@deWitLab

Computational & Genomics Lab studying 3D genome function and dynamics @ Netherlands Cancer Institute

 Amsterdam, Netherlands
github.com/deWitLab
Joined August 2016
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You may know ZNF143 as a looping factor. We show together with the @hansen_lab that this is not the case! If you want to know why and what it does instead do read our thread below: biorxiv.org/content/10.1101/…

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independen...

Gene expression is orchestrated by transcription factors, which function within the context of a three-dimensional genome. Zinc finger protein 143 (ZNF143/ZFP143) is a transcription factor that has...

biorxiv.org
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📢 We are very excited to announce the first International Dutch Embryo Model Meeting in Nijmegen on March 27-28. See below for details. Don't miss this fantastic opportunity to connect with the embryo model community!
Hendrik Marks@hendrik_marks11 Nov 2024
📢 Save the date! I am excited to announce the International Dutch Embryo Model Meeting 2025 in Nijmegen (NL) on Thursday 27 March and Friday 28 March! Registration is open now, or more information: ru.nl/en/about-us/events/int…. Direct link to registration webforms.ru.nl/0d5d3b2f-3d7f….
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Come and join us!
MIT Dept of BE@MITdeptofBE7 Nov 2024
LECTURER position open in the MIT Department of Biological Engineering to join the department as a lecturer focused on teaching the computational aspects of biological engineering. ow.ly/xSbu50U2y8U
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Check out our latest review on how cooperativity influences transcriptional bursting. Kudos to the first author Charis Fountas! sciencedirect.com/science/ar…
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Delighted to see the completed Special Issue of Current Opinion in Genetics and Development on "Genome Architecture and Expression” It was a pleasure putting this together with Maya Capelson. Thanks to all the authors that contributed articles sciencedirect.com/special-is…
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The protein factories of our cells are much more diverse than we thought. NKI scientists have shown that cancer cells can use ribosomes to boost their invisibility, helping them hide from the immune system. They publish their findings in Cell today ➡️ bit.ly/4ePmIVW
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Researchers from the Netherlands Cancer Institute and @prinsesmaximac are launching a new study looking into rhabdoid tumors, a rare and highly aggressive form of childhood cancer, thanks to financial contributions from @kika8118 ➡️ bit.ly/3zPw9Wc
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Happy to share work with Hadi, Yao & @Maxime_Tortora characterizing the impact of dynamic CTCF barriers for cohesin loop extrusion biorxiv.org/content/10.1101/…

Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy

In mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This interplay leads to the enrichment of cohesin at barriers, isolation between...

biorxiv.org
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Want to do a DPhil @BiochemOxford ? Here is a link (bioch.ox.ac.uk/graduate-abou…) to programmes that admit students. Great labs to choose from. Have a look at kloselab.co.uk if you want to know more what we do in my group! Please RT!
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🚨🚨🚨 Call is now open!!! Wanna become our new beloved colleague 🫶🏻🫶🏻🫶🏻 and be part of a stimulating (and friendly) scientific community ??? We are perfectly located in beautiful Paris with exciting work environment and state-of-the-art core facilities APPLY 👇🏻👇🏻👇🏻👇🏻
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👀 We're looking for a junior group leader! Join our innovative, curiosity-driven institute in a collaborative, international environment. Full freedom to pursue your research, competitive salary & relocation support. 📅 Apply by Dec 1 Info & application: bit.ly/3BLA3j8
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First preprint from the lab 🚨 How can enhancers regulate target promoters across vast genomic distances, and what is the role of cohesin loop extrusion in the process? biorxiv.org/content/10.1101/… (1)

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

Enhancers are critical genetic elements controlling transcription from promoters, but the mechanisms by which they convey regulatory information across large genomic distances remain elusive. Here,...

biorxiv.org
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Paper 🚨! Ecstatic, proud, grateful …Years of dedication from the whole lab, with the exceptional @djkloosterman and the one of a kind #JohannaErbani at its helm. What a journey all the way to @CellCellPress! How did it start (& end)? A 🧵1/n cell.com/cell/fulltext/S0092…

Macrophage-mediated myelin recycling fuels brain cancer malignancy

Recycling of cholesterol-rich myelin debris by macrophages leads to the emergence of lipid-laden macrophages (LLMs) in glioblastoma. LLMs support glioblastoma malignancy through transfer of myelin-...

cell.com
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(1/16) Check out our @SimonMJGaudin paper tiny.cc/icuazz from the Canzio lab out in @ScienceMagazine today on how tuning local cohesin trajectories enables differential readout of the clustered Protocadherin (Pcdh) locus across different types of neurons.
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I'm #hiring a PhD student! Join the Lindeboom Lab at the @NKI_nl on an exciting project to explore oncogenic transcription factor binding kinetics and biophysics using state-of-the-art technologies! Apply now or share this exciting opportunity! nki.nl/careers-study/vacanci…
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Immunotherapy before surgery for patients with metastatic melanoma appears to be successful as 59% of patients responds so well that adjuvant treatment is no longer needed, show the results of the NADINA trial presentend at #ASCO24 today by @ProfCUBlankNKI bit.ly/3Vo1hnn
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Might attempt to model a flotillin cage using the AlphaFold3 web server was super fun (original paper: biorxiv.org/content/10.1101/…). Read the thread for a crazy plot twist!🧵👇
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Demis -- I think AlphaFold3 is really exciting. As Reviewer #3, I got great results from the server. I tried hard to get @Nature to urge you to release the code but was unsuccessful. I did not get it for re-review so I don't know if you responded. So why no code? @GoogleDeepMind
Demis Hassabis
@demishassabis8 May 2024
Thrilled to announce AlphaFold 3 which can predict the structures and interactions of nearly all of life’s molecules with state-of-the-art accuracy including proteins, DNA and RNA. Biology is a complex dynamical system so modeling interactions is crucial blog.google/technology/ai/go…
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Interested in using degron tagging to study the function of your favourite protein in genetically engineered mouse models? Check out our review covering recent work in this area: doi.org/10.1242/dmm.050613

Degron tagging for rapid protein degradation in mice

Summary: We review recent applications of degron tagging in mouse models, focusing on the challenges and opportunities for using this technology to rapidly degrade proteins of interest in mammalian...

journals.biologists.com
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Come join us in Oxford as an Associate Professor in Molecular and Cellular Biochemistry. We are considering a wide range of research areas, but I would note that we have a vibrant chromatin and gene regulation community. Happy to answer questions if you are interested. Please RT!
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Save the date! June 7th @cdf1530 in Paris, the latest developments in the making of human pseudo-embryos in vitro🤘Open access👍 no registration 🙏RT @AMartinezArias @jacob_hanna @NRivron @nmoris @AlainChedotal @TreutleinLab #JFGuerin #ERialSebbag @the_Node
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