The role of the RNA structure in determining the level of A to I editing

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. Several methods have recently been developed to use ADAR for RNA engineering. With the help of a specific guide RNA, the ADAR protein is recruited to edit selected adenosine in a specific transcript, an approach known as site-directed RNA editing. Importantly, the specificity and efficiency of ADAR-mediated editing are affected by the structural properties of double-stranded RNA. While sequence preferences for ADARs have been previously documented, the structural mechanisms underlying ADAR activity are not well characterized, rendering it challenging to predict editing efficiency. In this work, we seek to examine how the spatial structure of a double-stranded RNA molecule affects the frequency of editing events. We characterized the frequency of editing events in 13 Alu sequences in which the spatial structure could be deciphered with high probability. The frequency of editing events on these sites was determined through a systematic analysis of RNA sequences taken from the GTEx database. By comparing editing efficiencies among individuals across different tissues, we identified sites edited at high or low levels in all the examined samples. In addition, specific RNA structures associated with those sites were characterized, and their role in determining editing efficiency will be studied experimentally. We believe that the findings of this work will form the basis for improved RNA guide designs that may enable the use of RNA engineering in clinical settings.