MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation

Survival rates for children and adults carrying mutations in the Mixed Lineage Leukemia (MLL) gene continue to have a very poor prognosis. The most common MLL mutation in ALL is the t(4;11)(q21;q23) chromosome translocation that fuses MLL in frame with the AF4 gene producing MLL-AF4 and AF4-MLL fusion proteins. Previously, we demonstrated that MLL-AF4 binds to the BCL-2 gene and directly activates it through DOT1L recruitment and increased H3K79me2/3 levels. Here, we perform a detailed analysis of MLL-AF4 regulation of the entire BCL-2 family. By measuring nascent RNA production in MLL-AF4 knockdowns, we find that of all the BCL-2 family genes, MLL-AF4 directly controls the active transcription of both BCL-2 and MCL-1, and also represses BIM via binding of the polycomb group repressor 1 (PRC1) complex component CBX8. We further analyze MLL-AF4 activation of the BCL-2 gene using Capture C and identify a BCL-2 specific enhancer, consisting of two clusters of H3K27Ac at the 3’end of the gene. Loss of MLL-AF4 activity results in a reduction of H3K79me3 levels in the gene body and H3K27Ac levels at the 3’ BCL-2 enhancer, revealing a novel regulatory link between these two histone marks and MLL-AF4 mediated activation of BCL-2.