GEO series

CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [hela rad21-aid RNA-seq]

GSE273618 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/11/08 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 12 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 12 samples: 3 × RAD21wt_NT vs 3 × RAD21wt_hs vs 3 × 15D_NT vs 3 × 15D_hsGroups 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 GSE273618 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 GSE273618_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1142511 and SRA study SRP523441. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39984730) ↗

Study design

3 × RAD21wt_NT vs 3 × RAD21wt_hs vs 3 × 15D_NT vs 3 × 15D_hs

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 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

GSM8433959 RAD21wt_NT1 RAD21wt_NT
GSM8433960 RAD21wt_NT2 RAD21wt_NT
GSM8433961 RAD21wt_NT3 RAD21wt_NT
GSM8433962 RAD21wt_hs1 RAD21wt_hs
GSM8433963 RAD21wt_hs2 RAD21wt_hs
GSM8433964 RAD21wt_hs3 RAD21wt_hs
GSM8433965 15D_NT1 15D_NT
GSM8433966 15D_NT2 15D_NT
GSM8433967 15D_NT3 15D_NT
GSM8433968 15D_hs1 15D_hs
GSM8433969 15D_hs2 15D_hs
GSM8433970 15D_hs3 15D_hs

Datasets on a similar topic

GSE248102 CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [RNA-Seq] 59 samples shares ctcf, chromatin-nuclear, organize, cohesin, speckle, rna-seq, ground
GSE268622 CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [CUT&RUN, CUT&Tag and RNA-seq] 24 samples shares ctcf, chromatin-nuclear, organize, cohesin, speckle, rna-seq, ground
GSE248043 CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [CUT&RUN] 40 samples shares ctcf, chromatin-nuclear, organize, cohesin, speckle, ground
GSE248103 CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association 135 samples shares ctcf, chromatin-nuclear, organize, speckle, ground
GSE217759 DNA methylation insulates exons from CTCF loops with nuclear speckles (RNA-Seq) 30 samples shares ctcf, speckle, rna-seq
GSE269856 Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program [RNA-seq] 14 samples shares ctcf, speckle, rna-seq
GSE275659 B-Type Lamins organize 3D chromatin architecture through associations with nuclear lamina and nuclear speckles [RNA-seq] 6 samples shares organize, speckle, rna-seq
GSE281733 CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis [RNA-seq] 18 samples shares ctcf, rna-seq

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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.