Elzo de Wit lab @ NKI
@dewitlab.bsky.social
Computational & Genomics Lab studying 3D genome function and dynamics @ Netherlands Cancer Institute
Pinned
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
doi.org
(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🧵:
Reposted by Elzo de Wit lab @ NKI
December 23, 2025 at 9:34 AM
Reposted by Elzo de Wit lab @ NKI
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
www.nature.com
December 22, 2025 at 11:45 AM
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Elzo de Wit lab @ NKI
@science.org Chromatin buffers torsional stress during transcription | Science www.science.org/doi/10.1126/...
Chromatin buffers torsional stress during transcription
During eukaryotic transcription, Pol II must overcome nucleosome obstacles and, because of DNA’s helical structure, must also rotate relative to DNA, generating torsional stress. However, there is lim...
www.science.org
December 19, 2025 at 10:31 PM
@science.org Chromatin buffers torsional stress during transcription | Science www.science.org/doi/10.1126/...
Reposted by Elzo de Wit lab @ NKI
As 2025 comes to a close, my university (Dalhousie U in Halifax, Canada) is recruiting faculty, including outstanding early career researchers, and Canada Research Chairs. Applications are due January 19 2026 (was just notified today!). Please repost.
Dalhousie University is recruiting up to 30 tenure and tenure-track faculty positions
Backed by the Government of Canada’s $1.7 billion Global Impact+ Research Talent Initiative, Dalhousie University is undertaking one of the most ambitious research-leader recruitment efforts in its hi...
www.dal.ca
December 19, 2025 at 8:17 PM
As 2025 comes to a close, my university (Dalhousie U in Halifax, Canada) is recruiting faculty, including outstanding early career researchers, and Canada Research Chairs. Applications are due January 19 2026 (was just notified today!). Please repost.
Reposted by Elzo de Wit lab @ NKI
My lab is hiring a postdoc (ERC funded)! If you're interested, get in touch!
December 18, 2025 at 8:36 AM
My lab is hiring a postdoc (ERC funded)! If you're interested, get in touch!
It was a pleasure to write this News & Views article for the 4D Nucleome flagship article: www.nature.com/articles/d41...
With great editorial support from @hollyasmith.bsky.social!
Read the 4D Nucleome paper here: www.nature.com/articles/s41...
With great editorial support from @hollyasmith.bsky.social!
Read the 4D Nucleome paper here: www.nature.com/articles/s41...
Systematic maps reveal how human chromosomes are organized
Our genomes are highly structured, which facilitates gene regulation. An ambitious project has catalogued the organization of DNA in the nuclei of human cells.
www.nature.com
December 17, 2025 at 10:16 PM
It was a pleasure to write this News & Views article for the 4D Nucleome flagship article: www.nature.com/articles/d41...
With great editorial support from @hollyasmith.bsky.social!
Read the 4D Nucleome paper here: www.nature.com/articles/s41...
With great editorial support from @hollyasmith.bsky.social!
Read the 4D Nucleome paper here: www.nature.com/articles/s41...
Reposted by Elzo de Wit lab @ NKI
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
www.nature.com
December 17, 2025 at 8:59 PM
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Elzo de Wit lab @ NKI
Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
December 13, 2025 at 7:00 AM
Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Reposted by Elzo de Wit lab @ NKI
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
SET1/MLL complexes control transcription independently of H3K4me3
Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...
www.biorxiv.org
December 11, 2025 at 6:09 AM
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Elzo de Wit lab @ NKI
Reminder: Tomorrow is VGZT day! 🚀
Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
Join us next week for another round of inspiring VGZT talks! 🤩
🗓️ Thursday, December 4th
⏰ 9:30 PST / 12:30 EST / 17:30 UTC / 17:30 GMT / 18:30 CET
Our speakers are
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
See you next week 👋
🗓️ Thursday, December 4th
⏰ 9:30 PST / 12:30 EST / 17:30 UTC / 17:30 GMT / 18:30 CET
Our speakers are
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
See you next week 👋
December 3, 2025 at 7:48 AM
Reminder: Tomorrow is VGZT day! 🚀
Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
Reposted by Elzo de Wit lab @ NKI
Apply for our Pathway to Independence (PI) programme, supporting postdocs in #devbio and #stemcell research during the transition to their first group leader position: www.biologists.com/grants/devel...
Application deadline: 2 February 2026.
Application deadline: 2 February 2026.
December 2, 2025 at 2:53 PM
Apply for our Pathway to Independence (PI) programme, supporting postdocs in #devbio and #stemcell research during the transition to their first group leader position: www.biologists.com/grants/devel...
Application deadline: 2 February 2026.
Application deadline: 2 February 2026.
Reposted by Elzo de Wit lab @ NKI
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
Reposted by Elzo de Wit lab @ NKI
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
December 2, 2025 at 2:18 PM
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Reposted by Elzo de Wit lab @ NKI
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
November 27, 2025 at 9:59 PM
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Reposted by Elzo de Wit lab @ NKI
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 8:57 PM
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Reposted by Elzo de Wit lab @ NKI
Very pleased to share our latest paper published in Cell:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
BRAIN-MAGNET, a convolutional neural network trained on 148,198 functionally tested
non-coding regulatory elements, predicts enhancer activity directly from DNA sequence
and identifies nucleotides ess...
www.cell.com
November 20, 2025 at 9:38 AM
Very pleased to share our latest paper published in Cell:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
Reposted by Elzo de Wit lab @ NKI
Very excited to host @efapostolou29.bsky.social for her talk on "Building, predicting and targeting 3D regulatory networks in development and cancer" in @enhancedgenomics.bsky.social's
seminar series "The 3D Regulatory Genome".
📅 13 November 2025 (today!)
⏰ 4 pm GMT
Please join: lnkd.in/eEKe4Z7H
seminar series "The 3D Regulatory Genome".
📅 13 November 2025 (today!)
⏰ 4 pm GMT
Please join: lnkd.in/eEKe4Z7H
November 13, 2025 at 12:32 PM
Very excited to host @efapostolou29.bsky.social for her talk on "Building, predicting and targeting 3D regulatory networks in development and cancer" in @enhancedgenomics.bsky.social's
seminar series "The 3D Regulatory Genome".
📅 13 November 2025 (today!)
⏰ 4 pm GMT
Please join: lnkd.in/eEKe4Z7H
seminar series "The 3D Regulatory Genome".
📅 13 November 2025 (today!)
⏰ 4 pm GMT
Please join: lnkd.in/eEKe4Z7H
Reposted by Elzo de Wit lab @ NKI
We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (www.nature.com/articles/s41...).
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
November 6, 2025 at 6:37 PM
We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (www.nature.com/articles/s41...).
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
Reposted by Elzo de Wit lab @ NKI
🚀 WE ARE HIRING 3️⃣ Independent Group Leaders for #mdcBerlin's new cutting-edge Bioengineering Cluster within our Biomedical Engineering Program.
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
October 9, 2025 at 11:00 AM
🚀 WE ARE HIRING 3️⃣ Independent Group Leaders for #mdcBerlin's new cutting-edge Bioengineering Cluster within our Biomedical Engineering Program.
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.
👉 Apply now: www.mdc-berlin.de/career/jobs/...
Reposted by Elzo de Wit lab @ NKI
Awesome stuff James and team! Thanks for giving @edimitrova.bsky.social and I the opportunity to contribute.
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 9:02 PM
Awesome stuff James and team! Thanks for giving @edimitrova.bsky.social and I the opportunity to contribute.
Exciting work from Hangpeng and James! Very nice explainer. Happy to have been able to contribute.
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 7:19 PM
Exciting work from Hangpeng and James! Very nice explainer. Happy to have been able to contribute.
Reposted by Elzo de Wit lab @ NKI
Are you excited to uncover the molecular mechanisms of actin filament assemblies that drive cell migration using cryo-EM?
Only 1.5 week to apply for this exciting PhD position in my newly established lab at the Netherlands Cancer Institute in Amsterdam: www.werkenbijavl.nl/vacatures/ph...
Only 1.5 week to apply for this exciting PhD position in my newly established lab at the Netherlands Cancer Institute in Amsterdam: www.werkenbijavl.nl/vacatures/ph...
PhD Student – Structural Biology of Actin Filament Assemblies | Werken bij AVL
www.werkenbijavl.nl
October 28, 2025 at 9:17 AM
Are you excited to uncover the molecular mechanisms of actin filament assemblies that drive cell migration using cryo-EM?
Only 1.5 week to apply for this exciting PhD position in my newly established lab at the Netherlands Cancer Institute in Amsterdam: www.werkenbijavl.nl/vacatures/ph...
Only 1.5 week to apply for this exciting PhD position in my newly established lab at the Netherlands Cancer Institute in Amsterdam: www.werkenbijavl.nl/vacatures/ph...
Reposted by Elzo de Wit lab @ NKI
Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
#JobOffer
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
October 28, 2025 at 1:51 PM
Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
Reposted by Elzo de Wit lab @ NKI
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
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...
Reposted by Elzo de Wit lab @ NKI
Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....
October 27, 2025 at 11:49 AM
Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....