Johannes Stein
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jmstein.bsky.social
Johannes Stein
@jmstein.bsky.social
1.3K followers 590 following 39 posts
Group Leader at Max Planck Institute for Molecular Genetics

Studying genome organization with quantitative super-resolution microscopy

https://www.molgen.mpg.de/stein-lab
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jmstein.bsky.social
Johannes Stein @jmstein.bsky.social · Aug 13
(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen!

Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵
Reposted by Johannes Stein
michellefrei17.bsky.social
🚨Curious how synthetic fluorophores simplify microscopy? Our review covers applications such as super-resolution microscopy and biosensing. 🎉👩‍🔬Congrats to my first PhD student, Agnese Nicoli, for the fearless deep dive! 🔬 ⚗️
D-CHAB @ethz.ch
www.nature.com/articles/s41...
Synthetic fluorophores for live-cell fluorescence microscopy and biosensing - Nature Chemical Biology
Performing live-cell microscopy experiments with high spatial and temporal resolution requires fluorophores with highly optimized properties. This Review examines the progress in developing synthetic ...
www.nature.com
November 5, 2025 at 9:29 PM
Reposted by Johannes Stein
scisonja.bsky.social
Single-molecule friends!

The prelim. program of next year's sm- #Gordon conference in Switzerland is online: www.grc.org/single-molec...
It'll be 3x fantastic: science, people, place in the alps ⛰️. Kevin & I hope to see you all next June:

Have a look, tell your friends, and register!
2026 Single Molecule Approaches to Biology Conference GRC
The 2026 Gordon Research Conference on Single Molecule Approaches to Biology will be held in Les Diablerets, Vaud (fr) Switzerland. Apply today to reserve your spot.
www.grc.org
November 2, 2025 at 7:23 PM
Reposted by Johannes Stein
distefanolab.bsky.social
1/ Excited to share our new study with @brumbaugh-lab.bsky.social, out in @natbiotech.nature.com! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵 www.nature.com/articles/s41...
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology
Stem cell differentiation is controlled by manipulating RNA condensates.
www.nature.com
October 28, 2025 at 4:02 PM
Reposted by Johannes Stein
campaslab.bsky.social
Really excited to present the results of a fantastic collaboration with Jesse Veenvliet @jesseveenvliet.bsky.social @mpi-cbg.de @poldresden.bsky.social 🤩

We find a unique mechanism for body axis elongation in mammals, different from other vertebrate species

➡️ www.biorxiv.org/content/10.1...
October 28, 2025 at 8:25 AM
Reposted by Johannes Stein
clairedeo.bsky.social
Our photoswitchable HaloTag is out in Angewandte Chemie @angewandtechemie.bsky.social ! We now also show that this system can be used to control emitter density in SMLM. Congrats to Franzi, Bego, and our amazing collaborators. Check it out: onlinelibrary.wiley.com/doi/full/10....
A Photoswitchable HaloTag for Spatiotemporal Control of Fluorescence in Living Cells
Photoswitchable fluorophores are critical for advanced bioimaging. Here, we develop a photoswitchable self-labeling HaloTag that can reversibly modulate the emission of a bound fluorogenic dye via a ....
onlinelibrary.wiley.com
October 25, 2025 at 8:56 AM
Reposted by Johannes Stein
fueyoraquel.bsky.social
My lab is seeking two PhD candidates to investigate the function and regulation of endogenous retroviruses in the early stages of human development 🦠👩‍🔬. Apply through the International Max Planck Research School (IMPRS) program: www.molgen.mpg.de/IMPRS/applic.... www.molgen.mpg.de/5094682/Fuey...
[2026] – Endogenous retroviruses in human embryogenesis
www.molgen.mpg.de
October 23, 2025 at 8:31 PM
Reposted by Johannes Stein
sedonamurphy.bsky.social
My new lab at the @molgen.mpg.de will be following up on some of the nuclear organization aspects of ecDNA so please do reach out if this is of interest :)
October 21, 2025 at 9:43 AM
Reposted by Johannes Stein
sedonamurphy.bsky.social
Here, we show that the unique regulatory landscape of ecDNA enables an ancient LINE to resurrect and act as an enhancer of Myc. This was so fun with @katerinakraft.bsky.social and @mattjones.bsky.social and others. www.nature.com/articles/s41...
Enhancer activation from transposable elements in extrachromosomal DNA - Nature Cell Biology
Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They show that EIE 14 integrat...
www.nature.com
October 21, 2025 at 9:43 AM
Reposted by Johannes Stein
juliusbrennecke.bsky.social
what you always wanted to know about the molecular choreography of nuclear mRNA packaging and export.

thought-provoking review by our colleagues (local or in the RNA community).

@plaschkalab.bsky.social
@rupertfaraway.bsky.social
@thezenklusen.bsky.social

www.annualreviews.org/content/jour...
Mechanisms of Messenger RNA Packaging and Export
The packaging and export of messenger RNA (mRNA) are essential cellular pathways that bridge the nuclear and cytoplasmic phases of eukaryotic gene expression. During their nuclear maturation, mRNAs ar...
www.annualreviews.org
October 18, 2025 at 3:08 PM
Reposted by Johannes Stein
cppape.bsky.social
Are you studying synapses in electron microscopy? Tired of annotating vesicles? We have the tool for you! SynapseNet implements automatic segmentation and analysis of vesicles and other synaptic structures and has now been published:
www.molbiolcell.org/doi/full/10....
SynapseNet is a deep learning based software tool that automates the segmentation of vesicles, mitochondria, synaptic compartments, and the active zone. This is visualized in three panels. On the left, a section of an electron tomogram with a synaptic compartment densely filled with vesicles, which appear as round structures with dark boundary and light body in the image, is shwon. The top right panel shows the segmentation result of vesicles, visualized by masks with an individual color per vesicle and outlines for the segmented compartment (red) and active zone (blue). The bottom right panels shows a 3D rendering of the segmentation with vesicles shown as yellow spheres.
October 17, 2025 at 11:09 AM
Reposted by Johannes Stein
danielibrahim.bsky.social
What is a promoter? And how does it work?

We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters

www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 3:06 PM
Reposted by Johannes Stein
eddaschulz.bsky.social
⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology
Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.
www.nature.com
October 6, 2025 at 1:02 PM
Reposted by Johannes Stein
fueyoraquel.bsky.social
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
A human-specific regulatory mechanism revealed in a pre-implantation model
Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.
rdcu.be
October 1, 2025 at 6:08 PM
Reposted by Johannes Stein
jungmannlab.bsky.social
Highly efficient 12-color multiplexing with speed-optimized DNA-PAINT. We are excited to share our latest paper in @natcomms.nature.com, using left-handed DNA to extend speed-optimized DNA-PAINT to 12 targets in a simple and straightforward way! 🧬👈🚀https://www.nature.com/articles/s41467-025-64228-x
October 2, 2025 at 11:37 AM
Reposted by Johannes Stein
basvansteensellab.bsky.social
Our reporter hopping scaled up to thousands of integrations in a single locus, to produce high-resolution functional maps, with plenty of interesting insights: www.science.org/doi/10.1126/...
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
www.science.org
September 24, 2025 at 8:56 AM
Reposted by Johannes Stein
sedonamurphy.bsky.social
Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...
www.science.org
September 19, 2025 at 6:20 AM
Reposted by Johannes Stein
christlet.bsky.social
Our new preprint is up! This is the main postdoc work of @wiesner-t.bsky.social focusing on exocytosis along the axon shaft and its regulation by the sub membrane actin-spectrin scaffold: www.biorxiv.org/content/10.1...
Read the thread below for a summary of our findings 🧵1/11
September 17, 2025 at 2:55 PM
Reposted by Johannes Stein
carmeloferrai.bsky.social
EpiSci - Hi there! Our review “Mechanotransduction in stem cells” is finally published. With @carstenschulte4.bsky.social we provided a comprehensive picture, that aims to cover the whole mechanotransductive pathway from the cell microenvironment to the nucleus. 1/3 pubmed.ncbi.nlm.nih.gov/38729084/
May 13, 2024 at 12:22 PM
Reposted by Johannes Stein
heilemannlab.bsky.social
And we are done --- #SMLMS2025 is over, and it was great. Thank you Uli & Ulrike & all the helpers 👍, and thanks to everyone joining this event 🙏 ... safe travels home & see you soon!
August 29, 2025 at 11:17 AM
Reposted by Johannes Stein
nadlerlab.bsky.social
Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism.
www.nature.com/articles/s41...
August 21, 2025 at 5:19 AM
Reposted by Johannes Stein
laurabreimann.bsky.social
Excited that our paper was published in Science Advances 🧪
Great work by first author Merrick Pierson Smela who will carry this work forward in his new start-up!
August 16, 2025 at 8:35 PM
Reposted by Johannes Stein
svenklumpe.bsky.social
Extremely excited for the second version of this workshop at the MPI of Biophysics l, Frankfurt, that will happen 12-20. April 2026. Absolutely amazing lineup of speakers, I am very much looking forward to learning from everyone! Apply here: meetings.embo.org/event/26-in-...
August 15, 2025 at 4:09 PM
Reposted by Johannes Stein
ericjoyce.bsky.social
🚨New preprint from the lab🚨
🧬 What keeps certain chromatin domains anchored at the nuclear periphery? Our new genome-wide HiDRO screen uncovers a key role for RNA-binding protein hnRNPK.
www.biorxiv.org/content/10.1...
Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen
The nuclear periphery is a key site for heterochromatin organization in eukaryotic cells, where lamina-associated domains (LADs) promote transcriptional repression and genome stability. Despite their ...
www.biorxiv.org
August 14, 2025 at 7:01 PM
jmstein.bsky.social
(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen!

Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵
August 13, 2025 at 2:19 PM