Gene expression profiles of epithelial cells infected with microRNA-negative and -positive Epstein-Barr viruses

The Epstein-Barr virus (EBV) encodes its own microRNAs (miRNAs); however, their biological roles remain elusive. The commonly used EBV B95-8 strain lacks a 12 kb genomic region, known as BamHI A Rightward Transcripts (BART) locus, which encodes a number of viral miRNAs (BART miRNAs). These miRNAs are expressed abundantly in EBV-positive epithelial malignancies, suggesting that the 12 kb region somehow contributes to EBV-mediated epithelial carcinogenesis. Bacterial artificial chromosome (BAC) technology was used to generate an EBV B95-8 strain in which the 12 kb region was fully restored at its native locus (BART-restored virus). HEK293 and AdAH cells infected with either the parental BART-deleted virus or the BART-restored virus were established. The gene expression profiles of these cells were examined to identify cellular target genes of BART miRNAs. Total RNAs of 2 independent v-miRNA-positive HEK293 (or AdAH) cells and 2 independent v-miRNA-negative cells HEK293 (or AdAH) cells were processed for Microarray analysis using 3D-Gene human Oligo chip 25k (Toray, Tokyo, Japan).