GEO series

ORCA-mediated Polycomb Repressive Complex stabilization maintains 3D-genome architecture and controls replication timing [Cut & Run]

GSE314620 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2026/06/15 Platform GPL24676

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: 6 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: Polycomb-mediated 3D-genome organization controls replication timingScience advances · 2026

Summary (written by the submitters)

Polycomb bodies, also called Polycomb group (PcG) protein complexes, are implicated in gene regulation, especially during development, differentiation, and during the maintenance of tissue-specific functions in multicellular organisms. Predominantly, in transformed cells, PcG bodies form distinct nuclear foci, within which PcG-bound DNA is localized.

Read the full summary ↓

These structures likely represent misregulated gene expression due to the loss of normal regulatory mechanisms, yet the molecular function of these bodies in cellular homeostasis remains unknown. Using TSA-Seq (Tyramide signal amplification), we provide the first-of-a-kind comprehensive view of the genomic regions, including specific centromeric and telomeric sites that are in proximity to the PcG bodies. Further, these regions are enriched for the repressive histone marks, H3K27me3, H3K9me3 and depleted for active marks, H3K4me3 consistent with a lack of accessible chromatin. We find high density of replication origins around PcG bodies, consistent with the replication factor, ORCA/LRWD1 localizing at these sites. ORCA interacts with the PRC complex, stabilizes the H3K27 methyltransferase, and facilitates the deposition of this histone mark at specific chromatin sites. Loss of ORCA impacts the chromatin organization around the PcG bodies, leading to decompaction of the repeat regions, and enhanced initiation from replication origins. Our results indicate that ORCA interacts with the PcG complex-bound chromatin and maintains a repressed heterochromatin environment to control the timing of replication origin firing.

Published in

Polycomb-mediated 3D-genome organization controls replication timing

Chetlangia N, Thakur BL, Redon CE et al. · Science advances 2026 · PMID 42361181 · doi:10.1126/sciadv.adx7445

This dataset

Open GSE314620 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 GSE314620_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 PRJNA1392312 and SRA study SRP657200. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42361181) ↗

Study design

6 conditions, mostly in duplicate

U2OS_Control_BMI1 ×2 U2OS_Control_RNF2 ×2 U2OS_Control_EZH2 ×2 U2OS_SiORCA_BMI1 ×2 U2OS_SiORCA_RNF2 ×2 U2OS_SiORCA_EZH2 ×2 U2OS_Control_IgG ×1 U2OS_siORCA_IgG ×1

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 14 sample titles; they account for 12 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

GSM9406906 U2OS_Control_BMI1_replicate1 U2OS_Control_BMI1
GSM9406907 U2OS_Control_BMI1_replicate2 U2OS_Control_BMI1
GSM9406908 U2OS_Control_RNF2_replicate1 U2OS_Control_RNF2
GSM9406909 U2OS_Control_RNF2_replicate2 U2OS_Control_RNF2
GSM9406910 U2OS_Control_EZH2_replicate1 U2OS_Control_EZH2
GSM9406911 U2OS_Control_EZH2_replicate2 U2OS_Control_EZH2
GSM9406912 U2OS_SiORCA_BMI1_replicate1 U2OS_SiORCA_BMI1
GSM9406913 U2OS_SiORCA_BMI1_replicate2 U2OS_SiORCA_BMI1
GSM9406914 U2OS_SiORCA_RNF2_replicate1 U2OS_SiORCA_RNF2
GSM9406915 U2OS_SiORCA_RNF2_replicate2 U2OS_SiORCA_RNF2
GSM9406916 U2OS_SiORCA_EZH2_replicate1 U2OS_SiORCA_EZH2
GSM9406917 U2OS_SiORCA_EZH2_replicate2 U2OS_SiORCA_EZH2
GSM9406918 U2OS_Control_IgG
GSM9406919 U2OS_siORCA_IgG

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GSE215323 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_BPK25_ChIP_Seq] 53 samples shares architecture
GSE278192 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T ChIP-seq] 45 samples shares architecture

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