Effect of mutations in Barley yellow dwarf virus genomic RNA on the 5′ termini of subgenomic RNAs

To investigate the role in transcription initiation of sequences upstream of the promoter for subgenomic RNA2 (sgRNA2) of Barley yellow dwarf virus PAV, deletion and insertion clones were constructed and the 5′ termini of all three sgRNAs were determined. Deletion and insertion of sequences upstream of the transcription start site of sgRNA2 altered the position and nucleotide used to initiate transcription of sgRNA2, but not of sgRNAs 1 or 3. Since the promoter for sgRNA2 is downstream of the mutations, these results show that sequences outside of the core promoter can influence transcription start site selection from the sgRNA2 promoter.