A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses

• DOI: 10.1261/rna.2326106
• Publication Date: 2006-03-16T01:45:21Z
• Authors: Adam Grundhoff; Christopher S. Su...; Don Ganem
• Keywords: 0301 basic medicine; Herpesvirus 4, Human; Base Sequence; Molecular Sequence Data; Chromosome Mapping; Computational Biology; Genome, Viral; Blotting, Northern; Cell Line; Alternative Splicing; MicroRNAs; Open Reading Frames; 03 medical and health sciences; Gammaherpesvirinae; Herpesvirus 8, Human; Humans; Nucleic Acid Conformation; RNA, Messenger; Algorithms; Oligonucleotide Array Sequence Analysis

We have developed an approach to identify microRNAs (miRNAs) that is based on bioinformatics and array-based technologies, without the use of cDNA cloning. The approach, designed for genomes small size (<2 Mb), was tested cells infected by either two lymphotropic herpesviruses, KSHV EBV. viral were scanned computationally pre-miRNAs using algorithm (VMir) we developed. Candidate hairpins suggested this analysis then synthesized as oligonucleotides microarrays, arrays hybridized with RNAs from cells. miRNAs scored positive subjected confirmatory Northern blot analysis. Using 10 known identified, well a novel pre-miRNA had earlier escaped detection. This method also led identification seven new EBV-encoded pre-miRNAs; additional computational approaches, identified total 18 EBV produce 22 mature miRNA molecules, thereby more than quadrupling number hitherto miRNAs. advantages limitations are discussed.