Elzo de Wit lab @ NKI

Open Call for Expressions of Interest in Max Planck Directorships: Expressions of interest can be submitted until 31 October 2025.

Director at Max Planck - a unique position! The Open Call for Expressions of Interest in Max Planck Directorships is open now and can be submitted by the 31st of October 2025. ➡️ mpg.de/directors - Please share the Open Call among potential candidates.

Group Leader - Genome Biology Unit Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Strong The Onion vibes with this one: www.nature.com/articles/d41...

We are looking for new colleagues to come join us in Galway as group leaders (Junior and Senior). The Centre for Chromosome Biology is a great place and it is a good time to join. Please reach out if you want to chat about the opportunity!
www.nature.com/naturecareer...

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...
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MRC Postdoctoral Research Scientists x 5 - MRC Laboratory of Medical Sciences Applications are now open for up to five postdoctoral positions in the area of developmental epigenetics.

Interested in developmental epigenetics? So are we! Apply now to join us for your postdoc!

Multiple positions across multiple groups @mrc-lms.bsky.social

Projects spanning germline demethylation, gene regulation, genome architecture in development & disease 👇👇

lms.mrc.ac.uk/work/vacanci...

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....

A little belated posting, but we (Emily Navarrete, Leonid Mirny, me) have an updated preprint in collaboration the Ines Drinnenberg, Héloïse Muller, José Gil Jr, + others on the strange and striking compartmentalization of silkworm chromatin: www.biorxiv.org/content/10.1...

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...

In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11

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/

Amazing, important work. Congratulations to all the authors.

Few dates left to apply for this tenure-track professorship on Single-Cell Systems Biology in my department at @uni-wuerzburg.de. Competitive package and highly attractive research environment at the Institute of Systems Immunology.

Full Professorship in Molecular Mechanisms of Disease - Vienna BioCenter, Austria job with Max Perutz Labs, University of Vienna | 12841053 Join theMax Perutz Labs as Full Professor to unravel disease mechanisms—from metabolism and stress to RNA regulation, epigenetics, and immunity.

Exciting and rare opportunity to join the @maxperutzlabs.bsky.social and the @viennabiocenter.bsky.social as a Full Professor!
www.nature.com/naturecareer...

That's interesting. The (for me) confusing part is that the fountain-like signal in the Chapard et al pre-print is observed in the Glucose condition so in the absence of transcription. Have tried the experiment you described above in the absence of topoisomerase activity by any chance?

They can be seen in Supp. Figure 1 and 2.

Transcription promotes discrete long-range chromatin loops besides organizing cohesin-mediated DNA folding The multi-layered arrangement of eukaryotic genomes and chromosome spatial organization dynamics are of functional importance for gene expression, DNA replication and segregation. SMC complexes are es...

Interesting point. This could very well be as cohesin is loaded at centromeres in yeast. The fountains that we observed are on the megabase scale (the size of yeast chromosomes). In a study by Fred Beckouet's lab there are similar features observed at the GAL locus: www.biorxiv.org/content/10.1...

Congrats!

Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec

(10/n) This study was led by the excellent Ning Qing Liu and later extended by the equally excellent Mikhail Magnitov. You can read the full manuscript here: doi.org/10.1093/nar/....

(9/n) Our study established fountains as an extrusion-mediated, fast-forming feature of the 3D genome, implicated in gene regulation and constrained by WAPL and CTCF activity.

Enrichment of downregulated genes following RAD21 depletion in fountain bases. And a cartoon suggesting a mechanism.

(8/n) Do fountains have a functional role? Our RNA-seq data revealed that their disruption resulted in downregulation of genes around fountains. This would be consistent with a model where cohesin loading at enhancers promotes enhancer-promoter communication and activates genes.

ChromHMM enrichment heatmap showing that enhancer categories are enriched in fountain bases.

(7/n) Where do fountains originate from? We found that fountains are enriched in enhancer chromatin features, consistent with observations in other species that fountains are formed at regions of active chromatin.

(6/n) Re-analysis of chromatin organisation data during cell cycle showed that fountains are formed rapidly after mitosis and their emergence corresponds to cohesin loading on chromatin. This pinpoints that cohesin is not only necessary but also required for fountains formation.

Hi-C maps directly showing the role of cohesin in the formation of fountains.

(5/n) Are fountains then a consequence of loop extrusion? To understand this, we tagged RAD21 in the WAPL/CTCF background, making it a triple degron cell line. Sequential depletion experiments clearly demonstrated that fountains are dependent on cohesin and reduced in its absence.

ChIPseq heatmaps suggesting that cohesin is loaded at fountain bases.

(4/n) What is the mechanism behind their formation? Regions making up the fountains exhibit strong cohesin binding, which is repositioned away upon WAPL and CTCF depletion. Additional analyses of WAPL and CTCF single depletions, suggests that cohesin might be loaded directly at the fountain base.

Hi-C maps and aggregate plots showing fountains in unperturbed and perturbed cells.

(3/n) Systematic analysis of fountains revealed that they can already be visible as a fountain-like pattern in the unperturbed cells. Fountains are extended upon depletion of WAPL and CTCF, which constrain fountain dynamics.

(2/n) Fountains are a newly discovered feature of chromosome organisation, recently reported in preprints from our lab and others. In the Hi-C maps they come out as interactions perpendicular to the main diagonal. We stumbled upon them when we depleted both WAPL and CTCF from mESCs.

Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec

(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators: doi.org/10.1093/nar/.... A Bluetorial🧵:

We are looking for a research assistant to join our lab and support ongoing projects with genome engineering in mouse embryonic stem cells! Please get in touch if you are interested.
www.fmi.ch/education-ca...

Jay, please stop gaslighting early career researchers.