To understand the basis of the alteration in mitochondrial gene expression in BCR-ABL/MSI2-HOXA9 leukemia and the concomitant increase in energy production, we tested whether MSI2-HOXA9 impacted mitochondrial gene expression directly in the mitochondria or indirectly through control of the polymerase and/or transcription factors. Here, HOXA9 is linked to leukemia.