Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts

ABSTRACT

Adar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome in a flexible manner. It has been a challenging task to identify beneficial editing sites from the sea of total editing events. The functional Ser>Gly auto-recoding site in insect Adar gene has uneditable Ser codons in ancestral nodes, indicating the selective advantage to having an editable status. Here, we extended this case study to more metazoan species, and also looked for all Drosophila recoding events with potential uneditable synonymous codons. Interestingly, in D. melanogaster, the abundant nonsynonymous editing is enriched in the codons that have uneditable counterparts, but the Adar Ser>Gly case suggests that the editable orthologous codons in other species are not necessarily edited. The use of editable versus ancestral uneditable codon is a smart way to infer the selective advantage of RNA editing, and priority might be given to these editing sites for functional studies due to the feasibility to construct an uneditable allele. Our study proposes an idea to narrow down the candidates of beneficial recoding sites. Meanwhile, we stress that the matched transcriptomes are needed to verify the conservation of editing events during evolution.

KEYWORDS:

• A-to-I RNA editing
• Adar
• auto-recoding
• beneficial
• editable
• metazoan

Abbreviations

AA	=	amino acid.
A-to-I	=	adenosine-to-inosine.
ADAR	=	adenosine deaminase acting on RNA.
CDS	=	coding sequence.
SNP	=	single nucleotide polymorphism.
dsRNA	=	double-stranded RNA.
edSer	=	editable serine codon.
unSer	=	uneditable serine codon.
edIle	=	editable isoleucine codon.
unIle	=	uneditable isoleucine codon.

Acknowledgments

We thank the members in Cai Lab for their help and suggestions to this work.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors’ contributions

Conceptualization & supervision: Y.D.

Data analysis: Y.D., L.M., S.X., and T.Z.

Writing – original draft: Y.D., T.Z., S.X., and L.M.

Writing – review & editing: T.Z., L.M., S.X., W.C., H.L., and Y.D.

Data availability statement

The analysis of the Adar auto-recoding codon involves the sequences in 13 species. Note that the Adar gene in insects is homologous to mammalian ADAD2 [30]. In total, 13 representative species with systematic RNA editing studies were listed as follows (Table 1), including 6 from Arthropoda, 4 from Chordata, 2 from Mollusca, and Acropora millepora from Cnidaria as an outgroup. The nucleotide and protein sequences were downloaded from NCBI https://www.ncbi.nlm.nih.gov/ (accession IDs listed in Table 1). The coding region of each mRNA sequence was extracted based on the annotation in NCBI.

Additional information

Funding

This study is financially supported by the National Natural Science Foundation of China [no. 32300371 and 31922012].