GSE116972
Chromatin changes in lateral organ founder cells of Arabidopsis thaliana detected by assay for transposase-accessible chromatin sequencing (ATAC-seq)
Two methods Fluorescence Activated Cell Sorting (FACS) and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) are combined to analyse the chromatin accessibility of Lateral Organ Founder Cells (LOFCs) in the peripheral zone of the apetala1 cauliflower double mutant Arabidopsis inflorescence meristem. Genome-wide we observed a striking correlation between Transposase Hypersensitive Sites (THS) detected in ATAC-seq and DNase I Hypersensitive Sites (DHS), covering mostly extended regions substructured into several individual THS that correspond to phylogenetically conserved sequence, enhancer elements and binding sites of MADS-box transcription factors. Relative to available RNA-seq data, chromatin configuration changes according to gene activation or repression, i.e. at cellular resolution chromatin regions gain or lose Tn5 transposase accessibility in direct correlation with gene expression levels. A pronounced THS priority immediately upstream of the transcription start and reduced numbers of THSs in the transcription unit are complementary to established H3K4me3 activation or H3K27me3 repressive marks. At this resolution, the FACS/ATAC-seq combination should be widely applicable to detect chromatin changes in course of cell type specification and facilitate the detection of regulatory promoter elements in plant promoters. Overall design: Examination of chromatin accessibility via ATAC-seq in Lateral organ founder cells and non founder cell neighbours. Three biological replicates were performed for each cell type. Two control samples of sheared DNA from the same tissue were sequenced.