The cis-acting 3'-element of rubella virus RNA has DNA promoter activity

The 3'-terminal region of the rubella virus (RV) positive-strand RNA, referred to here as the cis-acting element (CAE), is implicated in the initiation of negative-strand RNA synthesis. Sequence analysis of the 3'-CAE shows that there is a putative TATA box which is surrounded by G + C-rich sequences. To determine whether this element, in a DNA form, has the capability to initiate transcription, a 3'-end 165-bp NarI-EcoRI fragment from the RV cDNA was cloned upstream from a cat reporter gene. The level of CAT activity was dependent on the presence of the 3'-CAE and the SV40 enhancer. Primer extension analysis of the CAT mRNA showed that the transcription start point is in the RV 3'-CAE, 34 bp downstream from the putative TATA box. DNA-gel shift analysis revealed that three nucleoprotein-specific complexes were formed with the 3'-CAE and the binding sites for these proteins were between bp -64 to -108. The possible promoter function of the RV 3'-CAE is discussed in context to RV persistence.