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Inducible fusion with the CHASERR long noncoding RNA transcript upregulates haploinsufficient CHD2 expression

GSE298095 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 141 samples Submitted 2026/05/10 Platform GPL34328Platform GPL34281
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 141 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
141 samples: 39 conditions, mostly with about 4 replicates eachGroups 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.
Summary (written by the submitters)
Long noncoding RNAs are now realized to function in various biological processes via multiple, and as of yet not fully understood, modes of action. CHASERR is a long noncoding RNA conserved throughout vertebrates, located immediately upstream of the promoter of the CHD2 gene. CHD2 haploinsufficiency leads to a neurodevelopmental disorder that includes epilepsy and intellectual disability.
Read the full summary ↓
Homozygous loss of CHASERR promoter leads to embryonic lethality in mice, and heterozygous deletions lead to pleiotropic phenotypes in mice and a recently characterized syndromic human developmental disorder. Short highly conserved sequence motifs are present in the last exon of CHASERR and blocking them with antisense oligonucleotides (ASOs) up-regulates CHD2 expression. Here, we decipher the mechanism of action of these ASOs and show that they stimulate the formation of a fusion transcript connecting the first four exons of CHASERR with exons 2–39 of CHD2. These fusion transcripts are exported to the cytoplasm and translated to produce full-length CHD2 proteins. They are expressed endogenously, albeit at low levels, and are induced in activated neurons. Deletion of these conserved regions in mice mimics the effects of the ASO, leading to increased CHD2 levels, altered chromatin accessibility and altered neuronal responses. Perinatal introduction of the ASO into the brains of Chd2+/– mice up-regulates CHD2 expression and alleviates behavioral phenotypes caused by CHD2 haploinsufficiency, providing a therapeutic route to CHD2 haploinsufficiency. The concept of targeting upstream genes with ASOs to induce transcript fusion can be extended to other gene pairs.
This dataset
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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 GSE298095_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 PRJNA1268348 and SRA study SRP588120. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
39 conditions, mostly with about 4 replicates each
ATAC-seq in MCR_S/MCR_S primary cortical neur… ×5 RNA-seq in MCR_S/MCR_S primary cortical neuro… ×5 RNA-seq in MCR_S/MCR_S primary cortical neuro… ×5 RNA-seq in MCR_S/MCR_S primary cortical neuro… ×5 RNA-seq in MCR_S/MCR_S primary cortical neuro… ×5 RNA-seq in MCR_S/MCR_S primary cortical neuro… ×5 ATAC-seq in MCR_S/MCR_S primary cortical neur… ×4 ATAC-seq in MCR_S/MCR_S primary cortical neur… ×4 +41 more

Supports a case/control comparison: 16 samples read as cases, 16 as controls.

How we read this: 39 replicated groups read from 141 sample titles; they account for 131 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

+ 101 more — browse all 141 samples with per-sample file links →

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