Detection of APOBEC3B's RNA binding sites in T-47D cells using eCLIP-seq

RNA editing is a crucial post-transcriptional process that diversifies proteomic outcomes and influences gene expression. Particularly, the APOBEC3 family has emerged as a significant player in this mechanism, with APOBEC3A (A3A) showing notable roles in immune response and stress conditions. APOBEC3B (A3B), another family member, has garnered attention for its potential role in breast cancer genomic mutations. In this study, we employ an inducible expression cell model and eCLIP-seq to detect the RNA binding sites for A3B a breast cancer cell model. Our findings indicate that A3B engages in selective RNA editing and targets NEAT1 and MALAT1 long non-coding RNAs. Notably, the binding of these RNAs sequesters A3B's catalytic activity, and thereby affects A3A's activity through a feedback loop. Overall design: eCLIP-seq was conducted on T-47D cell line expressing inducible A3B. The inducible A3B was tagged with flag peptide, allowing affinity purification of protein-RNA complex using anti-Flag (M2) antibody.