Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

Clicks: 353
ID: 59948
2010
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Abstract

Abstract

Background

Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identified weak sequence motifs characterizing the editing sites, but these alone do not account for the large diversity observed.

Results

Here we build a dataset of 29,971 editing sites and use it to characterize editing preferences. We focus on structural aspects, studying the double-stranded RNA structure of the Alu repeats, and show the editing frequency of a given site to depend strongly on the micro-structure it resides in. Surprisingly, we find that interior loops, and especially the nucleotides at their edges, are more likely to be edited than helices. In addition, the sequence motifs characterizing editing sites vary with the micro-structure. Finally, we show that thermodynamic stability of the site is important for its editing.

Conclusions

Analysis of a large dataset of editing events reveals more information on sequence and structural motifs characterizing the A-to-I editing process

Reference Key
eli2010largescalebmc Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Eli, Eisenberg;Yoav, Kleinberger;
Journal BMC genomics
Year 2010
DOI
DOI not found
URL
http://www.biomedcentral.com/1471-2164/11/453
Keywords
Medicine Biotechnology Science genetics internal medicine evolution

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