Happy to share our new software SIMworks out today in Nature Protocols (1/3) SIMworks is a software suite built on our previous tools SIMCheck, Chromagnon, ChaiN and SIMinspector and enables data augmentation, quantitative processing and analysis. Link to publication: www.nature.com/articles/s41...

SIMworks—an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy

Nature Protocols - SIMworks is an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy (SIM), enabling both new learners and experienced users...

nature.com

My lab at the Center for Gene Expression (CGEN), University of Copenhagen is looking for a motivated Postdoc interested in cohesin biology, 3D chromatin, and super-resolution microscopy. 📩 Please email your CV and letter of intent to fena.ochs(at)sund.ku.dk.

Incredibly happy to share the first publication from our lab, now published in Nature Cell Biology! 🎉 How do cells coordinate RNA processing with nuclear organization and the cell cycle? www.nature.com/articles/s41...

🧬 1/ HP1α marks silenced heterochromatin, but how does it repress, and what happens when transcription is switched on? On mouse fibroblast chromocenters, HP1α stays bound, its barrier is local, and the domain reorganizes nanodomain by nanodomain. 👉 @cp-molcell.bsky.social doi.org/10.1016/j.mo...

Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)

Check out our preprint on the structural mechanisms of how LEM2 and ESCRTs seal the nuclear envelope. Awesome collaboration with @karenpalacior.bsky.social who brought my structures to life 💃🔬❄️🌀 @hummerlab.bsky.social www.biorxiv.org/content/10.6...

Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...

Mechanisms and functional implications of long-range enhancer-dependent gene regulation - Nature Genetics

Development depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...

nature.com

🚨the latest from the lab! 😃👇🏻 www.science.org/doi/10.1126/...

3D genome organization in tissue regeneration involves long-range chromatin loops

Chromosome conformation analysis in Drosophila wing discs reveals the requirement of specific meta-loops during regeneration.

science.org

Now out from Bintu lab: compaction following transient KRAB recruitment tracks long-term epigenetic memory. But K9me3 decays after KRAB release and is replaced by DNA methylation. Does compaction help maintain K9me3, or slow its loss enough to facilitate the handoff to DNAme? tinyurl.com/ycay4mrh

Single-cell chromatin state transitions during epigenetic memory formation

Large-scale chromatin compaction quantitatively predicts the percentage of cells with durable epigenetic memory of gene silencing.

tinyurl.com

@mileshuseyin.bsky.social and the lab have put together a comprehensive protocol for genome-wide Micro-C and for Region-Capture Micro-C in @natprot.nature.com : www.nature.com/articles/s41... See also the GitHub for a user-friendly end-to-end computational pipeline: github.com/ahansenlab/M...

Nature Protocols@natprot.nature.com · 3mo ago

New Article! Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC)

Out now in Science! Our study challenges long-standing assumptions about transcription factor specificity in eukaryotes. Novel single-molecule measurements of TF behavior in living cells reveal an independence of locus-specific binding from DNA sequence recognition.🧵 www.science.org/doi/10.1126/...

Unstructured transcription factor interactions enable emergent specificity

How intrinsically disordered regions (IDRs) shape chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We used proximity-assisted photoactivation (PAPA), a single...

science.org

Today, it was Lisa's turn to defend her PhD thesis and she did an absolutely fantastic job 😍 Especially going into full structure of the RNA Pol2 catalytic core and explaining the mutants. It was an outstanding discussion! I am really proud of her performance today 🥹

Very excited to share our newest findings! A very long team effort pursued by multiple team members -to frantically reproduce everything over and over-, we show mTOR-Polycomb synergy at promoters of developmental master regulator TFs in ESCs prior to their expression. www.biorxiv.org/content/10.6...

Excited to share our latest work in Molecular Cell: www.cell.com/molecular-ce... We show that PRC1 condensates exclude SWI/SNF from chromatin, revealing a physical mechanism for how opposing regulators compete to control gene expression. Huge thanks to all collaborators and mentors!

Mutual antagonism between PRC1 condensates and SWI/SNF in chromatin regulation

Niekamp et al. show that biomolecular condensates formed by Polycomb repressive complexes can physically restrict access of the activating remodeler SWI/SNF to chromatin. Establishing this barrier dep...

cell.com

Johannes Stein's new lab at the MPIMG will use microscopy to study the organization of the genome at a molecular level. We talked to him about how, despite being a trained physicist, he ended up in biology, the potential of his research and the power of interdisciplinary teams. @jmstein.bsky.social

A nanoscopic look at gene regulation

Johannes Stein joined the MPIMG in 2025. His lab will use state-of-the-art microscopy techniques to examine the organisation of the genome at a molecular level. We talked to him about how, despite bei...

molgen.mpg.de

The next iteration of O-MAP targeting genomic loci is now at eLife!! DNA O-MAP enables proximity labeling at specific DNA loci took a ton of work from many lab members and collaborators, so it's really exciting to wrap up this paper with @oligopain.bsky.social! elifesciences.org/articles/102...

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

DNA O-MAP enables proximity labeling at specific genomic loci in fixed cells using programmable oligonucleotides, revealing locus-proximal proteomes and chromatin interactions without genetic modifica...

elifesciences.org

Delighted to share our preprint describing COMET, a new approach to drift correction for #SMLM, which performs exceptionally well in practice. Check out the benchmarking results compared to other methods! :) Thanks to @lreinkensmeier.bsky.social for a superb effort. www.biorxiv.org/cgi/content/...

Please check out our newest work on fluorogenic speed imager probes, in which we combine the strengths of speed-optimized imagers and fluorogenic imagers. #SuperResolution #DNAPAINT #microscopy www.biorxiv.org/content/10.6...

It’s incredibly hard to study lipids in biological membranes on the nanoscale. You need near-perfect information on both membrane ultrastructure and lipid density. Lipid-CLEM, now out in @natcellbio.nature.com brought to you by @mathilda95.bsky.social changes that: www.nature.com/articles/s41...

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.

🚨 We’re happy to announce (finally!) the publication of METALoci, in collaboration with @dariloops.bsky.social and heroes: @jrotwitguez.bsky.social & @imotagom.bsky.social. METALoci integrates #3DGenome and #Epigenetics data into a unified framework we believe is very useful! Here 👉🏻 rdcu.be/e5sm2

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs

Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...

rdcu.be

Get to know Thomas Schlichthärle, our newly appointed professor of #AI-guided #ProteinDesign, in the latest NewIn episode. He wants to use custom-designed #proteins to advance the development of new #medicines: go.tum.de/484027 #HightechAgendaBayern ▶️ youtu.be/G-pt28HJpA8 📹& 📷ProLehre

Designing proteins for targeted cell activation

Prof. Thomas Schlichthärle spricht über seine Arbeit als Professor für AI-guided Protein Design.

go.tum.de

We;re hiring Junior Group Leaders! 🔬✨ We’re looking for researchers in immunology, chemical biology, AI in biology, or protein design to launch their own independent groups in our collaborative, international environment. www.nki.nl/news-events/...

Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. 🥳 mrc.tal.net/vx/mobile-0/...

Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package: - fully bootstrapped Java setup (just pip install) - lazy, repeatably-indexable Array object - fully spec-compliant OME-Zarr group obj. - xarray/dask exports github.com/imaging-form... v0.0.rc1 on PyPI

GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API

Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile

github.com

New paper alert!🤩Super proud that our story led by superstar postdocs @liujinghui.bsky.social and @nerlielisa.bsky.social is finally out! We found how electrical signals are key for promoting organ regenerative growth!!! A thread 🧵https://www.science.org/doi/10.1126/sciadv.aec0687

Injury-induced electrochemical coupling triggers organ growth

Organ repair and growth rely on coupling tissue-wide membrane depolarization with intracellular proliferative signaling.

science.org

I’m excited to share my first-author paper, with co-first author @rongqinxiaoxiao.bsky.social, now out in @nature.com. We developed a live-cell single-particle tracking platform to see how TRiC & prefoldin engage proteins during co- and post-translational folding. 1/9 www.nature.com/articles/s41...

Single-molecule dynamics of the TRiC chaperonin system in vivo - Nature

Single-particle tracking experiments in intact cells reveal dynamic co- and post-translational interactions of the TRiC–PFD chaperonin complex with client proteins during in vivo protein folding.

nature.com

Great to see our Science Review on emerging multiplexed single-molecule methods that use libraries to link sequence to dynamics. A fun collaborative writing project! From sequence to function: Bridging single-molecule kinetics and molecular diversity | Science www.science.org/doi/10.1126/...

From sequence to function: Bridging single-molecule kinetics and molecular diversity

Biological function is fundamentally determined by nucleic acid and protein sequence. Beyond encoding genetic information, nucleic acids also display complex physicochemical parameters that shape stru...

science.org

Formation & function of #MembranelessOrganelles! #CryoET structures of #proteasome storage granules inside cells! Read our paper @cp-cell.bsky.social! ❕Publication: doi.org/10.1016/j.ce... ❕Press Release: www.biochem.mpg.de/en/pressroom @uoftmedicine.bsky.social @erc.europa.eu #UPSmeetMet

Join our virtual seminar! @sedonamurphy.bsky.social presents cutting-edge research on 3D genome organisation & epigenetic memory in development, moderated by @stefanschoenfelder.bsky.social 📅 Jan 8, 4pm UK 💻 Zoom Register: us02web.zoom.us/webinar/regi... #3DGenome #Epigenetics #ChromatinBiology