Ed Banigan

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...

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.

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?

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...

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

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...

Also interesting is that w/ motor activity, chromatin constraints—polymer-polymer bridging + linkages to lamina (like several other models)—are essential to maintain conventional organization
We discuss mechanism in detail, connect to nuclear shape, & more. Read more: arxiv.org/abs/2507.17883

For ex., simply having a higher concentration of chromatin constraints at the periphery + motors is enough to achieve conventional chromatin organization (in terms of density) in steady state, with denser regions at the periphery, less dense in the interior (again, e.g., hetero- and euchromatin)

Uniform motor activity (e.g. RNAP) combined with a nonuniform spatial profile of chromatin crosslinkers (such as HP1) can sustain this nonuniform chromatin density profile. This works especially well w/ contractile motors that each draw chromatin inward toward a point. And not at all w/out motors!

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...

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

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.

tagging co-first author Emily Navarrete
@emily-nav.bsky.social
who did the model development and simulation work along with some analysis of the Hi-C

These compartments change through development, have a specific epigenetic profile, have an unusual 3D radial organization, and lots of other interesting findings. Read the preprint! www.biorxiv.org/content/10.1...

This is a unique interplay of 2 basic mechanisms of chrm org!

Usually we think extrusion inhibits compartment patterns- but here it's essential to forming S comps

Preferential loading of extruders (cohesin to enhancers) can make jets/fountains, but this is loading to extended chromatin domain

Left: Contact frequency curves for the whole chromosome, and A, B, and S comps, along with the log-derivative curves, showing an extrusion shoulder around 40-60 kb in S compartments. Right: a snippet of a contact map showing extrusion features — local contact enrichment along dots and lines that are especially visible in S compartments.

Interestingly, the Hi-C expts display features of loop extrusion - dots of contact enrichment, stripes emanating from S compartment boundaries, and a characteristic extrusion shoulder in the contact frequency curve P(s) that is most notable in S comps

Two contact maps. Left: split map showing contacts and observed-over-expected for a simple compartment model in which loop extruders preferentially load within S compartments (indicated by purple on axes). All 3 features: i) on-diagonal contact enrichment, ii) off-diagonal inter-S depletion, and iii) depletion of contacts between S and entire chromosome are visible. Right: split map showing the agreement of the best simulation model of an experimentally observed compartment configuration and the corresponding Hi-C map from experiments.

But a cooperative combination of these two mechanisms can generate S compartment patterns! When loop extrusion is targeted to S compartments, we observe local contact enrichment in S, depletion of inter-S contacts, and sequestration from the rest of the chromosome

Hi-C maps from simple models of compartmentalization. Two maps in the top row show the result of weak and strong affinity-mediated microphase separation: on-diagonal S contacts are always correlated with off-diagonal inter-S compartment contacts. Two maps in the bottom row show that increasing the abundance of loop-extruding motors uniformly suppresses compartmentalization and does not give unique S compartment patterning.

Ok it’s unusual but is this just microphase separation or loop extrusion? No!



Emily’s simulations show S compartments can't be generated by either of these mechanisms alone! Phase separation makes unwanted inter-S contacts & extrusion can't deplete inter-S contacts w/out erasing all comps

A 7 Mb window of a Hi-C map of silkworm genome showing the newly observed “S compartments” as well as typical Hi-C features (checkerboard A/B compartment patterning and small on-diagonal TAD-like domains). Thin filled colored boxes along the axes mark A, B, and S compartments (red, green, purple). Boxes on the map outline 3 features of S compartments: i) on-diagonal contact enrichment, ii) off-diagonal contact depletion between S compartments, iii) smooth depletion of S and all other parts of the chromosome.

How are S compartments are strange? 3 key features: i) on-diagonal contacts enriched, ii) off-diagonal contact depletion bet/ S comps. (unlike usual compartments, not typical of TADs), iii) smooth depletion of S & all other parts of the chrm (extreme sequestration!)

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...

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

(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 Bluetorial🧵:

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...

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).

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.

(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...

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

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.

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

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.

Opinion | No One Has Ever Defeated Autocracy From the Sidelines

„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

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...

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...

🧵

(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.

Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10

YouTube video by Johan Gibcus Rules of Engagement

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...

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

They are resegregating academic science