Today, Pim Rullens successfully defended his PhD thesis ‘Genome form and function in single cells’. In the Kind group, he investigated how the three-dimensional form of DNA in a cell nucleus influences how the cell uses it. Congratulations, Pim! 🎉 Read more here: www.hubrecht.eu/phd-rullens

Thrilled that our project received funding from the NWO Sustainable Science Fund! 🎉 We'll develop more sustainable single-cell epigenomic methods that cut plastic waste and energy use. www.nwo.nl/en/news/sust... @hubrechtinstitute.bsky.social @jopkind.bsky.social

Sustainable Science Fund; 20 projects granted funding to make research practices more sustainable | NWO

Research contributes to knowledge about sustainability, but how do we make research practices themselves more sustainable? Funding has been awarded to twenty projects from the call launched in 2025 by...

nwo.nl

Welcome, Tony Hyman! EMBL welcomes its new Director General, Tony Hyman, as he takes up the mandate of leading EMBL's six sites. www.embl.org/news/embl-an...

It’s well known that inflammation increases cancer risk, but how? The answer: the epigenome "remembers" inflammation and primes stem cells for cancer. Here is our paper: nature.com/articles/s41... And a special shoutout to the lead author @snaga13.bsky.social A 🧵

Epigenetic memory of colitis promotes tumour growth - Nature

Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...

nature.com

Life’s first kiss – what do we miss? The second annual #HubrechtSymposium2026 is off to a great start with keynote speaker Andrea Pauli on the molecular mechanisms of the egg-to-embryo transition. We're excited for this year's edition on the theme “Molecular Machines in Development”.

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

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.

rdcu.be

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...

🌱 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!

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

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...

doi.org

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

Hubrecht Institute@hubrechtinstitute.bsky.social · 11mo ago

Kim de Luca, Hubrecht alumna from the Kind group, was featured by MIT Technology Review in this year's Innovators Under 35! Swipe to read more. The full list can be found here: http://www.technologyreview.com/innovators-under-35/2025/.

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...

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 ...

biorxiv.org

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👇

kasitc.bsky.social@kasitc.bsky.social · 12mo ago

Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

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/

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....

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...

nature.com

🧬 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

🌎 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. 7/9

Exciting opportunity at @scilifelab.se

Ilaria Piazza lab@iplab.bsky.social · last yr.

We are accepting applications for a PhD opportunity at @scilifelab.se this is part of a MSCA Doctoral Network on the topic of metabolic regulation of genome function and cell identity. A EU funded generous fellowship is offered with possibility of industry experience. Apply here:

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/

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

nature.com

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

🧬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.

🚨 Preprint 🚨 Ever wondered how cells prepare their genomes to enable new cell-fates? In this team up with the Kind lab, we show that genes are repositioned in the nucleus to get ready for future activation and tissue formation. Read 🧵👇 to find out how and when this happens! doi.org/10.1101/2025...

Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates

Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell-fate...

biorxiv.org

Very excited to share our latest work revealing a prominent role for LADs in commisioning cell fates in mouse organ & tissue development, particularly of the limb. Amazing work by Isabel and Samy together with @stemundi.bsky.social & @drmrobson.bsky.social www.biorxiv.org/content/10.1...

Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates

Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell-fate...

biorxiv.org