Epstein-Barr virus (EBV) has been shown to encode at least 40 microRNAs (miRNAs), an important class of molecules that negatively regulate the expression of many genes through posttranscriptional mechanisms. Here, we have used real-time PCR assays to quantify the levels of EBV-encoded BHRF1 and BART miRNAs in latently infected cells and in cells induced into the lytic cycle. During latency, BHRF1 miRNAs were seen only in cells with detectable Cp-and/or Wp-initiated EBNA transcripts, while the BART miRNAs were expressed in all forms of latent infection. Surprisingly, levels of different BART miRNAs were found to vary up to 50-fold within a cell line. However, this variation could not be explained by differential miRNA turnover, as all EBV miRNAs appeared to be remarkably stable. Following entry into the virus lytic cycle, miR-BHRF1-2 and -1-3 were rapidly induced, coincident with the onset of lytic BHRF1 transcripts, while miR-BHRF1-1 expression was delayed until 48 h and correlated with the appearance of Cp/Wp-initiated EBNA transcripts. In contrast, levels of BART miRNAs were relatively unchanged during virus replication, despite dramatic increases in BART transcription. Finally, we show that BHRF1 and BART miRNAs were delayed relative to the induction of BHRF1 and BART transcripts in freshly infected primary B cell cultures. In summary, our data show that changes in BHRF1 and BART transcription are not necessarily reflected in altered miRNA levels, suggesting that miRNA maturation is a key step in regulating steady-state levels of EBV miRNAs.Epstein-Barr virus (EBV), a B lymphotropic gammaherpesvirus with potent growth-transforming properties, is etiologically linked to a number of malignancies of lymphoid and epithelial cell origin, including Burkitt's lymphoma (BL), posttransplant lymphoproliferative disease (PTLD), and nasopharyngeal carcinoma (NPC) (52). As illustrated in Fig. 1A, these different tumor settings can be distinguished by alternative patterns of EBV latent gene expression. Thus, EBV-driven PTLD lesions and growth-transformed lymphoblastoid cell lines (LCLs) display a latency III form of infection, characterized by the expression of six EBV nuclear antigens transcribed from one of two alternative promoters (Wp and Cp), and three latent membrane proteins (50, 63); in addition, a recent study (36) reported that LCLs also weakly express the viral Bcl2 homologue BHRF1 as a latent antigen. In contrast, most BL tumor cell lines which retain the original BL tumor phenotype in vitro show a more restricted pattern of latent antigen expression (termed latency I), in which the Cp, Wp, and LMP promoters are silent and a single nuclear antigen EBNA1 is transcribed from a novel promoter, Qp (46,54). However, a subset of BL lines display a third form of latency (termed Wp-restricted latency), in which Wp-initiated transcripts give rise to EBNA1, -3A, -3B, -3C, and BHRF1 (35,36,38). In addition to the above-mentioned latent antigens, two sets of RNAs are also expressed in all forms of EBV infection. These are ...