GEO series

RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [HiChIP]

GSE266412 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 4 samples Submitted 2025/09/30 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 4 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: 4 samples: 2 × hTERT1-RPE1, RB WT, G1, HiChIP biol vs 2 × hTERT1-RPE1, RB KO, G1, HiChIP biolGroups 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: RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactionsNature communications · 2026

Summary (written by the submitters)

The retinoblastoma protein (RB) is a well-characterized repressor of E2F transcriptional activity that controls genes involved in cell proliferation during the G1-phase. Here, we examine the effect of RB on chromatin organization and uncover a non-canonical role for RB in which it promotes the removal of cohesin from insulators and thereby induces the expression of adjacent genes.

Read the full summary ↓

We identify that RB colocalizes with cohesin across the human genome. During mitosis, RB facilitates the removal of cohesin from CTCF sites, with this effect persisting into early G1, impacting loop formation and extrusion at topologically associating domain (TAD) boundaries. Chromosome conformation capture assays revealed that RB reduces insulation at TAD boundaries and promotes enhancer-promoter interactions marked by histone 3 lysine 27 acetylation. In this way, RB enhances the transcription of hundreds of genes beyond the E2F transcriptional program, expanding our understanding of this key tumor suppressor and cell cycle regulator.

Published in

RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions

Lee H, Gkotinakou IM, McGrath CG et al. · Nature communications 2026 · PMID 41951674 · doi:10.1038/s41467-026-71655-x

This dataset

Open GSE266412 in finder → Find more human 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 GSE266412_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 PRJNA1107120 and SRA study SRP505305. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41951674) ↗

Study design

2 × hTERT1-RPE1, RB WT, G1, HiChIP biol vs 2 × hTERT1-RPE1, RB KO, G1, HiChIP biol

Supports a between-group comparison across 4 samples.

How we read this: 2 replicated groups read from 4 sample titles; they account for 4 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

GSM8246502 hTERT1-RPE1, RB WT, G1, HiChIP biol rep 1 hTERT1-RPE1, RB WT, G1,…
GSM8246503 hTERT1-RPE1, RB WT, G1, HiChIP biol rep 2 hTERT1-RPE1, RB WT, G1,…
GSM8246504 hTERT1-RPE1, RB KO, G1, HiChIP biol rep 1 hTERT1-RPE1, RB KO, G1,…
GSM8246505 hTERT1-RPE1, RB KO, G1, HiChIP biol rep 2 hTERT1-RPE1, RB KO, G1,…

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.