GEO series

Altering metabolism to program cell identity via NAD+ dependent deacetylation [ATAC-seq]

GSE173542 Mus musculus Genome binding/occupancy profiling by high throughput sequencing 8 samples Submitted 2025/04/01 Platform GPL19057

Summary

Cells change their metabolic profiles in response to an underling gene regulatory network, but how can alterations in metabolism encode specific transcriptional instructions? Here we show that forcing metabolic change in embryonic stem cells (ESCs) promotes a developmental identity that better approximates the inner cell mass (ICM) of the mammalian blastocyst in cultures we refer to as enhanced metabolic ESCs (EMESCs). The creation of EMESCs depends on the inhibition of glycolysis and stimulation of oxidative phosphorylation (OXPHOS), that in turns activates NAD+-dependent deacetlylases of the Sirtuin family. The activation of this pathway leads to the deacetylation of histones and key transcription factors leading to a revised ICM-like gene regulatory network. The exploitation of the NAD+/NADH coenzyme normally coupled to elevated OXPHOS to program lineage specific transcription suggests new paradigms for how cells respond to alterations in their environment.

Published in

Altering metabolism programs cell identity via NAD(+)-dependent deacetylation

Bone RA, Lowndes MP, Raineri S et al. · The EMBO journal 2025 · PMID 40281356 · doi:10.1038/s44318-025-00417-0

This dataset

Open GSE173542 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →

Download

Direct links to NCBI, no account and no request form: the whole study as GSE173542_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 8 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA726044 and SRA study SRP316856. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40281356) ↗

Samples in this study

The sample list for this study is not cached yet. Press Sort into groups and it will be fetched from NCBI.

+ 8 more — browse all 8 samples with per-sample file links →

Similar datasets

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.