DNA secondary structures in <i>BCL2</i> and <i>MYC</i> elicit activation-induced cytidine deaminase binding and activity

Activation-induced cytidine deaminase (AID) diversifies the immunoglobulin repertoire by targeting cytosines in specific hotspots. While AID is tightly regulated and largely confined to immunoglobulin loci, its activity at nonimmunoglobulin sites is linked to oncogenic mutagenesis. Mechanisms underlying AID targeting are not completely understood, though recent evidence indicates G4 structures are preferred AID substrates. Here, we use well-characterized structure-forming sequences from the BCL2 and MYC promoters, proposed AID off-targets in lymphoma, to investigate AID recognition of oncogene-associated secondary structures. Our work shows AID binds and deaminates G4s from both oncogenes. AID deaminates two specific cytosines in the BCL2 G4, each three nucleotides from a G-tetrad confirming previous position-dependent AID activity. Oligo-seq reveals distinct sequence contexts required for efficient deamination of these cytosines. In assessing the complementary DNA to the G4, we identify the i-Motif as a novel determinant of AID interaction. Using AID paralogs A3C, A3A, and A2, our findings highlight that DNA secondary structures differentially influence APOBEC deaminase binding and activity. Furthermore, mutation of AID residue glutamine 135 to its A3C cognate alanine disrupts both binding and deamination. This study establishes AID interacts with nonimmunoglobulin DNA structures implicating these promoter elements in AID recruitment to off-target sites in oncogenes.