RNA localization signals: deciphering the message with bioinformatics

mRNA localization is an important posttranscriptional method of targeting proteins to their site of function. The sorting of transcripts to their correct intracellular destination is achieved by a number of mechanisms, including selective degradation or transport by molecular motors along the cytoskeleton. In all cases, this involves mRNA localization signals, or so called zip codes, being recognized by trans-acting cellular factors. In a few cases, primary sequence motifs for RNA localization can be identified, but in general, localization signals operate at the level of secondary (2D) and tertiary (3D) structure. This inevitably means that searching for localization signal motifs is a complex task requiring specialist knowledge of bioinformatics. Furthermore, the publications describing these searching methods tend to be aimed at the bioinformatics community. In this review, we have surveyed the major tools for folding, comparing, and searching potential mRNA localization signals in transcripts or across genomes. Our aim is to provide an overview for biologists, who lack specialist computer and bioinformatics training, of the major RNA bioinformatics tools that are available. The examples provided are focused on mRNA localization signals and RNA stem-loop structures, however, these tools can be applied to the study of any RNA signals.