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A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform
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A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform

Siddhant U. Jain, Kaylyn E. Williamson, Alexander W. Ying +18 more
December 2025
 ·
bioRxiv
 ·
DOI 
10.1101/2025.08.01.667725
94
%
Reproducible
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This paper passed independent validation.
QED's automated review checked the evidence supporting each claim, the statistical methods, and whether the results are reproducible from the data provided.

It ranks in the top 1% of preprints assessed in Molecular Biology this quarter.
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Why this is interesting

Resolving how SWI/SNF complexes—lacking sequence-specific DNA binding—find their genomic targets, this study defines the SWIFT domain as a conserved TF-recruitment interface, explaining paralog-specific developmental switches and exposing a therapeutic vulnerability in TF-driven cancers.

QED claims analysis

Summary

The SWIFT domain, a conserved immunoglobulin-like fold within mSWI/SNF SMARCD subunits, functions as a direct transcription factor binding platform that mediates genome-wide chromatin remodeling complex recruitment through allovalent interactions with diverse transcription factor transactivation domains, with SMARCD paralog-specific binding preferences enabling tissue-specific gene regulation and representing a critical dependency in transcription factor-addicted cancers.

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Main Claim 1 –

TF expression recruits mSWI/SNF genome-wide via motif density

Main Claim 2 –

PU.1 transactivation domain directly binds mSWI/SNF complexes

Supporting evidence

  • PU.1 binds the mSWI/SNF structural core via SMARCD/SMARCC
  • TF–mSWI/SNF binding occurs without the ATPase catalytic module
Main Claim 3 –

SMARCD SWIFT domain is necessary and sufficient for TF binding

Supporting evidence

  • PU.1 tAD engages SWIFT via multiple allovalent binding sites
  • SWIFT R290W mutation disrupts TF binding and mSWI/SNF recruitment
  • Isolated SWIFT sequesters TFs and blocks endogenous mSWI/SNF recruitment
  • SWIFT is a broad TF-binding platform across diverse TF families
Main Claim 4 –

SWIFT–PU.1 binding sustains oncogenic transcription and AML proliferation

Supporting evidence

  • SWIFT overexpression poisons TF-addicted cancers by blocking mSWI/SNF binding

Abstract

Mammalian SWI/SNF (BAF) chromatin remodeling complexes modulate DNA accessibility and gene expression, however, their genomic targeting mechanisms remain incompletely understood. Here, we identify SWIFT (SWI/SNF Ig-Fold for Transcription Factor Interactions), a conserved, broad transcription factor (TF) binding platform on the SMARCD subunits. SWIFT is necessary and sufficient for direct engagement with the transactivation domain of PU.1, a single mutation in which disrupts PU.1-mSWI/SNF binding, impairs complex targeting, and attenuates oncogenic transcription and proliferation in PU.1-dependent cancer cells. Dominant expression of the SWIFT domain in isolation sequesters TFs from mSWI/SNF and poisons TF-addicted cancer cells. Finally, TFs across diverse families interact with SMARCD paralog-specific SWIFT domains. These results define a major mechanism of cell type- and disease-specific mSWI/SNF chromatin targeting and inform approaches toward therapeutic modulation.

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