Cis regulatory effects on A-to-I RNA editing in related Drosophila species.

Jin Billy Li,Rui Zhang,Anne L. Sapiro,Patricia Deng

doi:10.1016/j.celrep.2015.04.005

Abstract

Adenosine-to-inosine RNA editing modifies maturing mRNAs through the binding of adenosine deaminase acting on RNA (Adar) proteins to double-stranded RNA structures in a process critical for neuronal function. Editing levels at individual editing sites span a broad range and are mediated by both cis-acting elements (surrounding RNA sequence and secondary structure) and trans-acting factors. Here, we aim to determine the roles that cis-acting elements and trans-acting factors play in regulating editing levels. Using two closely related Drosophila species, D. melanogaster and D. sechellia, and their F1 hybrids, we dissect the effects of cis sequences from trans regulators on editing levels by comparing species-specific editing in parents and their hybrids. We report that cis sequence differences are largely responsible for editing level differences between these two Drosophila species. This study presents evidence for cis sequence and structure changes as the dominant evolutionary force that modulates RNA editing levels between these Drosophila species.

Highlights

Adenosine-to-inosine (A-to-I) RNA editing is a co-transcriptional process mediated by adenosine deaminase acting on RNA (Adar) proteins that bind double-stranded RNA structures to convert adenosines into inosines, which are recognized as guanosine by the cellular machinery (Bass, 2002; Gott and Emeson, 2000; Nishikura, 2010; Rodriguez et al, 2012)
We designed 493 pairs of PCR primers that assayed a total of 1,036 editing sites in D. melanogaster that have conserved adenosines in D. sechellia, requiring high conservation within the primer sequences to allow amplification in both species (Table S1)
In F1 hybrids, many of these differences are maintained in the species-specific alleles, suggesting that cis sequence differences are largely responsible for the changes in editing between these species

Summary

Introduction

Adenosine-to-inosine (A-to-I) RNA editing is a co-transcriptional process mediated by adenosine deaminase acting on RNA (Adar) proteins that bind double-stranded RNA (dsRNA) structures to convert adenosines into inosines, which are recognized as guanosine by the cellular machinery (Bass, 2002; Gott and Emeson, 2000; Nishikura, 2010; Rodriguez et al, 2012). Adar proteins show primary sequence preferences in the bases adjacent to the edited adenosine (Eggington et al, 2011), suggesting that sequences both next to and far from the editing site contribute to establishing the editing levels at specific sites

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