ChIP-seq of histone marks 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 histone modifications (H3K27ac, H3K27me3, H3K4me3 and H3K9me3) in the absence of H3K9me3-dependent heterochromatin by performing ChIP-seq in primary immune cells deficient in both Suv39h1 and Suv39h2 (Suv39DKO), the major mammalian histone methyltransferase enzymes which catalyse heterochromatic H3K9me3 deposition. Overall design: CD4+CD8+ double positive mouse thymocyte cells were flow-sorted (Ly5.2+CD19-CD4+CD8+) and analysed. H3K27ac, H3K27me3, H3K4me3 and H3K9me3 ChIP-seq libraries from Suv39h1+/y Suv39h2+/- (control) mice were prepared and sequenced along with an IgG and whole-cell extract (input) library. H3K27ac, H3K27me3 and H3K4me3 ChIP-seq libraries from Suv39h1-/y Suv39h2-/- double knock-out (Suv39DKO) mice were prepared and sequenced along with an IgG and whole-cell extract (input) library. For the bioinformatics analysis, the reads were aligned to mm10 and duplicates were removed.