Transcription of the Epstein-Barr virus genome during latency in growth-transformed lymphocytes

Nuclear run-on assays revealed extensive transcription of the Epstein-Barr virus genome during latent infection in in vitro-infected human fetal lymphoblastoid cells (IB-4). The EBER genes were the most heavily transcribed viral genes in these cells. Their transcription was partially inhibited in the presence of 1 microgram of alpha-amanitin per ml and fully inhibited at 100 micrograms/ml, consistent with RNA polymerase III transcription. All other transcription was inhibited at 1 microgram of alpha-amanitin per ml, consistent with RNA polymerase II sensitivity to alpha-amanitin. Other than EBER transcription, almost no transcription occurred from the U1 region. Specifically, no transcription was detected from the U1 latent promoter. RNA polymerase II transcription was highest in IR1, extending rightward through U2 and IR2 into the U3 domain and gradually decreased, but was measurable throughout the rest of the genome. This is consistent with EBNA gene transcription initiation within IR1. The higher level of transcription of the IR1 and U2 domains, which encode EBNA-LP and EBNA-2, as opposed to the domains which encode EBNA-3A, EBNA-3B, or EBNA-3C or EBNA-1, correlated with a higher level of EBNA-LP/EBNA-2 mRNA. Transcription extended through U4 into U5, even though no known latent-gene mRNAs are expressed from U4 downstream of the EBNA-1 open reading frame. This may result from inefficient termination of EBNA gene transcription. Leftward transcription from the latent membrane protein promoter was lower than EBNA transcription, although the latent membrane protein mRNA was the most abundant of the latent-gene mRNAs, indicating that this mRNA is more efficiently processed or has a longer half-life. Although transcription was detected from the DL strong early promoters and to a lesser extent from other early promoters, early mRNAs were less abundant than EBNA mRNAs or undetectable, suggesting that there may be posttranscriptional as well as transcriptional control over early mRNA expression in these latently infected cells.