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Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin [ChIP-Seq]

GSE273678 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 55 samples Submitted 2025/08/05 Platform GPL16791Platform GPL34284
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 55 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
55 samples: 23 conditions, mostly in duplicateGroups 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
Phase-separated NDF-FACT condensates facilitate transcription elongation on chromatinNature cell biology · 2025
Summary (written by the submitters)
How the facilitates chromatin transcription (FACT) complex enables RNA polymerase II to overcome chromatin barriers in cells remains poorly understood—especially given the limited direct interactions of FACT with polymerases, DNA or nucleosomes. Here we demonstrate that phase separation, mediated by nucleosome destabilizing factor (NDF), is a key mechanism enabling the function of FACT during transcription elongation.
Read the full summary ↓
Through biochemical and single-molecule assays, we found that NDF−FACT condensates create specialized biochemical environments that enhance transcription efficiency approximately 20-fold compared with FACT alone. These dynamic condensates form on transcribing RNA polymerase II and travel along chromatin, where they promote efficient nucleosome disassembly at barriers while retaining histones on DNA to preserve chromatin integrity. In human stem cells, disruption of these condensates leads to genome-wide transcriptional defects and chromatin instability, mirroring the effects of FACT depletion. By showing that phase separation enhances FACT function during transcription elongation, our study reveals a key mechanism that preserves chromatin integrity and transcriptional homeostasis in human stem cells.
Published in
Phase-separated NDF-FACT condensates facilitate transcription elongation on chromatin
Li Z, Burgos-Bravo F, Xu K et al. · Nature cell biology 2025 · PMID 41028835 · doi:10.1038/s41556-025-01778-8
This dataset
Open GSE273678 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 GSE273678_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 PRJNA1142607 and SRA study SRP523453. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41028835) ↗
Study design
23 conditions, mostly in duplicate
NDF-degron, Spt16, ChIP_DMSO1h ×3 NDF-degron, Spt16, ChIP_Aux1h ×3 NDF-degron, Spt16, ChIP_DMSO2h ×3 NDF-degron, Spt16, ChIP_Aux2h ×3 iPSC, NDF, ChIP ×2 iPSC, Spt16, ChIP ×2 iPSC, Pol II, ChIP ×2 iPSC, NDF, ChIP_Con ×2 +20 more

Supports a between-group comparison across 50 samples.

How we read this: 23 replicated groups read from 55 sample titles; they account for 50 of them. 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

+ 15 more — browse all 55 samples with per-sample file links →

Datasets on a similar topic

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