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MRNA-seq time course (in parallel to ATAC-seq time course), of control or GRH-1 depleted C. elegans larvae sampled at 20oC [RNAseq_GRH1degron]

ABSTRACT: The goal of these experiments were to evaluate how dynamic changes to gene expression (mRNA-seq) and chromatin accessibility (ATAC-seq) were affected by the acute depletion of the transcription factor GRH-1. To do so, we employed a strain that incorporated an auxin-inducible degron at the endogenous grh-1 locus (Meeuse et al., 2023, EMBO J). We can thereby acutely deplete GRH-1 in growing larvae. Based on linear modeling incorporating ATAC-seq dynamics and ChIP-seq data, we hypothesized that GRH-1 depletion should affect accessibility at a specific set of chromatin regions and expression of a specific set of genes.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE288871 | GEO | 2025/09/17

REPOSITORIES: GEO

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ATAC-seq time course (in parallel to mRNA-seq time course), of control or GRH-1 depleted C. elegans larvae sampled at 20oC

Project description:The goal of these experiments were to evaluate how dynamic changes to gene expression (mRNA-seq) and chromatin accessibility (ATAC-seq) were affected by the acute depletion of the transcription factor GRH-1. To do so, we employed a strain that incorporated an auxin-inducible degron at the endogenous grh-1 locus (Meeuse et al., 2023, EMBO J). We can thereby acutely deplete GRH-1 in growing larvae. Based on linear modeling incorporating ATAC-seq dynamics and ChIP-seq data, we hypothesized that GRH-1 depletion should affect accessibility at a specific set of chromatin regions and expression of a specific set of genes.

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Project description:We collected timecourse samples for RNA-seq, in parallel to ATAC-seq, in order to have matching samples for comparisson. The overall goal was to link oscillating gene expression (RNA-seq) to oscillating changes in chromatin accessibility (ATAC-seq), in order to identify enhancer elements that are critical to oscillatory regulation.

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GRH-inducible genes in rice plants

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The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [ATAC-seq]

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