Simian virus 40-associated small RNA: mapping on the simian virus 40 genome and characterization of its synthesis.

The simian virus 40 (SV40)-associated small RNA (SAS-RNA) has previously been shown to arise late in SV40 lytic infection and to bear homology with the SV40 early mRNA's, or the SV40 genome, at map position 0.21. By using hybridization analysis, we determined that the SAS-RNA is between 62 and 65 nucleotides in length and its homology region lies between nucleotides 2760 and 2825 of the SV40 late(+) DNA strand. Viable deletion mutants which lacked part or all of this region made no SAS-RNA, strongly indicating that this is the coding region of the SAS-RNA. The expected sequence for the SAS-RNA, determined from the DNA sequence between nucleotides 2760 and 2825, appeared to be very pyrimidine rich (76% uridine and cytidine). Deletion or alteration of sequences immediately preceding the SAS-RNA coding region (approximately nucleotides 2716 to 2748) resulted in the loss of SAS-RNA production. These sequences may be part of a promotor for SAS-RNA synthesis or a processing site for its excision from long nuclear late transcripts. Under growth conditions where late transcription was not fully initiated (tsA58 at 41 degrees C; wild-type SV40 in the presence of 1-beta-D-arabinofuranosylcytosine), no SAS-RNA was produced, indicating that the expression of the SAS-RNA is regulated by a mechanism related to the control of late transcription.