Strand-specific DNA:RNA immunoprecipitation sequencing on T-47D breast cancer cells.

Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B) is a key molecular driver inducing mutations in multiple human cancer. A3B is a member of the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). Using a cell model that lacks base excision repair function, we sampled A3B editing sites in bulk. Analyses conducted on these A3B editing sites point to a function of A3B in editing DNA:RNA hybrid structure known as R-loops. In order to verify this result, we conducted strand-specific DNA:RNA immunoprecipitation sequencing (ssDRIP-seq; S9.6, KeraFAST, ENH001) on T-47D breast cancer cells. DNA:RNA immunoprecipitation (DRIP) were carried out on T-47D samples using an optimised method that minimise sampling bias (PMID: 28341774). Strand-specific libraries were constructed using input or immunoprecipitated DNA:RNA hybrids and compared.