Systematic Identification and Repository of RNA Editing Site in Human Genome

Abstract

RNA editing is the modification of RNA sequence through nucleotide deletion, insertion or substitution mechanisms. RNA editing mechanisms can affect pre-mRNA splicing, frameshifts, RNA structural changes and mRNA translation. A database comprising RNA editing sites in mammalian genomes is crucial for deciphering RNA editing mechanism. Since two types of substitution RNA editing in human such as A-to-I editing and C-to-U editing were investigated recently, this work mainly focuses on the substitution RNA editing sites in human and excludes the insertion and deletion RNA editing. In this work, we present a database, namely EdRNA, comprising the RNA editing sites which are computationally predicted based on the expressed sequences such as mRNA sequences and EST sequences. Computational methods based on comparative sequence analysis were applied for identifying RNA editing sites. The RNA editing site candidates are also cross-referenced to gene structures, repeats and SNP. Moreover, cross-species comparison between human and mouse is performed to confer the evolution meanings of the RNA editing sites. Both textual and graphical interface are provided for effectively retrieving the RNA editing sites in EdRNA. The resource is now freely available at http://EdRNA.mbc.nctu.edu.tw/.