RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout 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. We investigated the effects of loss of H3K9me3-dependent heterochromatin 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 thymocyte cells from control and Suv39h1/Suv39h2 double knockout mice were analysed by RNA-seq, LaminB1 ChIP-seq and in situ Hi-C. Three biological replicates were undertaken for RNA-seq and two biological replicates for LaminB1 ChIP-seq and Hi-C.