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RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcription
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RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcription

Krista A. Budinich, Xinyi Yao, Chujie Gong +12 more
November 2025
 ·
bioRxiv
 ·
DOI 
10.1101/2025.07.29.665963
94
%
Reproducible
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It ranks in the top 1% of preprints assessed in Molecular Biology this quarter.
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Why this is interesting

By revealing that locally produced RNA actively nucleates oncogenic chromatin condensates rather than merely resulting from them, this work reframes transcription as a self-amplifying oncogenic loop and opens RNA–condensate interactions as a direct therapeutic target.

QED claims analysis

Summary

Locally produced RNA transcripts reinforce the nucleation and chromatin engagement of oncogenic ENL mutant condensates through interactions with a conserved basic patch in the YEATS domain, preferentially enhancing condensate formation at permissive genomic loci to drive persistent transcriptional bursting and hyperactivation of leukemogenic gene programs, such that even partial disruption of ENL-RNA interactions effectively abolishes leukemogenesis in mouse models.

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Main Claim 1 –

ENL YEATS-domain basic patch mediates RNA binding

Supporting evidence

  • ENL binds intronic RNA in cells; 3A reduces binding
  • ENL 3A mutation selectively impairs RNA binding specificity
Main Claim 2 –

RNA binding promotes oncogenic ENL mutant condensates in cells

Supporting evidence

  • RNA dose-dependently enhances ENL droplet formation in vitro
Main Claim 3 –

RNA interactions promote ENL condensates at endogenous target loci

Supporting evidence

  • RNA interactions increase transcriptional bursting at ENL target loci
  • RNA binding and transcription enable ENL condensate re-nucleation
Main Claim 4 –

RNA binding preferentially boosts ENL occupancy at top-bound loci

Supporting evidence

  • ChIP-seq top-bound ENL sites correspond to condensate loci
  • RNA binding enhances activation of condensate-permissive ENL targets

Abstract

Aberrant chromatin-associated condensates have emerged as drivers of transcriptional dysregulation in cancer. Although extensive studies have elucidated intrinsic protein sequence features governing their formation, how extrinsic factors within the chromatin environment modulate their assembly and pathogenic function remains poorly understood. Gain-of-function mutations in the histone acetylation reader ENL, found in pediatric leukemia and Wilms tumor, drive oncogenesis by inducing condensate formation at highly selective genomic loci. Here, we uncover a critical role for locally produced gene transcripts in reinforcing the nucleation, chromatin engagement, and oncogenic activity of ENL mutant condensates. Mutant ENL binds RNA in part through a conserved basic patch within its YEATS domain, and this interaction enhances condensate formation both in vitro and across diverse cellular contexts. Using a chemically inducible condensate displacement and re-nucleation system, we show that blocking ENL–RNA interactions or transcription impairs condensate reformation at endogenous targets. RNA interactions preferentially enhance mutant ENL occupancy at top-bound, condensate-permissive loci, leading to increased transcriptional bursting and robust gene activation at the single-cell and single-allele level. In mouse models, disrupting ENL–RNA interactions reduces condensate formation and oncogenic transcription in hematopoietic stem and progenitor cells, thereby suppressing ENL mutant-driven leukemogenesis. Together, these findings demonstrate that locally produced RNA transcripts can promote locus-specific nucleation of pathogenic condensates on chromatin, which in turn drive persistent and hyperactive transcription of oncogenic targets and lead to tumorigenesis.

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