Rev response elements (RRE) in lentiviruses: An RNAMotif algorithm-based strategy for RRE prediction

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Abstract
Lentiviruses (a sub‐family of the retroviridae family) include primate and non‐primate viruses associated with chronic diseases of the immune system and the central nervous system. All lentiviruses encode a regulatory protein Rev that is essential for post‐transcriptional transport of the unspliced and incompletely spliced viral mRNAs from nuclei to cytoplasm. The Rev protein acts via binding to an RNA structural element known as the Rev responsive element (RRE). The RRE location and structure and the mechanism of the Rev‐RRE interaction in primate and non‐primate lentiviruses have been analyzed and compared. Based on structural data available for RRE of HIV‐1, a two step computational strategy for prediction of putative RRE regions in lentivirus genomes has been developed. First, the RNAMotif algorithm was used to search genomic sequence for highly structured regions (HSR). Then the program RNAstructure, version 3.6 was used to calculate the structure and thermodynamic stability of the region of ∼ 350 nucleotides encompassing the HSR. Our strategy correctly predicted the locations of all previously reported lentivirus RREs. We were able also to predict the locations and structures of potential RREs in four additional lentiviruses. © 2002 Wiley Periodicals, Inc. Med Res Rev, 22, No. 6, 617–636, 2002; Published online in Wiley InterScience ( www.interscience.wiley.com). DOI 10.1002/med.10027