Elzo de Wit lab @ NKI @dewitlab

Terrific paper on a new chromosomal
compartment where extensive loop
extrusion isolates domains from
other such domains

03.02.2026 21:55 — 👍 28 🔁 15 💬 0 📌 0

SS18-SSX co-opts P300 to sustain oncogenic transcription independent of SWI/SNF activity Synovial sarcoma is driven by the SS18-SSX fusion oncoprotein, which has been assumed to promote tumorigenesis through its incorporation into the SWI/SNF chromatin remodeling complexes. Accordingly, therapeutic efforts have focused on targeting SS18-SSX containing SWI/SNF assemblies, yet these approaches have produced limited clinical benefit. Here, we demonstrate that SS18-SSX sustains oncogenic transcription independent of SWI/SNF activity. Despite efficient degradation and dismantling of SWI/SNF complexes, fusion occupancy at target loci and associated gene expression programs remain largely intact. Instead, we identify the acetyltransferase P300 as an essential co-factor supporting SS18-SSX chromatin binding and transcriptional activation. Targeting P300 displaces the fusion from chromatin, suppresses its transcriptional output, compromising synovial sarcoma viability. Notably, dual PROTAC mediated degradation of P300 and SWI/SNF produces strong synergistic effects, broadly disrupting SS18-SSX localization and function. These findings redefine the mechanistic basis of synovial sarcoma and reveal a mechanistically anchored therapeutic strategy for targeting its core oncogenic driver. ### Competing Interest Statement C.R.V. has been a consultant for Flare Therapeutics, Roivant Sciences and C4 Therapeutics; has served on the advisory boards of KSQ Therapeutics, Syros Pharmaceuticals and Treeline Biosciences; has received research funding from Boehringer Ingelheim and Treeline Biosciences; and owns stock in Treeline Biosciences. S.A.A. has been a consultant and/or shareholder for Neomorph, Imago Biosciences, Hyku Therapeutics, C4 Therapeutics, Accent Therapeutics and Nimbus Therapeutics; and has received research support from Janssen and Syndax. N.O.C. is a co-founder, shareholder and management consultant for PhenoTherapeutics Ltd; and a shareholder in Amplia Therapeutics Ltd All other authors declare no financial interests UKRI, EP/X039633/1 Worldwide Cancer Research, https://ror.org/031tfbz57, 21-0271 Science Foundation Ireland, https://ror.org/0271asj38, 18/SIRG/5573

Synovial sarcoma is driven almost exclusively by a single oncofusion – SS18-SSX

For years, the assumptions on disease mechanisms were simple:

➡️ SS18-SSX works by hijacking SWI/SNF chromatin remodeling activity

Our new study shows that assumption was wrong 🧵👇

www.biorxiv.org/content/10.6...

28.01.2026 09:54 — 👍 23 🔁 10 💬 2 📌 2

Full Professor and Chair Laboratory of Biophysics We are looking for a Full Professor in the Biophysics chair group, part of Wageningen University & Research (WUR)

www.wur.nl/en/vacancy/f...

Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!

28.01.2026 05:20 — 👍 23 🔁 47 💬 0 📌 0

CAD-C: An engineered nuclease enables repair-free in situ proximity ligation and nucleosome-resolution chromosome walks in human cells Chromosome conformation capture (3C)-derived methods have become an indispensable tool in the study of gene regulation. The three-dimensional contacts they are able to assay depend strongly on the properties of the enzyme used to fragment chromatin prior to proximity-driven ligation. Micrococcal nuclease (MNase), used in Micro-C, increases resolution at the expense of low ligation efficiency and the need for extensive enzyme titration. To overcome these limitations, we engineered a highly active, TEV protease-activatable caspase-activated DNase (CAD) to enable an efficient, low-sequence-bias, and high-resolution proximity ligation assay we call CAD-C. CAD-C was successful on the first attempt for each human cell line tested and the resulting datasets capture loops, TADs, compartments, and stripes similarly to Micro-C. However, compared to Micro-C and Hi-C, CAD-C shows enhanced sensitivity for promoter-enhancer loops. Leveraging the ligation-competent DNA ends produced by CAD cleavage, we show that CAD-C is compatible with a highly streamlined, repair-free protocol and produces multi-step CADwalks, consecutive ligations between nucleosomal or sub-nucleosomal fragments. With these walks, we probe local chromatin fiber folding contacts, nucleosomal and sub-nucleosomal footprints, and long-range nuclear organization regimes in human cell lines. CAD-C is an efficient, robust chromatin structure assay that can span sub-nucleosomal to chromosomal length scales in a single experiment. ### Competing Interest Statement V.I.R. and J.S. are inventors on a related patent application covering CAD-C (PCT application filed 2024). NIH Common Fund, https://ror.org/001d55x84, 1DP2GM150021 Irma T. Hirschl Trust, https://ror.org/01yaqvf46, Career Scientist Award Rita Allen Foundation, https://ror.org/0515k5w36, Scholar Award Stavros Niarchos Foundation, https://ror.org/0210rze73, Institute for Global Infectious Disease Research at Rockefeller University Grant Robertson Technology Development Fund at Rockefeller University Boehringer Ingelheim (Germany), https://ror.org/00q32j219, PhD Fellowship to JS U.S. National Science Foundation, https://ror.org/021nxhr62, GRFP to LAW International Human Frontier Science Program Organization, https://ror.org/02ebx7v45, Postdoctoral Cross-Disciplinary Fellowship to AO Natural Sciences and Engineering Research Council of Canada, Postgraduate fellowship to HC, Postgraduate fellowship to JLY

Excited to share my PhD work from @riscalab.bsky.social on @biorxivpreprint.bsky.social CAD-C & CADwalks –repair-free, nucleosome-resolution chromosome conformation capture with engineered TEVp-activatable CAD. CADwalks: chromosome walks of ligated CAD footprints. doi.org/10.64898/202...
1/

21.01.2026 19:32 — 👍 16 🔁 5 💬 1 📌 1

Very interesting!

24.01.2026 07:46 — 👍 0 🔁 0 💬 0 📌 0

Seeing into Hi-C: How our scientific connectivity revealed the close connections in our DNA to be a work of art Scientific data can be beautiful. An example where the data itself have a particularly striking appearance even before any scientific meaning has been ascribed

I had the privilege to meet artist Mary Griffiths. Mary got inspired by Hi-C maps and over zooms we spoke about Hi-C maps, patterns and drawings. Mary’s Hi-C inspired art has been exhibited eg the Royal Academy. We wrote this piece about this art-science collaboration

pubs.aip.org/aip/bpr/arti...

24.01.2026 00:50 — 👍 30 🔁 10 💬 1 📌 0

View from the hotel room

Poster session 2024, with Valentina Boeva, Constantin Ahlmann-Eltze and others

Wednesday afternoon hike incl. swim in the mountain river

Another view from the hotel room

Apply for the Ascona workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems", 28 Jun-3 Jul 2026 on Monte Verità, Lago Maggiore at the foot of the Swiss Alps.

ascona2026.sciencesconf.org

15.01.2026 16:16 — 👍 19 🔁 15 💬 0 📌 1

And tangerine is mandarijn (mandarin).

14.01.2026 14:20 — 👍 2 🔁 0 💬 0 📌 0

Start your independent as an ELISIR fellow right after your PhD, in one of the most terrific places in Europe !

14.01.2026 13:12 — 👍 16 🔁 11 💬 0 📌 1

Job offer 2026.pdf

🧬 We’re #Hiring a #Bioinformatician/ Computational Biologist!
#Single-cell genomics, #Epigenomics & #3Dgenome biology in #Zebrafish #DevBio 🐟
📍 @cabd-upo-csic.bsky.social, CABD, Seville (Spain)
🕒 Full-time, 3-year position (start March 2026)
📅 Apply by Feb 15, 2026
👉 drive.google.com/file/d/1M8rp...

12.01.2026 15:57 — 👍 17 🔁 22 💬 1 📌 2

We’re hiring!
@jcellsci.bsky.social is looking for a Reviews Editor to join the team. This is a fantastic opportunity for someone who loves #cellbiology and wants to stay connected with the field. A great chance to work for an organisation that believes in helping the community!

Details below👇

09.01.2026 10:13 — 👍 29 🔁 42 💬 1 📌 0

International Genome Dynamics course in Institut Curie-Paris (April 8-15), experimental and computational methods in multiomics,with a #TE centered session.
Free registration, until Jan 15th
Don’t miss it!
👉https://training.institut-curie.org/courses/Genome-Dynamics-2026
@institutcurie.bsky.social

09.01.2026 10:54 — 👍 16 🔁 12 💬 1 📌 2

DDLS Research School Postdoc call 2026 Call for Academic and Industrial Postdoctoral Fellowships in Data-Driven Life Science 2026 Generic Description of the DDLS Postdoc Program The SciLifeLab and Wallenberg National Program for Data-Drive...

Planning to apply to the @scilifelab.se DDLS Research School Postdoc Call 2026?
Our lab will be happy to host prospective computational postdocs at @ki.se Karolinska Institutet / @scilifelab.se .
#Postdoc #ComputationalBiology #RNA #InfectionBiology #AntimicrobialResistance #Bioinformatics

08.01.2026 15:39 — 👍 6 🔁 3 💬 1 📌 0

Bella Chow, same thing.

08.01.2026 08:10 — 👍 1 🔁 0 💬 0 📌 0

The 5 stages of the ‘enshittification’ of academic publishing Academic publishing now shows the same decline that has hit social media and online marketplaces.

Reading “The 5 stages of the ‘enshittification’ of academic publishing”
theconversation.com/the-5-stages...

07.01.2026 09:32 — 👍 91 🔁 35 💬 2 📌 7

DNA sequence quantitatively encodes CTCF-binding affinity at genome scale https://www.biorxiv.org/content/10.64898/2026.01.05.696797v1

06.01.2026 07:31 — 👍 3 🔁 4 💬 0 📌 0

Yeah, no. I’m not your monkey.

05.01.2026 20:12 — 👍 2 🔁 0 💬 0 📌 0

🌱 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.

02.01.2026 13:56 — 👍 29 🔁 4 💬 3 📌 2

Apply soon: Full professorship in Systems #Neuroscience @uni-muenster.de
See shorturl.at/VczFp

23.12.2025 09:34 — 👍 9 🔁 8 💬 0 📌 0

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.

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...

22.12.2025 11:45 — 👍 75 🔁 39 💬 1 📌 1

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...

@science.org Chromatin buffers torsional stress during transcription | Science www.science.org/doi/10.1126/...

19.12.2025 22:31 — 👍 31 🔁 11 💬 0 📌 0

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...

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.

19.12.2025 20:17 — 👍 23 🔁 33 💬 4 📌 1

My lab is hiring a postdoc (ERC funded)! If you're interested, get in touch!

18.12.2025 08:36 — 👍 59 🔁 67 💬 3 📌 2

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.

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...

17.12.2025 22:16 — 👍 30 🔁 11 💬 1 📌 1

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...

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...

17.12.2025 20:59 — 👍 106 🔁 54 💬 2 📌 5

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.

13.12.2025 07:00 — 👍 150 🔁 55 💬 4 📌 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...

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...

11.12.2025 06:09 — 👍 133 🔁 64 💬 10 📌 6

Reminder: Tomorrow is VGZT day! 🚀

Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)

03.12.2025 07:48 — 👍 8 🔁 5 💬 0 📌 0

Pathway to Independence Support postdocs on the job market Line drawing of a person at a bench transitioning to working at a desk Development

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.

02.12.2025 14:53 — 👍 38 🔁 36 💬 2 📌 6

Intro to Bedder – The Quinlan Lab

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

02.12.2025 02:28 — 👍 298 🔁 152 💬 5 📌 11

Elzo de Wit lab @ NKI

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