Structural analysis of the major immediate early gene of human cytomegalovirus

The most abundant species of human cytomegalovirus (Towne) immediate early polysome-associated RNA originates from a region of ca. 2.8 kilobases (0.739 to 0.755 map units) within the XbaI-E DNA fragment. These sequences code for a 1.95-kilobase mRNA and are referred to as immediate early coding region one (M. F. Stinski, D. R. Thomsen, R. M. Stenberg, and L. C. Goldstein, J. Virol. 46:1-14, 1983). We have utilized the nuclease mapping technique of Berk and Sharp (A. J. Berk and P. A. Sharp, Cell 12:721-732, 1977) to examine this gene in detail. Cloned fragments of human cytomegalovirus DNA, either labeled with 32P in vivo or end labeled in vitro at the 5' or 3' termini, were hybridized to immediate early polysome-associated RNA. The hybrids were treated with single-strand-specific nuclease and subjected to electrophoresis in either neutral or denaturing gels. The major transcript was shown to be a spliced molecule containing a 3' terminal exon of 1,341 nucleotides. Upstream of the major body of the mRNA are three small exon sequences of 185, 88, and 121 nucleotides. The sequence of the exons as well as the locations of the intron-exon splice junctions were determined. Based on the DNA sequence, the viral mRNA molecule has one open reading frame which begins within the second exon and extends for 491 amino acid residues. The predicted molecular weight of the polypeptide originating from this region was estimated to be 64,000. It is hypothesized that this viral gene codes for the major regulatory protein controlling transcription of the viral genome at early times. The properties of the viral gene and its protein product are discussed.