Genome-wide mapping of histone H3 lysine 9 dimethylation in normal myeloid cells and acute myeloid leukemia

Histone H3 lysine 9 (H3K9) is a target for posttranslational histone methylation associated with gene repression. Most of H3K9me2 modification in mammalian cells is mediated by histone methyltransferase G9a that is essential for mouse embryo development and plays an oncogenic role in acute myeloid leukemia (AML), a highly malignant blood cancer. In this study, ChIP-sequencing was used to conduct a detailed whole-genomic characterization of the localization and expression of H3K9me2 and to identify epigenetic changes associated with normal myeloid differentiation and AML. Genome-wide computational analysis using hidden Markov model was employed to map multiple associations of chromatin modification topographies with transcription in leukemia and define chromosomal domains undergoing epigenetic changes in AML Overall design: ChIP-Seq with antibodies against H3K9me2 was used with normal human granulocytes (2 samples), CD34+ hematopoietic progenitors (2 samples), K562 cells (2 intact samples and 2 samples treated with G9a inhibitor UNC0638), and primary myeloblasts from 8 different acute myeloid leukemia samples. Each H3K9me2 ChIP-seq was repeated twice. In addition, control experiments for antibody specificity were conducted with ChIP input DNA (16 samples), and ChIP-seq with antibodies against histone H3K9me3 (4 samples), histone H3K4me2 (1 sample), and nonmodified histone H3 C-tail (2 samples).