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Autism-associated mutations in Kdm6b affect its role as a chromatin regulator in brain development

GSE267688 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2025/05/14 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 5 × CGNs, Control vs 5 × CGNs, shKDM6B vs 5 × CGNs, shKDM6B Cat Rescue vs 5 × CGNs, shKDM6B dCat RescueGroups 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)
The regulation of gene expression in the developing brain is coordinated by changes in chromatin regulation. Chromatin regulation involves the deposition and removal of molecular modifications on the histone proteins that give structure to and control the function of genomic DNA. The trimethylation of histone H3 at lysine 27 (H3K27me3) is a chromatin mark that recruits transcriptional repressors, silencing gene transcription.
Read the full summary ↓
The JmjC family lysine demethylase KDM6B has been identified as an enzyme that removes H3K27me3, allowing for expression of genes critical for brain development. Genetic variants in human KDM6B have been found to be associated with intellectual disability and autism spectrum disorder (ASD); however, the molecular mechanisms by which these genetic variants affect KDM6B function remain unknown. We mapped these variants into the structure of KDM6B, and computationally assessed their likely effects on KDM6B protein function. To experimentally determine how ASD-associated sequence variants in KDM6B affect the function of this protein in cells, we generated ASD-associated mutations into a KDM6B expression construct and assessed their effects on the enzymatic function of this protein as well as its stability and nuclear localization. We found that several ASD-associated mutations occur in the H3K27me3 binding pocket of KDM6B and impair the ability of this enzyme to demethylate histones. In parallel, through RNA sequencing experiments in cerebellar granule neurons from mouse, we found that expression of the enzymatically active form but not the enzymatically dead form of KDM6B was sufficient to rescue synaptic gene expression following knockdown of endogenous KDM6B. Together, these findings elucidate a novel role of KDM6B in controlling gene expression in maturing neurons, and they expand our knowledge on how chromatin dysregulation can lead to neurodevelopmental disorders like ASD.
This dataset
Open GSE267688 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 GSE267688_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 PRJNA1112409 and SRA study SRP508193. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × CGNs, Control vs 5 × CGNs, shKDM6B vs 5 × CGNs, shKDM6B Cat Rescue vs 5 × CGNs, shKDM6B dCat Rescue

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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
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