GEO series

PRMT1-methylated MSX1 phase separates to control palate development

GSE285740 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/01/07 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 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: Homo sapiens (human)
Samples: 12 samples: 3 × HEPM, MSX1, 6h, vs 3 × HEPM, R157F, 6h, vs 3 × HEPM, R157S, 6h, vs 3 × HEPM, R157K, 6h,Groups 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: PRMT1-methylated MSX1 phase separates to control palate developmentNature communications · 2025

Summary (written by the submitters)

Little is known about the regulation and function of liquid‒liquid phase separation (LLPS) in craniofacial developmental disorders, where Msh homeobox 1 (MSX1) and protein arginine methyltransferase 1 (PRMT1) are two important regulators. MSX1 mutations are associated with human cleft palate, the most common craniofacial birth defect.

Read the full summary ↓

Here, we show that MSX1 LLPS, regulated by PRMT1-catalyzed methylation, is a vertebrate-conserved mechanism underlying the proliferation of embryonic palatal mesenchymal cells (EPMs) and palatal fusion. MSX1 LLPS is triggered by its N-terminal intrinsically disordered protein region (IDR) and regulated by PRMT1-catalyzed methylation, specifically asymmetric dimethylation of arginine (R). Biochemically, PRMT1 methylates MSX1 by dimethylating the residues R150 and R157 in the MSX1 IDR. Physiochemically, the R157 to serine (R157S) mutant, R150S mutant, and hypomethylated MSX1 under PRMT1 deficiency consistently cause abnormal MSX1 LLPS to form less dynamic gel-like condensates. PRMT1 and its methylation target R residues in MSX1 are conserved in vertebrates, from zebrafish to humans. Phenotypically, less dynamic gel-like condensates formed by abnormal MSX1 LLPS cause EPM proliferation defects and cleft palate.In this study, rna-seq was used to reveal the differences between the effects of Msx1 and its mutants on hepm cells. Our findings provide a new paradigm for further exploration of LLPS underlying genetic disorders for future innovation of genetic disorder treatment by direct modulation of LLPS.

Published in

PRMT1-methylated MSX1 phase separates to control palate development

Meng L, Jiang Y, You J et al. · Nature communications 2025 · PMID 39843447 · doi:10.1038/s41467-025-56327-6

This dataset

Open GSE285740 in finder → Find more human 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 GSE285740_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 PRJNA1205740 and SRA study SRP554987. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39843447) ↗

Study design

3 × HEPM, MSX1, 6h, vs 3 × HEPM, R157F, 6h, vs 3 × HEPM, R157S, 6h, vs 3 × HEPM, R157K, 6h,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8707953 HEPM, MSX1, 6h, rep1 HEPM, MSX1, 6h,
GSM8707954 HEPM, MSX1, 6h, rep2 HEPM, MSX1, 6h,
GSM8707955 HEPM, MSX1, 6h, rep3 HEPM, MSX1, 6h,
GSM8707956 HEPM, R157F, 6h, rep2 HEPM, R157F, 6h,
GSM8707957 HEPM, R157F, 6h, rep1 HEPM, R157F, 6h,
GSM8707958 HEPM, R157F, 6h, rep3 HEPM, R157F, 6h,
GSM8707959 HEPM, R157S, 6h, rep2 HEPM, R157S, 6h,
GSM8707960 HEPM, R157S, 6h, rep3 HEPM, R157S, 6h,
GSM8707961 HEPM, R157S, 6h, rep1 HEPM, R157S, 6h,
GSM8707962 HEPM, R157K, 6h, rep1 HEPM, R157K, 6h,
GSM8707963 HEPM, R157K, 6h, rep2 HEPM, R157K, 6h,
GSM8707964 HEPM, R157K, 6h, rep3 HEPM, R157K, 6h,

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