Jop Kind

Pre-assembly of biomolecular condensate seeds drives RSV replication Nature - Viral ribonucleoprotein–viral protein networks form pre-replication centres that nucleate viral factories and drive respiratory syncytial virus replication.

Now out in Nature! We visualize infection of the RNA virus RSV in real-time with single-vRNP resolution to understand how RSV establishes viral factories, biomolecular condensates that act as sites of viral replication. A huge collaborative effort led by Dhanushika Ratnayake!

rdcu.be/e1bBW

Image with overview of Hubrecht Symposium 2026 information, including title, speakers, etc.

There are still spots available for our Hubrecht Symposium 2026, taking place on Thursday March 26!

📝 Abstract submission deadline: February 1st.
🎟️ Registration deadline: February 15th.

Learn more and register 👇
www.hubrecht.eu/hubrecht-sym...

So many exciting things ahead, Robin. Enjoy it all!

🌱 As of Jan 1, I started as Assistant Professor at UMC Utrecht – Center for Molecular Medicine.

Very grateful to @dewitlab.bsky.social and @jopkind.bsky.social and to the many other people who supported me along the way.

I’ll be launching the lab soon, focusing on Chromatin Systems Biology.

Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty

1/

🧬 Very excited to share our work on dissecting imputation strategies for single-cell histone modification data! academic.oup.com/nargab/artic...

A huge thank you to @robinhweide.bsky.social, @jopkind.bsky.social and Jeroen de Ridder for their collaboration in this project!

6/ Together, our work links nuclear architecture, epigenetic state, and MeCP2 activity to the spatiotemporal control of long neuronal genes.

With implications for understanding Rett syndrome and broader mechanisms of cortical development.

Great collaboration with Basak (UMC Utrecht) team
🧵//

5/ Strikingly, MeCP2’s function appears context-dependent:

• In prenatal cortex: MeCP2 promotes activation of long genes.
• In postnatal cortex: MeCP2 represses the same genes

4/ Mechanistically, we identify MeCP2 (mutated in Rett syndrome) as a candidate regulator.
MeCP2 binds long LAD genes before they are released and transcribed, pointing to a stage-specific role in gene priming.

3/ These long neuronal genes often detach from the nuclear lamina before activation, suggesting lamina release is an early regulatory step in corticogenesis.
This spatial reorganization aligns with their role in neurodevelopmental disorders, including ASD.

2/ Using in utero electroporation + scDam&T-seq, we jointly profiled transcriptomes and lamina-associated domains (LADs) in embryonic cortex.

We found widespread lamina reorganization during differentiation, strongly enriched at long neuronal genes (≥100 kb).

MeCP2 binding and genome–lamina reorganization precede long gene activation during mouse corticogenesis During corticogenesis, neural gene expression is tightly coordinated by chromatin and epigenetic changes, whose misregulation can lead to neurodevelopmental disorders[1][1]–[4][2]. The role of spatial...

1/ 🧵 I am excited to share a new preprint from our group:
Single-cell Dam&T-seq during mouse corticogenesis reveals how genome–lamina interactions regulate long neuronal genes.
doi.org/10.1101/2025...
#Neurodevelopment #Epigenetics @hubrechtinstitute.bsky.social @oncodeinstitute.bsky.social

Join this year's CSH Asia Systems Biology of Gene Regulation & Genome Editing meeting in beautiful Suzhou, China, Oct 20-24. Let's bring the international communities together! Abstract deadline Sept 19! Infos and registration at csh-asia.org?content/2767. Please repost!

Very proud of Kim to be featured by MIT Technology Review as one of this year's innovators under 35 for her pioneering work on mapping DNA repair in single cells! @oncodeinstitute.bsky.social @hubrechtinstitute.bsky.social

NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...

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...

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

Extensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....

We’re looking for curious, innovative science leaders at EMBL Heidelberg! 🔬🧬🦠

Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels.

Take a look at these four open positions 👇

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/

🧬 Looking for a PhD position in molecular or developmental biology? 🔬

✉️ The Hubrecht Institute now has its very own PhD program! Applications are open and will be accepted until September 15th. Read more here 👉 www.hubrecht.eu/hipp/

Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation - Nature Cell Biology Kefalopoulou, Rullens et al. develop Dam&ChIC to assay chromatin state at two different time points in the same cell. The method was used to study the reorganization of LADs during cell division a...

I am very excited to share our latest work where we describe a new method to profile genome-wide chromatin transitions over time in single cells. Great collaborative effort with the van Oudenaarden group @hubrechtinstitute.bsky.social @oncodeinstitute.bsky.social www.nature.com/articles/s41....

🧬 How do epigenetic modifications change over time in the same cell? Are they maintained during cell divisions?

Researchers from the Kind and Van Oudenaarden groups have found a way to study these types of questions: www.nature.com/articles/s41.... Read more below! 👇

@jopkind.bsky.social

⚡ I developed VIS-seq with the help of dougfowler.bsky.social and others at UW Genome Sciences. Check out my preprint:
www.biorxiv.org/content/10.1...

2/9

UMAP of LMNA variant profiles (left) colored by Louvain-derived clusters. Colors legend at bottom. Graphical representation (right) of lamin A processing, localization, aggregation, and degradation, annotated with their relationship to dimerization, multimerization and variant clusters.

🌎 LMNA variant ➡️ structure ➡️ abundance and localization ➡️ function! VIS-seq maps LMNA variant effects across scales of cellular organization and discovered a new subset of gain-of-function LMNA variants.

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Exciting opportunity at @scilifelab.se

Beautiful work Grace!! Congratulations!

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Delighted that our work on positional memory is now published. We asked how axolotl cells 'know' which part of the limb to regenerate after injury.
www.nature.com/articles/s41...
A joy to work with super team Sarah Plattner, Yuka Sugiura, Francisco Falcon and Elly Tanaka.
🧵1/14

Thesis cover image

🧬What makes one cell different from another? Kim de Luca developed methods that help answer this question. They can be used to study DNA organization, regulation and repair in single cells. Today she successfully defended her thesis. Congratulations Kim!🎓 Read more 👉 www.hubrecht.eu/phd-kim-de-l...

Today, on ‘Be Open about Animal Research Day’, we spotlight how research with zebrafish brings us closer to healthier hearts. #BOARD25

Sharing about 80% of heart disease–causing genes with humans, the zebrafish is an excellent model to study how hearts develop, become diseased and might regenerate.