, the lab of Jan-Michael Peters just reported largely concordant findings: The PDS5:NIPBL balance in cells tunes the rate/velocity of cohesin loop extrusion, shaping chromosomes from loops to compartments đźš…âž°
www.biorxiv.org/content/10.1...
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paper with
@erbash.bsky.social
now published in
@narjournal.bsky.social
academic.oup.com/nar/article/...
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4 months ago
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Nidhi Subbaraman
5 months ago
Update: A Trump administration effort to block all funding that flows to outside health researchers was scrapped Tuesday evening after senior White House officials intervened
www.wsj.com/politics/pol...
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Max Kozlov
5 months ago
The NIH can’t award ANY grants to outside researchers under new WH restriction, reports
@wsj.com
. The pause came in the form of a footnote from OMB Director Vought, in a document that doles out federal funds to the NIH. Prelude to rescissions, especially after his comments over the weekend?
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Trump Administration Puts New Chokehold on Billions in Health-Research Funding
The National Institutes of Health can’t award grants to outside researchers under a new White House restriction.
https://www.wsj.com/politics/policy/trump-administration-puts-new-chokehold-on-billions-in-health-research-funding-19660215?st=YWVyJH&reflink=desktopwebshare_permalink
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Ligesh Theeyancheri, Jen Schwarz, and I have a new preprint out presenting a nonequilibrium mechanism that can spatially segregate dense polymer from less compacted polymer, e.g., heterochromatin and euchromatin.
arxiv.org/abs/2507.17883
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Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euc...
https://arxiv.org/abs/2507.17883
5 months ago
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Ligesh Theeyancheri, Jen Schwarz, and I have a new preprint out presenting a nonequilibrium mechanism that can spatially segregate dense polymer from less compacted polymer, e.g., heterochromatin and euchromatin.
arxiv.org/abs/2507.17883
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Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euc...
https://arxiv.org/abs/2507.17883
5 months ago
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Flavia Corsi
5 months ago
Happy to share my postdoc work—our new preprint is out! 🧬 It’s been a privilege to lead this project. I'm immensely grateful to Anton
@golobor.bsky.social
for being such an inspiring and supportive supervisor. Also truly thankful to
@danielgerlich.bsky.social
for his guidance and collaboration.
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A little belated posting, but we (Emily Navarrete, Leonid Mirny, me) have an updated preprint in collaboration the Ines Drinnenberg, Héloïse Muller, José Gil Jr, + others on the strange and striking compartmentalization of silkworm chromatin:
www.biorxiv.org/content/10.1...
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Unique territorial and compartmental organization of chromosomes in the holocentric silkworm
Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these are mainly observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is “secluded” from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. Polymer simulations show that this contact pattern can only be explained by high loop-extrusion activity within compartment S, combined with low extrusion elsewhere through the genome. This unique, targeted extrusion represents a novel phenomenon and underscores how evolutionarily conserved mechanisms—compartmentalization and loop extrusion—can be repurposed to create new 3D genome architectures. ### Competing Interest Statement The authors have declared no competing interest.
https://www.biorxiv.org/content/10.1101/2023.09.14.557757v3
6 months ago
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Elzo de Wit lab @ NKI
6 months ago
(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators:
doi.org/10.1093/nar/...
. A Bluetorialđź§µ:
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Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec
https://doi.org/10.1093/nar/gkaf549
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Ashamed of my PhD institution Penn deciding to ban and erase trans athletes today. Could just barely wait to get out of Pride month. Another university trying to make an impossible deal with Trump or is this what the suits wanted anyway? Gross either way
www.espn.com/college-spor...
6 months ago
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Cees Dekker
6 months ago
Latest
#CDlab
paper online now: Cohesin supercoils DNA during loop extrusion
www.cell.com/cell-reports...
This extensive study was led by Jan Michael Peters at Vienna; our lab contributed mostly modeling of plasmid supercoiling (
@romanbarth.bsky.social
‬) and single-molecule data (Richard Janissen).
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Jeremy Berg
7 months ago
Getting confirmation from several sources that the review branch at the National Institute of General Medical Sciences (NIGMS) at NIH no longer exists. I am sure this is true across many/all institutes and centers at NIH. I hope the Center for Scientific Review will be up to the task.
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Anders Sejr Hansen
7 months ago
(1/n) Thread
@matteomazzocca.bsky.social
@domenicnarducci.bsky.social
Simon Grosse-Holz
@jessematthias.bsky.social
preprint Q: how does chromatin move? Using MINFLUX, SPT & SRLCI, we track chromatin dynamics across 7 orders of magnitude in time to provide answers
www.biorxiv.org/content/10.1...
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Aykut Erbas
8 months ago
How Can Mesoscale Phases of Lamin Fibrous Structure Form on the Nuclear Surface? 🔍🧬 Lamina is a protective meshwork at the nuclear periphery, but in diseases like HGPS, its structure becomes disrupted and becomes thicker with the traces of nematically ordered lamin fibers.
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Phase behavior and dissociation kinetics of lamins in a polymer model of progeria
One of the key structural proteins in the eukaryotic cell nucleus is lamin. Lamins can assemble into a two-dimensional protein meshwork at the nuclear periphery
https://pubs.aip.org/aip/jcp/article/162/18/185101/3346472/Phase-behavior-and-dissociation-kinetics-of-lamins
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Science Magazine
8 months ago
Exclusive: National Science Foundation staff were told today that the agency’s 37 divisions—across all eight directorates—are being abolished and the number of programs within those divisions will be drastically reduced.
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Exclusive: NSF faces radical shake-up as officials abolish its 37 divisions
Changes seen as a response to presidential directives on what research to fund
https://scim.ag/3YCFvO3
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Kai Kupferschmidt
8 months ago
„Americans are living under a new regime. The question now is whether we will allow it to take root. So far, American society’s response to this authoritarian offensive has been underwhelming — alarmingly so.“ Written by political scientists who study how democracies come to an end
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Opinion | No One Has Ever Defeated Autocracy From the Sidelines
https://www.nytimes.com/2025/05/08/opinion/trump-authoritarianism-democracy.html?unlocked_article_code=1.Fk8.JhE1.lb_mzlYu3hC_&smid=url-share
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Annie Waldman
8 months ago
NEW: Whistleblower records show that the NIH axed research grants – even after a federal judge blocked the cuts with an injunction.
www.propublica.org/article/trum...
đź§µ
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Trump’s NIH Axed Research Grants Even After a Judge Blocked the Cuts, Internal Records Show
A lawsuit led by the Washington state attorney general offers an unprecedented view of the termination of more than 600 NIH grants, including transgender research grants threatened by Trump’s executiv...
https://www.propublica.org/article/trump-nih-cuts-transgender-research-grants
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Anders Sejr Hansen
8 months ago
(1/n) New preprint from
@claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu. Q: How do we get ultra-high-res 3D genome maps? A: New deep learning model, Cleopatra. Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
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Carl Zimmer
8 months ago
Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10
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Anton Goloborodko
9 months ago
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
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Rules of Engagement
YouTube video by Johan Gibcus
https://www.youtube.com/watch?v=pmvOrmErhhc
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American Society for Cell Biology
9 months ago
From MBoC DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture, by Andrew Stephens, UMass Amherst, et al.
doi.org/10.1091/mbc....
#ASCB
#CellBiology
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Needhi Bhalla 💅🏽
9 months ago
They are resegregating academic science
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Jason Koebler
9 months ago
Petabytes of critical government research that is marked for possible deletion cannot be archived because of technical and legal restrictions, meaning it is very likely to be lost forever:
www.404media.co/nih-archives...
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Massive, Unarchivable Datasets of Cancer, Covid, and Alzheimer's Research Could Be Lost Forever
Days before Robert F. Kennedy Jr. announced that 10,000 HHS staffers would lose their jobs, a message appeared on NIH research repository sites saying they were "under review."
https://www.404media.co/nih-archives-repositories-marked-for-review-for-potential-modification/
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Jeremy Berg
9 months ago
Reach out to your Senators with your concerns and suggestions. HELP committee…
www.help.senate.gov/about/members
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Unacceptable. As long as Musk/Trump admin act outside of law and Constitution, this is meaningless bullshit. Vote no.
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10 months ago
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Jonathan M. Katz
10 months ago
“The president of the United States is illegally impounding critical research funds in an attempt to silence members of the Columbia community. As a university committed to free inquiry, free expression and the rule of law, we categorically reject these efforts and will see him in court.”
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Markus Deserno
10 months ago
Straight up political influence interfering with science. This cannot end well. Your grant didn’t get canceled yet? Maybe next time! If your research could show that the world isn’t upside down like Trump claims it is, you’ll be a target. We cannot have science contradicting the king.
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Drug Monkey
10 months ago
These grants survived intense scientific competition and scrutiny by expert peer scientists. It’s a sham to suggest they are unworthy. Pure bigotry to revoke them.
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maybe sacrilegious for a transplanted yankees fan, but david ortiz is right
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10 months ago
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Usha Lee McFarling
10 months ago
SCOOP: The National Academies of Science, Engineering, and Medicine, arguably the nation's most powerful scientific organization, is bending to political pressure and removing terms like "health equity" from pending reports. Members are not happy. Story by me:
www.statnews.com/2025/02/20/n...
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National Academies is altering pending reports to appease Trump administration, some members say
Words such as “health equity” are being replacing with vaguer terms, and 100 members sent a letter of protest to NASEM leaders.
https://www.statnews.com/2025/02/20/national-academies-altering-pending-reports-to-appease-trump-administration-members-say/
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Jeremy Berg
10 months ago
“What is happening is that they’re basically blocking the process, just by an administrative, legal means, rather than by ordering staff not to make grants,” said Jeremy Berg, who directed the National Institute of General Medical Sciences at the N.I.H. for eight years... 2/n
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Jeremy Berg
10 months ago
New York Times article now up on Federal Register stuff.
www.nytimes.com/2025/02/21/s...
1/n
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Trump Administration Stalls Scientific Research Despite Court Ruling (Gift Article)
Using an arcane law, officials have effectively delayed funding from the National Institutes of Health, leaving medical studies in jeopardy.
https://www.nytimes.com/2025/02/21/science/nih-research-funding-delays.html?unlocked_article_code=1.yk4.qNQA.zVPAsVztAZ3p&smid=url-share
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@PhysGenCenter
10 months ago
Next Friday Feb. 28 @ 12pm CT, Andrew Stephens, PhD of UMass presents the Monthly Seminar on Physical Genomics: "Transcription Inhibition Suppresses Nuclear Blebbing And Rupture, Independent Of Nuclear Rigidity" Registration is free at
tinyurl.com/mr2s7fpy
#chromatin
#northwestern
#dna
#genomics
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Welcome to bluesky
@erbash.bsky.social
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10 months ago
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extrusion and extrusion barriers by archaeal SMC complexes?!
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10 months ago
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