ATAC-seq of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice

H3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes for healthy cellular function. Within all eukaryotic nuclei, heterochromatin and euchromatin are spatially segregated, with euchromatin typically located in the nuclear interior and heterochromatin at the nuclear periphery. Here we investigate the changes in DNA accessibilty in the absence of H3K9me3-dependent heterochromatin by performing ATAC-seq in primary immune cells deficient in both Suv39h1 and Suv39h2 (Suv39DKO), the major mammalian histone methyltransferase enzymes which catalyse heterochromatic H3K9me3 deposition. CD4+CD8+ double positive mouse thymocyte cells were flow-sorted (Ly5.2+CD19-CD4+CD8+) and analysed. ATAC-seq libraries from two replicates from Suv39h1+/y Suv39h2+/- (control) mice and two replicates from Suv39h1-/y Suv39h2-/- double knock-out (Suv39DKO) mice were independently prepared and sequenced . For the bioinformatics analysis, fastq files were aligned, filtered and then biological replicates were merged.