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]
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. Overall design: mRNA-seq of RNA isolated from larval C. elegans (HW2434 strain - grh-1::degron::3xFLAG), treated with either EtOH or 250 uM Auxin, and collected in a time course spanning 12-13 hours of development. Synchronized L1 animals were grown at a density of 1 animal/uL in liquid culture (S-Basal + OP50 at OD600=2.8) for 20-21 hours before splitting the culture to treat half the animals with EtOH, and the other half with 250 uM Auxin. Every hour following treatment, 2000-5000 animals were collected for RNA prep. RNA was isolated with Trizol and the Direct-zol RNA microprep kit (R2062, Zymo Research) including DNase treatment. Libraries were prepared according to the Illumina Stranded mRNA-seq protocol. Library was sequenced using NovaSeq SP 2x56bp Paired-end reads.