Four hours left. Do it. Two or three paragraphs of your own text are enough.

Alex Merz 🇺🇸🇨🇦🇺🇦@merz.bsky.social · 3w ago

There are only a few hours left to comment on the proposed OMB rule that would eviscerate American science. This is the single best summary, and guidance for how to write a comment, that I have seen. PLEASE submit something, even if it is only 2 or 3 paragraphs.

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...

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...

federalregister.gov

elizabethginexi.bsky.social@elizabethginexi.bsky.social · 2mo ago

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...

(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...

🧵 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

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.

Science Magazine@science.org · 2mo ago

The White House today announced it plans to make major changes in how the U.S. government manages research funding. https://scim.ag/43HgW4s

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...

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. 🌉

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

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 🧪 🧵👇

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

how does loop extrusion and chromatid cohesion interact in interphase? Find out in our latest collaboration with Gerlich lab | | | vvv

Gerlich Lab@gerlichlab.bsky.social · 3mo ago

New preprint out!🧬 How do cells keep replicated sister chromatids linked for DNA repair while folding 3D loops for gene expression? Extrusion folds DNA but separates sisters, while cohesion connects them, risking mutual interference. How do they coexist?🧵👇 🔗 doi.org/10.64898/2026.05.02.722390 1/6

(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...

Anders Sejr Hansen@andersshansen.bsky.social · last yr.

(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...

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...

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 ...

cell.com

Ed Banigan@irate-physicist.bsky.social · 11mo ago

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

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!

The EMBO Journal@embojournal.org · 5mo ago

Condensin loop extrusion properties, roadblocks, and role in homology search @aurelepiazza.bsky.social et al show yeast condensin unidirectionally extrudes long chromatin loops & contributes to biasing donor selection during recombinational DNA break repair link.springer.com/article/10.1...

Inter-lamin interactions control meshwork topologyin a polymer-gel model of nuclear lamina https://www.biorxiv.org/content/10.64898/2026.03.14.711786v1

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...

Daniel Jost - Physical Biology of Chromatin group@djost-physbiol.bsky.social · 10mo ago

New preprint from the lab !! Loop extrusion may provide mechanical robustness to chromatin. Great work by Hossein Salari. @cnrs.fr @lbmcinlyon.bsky.social www.biorxiv.org/content/10.1...

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

Ed Banigan@irate-physicist.bsky.social · last yr.

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

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...

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...

cell.com

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/...

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.

science.org

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

The EMBO Journal@embojournal.org · 6mo ago

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...

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 ...

link.springer.com

Ed Banigan@irate-physicist.bsky.social · last yr.

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...

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...

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 ...

link.springer.com

Healey is the only Democratic governor with a 287(g) agreement. Tell her: De-ICE Mass. #mapoli actionnetwork.org/letters/tell...

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...

actionnetwork.org

Taniel@taniel.bsky.social · 6mo ago

NEW: Abigail Spanberger this afternoon ordered that all state agencies leave ICE's 287(g) program. This means that the state police (and some other agencies) will no longer be empowered to detain and arrest people for ICE. Big, big move by the governor within weeks of coming into office.

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

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, ...

nature.com

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

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...

rdcu.be

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.

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...

rdcu.be

🚨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...

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...

link.springer.com

Daniel Jost - Physical Biology of Chromatin group@djost-physbiol.bsky.social · last yr.

🚨 new preprint from the lab. Combining modeling, new Hi-C data in yeast and data analysis, our study offers new insights into the spatial and dynamic organization of chromatin during replication in eukaryotes. Check the tweetorial below ⬇️ www.biorxiv.org/content/10.1...

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

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.

nature.com

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...

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.

nature.com

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...