Journal Article

Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus

Ramasamy, Adaikalavan, Heng, Jia Wei Joel, Fisher, Shira, Ng, Yan Ting, Nguyen, Tram Anh, Eisenberg, Eli, Tan, Meng How, Kaewsapsak, Pornchai, Reversade, Bruno, Oguz, Gokce, Sun, Rui, Xue, Shifeng

2023

Overview

Background Xenopus has served as a valuable model system for biomedical research over the past decades. Notably, ADAR was first detected in frog oocytes and embryos as an activity that unwinds RNA duplexes. However, the scope of A-to-I RNA editing by the ADAR enzymes in Xenopus remains underexplored. Results Here, we identify millions of editing events in Xenopus with high accuracy and systematically map the editome across developmental stages, adult organs, and species. We report diverse spatiotemporal patterns of editing with deamination activity highest in early embryogenesis before zygotic genome activation and in the ovary. Strikingly, editing events are poorly conserved across different Xenopus species. Even sites that are detected in both X. laevis and X. tropicalis show largely divergent editing levels or developmental profiles. In protein-coding regions, only a small subset of sites that are found mostly in the brain are well conserved between frogs and mammals. Conclusions Collectively, our work provides fresh insights into ADAR activity in vertebrates and suggest that species-specific editing may play a role in each animal’s unique physiology or environmental adaptation.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: ADAR / Adenosine / Adenosine Deaminase - genetics / Adenosine Deaminase - metabolism / Amphibians / Analysis / Animals / Biomedical and Life Sciences / Cell cycle / Datasets / Deamination / Depth profiling / Developmental stages / DNA / Editing / Embryogenesis / Embryonic development / Embryonic growth stage / Enzymes / Female / Frogs / Gametocytes / Gene Expression Profiling / Genetic aspects / Genomes / Genomics / Life Sciences / Mammals - genetics / Medical research / Medicine, Experimental / MicroRNAs / Mutation / Oocytes / Physiological aspects / Proteins / Research Article / RNA / RNA Editing / Transcriptome / Transcriptomes / Vertebrates / Wildlife conservation / Xenopus / Xenopus laevis - genetics / Xenopus laevis - metabolism