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NELF prevents transcriptional readthrough into DNA replication zones in cancer cells

GSE253121 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 70 samples Submitted 2025/12/13 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 70 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
70 samples: 35 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
NELF prevents transcriptional readthrough into DNA replication zones in cancer cellsEMBO reports · 2026
Summary (written by the submitters)
Regulation of RNA polymerase II (Pol II) transcription is closely associated with cell proliferation. However, it remains unclear how the Pol II transcription program is rewired in cancer to promote uncontrolled growth. Here, we find that expression of NELFCD, a known negative transcription elongation factor, is upregulated in colorectal tumors.
Read the full summary ↓
Auxin-dependent protein degradation of NELF-C in combination with nascent transcript sequencing demonstrates a direct role of NELF-C on Pol II transcription in this cancer. Strikingly, we demonstrate that the acute loss of NELF-C protein globally redistributes termination factors and perturbs Pol II transcription termination. These changes drive pervasive Pol II transcription into DNA replication zones, leading to transcription-replication conflict that may block the cell cycle in G1 or early S phase. Our findings reveal a previously unrecognized role of NELF in transcription termination and highlight NELF as a potential therapeutic target in colorectal cancer.
Published in
NELF prevents transcriptional readthrough into DNA replication zones in cancer cells
Nakayama C, Fang Q, Daigaku Y et al. · EMBO reports 2026 · PMID 41721097 · doi:10.1038/s44319-026-00700-z
This dataset
Open GSE253121 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 GSE253121_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 PRJNA1064075 and SRA study SRP483321. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41721097) ↗
Study design
35 conditions, mostly in duplicate
ATAC_0h ×2 ATAC_4h ×2 ATAC_24h ×2 RNAseq_pA_0h ×2 RNAseq_pA_4h ×2 RNAseq_Nuclear_pA_0h ×2 RNAseq_Nuclear_pA_4h ×2 RNAseq_Nuclear_pA_12h ×2 +27 more

Supports a between-group comparison across 70 samples.

How we read this: 35 replicated groups read from 70 sample titles; they account for 70 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

+ 30 more — browse all 70 samples with per-sample file links →

Datasets on a similar topic

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