Novel downstream elements upregulate transcription initiated from an Epstein-Barr virus latent promoter

The modulation of nuclear antigen expression from the Epstein-Barr virus (EBV) genome in virus-infected cells is crucial to the establishment and maintenance of the immortalized state. The EBV nuclear antigen (EBNA) genes are all transcribed from either of two promoters whose alternate usage is not understood. We have studied the EBNA transcriptional domain by using various promoter constructs to transfect a variety of EBV positive cell lines and then measured promoter activity by RNase protection analysis and nuclear run-on transcription assay. These experiments have shown that at least two distinct and novel DNA sequence elements are located in the intronic region situated between both promoters and that their presence results in a 100-fold stimulation of transcription initiated from the upstream promoter. One of these elements is shown to bind nuclear proteins from an EBV-positive cell line. In addition, an important sequence homology is noted between this element and the core sequences of a number of well known viral enhancers. Taken together, the results show that EBNA transcription is controlled by upstream and intronic elements in a regulatory domain that is at least 7 kb long.