GEO series

A functional overlap between actively transcribed genes and insulator elements [ATAC-seq]

GSE313787 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 15 samples Submitted 2026/01/31 Platform GPL19057

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 15 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: Mus musculus (mouse)
Samples: 15 samples
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: A functional overlap between actively transcribed genes and chromatin insulator elementsThe EMBO journal · 2026

Summary (written by the submitters)

Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation.

Read the full summary ↓

This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Insertion of actively transcribed fragments of the α-globin gene between the enhancers and native genes leads to a reduction in native α-globin expression and accumilation of cohesin at the insertion site. Together, these observations provide direct evidence that actively transcribed genes can behave as insulator elements.

Published in

A functional overlap between actively transcribed genes and chromatin insulator elements

Cornell LJ, Harrold CL, Holliman S et al. · The EMBO journal 2026 · PMID 41840057 · doi:10.1038/s44318-026-00730-2

This dataset

Open GSE313787 in finder → Find more mouse 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 GSE313787_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 PRJNA1381593 and SRA study SRP655277. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41840057) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 15 more — browse all 15 samples with per-sample file links →

Datasets on a similar topic

GSE313788 A functional overlap between actively transcribed genes and insulator elements [ChIP-seq] 8 samples shares transcribed, insulator, actively, elements, overlap
GSE313947 A functional overlap between actively transcribed genes and insulator elements 68 samples shares transcribed, insulator, actively, elements, overlap
GSE313785 A functional overlap between actively transcribed genes and insulator elements [RNA-seq] 28 samples shares transcribed, insulator, actively, elements, overlap
GSE256229 Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq [Mouse KAS-seq] 26 samples shares elements, atac-seq
GSE256231 Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq [Mouse KAS-ATAC-seq] 24 samples shares elements, atac-seq
GSE256311 Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements [ATAC-seq] 8 samples shares elements, atac-seq
GSE279024 cGAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation [ATAC-seq] 8 samples shares elements, atac-seq
GSE246040 Guanine- and cytosine-rich genes are actively transcribed at the nuclear Lmnb1 compartment 6 samples shares transcribed, actively

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.