APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast

•APOBEC3B mutagenic activity is 1000-fold more in tRNA than in mRNA genes.•APOBEC3B mutagenic lesions in tRNA genes are targeted to non-transcribed strand.•Reversion of trp1-289 can be used as a proxy for hypermutation in tRNA genes.•Efficacy of AP-site repair in tRNA genes is 99%, unlike only 83% in mRNA genes.•Base excision repair and error-free lesion bypass prevent tRNA genes’ hypermutation.