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

GSE313785 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2026/01/31 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 28 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
Mus musculus (mouse)
Samples
28 samples: 8 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
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 GSE313785 in finder → Find more mouse 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 GSE313785_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 PRJNA1381596 and SRA study SRP655273. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41840057) ↗
Study design
8 conditions, mostly in triplicate
RNA_WT_aYFP_PolyAMinus ×5 RNA_WT_aYFP_PolyAPlus ×5 RNA_Ins_aGonly_PolyAMinus ×3 RNA_Ins_aGonly_PolyAPlus ×3 RNA_Ins_aPonly_PolyAMinus ×3 RNA_Ins_aPonly_PolyAPlus ×3 RNA_Ins_aPandG_PolyAMinus ×3 RNA_Ins_aPandG_PolyAPlus ×3

Supports a between-group comparison across 28 samples.

How we read this: 8 replicated groups read from 28 sample titles; they account for 28 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
Datasets on a similar topic

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