Abstract
RNA editing is a relatively unexplored process in which transcribed RNA is modified at specific nucleotides before translation, adding another level of regulation of gene expression. Cephalopods use it extensively to increase the regulatory complexity of their nervous systems, and mammals use it too, but less prominently. Nevertheless, little is known about the specifics of RNA editing in most of the other clades and the relevance of RNA editing from an evolutionary perspective remains unknown. Here we analyze a key element of the editing machinery, the ADAR (adenosine deaminase acting on RNA) gene family, in an animal with a key phylogenetic position at the root of chordates: the cephalochordate amphioxus. We show, that as in cephalopods, ADAR genes in amphioxus are predominantly expressed in the nervous system; we identify a number of RNA editing events in amphioxus; and we provide a newly developed method to identify RNA editing events in highly polymorphic genomes using orthology as a guide. Overall, our work lays the foundations for future comparative analysis of RNA-editing events across the metazoan tree.
Highlights
Changes in the regulation of gene functions are at the basis of morphological evolution, from the simplest metazoans to the possessors of amazingly complex nervous systems
Using the available transcriptomic data from B. lanceolatum [18], we were able to retrieve two amphioxus genes belonging to the ADAR family
Adar was expressed at a five times higher level than Adarb in the neural tube, while they were expressed at similar levels in the gut; Adar but not Adarb was found in the gills
Summary
Changes in the regulation of gene functions are at the basis of morphological evolution, from the simplest metazoans to the possessors of amazingly complex nervous systems. Contemporary textbook examples of mechanisms that allow exquisite fine-tuning of this regulation are alternative splicing in vertebrates and RNA gene editing in cephalopods [1,2,3]. Both enable an increase of proteome and interactome complexity [4] without affecting genome complexity by addition of extra genes. In this regard, RNA-editing is a post-transcriptional modification that has not received much attention. RNA-editing is present in all eukaryotic organisms [6,7,8] in different forms, such as the C-to-U (cytidine to uracil) editing mediated by the Apobec protein family [7] or the most prevalent in metazoans, the A-to-I (adenosine to inosine) editing, mediated by the ADAR (adenosine deaminase acting on RNA) protein family [9]
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