I am very excited to share the work of my PhD with @eddaschulz.bsky.social, now on BioRxiv! 🎉 🧵⬇️ (1/9) How does the transcription↔️chromatin crosstalk ensure monoallelic expression?

bioRxivpreprint@biorxivpreprint.bsky.social · last wk.

Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome https://www.biorxiv.org/content/10.64898/2026.07.22.737064v1

An encyclopedia of enhancer-gene regulatory interactions — online today! nature.com/articles/s4158… Now with an improved model, expanded maps across 1400+ biosamples, larger validation CRISPR datasets, and guidance on applying the model 1/

Andreas Gschwind@argschwind.bsky.social · 3w ago

Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/

Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:

Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics

Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...

doi.org

Luca Giorgetti lab @FMI@lucagiorgetti.bsky.social · last yr.

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:

Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning

Nature Communications - How non-coding mutations in DNA contribute to phenotypes is a largely unresolved question. Here the authors integrate personal genomics and machine learning to identify...

rdcu.be

New paper! 🚀 A high-affinity anti- #mNeonGreen #nanobody turns #mNG into a #multifunctional Tag. @nanotag.bsky.social decided to openly share the #nanobody for research use. Not common, but we strongly believe well-defined reagents are key for reproducible science. We hope you find it useful! 💚

Does every enhancer work with every promoter? With @jengreitz.bsky.social and Will Greenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 www.biorxiv.org/content/10.6...

Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers

Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac...

biorxiv.org

My first PhD paper is out in Nucleic Acids Research! We describe "Ab-trapping" - an antibody artifact that distorts assays relying on antibody diffusion (microscopy, CUT&Tag, CUT&RUN). The revisions made the story much stronger. Check it out! doi.org/10.1093/nar/...

Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus

Abstract. Chromatin has a complex 3D structure and diverse binding proteins that coordinate the genome’s most essential functions. Many microscopy and geno

doi.org

Excited to see James' Genome-wide Absolute Quantification of Looping paper out in @natsmb.nature.com : www.nature.com/articles/s41... This has been in collaboration with @lucagiorgetti.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs. Brief thread below on some key updates

Anders Sejr Hansen@andersshansen.bsky.social · 2y ago

Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...

(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...

JIT 4 summer, the latest preprint from our lab, brilliantly led by @kaitezhang.bsky.social w/ support from Collepardo lab (@juliamaristany.bsky.social / @janhuemar.bsky.social). www.biorxiv.org/content/10.6... describes a new single-molecule epigenomic method, & discoveries it enables ... (1/n)

Single-molecule nucleosome spacing coordinates chromatin fiber interactions

Nucleosome spacing influences higher-order chromatin fiber organization in vitro but how this relates to cellular chromosome structure remains contentious. To address this, we developed Ligation Analy...

biorxiv.org

Interested in hearing about mechanisms of cohesin-dependent vs. -independent enhancer regulation? @karissalhansen.bsky.social will be presenting her work **Tues June 23rd 8am CET** www.biorxiv.org/content/10.6... www.science.org/doi/10.1126/... Thank you @genome-org-aus.bsky.social ! 👇

GOA - Genome Organisation Australia@genome-org-aus.bsky.social · 2mo ago

Only one week to go until our next GOA seminar! @karissalhansen.bsky.social will present here work on the mechanisms of long-range enhancer-promoter communication. Registration link: unimelb.zoom.us/webinar/regi...

Please join us for the next edition of the GOA monthly seminar series Dr Karissa Hansen Registration link: unimelb.zoom.us/webinar/regi...

📣 Preprint alert! We developed a method to analyze concurrent interactions between multiple chromatin regions at single alleles at sub-nucleosome resolution (multi-way Micro-Capture-C, mwMCC) & used this to study structural synergy within super-enhancers. 1/14 www.biorxiv.org/content/10.6...

🆕 ADVANCE ONLINE 🆕 RESEARCH PAPER: Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer By Martinovic et al., and Elzo de Wit ➡️ https://ow.ly/H1mH50YWiTO Elzo de Wit lab @ NKI Netherlands Cancer Institute #enhancer #cohesin

🚨🧪🧵URGENT INPUT NEEDED: NIH asks input for next strategic plan-including emphasis on non-animal models (NAMs) to replace animals. Per NIH insider, anti-animal responses now outnumber scientists 200-700x. Please please provide input. Deadline: May 26, 11:59 PM ET. grants.nih.gov/news-events/...

Many of you may have received pessimism from me over the years about using Hi-C to predict distal regulatory effects, mired with paradoxical optimism that cohesin loop extrusion is key. Well, the theoretical story underlying my seemingly paradoxical rambling is finally ready to be told. 👇

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 3mo ago

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 🧪 🧵👇

Beautiful new study from @elphegenoralab.bsky.social and Leonid Mirny's lab: Cohesin-bridged encounters mediate enhancer-promoter communication, predicting how enhancer effect scales with genomic distance and - for the first time - how CTCF sites modulate enhancer-promoter communciation! 🧵 below

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 3mo ago

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 🧪 🧵👇

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 🧪 🧵👇

Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...

Did you know that Pierre Chambon's laboratory was the first to use the term "nucleosome" in 1975 ? www.cell.com/cell/fulltex...

#RIP Pierre Chambon (1931-2026) via @alainberetz.bsky.social one of the last giants in biology: PARP, nuclear receptors, RNA Pol II, nucleosome, promoters, split genes

Although cohesin-sensitive, long-range enhancer activation is equivalent in nature to proximal activation. Cooperativity can arise from different levels of activation inputs operating on a non-linear response function. @eliasfriman.bsky.social @uoe-igc.bsky.social www.biorxiv.org/content/10.6...

Faculty search at the Institute for Human Genetics at UCSF. Come be my colleague! aprecruit.ucsf.edu/JPF06052

Faculty Positions - Institute for Human Genetics

University of California, San Francisco is hiring. Apply now!

aprecruit.ucsf.edu

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

Delighted to share our lab's latest (w/ inimitable @genophoria.bsky.social) in final form at @nature.com. Enormous lift by Sean Wang, @palindromephd.bsky.social & @martyyang.bsky.social to address extensive & constructive reviewer comments & see this through. (1/n) www.nature.com/articles/s41...

Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature

An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...

nature.com

(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...

Today in @nature.com, the @genophoria.bsky.social and & Vijay Ramani labs reveal that our picture of how nucleosomes regulate DNA accessibility has been too simple. They find that over 85% of nucleosomes in mammalian cells are structurally distorted, with DNA partially accessible even while wrapped.

Happy to see this paper in press @elphegenoralab.bsky.social together with the highly complementary study from Jan-Michael Peter's lab, and very much in line with Gerd Blobel's+@andersshansen.bsky.social recent results! Cohesin cofactor dosage controls rates of cohesin extrusion

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 3mo ago

📖 The final version of our paper is out in press Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption authors.elsevier.com/a/1m%7EU03vV... or www.cell.com/molecular-ce...

📖 The final version of our paper is out in press Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption authors.elsevier.com/a/1m%7EU03vV... or www.cell.com/molecular-ce...

Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption

Shah, Tortora, et al. show that cells can dial the rate of cohesin loop extrusion by balancing the relative dosage of NIPBL and PDS5. Their models provide a quantitative mechanistic basis for the gene...

cell.com

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 12mo ago

New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...

New paper in Genes & Dev: we dissected how Sox2 — a key pluripotency TF — is regulated by a distal enhancer cluster (SCR) 100 kb away. The results challenge simple models of cohesin-mediated loop extrusion of gene regulation. genesdev.cshlp.org/content/earl... 🧵