Termination sequences in the control region of the Ad2-specific VARNA2 gene

Both VARNA genes in the adenovirus genome are transcribed by host DNA-dependent RNA polymerase III. Nevertheless, late in infection the mass ratio of VARNA2 to VARNA1 in adenovirus-infected human KB or HeLa cells is about 1:40. This difference is most likely due to differences in promoter strength which may be attributed to sequence differences in the control regions of the two genes. To investigate this possibility, the two genes were cloned into separate plasmid molecules and their transcription efficiencies were compared in vitro. The VARNA2 gene was transcribed in vitro at least 50 times less efficiently than the VARNA1 gene. The competing strengths of the two genes were similar, which suggests that the B block sequence in the VARNA2 gene may be fully functional for sequestering factors. Therefore, the major difference must reside in the region upstream of the B block. By analyzing the hybrid RNAs transcribed from a hybrid gene and 27 fused genes in which only the control region of the VARNA1 gene was fused to various lengths of the 5'-flanking and the coding regions of the VARNA2 gene, one major and one minor termination site, which caused premature termination, were revealed downstream of the A block sequence and in the 5'-flanking region of the VARNA2 gene, respectively. The presence of termination sequences, a suboptimal interblock spacing, and an altered A block sequence in the control region may result in a weaker promoter in the VARNA2 gene.