Intrinsic DNA features are determinants of activation-induced cytidine deaminase (AID) recruitment and activity

Abstract

While most cells strive to guard their genomic DNA from damage, B lymphocytes of the immune system actively damage their genomic DNA in order to mount a more robust antibody response. They do so by expressing the DNA-mutating enzyme activationinduced cytidine deaminase (AID). Although AID action is critical to antibody diversification, AID-mediated damage outside of antibody loci is a leading cause of leukemia/lymphomas. It is known that AID acts on single-stranded DNA and mutates genes that are highly transcribed; however, the mechanisms for AID targeting to specific genes or loci have yet to be elucidated. It has been hypothesized that one of the many factors involved in the targeting of AID is the topology of the DNA itself, as it is thought that AID can only deaminate supercoiled but not relaxed double-stranded DNA (dsDNA). We hypothesized that features of the DNA inherent to a gene (i.e. sequence, structure and topology) are important determinants of AID recruitment. Contrary to the current model that transcription significantly increases AID activity, we found that transcription is not necessary for AID activity, as AID efficiently deaminated both supercoiled and relaxed linear DNA in the absence of transcription. Moreover, DNA secondary structure may be of greater importance than primary sequence in attracting AID to its target, and that these structures may be liberated through dsDNA breathing and/or in conjunction with transcription.