The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

• Published in: PLoS genetics Vol. 12; no. 7; p. e1006191
• Main Authors: Yu, Yao, Zhou, Hongxia, Kong, Yimeng, Pan, Bohu, Chen, Longxian, Wang, Hongbing, Hao, Pei, Li, Xuan
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 28.07.2016; Public Library of Science (PLoS)
• Subjects: Adenosine; Adenosine - genetics; Animals; Biology and life sciences; Conserved Sequence - genetics; Drosophila; Drosophila - genetics; Editing; Evolution; Evolution, Molecular; Exons - genetics; Genes; Genomes; Grants; Inosine - genetics; Insects; Methods; Nervous system; Phylogenetics; Phylogeny; Research and Analysis Methods; RNA Editing - genetics; RNA sequencing; Selection, Genetic - genetics; Transcriptome - genetics
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1006191

The hydrolytic deamination of adenosine to inosine (A-to-I editing) in precursor mRNA induces variable gene products at the post-transcription level. How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution, and very little is known about the selective constraints that drive the evolution of RNA editing events. Here we present a study on A-to-I RNA editing, by generating a global profile of A-to-I editing for a phylogeny of seven Drosophila species, a model system spanning an evolutionary timeframe of approximately 45 million years. Of totally 9281 editing events identified, 5150 (55.5%) are located in the coding sequences (CDS) of 2734 genes. Phylogenetic analysis places these genes into 1,526 homologous families, about 5% of total gene families in the fly lineages. Based on conservation of the editing sites, the editing events in CDS are categorized into three distinct types, representing events on singleton genes (type I), and events not conserved (type II) or conserved (type III) within multi-gene families. While both type I and II events are subject to purifying selection, notably type III events are positively selected, and highly enriched in the components and functions of the nervous system. The tissue profiles are documented for three editing types, and their critical roles are further implicated by their shifting patterns during holometabolous development and in post-mating response. In conclusion, three A-to-I RNA editing types are found to have distinct evolutionary dynamics. It appears that nervous system functions are mainly tested to determine if an A-to-I editing is beneficial for an organism. The coding plasticity enabled by A-to-I editing creates a new class of binary variations, which is a superior alternative to maintain heterozygosity of expressed genes in a diploid mating system.