Dynamic of H3K4me3-broad domains uncover an epigenetic switch between cell identity and cancer-related genes

Broad domains of H3K4 methylation have been associated with tissue specific, cell identity and tumor suppressor genes. Here, we identified broad H3K4me3 domains (BH4D)-associated genes in human thymic T cell populations and a collection of T-Acute Lymphoblastic Leukemia (T-ALL) primary samples and cell lines. We found that BH4D are highly dynamic throughout T cell differentiation, flag key leukemia associated oncogenes and distinguish between normal and neoplastic cells. Leukemic cells loss broad domains at T cell identity genes and gain broad domains at cancer-related genes. Moreover, the expression of genes, both coding and non-coding, associated with BH4D is frequently deregulated in T-ALL. Using an ex-vivo model we demonstrated that the ectopic expression of TLX3 oncogenic factor preferentially impact on the expression of BH4D-associated genes in T cell leukemia. Finally, an H3K4me3 demethylase inhibitor differentially targets T-ALL cell lines depending on the extend of the broad domains. Our results show that regulation of BH4D-associated genes is critical for leukemogenesis and suggest that association with BH4D might be used as epigenetic prioritization of cancer-relevant genes, including long non-coding RNAs Overall design: ChIP-seq of H3K4me3 from human T acute lymphoblastic blasts and cell lines