Transcription-wide impact by RESCUE-induced off-target single-nucleotide variants in mammalian cells

RNA base editing is a promising tool in precise molecular therapy. Currently, there are two widely used RNA base editors, REPAIR and RESCUE. REPAIR only facilitates A-to-I conversions, while RESCUE performs both A-to-I and C-to-U conversions. Thus, RESCUE can generate twice the number of mutations compared to REPAIR. However, transcription-wide impact due to RESCUE-induced off-target single-nucleotide variants (SNVs) is not fully appreciated. Therefore, to determine the off-target effects of RESCUE-mediated editing, we employed transcription-wide sequencing on cells edited by RESCUE. The SNVs showed different off-target effects on mRNA, circRNA, lncRNA, and miRNA expression patterns and their interacting networks. Our results illustrate the transcription-wide impact of RESCUE-induced off-target SNVs and highlight the need for careful characterization of the off-target impact by this editing platform.

Automated summary

RNA base editing is a promising tool for precise molecular therapy, and currently there are two widely used RNA base editors, REPAIR and RESCUE. REPAIR only facilitates A-to-I conversions, while RESCUE performs both A-to-I and C-to-U conversions, and can generate twice the number of mutations compared to REPAIR. However, the transcription-wide impact caused by RESCUE-induced off-target single-nucleotide variants (SNVs) is not fully understood. Therefore, this study used transcription-wide sequencing to determine the off-target effects of RESCUE-mediated editing and found different off-target effects on various RNA types.