Comparative genomic and bioinformatic approaches for the identification of new adenosine-to-inosine substrates.

Adenosine-to-inosine (A-to-I) RNA editing is the enzymatic deamination of A-to-I catalyzed by ADAR (adenosine deaminase acting on RNA). Adenosine is read by ribosomes as guanosine causing a codon change and potentially protein recoding. A-to-I RNA editing can be either promiscuous, where the editing is nonspecific, or site specific, which requires a complex target RNA secondary structure formed by intramolecular base pairings between editing sequences and intronic or exonic editing site complementary sequences (ECSs). The most numerous editing sites have been found in noncoding regions containing Alu repeats, such as 3' untranslated regions, while specific editing sites are mostly found in transcripts involved in the transmission of neuronal signals. Previously A-to-I RNA editing sites were discovered by chance, but recently investigators have used comparative genomic and bioinformatics methods to identify novel sites. In this chapter, we discuss these approaches to identifying new editing sites.