GEO series

Induction of a transcriptional adaptation response via perturbations at the DNA and RNA levels [dst233]

GSE255120 Mus musculus Genome binding/occupancy profiling by high throughput sequencing 6 samples Submitted 2025/03/17 Platform GPL30172

Summary

Transcriptional adaptation (TA) is a cellular process whereby mRNA-destabilizing mutations lead to the transcriptional upregulation of so-called adapting genes. The nature of the TA-triggering factor(s) remains unclear. Here, we first generated Cas9-induced mutations in mouse Actg1, including an mRNA-destabilizing allele and an RNA-less allele. We find in the Actg1 mRNA-destabilizing allele, higher levels of Actg2 mRNA as well as increased chromatin accessibility at the Actg2 locus compared with wild-type and the RNA-less allele. Notably, Cas13d experiments show that Actg1 mRNA cleavage, but not Actg1 pre-mRNA cleavage, also triggers Actg2 upregulation; however, this upregulation is not associated with increased chromatin accessibility at the Actg2 locus. Furthermore, time course experiments show that increased Actg2 expression persists even after Actg1 mRNA degradation by Cas13d ceases. Together, our data highlight the importance of cytoplasmic mRNA degradation as a trigger for the TA response and suggest that chromatin remodeling is not necessary for TA.

This dataset

Open GSE255120 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 GSE255120_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 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 PRJNA1073554 and SRA study SRP488284. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

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.

+ 6 more — browse all 6 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.