GEO series

RNA promotes nucleation and oncogenic activity of chromatin-associated condensates [ChIP-Seq]

GSE300421 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2025/11/28 Platform GPL30173

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 14 samples: 14 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcriptionbioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

Aberrant chromatin-associated condensates have emerged as drivers of gene dysregulation in cancer, yet the mechanisms regulating their formation and function remain poorly understood. Mutations in the histone acetylation reader ENL, recurrent in leukemia and Wilms tumor, drive oncogenesis by inducing condensate formation at selective target loci.

Read the full summary ↓

Here, we show that RNA promotes the nucleation, chromatin engagement, and oncogenic activity of ENL mutant condensates. Mutant ENL binds RNA via a conserved basic patch within the YEATS domain, and this interaction enhances condensate formation in vitro and in cells. Acute displacement and reassembly experiments demonstrate that interactions with local RNA transcripts facilitate condensate nucleation efficiency at endogenous target loci. Partial disruption of RNA binding preferentially impairs chromatin occupancy of ENL mutants at condensate-permissive loci, leading to reduced transcriptional bursting and target gene expression. In mouse models, disrupting RNA binding compromises mutant ENL-driven gene expression and malignant self-renewal, halting disease progression and prolonging survival. These findings uncover a previously unrecognized role of RNA in promoting the formation and oncogenic function of chromatin-associated condensate.

Published in

RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcription

Budinich KA, Yao X, Gong C et al. · bioRxiv : the preprint server for biology 2025 · PMID 40766627 · doi:10.1101/2025.07.29.665963

This dataset

Open GSE300421 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE300421_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1280926 and SRA study SRP594102. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40766627) ↗

Study design

14 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 14 sample titles: 14 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM9060284 HEK293 cells, ENL-WT, input, batch1, ChIP
GSM9060285 HEK293 cells, ENL-WT, Flag-ChIP, batch1, ChIP
GSM9060286 HEK293 cells, ENL-T1, Flag-ChIP, batch1, ChIP
GSM9060287 HEK293 cells, ENL-T1-3A, Flag-ChIP, batch1 ChIP
GSM9060288 HEK293 cells, ENL-WT, input, batch2, ChIP
GSM9060289 HEK293 cells, ENL-WT, Flag-ChIP, batch2, ChIP
GSM9060290 HEK293 cells, ENL-T2, Flag-ChIP, batch2, ChIP
GSM9060291 HEK293 cells, ENL-T2-3A, Flag-ChIP, batch2, ChIP
GSM9060292 MDA231 cells, ENL-WT, input, ChIP
GSM9060293 MDA231 cells, ENL-WT, Flag-ChIP, ChIP
GSM9060294 MDA231 cells, ENL-T1, Flag-ChIP, ChIP
GSM9060295 MDA231 cells, ENL-T1-3A, Flag-ChIP, ChIP
GSM9060296 MDA231 cells, ENL-T2, Flag-ChIP, ChIP
GSM9060297 MDA231 cells, ENL-T2-3A, Flag-ChIP, ChIP

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