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Series GSE280488 Query DataSets for GSE280488
Status Public on Nov 22, 2024
Title A histone hyperacetylation pulse induces cellular memory of gene expression and 3-dimensional genome folding [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Epigenetic memory enables the stable propagation of gene expression patterns in response to transient developmental and environmental stimuli. Although 3-dimensional (3D) organisation is emerging as a key regulator of genome function due its role in gene expression control, it is unknown whether it contributes to cellular memory. Here, we establish that acute perturbation of the epigenome can induce cellular memory of gene expression in mouse embryonic stem cells (mESCs). Specifically, we uncover how a pulse of histone deacetylase inhibition translates to changes in the histone acetylation and methylation landscape, as well as global and local genome folding. While most epigenomic and transcriptional changes are readily reversible once the perturbation is removed, architectural features are not fully reestablished. Upon a second transient pulse of hyperacetylation, hundreds of genes maintain their dysregulated state. Using ultra-deep Micro-C, we associate memory of gene expression with enhancer-promoter contacts and repressive chromatin topology mediated by Polycomb. These results uncover the complex interplay between different epigenetic regulatory layers and establish a novel link between genome folding and cellular memory.
 
Overall design Micro-C experiments in mouse ESCs in control (DMSO), TSA-treated or 24-hour recovery (REC) conditions.
Web link https://doi.org/10.1101/2024.11.21.624660
 
Contributor(s) Paldi F, Szalay M, Di Stefano M, Cavalli G
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BioProject PRJNA1117356
Submission date Oct 28, 2024
Last update date Nov 26, 2024
Contact name Marco Di Stefano
E-mail(s) [email protected]
Organization name Institut de Génétique Humaine - CNRS / University of Edinburgh
Lab Giacomo Cavalli lab
Street address 141 rue de la Cardonille
City Montpellier
ZIP/Postal code 34396
Country France
 
Platforms (1)
GPL28457 DNBSEQ-G400 (Mus musculus)
Samples (33)
GSM8599173 RNA-seq mESC DMSO control expt1 r1
GSM8599174 RNA-seq mESC DMSO control expt1 r2
GSM8599175 RNA-seq mESC DMSO control expt1 r3
This SubSeries is part of SuperSeries:
GSE281151 Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding

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Supplementary file Size Download File type/resource
GSE280488_RAW.tar 75.8 Mb (http)(custom) TAR (of TSV)
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Raw data are available in SRA

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