H3K9me3 ChIP-seq in MLL-rearranged leukemic stem cells and hematopoietic stem cells

Acute myeloid leukemia (AML) with rearrangement of the mixed-lineage leukemia (MLL) gene are the most aggressive hematopoietic malignancies. Previous studies demonstrated the distribution of several epigenetic modifications including H3K9me3, H3K79me2, H3K36me3, H3K4me3 and H3K27me3, in MLL-AF9 transformed murine cells. Here, we examined the H3K9me3 distribution in c-Kit+ cells (enriched with stem/progenitor cells) from both MLL-AF9 transformed murine cells in parallel with control wild-type cells, and found an overall lower distribution of H3K9me3 in leukemia stem cells than normal hematopoietic stem/progenitor cells. c-Kit+ cells were isolated with CD117 beads from bone marrow of wild-type and moribund leukemic mice (MLL-AF9 and MLL-NRIP3 fusion transformed murine c-Kit+ cells). c-Kit+ cells were then cross-linked, sonicated and incubated with H3K9me3 antibody. ChIPed DNA were purified with classic phenol chloroform extraction protocol. H3K9m3 ChIPed DNA profiles of these c-Kit+ cells were generated by DNA sequencing using Illumina Hiseq2500.