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The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation

GSE271983 Mus musculus (mouse) RNA-seq (gene expression) 35 samples Submitted 2025/02/28 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 35 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
35 samples: 10 × Double-LOF-embryo vs 9 × Dux-LOF-embryo vs 9 × Ctrl-embryo vs 7 × Srf-LOF-embryoGroups 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 transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activationGenes & development · 2025
Summary (written by the submitters)
The regulatory circuitry of cell-specific transcriptional programmes is thought to be influenced by transposable elements (TEs) whereby TEs serve as raw material for the diversification and genome-wide distribution of genetic elements that contain cis-regulatory elements. However, the transcriptional activators of TEs in relevant physiological contexts are largely unknown.
Read the full summary ↓
Here, we undertook an evolutionary approach to identify regulators of two main families of MERVL, a major regulator of transcription during early mouse development. Using a combination of phyloregulatory, transcriptomics and loss-of-function approaches we demonstrate that SRF is a novel regulator of MERVL and of embryonic transcription during zygotic genome activation. By resolving the phylogenetic history of two major MERVL families, we delineate the evolutionary acquisition of SRF and DUX binding sites and show that the acquisition of the SRF site precedes that of DUX. SRF contributes to embryonic transcription through the regulation of MERVLs, which in turn serves as promoter for host genes. Our work identifies new transcriptional regulators and TEs that shape the gene expression programmes in early embryos and highlights the process of TE domestication via the sequential acquisition of transcription factor binding sites and co- evolution with the host.
Published in
The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation
Hermant C, Mourra-Díaz CM, Oomen ME et al. · Genes & development 2025 · PMID 40015990 · doi:10.1101/gad.352270.124
This dataset
Open GSE271983 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 GSE271983_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 PRJNA1134243 and SRA study SRP519184. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40015990) ↗
Study design
10 × Double-LOF-embryo vs 9 × Dux-LOF-embryo vs 9 × Ctrl-embryo vs 7 × Srf-LOF-embryo

Supports a between-group comparison across 35 samples.

How we read this: 4 replicated groups read from 35 sample titles; they account for 35 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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