Revealing epigenetic processes in Populus by looking at Chromatin accessibility with ATAC-seq

Stress induces changes in gene expression by altering chromatin accessibility. The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a widely used method to survey genomic patterns of chromatin accessibility. Previous ATAC-seq research in Populus has focused on leaf tissue and single time points. However, changes in chromatin accessibility of Populus wood tissue under gravitropism stress have not been investigated. This investigation aims to (1) identify accessible regions of chromatin in developing xylem in different wood types of Populus alba x Populus tremula INRA 717 IB4 trees, (2) Identify temporal changes in chromatin accessibility between wood types using a time-series experiment, (3) Identify how chromatin accessibility is associated with gene expression clusters from a previous RNA-seq gravi-stimulation experiment by Zinkgraf et al., 2018. A time-series experiment was conducted and compared accessible regions of chromatin between time points (0,24,48, and 96hr) and across wood types. This investigation concluded that accessible chromatin in developing xylem was predominately observed in regions proximal to the transcription start site (TSS) across all treatments. Additionally, differentially accessible regions (DAR) peaks showed temporal changes observed throughout all 19 chromosomes and were identified around pivotal genes. These include the MYB transcription factor, and starch biosynthesis genes that were previously implicated in tension wood development. Finally, DAR peaks associated with mRNA expression clusters suggesting that changes in accessibility are important for differential gene expression previously observed in a gravi-stimulation time series experiment in Populus by Zinkgraf et al., 2018.