Interaction of Cancer Cytosine Deaminase APOBEC3B With Nucleic Acid Structures

APOBEC3A (A3A) and APOBEC3B (A3B) are closely related DNA-cytosine deaminases that are implicated in cancer mutagenesis and result in a single-base substitution signature of C>T and C>G mutations in a TC dinucleotide context. This mutation signature is, in some cancers and particularly in metastasis, the largest fraction of the overall mutation burden. Furthermore, high expression levels of A3B correlate with poorer prognosis in breast cancer patients and APOBEC3 signature mutations are a likely cause of some driver mutations (e.g. E542K and E545K in PIK3CA). Therefore, understanding how APOBEC3 enzymes interact with their substrates is likely to provide avenues for reducing their effect on cancer and help inform the design of inhibitors that target these cytosine deaminases. We know, from previous work, that the single-stranded loop regions of DNA hairpin structures can be bound by both A3A and A3B. A3A has been shown to have extensive activity on such hairpin structures but A3B has been less studied on nucleic acid structures with some work even claiming no activity. To elucidate the activity of A3B on nucleic acid structures, we have performed biochemical DNA deamination assays on various substrates as well as performing EMSA with A3B on DNA, RNA, and R-loop structures. We show that A3B can bind to and deaminate different hairpins as well as bind to and globally affect R-loop structures. RSH is a Howard Hughes Medical Institute Investigator and MAC and RSH are funded by the National Cancer Institute P01-CA234228 with RSH also awarded The Cancer Prevention and Research Institute of Texas RR220053. SH, GBJ, VVF, and EH are funded by KiwiNet and Massey Ventures Ltd.