Substrate specificity and RNA-based regulation of AID orthologs

Activation-induced cytidine deaminase (AID) is a DNA editing enzyme which facilitates antibody maturation through somatic hypermutation (SHM) and class switch recombination (CSR) in activated B cells. Lack of functional AID in human and mouse models impairs class switch recombination resulting in hyper IgM syndrome. Furthermore, it is thought that dysregulated activity of AID can contribute to the onset and progression of various types of cancer. AID binds ssDNA and deaminates deoxycytidine to deoxyuridine at the Ig loci. To date, several cofactors have been proposed to bind AID, but unlike the well-established role of AID itself in CSR and SHM, whether there is any potential regulation on its deamination activity has remained unclear. In addition, AID has some conserved and non-conserved biochemical features among species, of which substrate specificity for different topologies of DNA/DNA and DNA/RNA is not identified yet. In chapter 3, we focused on the characterization of AID orthologs from divergent species, aiming to find the structural determinants that regulate the enzyme's targeting of specific genes. The results of this study reveal variations in activity and thermal sensitivity among AID orthologs. In addition, we showed that the activity of AID orthologs varies to different extents by removing the bound RNAs from the enzyme. In chapter 4, we discovered that specific RNA fragments can inhibit human AID activity, with stronger inhibition observed in sequences found in class switch regions (AID's target for CSR), as opposed to variable regions (AID's target for SHM). This study presents novel insights into the potential regulation of AID activity through RNA interactions.