RNA encoded by the IR1-U2 region of Epstein-Barr virus DNA in latently infected, growth-transformed cells

The IR1-U2 region of Epstein-Barr virus DNA consists of multiple copies of a 3.1-kilobase (kb) repeat sequence, IR1, which maps to the left of a 3.3-kb unique region, U2. Although hybridizations of cytoplasmic polyadenylated RNA from latently infected cells to viral DNA indicate that the IR1-U2 region encodes a substantial fraction of the viral RNA in these cells, only a single low-abundance 3-kb cytoplasmic polyadenylated RNA has been identified on Northern blots. Further analysis of the cytoplasmic polyadenylated RNA encoded by the IR1-U2 region indicates that (1) the RNA is transcribed from left to right; (ii) there are only three copies of the 3-kb RNA per cell; and (iii) the RNA is spliced. The RNA hybridizes to possibly contiguous 0.56- and 1.3 U2 domains. These domains and part of IR1 hybridize to the 3-kb cytoplasmic RNA. DNA between IR1 and the 0.56-kb U2 domain does not hybridize to the 3-kb RNA. The CCAAT-34 nucleotide-TATAA sequence in IR1 may be part of the promotor for the 3-kb cytoplasmic polyadenylated RNA since (i) it enables left-to-right transcription of IR1 by a HeLa cell extract, and (ii) latently infected cells contain giant polyadenylated nuclear RNAs which differ in size by 3 kb, as would be expected if transcription initiates in any copy of IR1 and continues through the rightward remaining copies into UR2.