Elzo de Wit lab @ NKI
@dewitlab.bsky.social
📤 648
📥 260
📝 60
Computational & Genomics Lab studying 3D genome function and dynamics @ Netherlands Cancer Institute
pinned post!
(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🧵:
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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
https://doi.org/10.1093/nar/gkaf549
6 months ago
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Stefan Luschnig
3 days ago
Apply soon: Full professorship in Systems
#Neuroscience
@uni-muenster.de
See
shorturl.at/VczFp
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Elzo de Wit lab @ NKI
Job Dekker
4 days ago
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...
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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.
https://www.nature.com/articles/s41556-025-01828-1
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Di Jiang
7 days ago
@science.org
Chromatin buffers torsional stress during transcription | Science
www.science.org/doi/10.1126/...
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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...
https://www.science.org/doi/10.1126/science.adv0134
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Angelo Iulianella
7 days ago
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.
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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...
https://www.dal.ca/research-and-innovation/support-for-researchers/external-funding/federal-funding/the-cerc-opportunity.html
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Agathe Chaigne
8 days ago
My lab is hiring a postdoc (ERC funded)! If you're interested, get in touch!
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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...
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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.
https://www.nature.com/articles/d41586-025-03808-9
9 days ago
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Job Dekker
9 days ago
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...
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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...
https://www.nature.com/articles/s41586-025-09890-3
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Claudio Cantù
13 days ago
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.
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Rob Klose
15 days ago
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...
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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...
https://www.biorxiv.org/content/10.64898/2025.12.08.692985v1
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Virtual Gastrulation Zoom Talks
23 days ago
Reminder: Tomorrow is VGZT day! 🚀 Don’t miss great talks from 👉 Luca Braccioli (
@bracciolilab.bsky.social
) 👉 Komal Makwana (on X: @Komal_Makwana4)
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Elzo de Wit lab @ NKI
Development
24 days ago
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.
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Aaron Quinlan (he/him)
25 days ago
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
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Intro to Bedder – The Quinlan Lab
http://quinlanlab.org/blogposts/bedder_intro.html
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Bart Deplancke
24 days ago
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
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Elzo de Wit lab @ NKI
Elphege Nora Lab at UCSF
29 days ago
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/...
🧵👇
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Zeitlinger Lab
about 1 month ago
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!)
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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...
https://www.biorxiv.org/content/10.1101/2025.11.18.685822v1
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Stefan Barakat
about 1 month ago
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:
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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...
https://www.cell.com/cell/fulltext/S0092-8674%2825%2901234-6
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Elzo de Wit lab @ NKI
Stefan Schoenfelder
about 1 month ago
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
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Elzo de Wit lab @ NKI
Rada-Iglesias Lab
about 2 months ago
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 👇
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Elzo de Wit lab @ NKI
Max Delbrück Center
3 months ago
🚀 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/...
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Elzo de Wit lab @ NKI
Rob Klose
about 2 months ago
Awesome stuff James and team! Thanks for giving
@edimitrova.bsky.social
and I the opportunity to contribute.
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Exciting work from Hangpeng and James! Very nice explainer. Happy to have been able to contribute.
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about 2 months ago
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Elzo de Wit lab @ NKI
Wout Oosterheert
about 2 months ago
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...
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PhD Student – Structural Biology of Actin Filament Assemblies | Werken bij AVL
https://www.werkenbijavl.nl/vacatures/phd-student-structural-biology-of-actin-filament-assemblies-to-understand-cell-migration/
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Elzo de Wit lab @ NKI
Maxim Greenberg
about 2 months ago
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!
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Elzo de Wit lab @ NKI
Bruno Di Stefano
about 2 months ago
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...
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Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology
Stem cell differentiation is controlled by manipulating RNA condensates.
https://www.nature.com/articles/s41587-025-02853-z
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Elzo de Wit lab @ NKI
Marieke Oudelaar
2 months ago
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....
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Elzo de Wit lab @ NKI
Anders Sejr Hansen
2 months ago
Our collab w. V Goel,
@nicholas-aboreden.bsky.social
, J Jusuf, G Blobel, L Mirny,
@irate-physicist.bsky.social
out in
@natsmb.nature.com
www.nature.com/articles/s41...
Was co-submitted with
@allanaschooley.bsky.social
@jobdekker.bsky.social
whose paper should also come out soon Brief thread 👇
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Elzo de Wit lab @ NKI
Rob Klose
2 months ago
Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost!
www.keystonesymposia.org/conferences/...
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Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia
Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!
https://www.keystonesymposia.org/conferences/conference-listing/meeting/C12026
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Elzo de Wit lab @ NKI
Rob Klose
2 months ago
We are recuiting two new Associate Professors here in Oxford Biochemistry. Come join us! Reach out to me if you have any questions. Please repost!
tinyurl.com/mr3m7bd3
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Ed Banigan
2 months ago
Excited to share our paper on dynamics of microcompartments during M-to-G1 is now published in
@natsmb.nature.com
www.nature.com/articles/s41...
Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from
@andersshansen.bsky.social
lab) on transcriptional spiking
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The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project! If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
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Characterization of induced cohesin loop extrusion trajectories in living cells
Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...
https://rdcu.be/eLiT5
2 months ago
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Elzo de Wit lab @ NKI
Daniel Ibrahim
2 months ago
What is a promoter? And how does it work? We very happy to share our latest work trying to understand enhancer-promoter compatibility. I am very excited about the results of
@blanka-majchrzycka.bsky.social
, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
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Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
https://www.biorxiv.org/content/10.1101/2025.10.14.682013v1
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Stephan Gruber
2 months ago
And also the bacterial telomere protection paper by Maya, Nicolas, & Ania is out:
doi.org/10.1038/s443...
Great experience with
@reviewcommons.org
&
@embojournal.org
Feels just right to have the manuscript reviewed without having to target a specific journal from the start.
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Elzo de Wit lab @ NKI
Wout Oosterheert
2 months ago
Very excited that my final postdoctoral work is now online in Cell
@cellpress.bsky.social
.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
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Di Jiang
2 months ago
Last week
@science.org
mRNA initiation and termination are spatially coordinated | Science
www.science.org/doi/10.1126/...
from
@anafiszbein.bsky.social
@athmapai.bsky.social
et al.
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Elzo de Wit lab @ NKI
Daniel Durocher
3 months ago
9 days to go: * 2 x open positions! * Exceptional environment, competitive start-up package * University of Toronto appointments * Toronto has great (and peaceful) quality of life!
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Elzo de Wit lab @ NKI
James Briscoe
3 months ago
The
@crick.ac.uk
is recruiting Early Career Group Leaders - Lab set-up, research costs, salaries for up to 5 researchers - Support for up to 12 years - Access to our core facilities - Competitive salary - Fantastic colleagues - All areas of biology Deadline 27 Nov
www.crick.ac.uk/careers-stud...
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Early career group leaders
We appoint researchers from across biology and biomedicine to set up their first groups at the Crick.
https://www.crick.ac.uk/careers-study/faculty/early-career-group-leaders
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Elzo de Wit lab @ NKI
Naomi Moris
3 months ago
The Crick is looking for new junior group leaders! Any postdocs or early career researchers wanting to be our colleagues should apply 👍
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Elzo de Wit lab @ NKI
Carl Zimmer
3 months ago
Today my
@nytimes.com
colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link:
nyti.ms/3IWXbiE
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https://nyti.ms/3IWXbiE
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Elzo de Wit lab @ NKI
Arnau Sebé-Pedrós
3 months ago
A thoughtful and beautifully written
@quantamagazine.bsky.social
article about genome regulatory innovation at the origin of animals. Featuring some of our work and highlighting key open questions. Thanks to
@philipcball.bsky.social
for this fantastic piece.
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Elzo de Wit lab @ NKI
Emilia Dimitrova
3 months ago
If you are a computational biologist interested in how chromatin states are established and maintained to regulate transcription, this is the dream job for you! This will be in close collaboration with the Klose lab in Oxford and we have a lot of cool projects you can get involved in. Apply!
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Elzo de Wit lab @ NKI
Bart Deplancke
3 months ago
🧵1/ Excited to share our new paper introducing a new
#singlecell
assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗
www.nature.com/articles/s41...
Big congrats to the entire team @EPFL & @SIAT_China
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Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics
This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.
https://www.nature.com/articles/s41588-025-02343-7
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Elzo de Wit lab @ NKI
Tung Le
3 months ago
Independent research fellowships leading to tenured positions at the John Innes Centre. Repost = nice. Thank you very much!!!
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Edda Schulz
3 months ago
⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation. 👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
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Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology
Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.
https://www.nature.com/articles/s41594-025-01686-3
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Elzo de Wit lab @ NKI
Benoit Bruneau
3 months ago
awesome new work by my
@gladstoneinst.bsky.social
and
@ucsanfrancisco.bsky.social
colleagues incl
@vram142.bsky.social
on how chromatin remodelers affect mesoscale chromatin organization
www.science.org/doi/10.1126/...
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ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes
Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...
https://www.science.org/doi/10.1126/science.adr0018
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Elzo de Wit lab @ NKI
Francesca Mattiroli
3 months ago
Join us at the Hubrecht Institute in Utrecht to start your research group! Fantastic scientific environment, strong support, and nice colleagues :) Apply and please share broadly in your network.
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Elzo de Wit lab @ NKI
Seema Sheth
3 months ago
Tenure-track Assistant Professor position in Bioinformatics in the Department of Biology at the University of San Francisco
usfca.wd5.myworkdayjobs.com/en-US/USF_Fu...
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Assistant Professor, Tenure-Track, Department of Biology, University of San Francisco
Job Title: Assistant Professor, Tenure-Track, Department of Biology, University of San Francisco Job Summary: The Department of Biology at the University of San Francisco invites applications for a fu...
https://usfca.wd5.myworkdayjobs.com/en-US/USF_Full-Time_Faculty/job/USF-Hilltop-Campus/Assistant-Professor--Tenure-Track--Department-of-Biology--University-of-San-Francisco_R0011691
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Elzo de Wit lab @ NKI
Bas van Steensel lab (NKI)
3 months ago
Our reporter hopping scaled up to thousands of integrations in a single locus, to produce high-resolution functional maps, with plenty of interesting insights:
www.science.org/doi/10.1126/...
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Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
https://www.science.org/doi/10.1126/science.ads6552
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Elzo de Wit lab @ NKI
Luca Giorgetti lab @FMI
3 months ago
Really excited to share our latest work led by
@mattiaubertini.bsky.social
and
@nesslfy.bsky.social
: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
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Nature Methods
3 months ago
scEpi2-seq: a method for simultaneous single-cell profiling of DNA methylation and histone modifications.
@jervdberg.bsky.social
@hubrechtinstitute.bsky.social
www.nature.com/articles/s41...
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Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance - Nature Methods
This work presents scEpi2-seq, a method for simultaneous single-cell profiling of DNA methylation and histone modifications, enabling direct investigation of the interplay between these two epigenomic marks.
https://www.nature.com/articles/s41592-025-02847-4
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Elzo de Wit lab @ NKI
Tobias Raisch
3 months ago
We just published this paper of which I am immensely proud:
www.nature.com/articles/s41...
In the study, we uncover how the enzyme MPO disassembles
#nucleosomes
in a process called NETosis, a funky mechanism of
#neutrophils
to kill
#pathogens
that you might have never heard of. Let's dive in... 🧵
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Myeloperoxidase transforms chromatin into neutrophil extracellular traps - Nature
Myeloperoxidase, a highly expressed neutrophil protein, disassembles nucleosomes, facilitating neutrophil extracellular trap (NET) formation, and binds stably to NETs extracellularly.
https://www.nature.com/articles/s41586-025-09523-9
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