DOT1L limits RNAPII promoter-proximal pause release thus enabling Activation Induced Deaminase activity genome-wide

Abstract Activation induced deaminase (AID) initiates class switch recombination (CSR) and somatic hypermutation of the antibody genes but also mutates “off-target” genes, with oncogenic consequences. Understanding the mechanisms that render such loci susceptible to AID is therefore necessary. We identify the H3K79 histone methyltransferase DOT1L as a nuclear AID-proximal factor required for CSR and AID off-target activity, including IgH-cMyc translocations. Mechanistically, DOT1L limits promoter-proximal transcriptional pause release. DOT1L inactivation reduced promoter-proximal paused RNA polymerase II (RNAPII) occupancy, while concomitantly increasing RNAPII Serine 2 phosphorylation and reducing cohesin at gene bodies. These changes were proportional to the amount of H3K79me3 lost and perturbed transcription elongation, as evidenced by downregulation of highly expressed long genes but upregulation of shorter primed genes. Thus, DOT1L restricting promoter-proximal pause release can explain the hitherto puzzling predominance of gene upregulation in DOT1L-deficient mammalian cells and establishes regulated pause release as a critical step for AID activity.