IRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences

Wei Chen,Hao Lin,Hui Yang,Hui Ding,Kuo-Chen Chou,Pengmian Feng

doi:10.18632/oncotarget.13758

Abstract

Catalyzed by adenosine deaminase (ADAR), the adenosine to inosine (A-to-I) editing in RNA is not only involved in various important biological processes, but also closely associated with a series of major diseases. Therefore, knowledge about the A-to-I editing sites in RNA is crucially important for both basic research and drug development. Given an uncharacterized RNA sequence that contains many adenosine (A) residues, can we identify which one of them can be of A-to-I editing, and which one cannot? Unfortunately, so far no computational method whatsoever has been developed to address such an important problem based on the RNA sequence information alone. To fill this empty area, we have proposed a predictor called iRNA-AI by incorporating the chemical properties of nucleotides and their sliding occurrence density distribution along a RNA sequence into the general form of pseudo nucleotide composition (PseKNC). It has been shown by the rigorous jackknife test and independent dataset test that the performance of the proposed predictor is quite promising. For the convenience of most experimental scientists, a user-friendly web-server for iRNA-AI has been established at http://lin.uestc.edu.cn/server/iRNA-AI/, by which users can easily get their desired results without the need to go through the mathematical details.

Highlights

RNA editing is a post-transcriptional modification that changes the genomic template through the insertion, deletion, deamination or substitution of nucleotides within the edited RNA molecule
Knowledge about the adenosine to inosine (A-to-I) editing sites in RNA is crucially important for both basic research and drug development
Given an uncharacterized RNA sequence that contains many adenosine (A) residues, can we identify which one of them can be of A-to-I editing, and which one cannot? so far no computational method whatsoever has been developed to address such an important problem based on the RNA sequence information alone

Summary

Introduction

RNA editing is a post-transcriptional modification that changes the genomic template through the insertion, deletion, deamination or substitution of nucleotides within the edited RNA molecule. It would be very useful for in-depth genome analysis or drug development to develop a sequence-based computational method that can effectively predict which adenosine sites in a RNA sequence can be “A-to-I” edited, and which ones cannot.

Results

Conclusion