Systematic identification of A-to-I RNA editing in zebrafish development and adult organs

Abstract

A-to-I RNA editing is a common post transcriptional mechanism, mediated by the Adenosine deaminase that acts on RNA (ADAR) enzymes, that increases transcript and protein diversity. The study of RNA editing is limited by the absence of editing maps for most model organisms, hindering the understanding of its impact on various physiological conditions. Here, we mapped the vertebrate developmental landscape of A-to-I RNA editing, and generated the first comprehensive atlas of editing sites in zebrafish. Tens of thousands unique editing events and 149 coding sites were identified with high-accuracy. Some of these edited sites are conserved between zebrafish and humans. Sequence analysis of RNA over seven developmental stages revealed high levels of editing activity in early stages of embryogenesis, when embryos rely on maternal mRNAs and proteins. In contrast to the other organisms studied so far, the highest levels of editing were detected in the zebrafish ovary and testes. This resource can serve as the basis for understanding of the role of editing during zebrafish development and maturity.

Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish

“…The A-to-I RNA editing enzyme Adar and Adarb1b are expressed in the developing zebrafish embryo To determine whether A-to-I editing activity exists during embryonic development, we revisited our transcriptome data [35] to check whether the enzymes responsible for A-to-I editing were expressed. In agreement with other recently published data [23] , we detected transcripts of at least two deaminase paralogs, adar and adarb1b, from egg to 5.3 hpf (Fig. 1A).…”

“…Editing primarily in the 3'-UTRs and outside the coding regions of transcripts is expected based on similar patterns observed in mammals [51] . It is also consistent with a recent data for zebrafish [23] that editing within the proteincoding regions of transcripts sets in after 24 hours. However, we also note that the previous study applied very conservative criteria for editing (to keep the false positive rate low) and called editing sites in embryonic transcripts based on a catalogue of editing sites for adult brain samples [23] .…”

“…It is also consistent with a recent data for zebrafish [23] that editing within the proteincoding regions of transcripts sets in after 24 hours. However, we also note that the previous study applied very conservative criteria for editing (to keep the false positive rate low) and called editing sites in embryonic transcripts based on a catalogue of editing sites for adult brain samples [23] . Therefore, this study may systematically miss editing sites that are unique for the embryo and not found in the brain.…”

“…In adult organs, adar was most highly expressed in testis and heart, whereas adarb1a was highly expressed in heart and brain. Overall Ato-I editing was most pervasive in testes and ovaries [23] . In contrast to the detailed information about the occurrence of editing, very little is known about functional consequences.…”

“…In human and mouse, A-to-I editing contributes to germline integrity, by preventing the spread of Alu [19][20][21] and SINE elements [22] , respectively. Higher editing prevalence in zebrafish testis and ovary compared to other organs [23] may hint to a role of A-to-I editing for germline integrity in non-mammalian vertebrates. However, to our knowledge, there is no evidence for this role in invertebrates yet.…”