Fig. 4

Engineered ascorbate peroxidase (APEX2)-based proximity labeling. A APEX-Seq. APEX2 generates biotin‒phenoxyl radicals in the presence of biotin‒phenol and hydrogen peroxide. These radicals are highly reactive and covalently bind to RNA in proximity to APEX2, but their short-lived nature limits the labeling radius. B APEX-Seq with alkyne-phenol. Alkynylated RNAs are conjugated with azide-biotin via a click reaction. C APEX2 is recruited to a target RNA using the MS2 system or inactive Cas13. D Hybridization-proximity (HyPro)-Seq. In fixed cells, digoxigenin (DIG)-labeled probes hybridize to the target RNA, and APEX2 is subsequently recruited via a DIG-binding protein