The present invention relates to MLL fusion proteins (e.g., AF9 and ENL), which activate target genes in part via recruitment of histone methyltransferase DOT1L. In particular, the present invention provides the AF9/ENL binding site in DOT1L and agents that block the protein-protein interactions between AF9/ENL and DOT1L, therefore inhibiting the activity of DOT1L, and inhibiting MLL-fusion protein associated leukemia.