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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article number251
JournalBMC biology
Volume21
Issue number1
DOIs
StatePublished - Dec 2023

Bibliographical note

Publisher Copyright:
© 2023, The Author(s).

Keywords

  • ADAR
  • RNA editing
  • Xenopus

ASJC Scopus subject areas

  • Biotechnology
  • Structural Biology
  • Ecology, Evolution, Behavior and Systematics
  • Physiology
  • General Biochemistry, Genetics and Molecular Biology
  • General Agricultural and Biological Sciences
  • Plant Science
  • Developmental Biology
  • Cell Biology

Fingerprint

Dive into the research topics of 'Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus'. Together they form a unique fingerprint.

Cite this