GEO series

CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [CUT&RUN, CUT&Tag and RNA-seq]

GSE268622 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2024/11/08 Platform GPL30882

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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: 24 samples: 6 conditions, mostly in triplicateGroups 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: CTCF/RAD21 organize the ground state of chromatin-nuclear speckle associationNature structural & molecular biology · 2025

Summary (written by the submitters)

The interchromatin space in the cell nucleus contains various membrane-less nuclear bodies. Recent findings indicate that nuclear speckles, comprising a distinct nuclear body, exhibit interactions with certain chromatin regions in a ground state. Key questions are how this ground state of chromatin-nuclear speckle association is established and what are the gene regulatory roles of this layer of nuclear organization.

Read the full summary ↓

We report here that chromatin structural factors CTCF and cohesin are required for full ground state association between DNA and nuclear speckles. Disruption of ground state DNA-speckle contacts via either CTCF depletion or cohesin depletion had minor effects on basal level expression of speckle-associated genes, however we show strong negative effects on stimulus-dependent induction of speckle-associated genes. We identified a putative speckle targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association. In contrast to reduction of CTCF or RAD21, depletion of the cohesin releasing factor WAPL stabilized cohesin on chromatin and DNA-speckle contacts, resulting in enhanced inducibility of speckle-associated genes. In addition, we observed disruption of chromatin-nuclear speckle association in patient derived cells with Cornelia de Lange syndrome (CdLS), a congenital neurodevelopmental diagnosis involving defective cohesin pathways, thus revealing nuclear speckles as an avenue for therapeutic inquiry. In summary, our findings reveal a mechanism to establish the ground organizational state of chromatin-speckle association, to promote gene inducibility, and with relevance to human disease.

Published in

CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association

Yu R, Roseman S, Siegenfeld AP et al. · Nature structural & molecular biology 2025 · PMID 39984730 · doi:10.1038/s41594-024-01465-6

This dataset

Open GSE268622 in finder → Find more human RNA-seq 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 GSE268622_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 PRJNA1117915 and SRA study SRP510683. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39984730) ↗

Study design

6 conditions, mostly in triplicate

NegHS ×3 NegRT ×3 SONHS ×3 SONRT ×3 HCT116_DMSO ×2 HCT116_halo ×2 HelaDMSO1_IGG ×1 HelaDMSO1_SON ×1 +6 more

Supports a between-group comparison across 16 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 16 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

GSM8295453 HelaDMSO1_IGG
GSM8295454 HelaDMSO1_SON
GSM8295455 HelaDMSO2_IGG
GSM8295456 HelaDMSO2_SON
GSM8295457 HelaIAA1_IGG
GSM8295458 HelaIAA1_SON
GSM8295459 HelaIAA2_IGG
GSM8295460 HelaIAA2_SON
GSM8295461 NegHS1 NegHS
GSM8295462 NegHS2 NegHS
GSM8295463 NegHS3 NegHS
GSM8295464 NegRT1 NegRT
GSM8295465 NegRT2 NegRT
GSM8295466 NegRT3 NegRT
GSM8295467 SONHS1 SONHS
GSM8295468 SONHS2 SONHS
GSM8295469 SONHS3 SONHS
GSM8295470 SONRT1 SONRT
GSM8295471 SONRT2 SONRT
GSM8295472 SONRT3 SONRT
GSM8295473 HCT116_DMSO1 HCT116_DMSO
GSM8295474 HCT116_DMSO2 HCT116_DMSO
GSM8295475 HCT116_halo1 HCT116_halo
GSM8295476 HCT116_halo2 HCT116_halo

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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.