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The Sotos syndrome gene Nsd1 safeguards bivalent developmental enhancers in poised states through restraining excessive H3K27me3 deposition [RNA-Seq]

GSE271862 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/02/25 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 samples: 9 conditions, mostly in duplicateGroups 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
The sotos syndrome gene Nsd1 safeguards developmental gene enhancers poised for transcription by maintaining the precise deposition of histone methylationThe Journal of biological chemistry · 2025
Summary (written by the submitters)
Germline haploinsufficiency of Nsd1 is implicated as the etiology of Sotos syndrome, a developmental genetic disorder manifesting skeletal overgrowth and intellectual disability. However, the underlying molecular mechanisms remain largely elusive to date. Here we employed mouse embryonic stem (ES) cell in vitro differentiation as a developmental model system to tackle this question.
Read the full summary ↓
We found that Nsd1 is indispensable for faithful differentiation of mouse ES cells into three primary germ layers, particularly the meso-endoderm lineages such as heart, vascular, and skeletal systems. Time-series gene expression profiling revealed that Nsd1 facilitates not only the basal expression but also differentiation-accompanied rapid induction of certain key meso-endoderm linage-specifying transcription factor genes such as T and Gata4. Mechanistically, Nsd1 directly binds to putative distal bivalent enhancers of these genes under ES state, where it antagonizes excessive H3K27me3 through depositing H3K36me2 and conversely maintains the active H3K27ac mark, thereby safeguarding these enhancers at poised or primed states that are highly responsive to developmental cues. In agreement, rescue assays showed that Nsd1-catalyzed H3K36me2 depends on intact PHD1-4, PWWP2, and SET domains to a similar degree, disruption of either one severely abolished Nsd1’s ability to revert the defective differentiation phenotype. Additionally, Nsd1 is likely continuously required to sustain the activation of certain developmental genes, as it continues to reside at these genes after differentiation induction, albeit recruited by a different set of transcription factors. Altogether, our results provide novel molecular insights into how Nsd1 perturbations derail the normal developmental pathways and cause human disease.
Published in
The sotos syndrome gene Nsd1 safeguards developmental gene enhancers poised for transcription by maintaining the precise deposition of histone methylation
Li J, Li Z, Yin J et al. · The Journal of biological chemistry 2025 · PMID 40118455 · doi:10.1016/j.jbc.2025.108423
This dataset
Open GSE271862 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 GSE271862_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 PRJNA1133766 and SRA study SRP518900. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40118455) ↗
Study design
9 conditions, mostly in duplicate
mESC, WT, day 0, biol ×2 mESC, Nsd1-KO-1, day 0, biol ×2 mESC, Nsd1-KO-2, day 0, biol ×2 mESC, WT, day 2, biol ×2 mESC, Nsd1-KO-1, day 2, biol ×2 mESC, Nsd1-KO-2, day 2, biol ×2 mESC, WT, day 4, biol ×2 mESC, Nsd1-KO-1, day 4, biol ×2 +1 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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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