#SWI/SNF
Excited to share our latest work in Molecular Cell: www.cell.com/molecular-ce...

We show that PRC1 condensates exclude SWI/SNF from chromatin, revealing a physical mechanism for how opposing regulators compete to control gene expression.

Huge thanks to all collaborators and mentors!
Mutual antagonism between PRC1 condensates and SWI/SNF in chromatin regulation
Niekamp et al. show that biomolecular condensates formed by Polycomb repressive complexes can physically restrict access of the activating remodeler SWI/SNF to chromatin. Establishing this barrier dep...
www.cell.com
April 25, 2026 at 12:43 PM
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...
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
www.biorxiv.org
January 28, 2026 at 9:54 AM
where are the polycomb and swi/snf starter packs
November 15, 2024 at 11:18 PM
🎉 Excited to share my postdoc work in the Bernstein lab now online @cp-molcell.bsky.social!
🔎We explored the unique functions of the SWI/SNF PBAF complex and its relationship with TFs, and unveiled a PBAF/REST-controlled neuronal-like signature with potential implications in #melanoma brain mets🧬
The SWI/SNF PBAF complex facilitates REST occupancy at repressive chromatin
By mapping SWI/SNF complex subfamilies in the melanocytic lineage, Grossi and Nguyen et al. find that PBAF-only sites harbor PRC1/2 modifications and the repressive transcription factor REST. PBAF is ...
www.cell.com
April 21, 2025 at 12:38 PM
How do chromatin remodelers use #IDRs to find TF binding partners? In our new Molecular Cell paper, we show that β-catenin is an adaptor that links SWI/SNF (cBAF) subunit ARID1A with binding partners via IDR-domain interactions.
www.cell.com/molecular-ce...
July 22, 2025 at 6:42 PM
Now online! Structural basis of a SWI/SNF-associated transcription pre-initiation complex
Structural basis of a SWI/SNF-associated transcription pre-initiation complex
Cryo-EM and genetic analyses reveal that the SWI/SNF chromatin remodeler is an integral component of the transcription pre-initiation complex. The structures demonstrate how SWI/SNF facilitates transcription initiation through stabilization of PIC organization and concerted remodeling of the +1 nucleosome.
dlvr.it
September 8, 2026 at 2:59 PM
A bit late posting here- but very excited that our SWI/SNF paper is now published (following preprint in March)!!

Rather than a full thread, let me summarize by #ChromatinHaiku 😀

At most promoters
P400 compensates
For loss of SWI/SNF

bit.ly/3G6Cqw3
November 25, 2023 at 9:54 PM
Very happy to share the updated version of our bioRxiv preprint. New experiments further support a role for SWI/SNF in regulating epiblast and trophectoderm specification in early human embryos and blastoids. Congrats Sam van Knippenberg, Maria Tryfonos & all involved
www.biorxiv.org/content/10.6...
September 25, 2026 at 3:58 PM
What do SWI/SNF-addicted cancers have in common? And when are they most sensitive to SWI/SNF inhibition? Check out Katka’s thread highlighting our most recent paper
For the first time, we find a common mechanism for SWI/SNF addiction in cancer! Our paper reveals that G1 phase is a critical junction for SWI/SNF activity in several addicted cancers, including neuroblastoma, AML, prostate cancer, and uveal melanoma academic.oup.com/nar/advance-... (1/6)
November 27, 2023 at 2:25 PM
New preprint of @trono-lab.bsky.social and my PhD work!
By modulating SWI/SNF remodeling at ancient transposable elements - LINE/L2s and SINE/MIRs, a "noncanonical" KZFP called ZNF436 protects cardiomyocytes from losing their identity.
🫀heartbeat on 🔁 repeat
www.biorxiv.org/content/10.1... #TEsky
May 19, 2025 at 2:01 PM
Some Friday reading...new review in Open Biology where we discuss how SWI/SNF maintains the chromatin environment around centromeres, building on recent work from ourselves and others. Lots of fun putting this together with @alison-harrod.bsky.social and @thedownslab.bsky.social!
Boundary issues: SWI/SNF shapes chromatin patterns in and around centromeres
Abstract. The SWI/SNF family of chromatin remodelling complexes, comprising BAF, PBAF and ncBAF, is known for their critical roles in regulating chromatin
royalsocietypublishing.org
December 5, 2025 at 10:30 AM
January 2, 2026 at 1:13 AM
Check out this study by Oo et al. revealing how trans-acting lncRNAs target SWI/SNF complex to lineage-specific enhancers to maintain open chromatin:

www.nature.com/articles/s41...
Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers - Nature Communications
The mechanisms directing chromatin remodeling complexes to genomic regions have remained elusive. Here, the authors show that lncRNAs direct SWI/SNF to cell type-specific enhancers, investigating an R...
www.nature.com
January 6, 2025 at 2:31 PM
CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly www.nature.com/articles/s4...
May 31, 2025 at 2:15 PM
Getting ready for an exciting discussion section in the UCSF #BioReg grad course! Classic paper Coté 1994 on swi/snf facilitating GAL4 binding to nucleosomal DNA.
February 5, 2025 at 2:59 PM
Over 20% of cancers have mutations in SWI/SNF (BAF) chromatin remodelers, linking them to oncogenesis & neurodevelopmental disorders. #CancerResearch PMID:39014081, Nat Rev Drug Discov 2024, @NatRevDrugDisc
Chromatin remodellers as therapeutic targets
Mutations in genes that encode subunits of the SWI/SNF chromatin remodelling complexes are found in more than 20% of cancers as well as in certain neurodevelopmental disorders. This Review discusses mechanisms...
buff.ly
January 15, 2025 at 9:00 PM
Our new review, looking into the roles of SWI/SNF in the chromatin environment around centromeres, is just out in Open Biology! @kezlane.bsky.social @thedownslab.bsky.social
Some Friday reading...new review in Open Biology where we discuss how SWI/SNF maintains the chromatin environment around centromeres, building on recent work from ourselves and others. Lots of fun putting this together with @alison-harrod.bsky.social and @thedownslab.bsky.social!
Boundary issues: SWI/SNF shapes chromatin patterns in and around centromeres
Abstract. The SWI/SNF family of chromatin remodelling complexes, comprising BAF, PBAF and ncBAF, is known for their critical roles in regulating chromatin
royalsocietypublishing.org
December 5, 2025 at 4:57 PM
For the first time, we find a common mechanism for SWI/SNF addiction in cancer! Our paper reveals that G1 phase is a critical junction for SWI/SNF activity in several addicted cancers, including neuroblastoma, AML, prostate cancer, and uveal melanoma academic.oup.com/nar/advance-... (1/6)
November 27, 2023 at 2:17 PM
Disruption of the ARID1A-containing SWI/SNF complex reprograms tumor-associated macrophages and enhances immunotherapy response https://www.biorxiv.org/content/10.64898/2026.09.25.754528v1
September 28, 2026 at 11:46 AM
Canonical PRC1 excludes SWI/SNF, and its subunit composition (e.g., which CBX) can change the competition outcome.

Fig 1D (magenta: cPRC1, cyan: SWI/SNF)
April 27, 2026 at 2:34 AM
New paper on bioRxiv by YounJu So in our lab! She shows that while SMARCD paralogs compensate for each other during neurodevelopment, each still drives distinct gene expression programs, explaining selective vulnerability of these SWI/SNF subunits in brain disorders.
www.biorxiv.org/content/10.6...
Redundancy masks functional specificity of SMARCD paralogs in neurodevelopment
The SWI/SNF complex is an essential chromatin remodeler that regulates DNA accessibility during brain development. Through combinatorial assembly of subunits encoded by paralogous genes, SWI/SNF compl...
www.biorxiv.org
December 8, 2025 at 4:12 PM
We depleted SWI/SNF-ATPases 𝗦𝗠𝗔𝗥𝗖𝗔𝟮 𝗮𝗻𝗱 𝗦𝗠𝗔𝗥𝗖𝗔𝟰 during 𝘁𝗿𝗼𝗽𝗵𝗲𝗰𝘁𝗼𝗱𝗲𝗿𝗺 𝗱𝗶𝗳𝗳𝗲𝗿𝗲𝗻𝘁𝗶𝗮𝘁𝗶𝗼𝗻, 𝗵𝘂𝗺𝗮𝗻 𝗯𝗹𝗮𝘀𝘁𝗼𝗶𝗱 𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗼𝗻, and 𝗵𝘂𝗺𝗮𝗻 𝗯𝗹𝗮𝘀𝘁𝗼𝗰𝘆𝘀𝘁 𝗱𝗲𝘃𝗲𝗹𝗼𝗽𝗺𝗲𝗻𝘁. We then performed 𝘀𝗶𝗻𝗴𝗹𝗲-𝗻𝘂𝗰𝗹𝗲𝗶 𝗺𝘂𝗹𝘁𝗶-𝗼𝗺𝗶𝗰 𝗴𝗲𝗻𝗲 𝗲𝘅𝗽𝗿𝗲𝘀𝘀𝗶𝗼𝗻 𝗮𝗻𝗱 𝗔𝗧𝗔𝗖 𝗽𝗿𝗼𝗳𝗶𝗹𝗶𝗻𝗴 of SWI/SNF-perturbed human blastoids.
December 3, 2025 at 6:53 PM