Initiation of transcription by RNA polymerase II in permeable, SV40-infected or noninfected, CVI cells; evidence for multiple promoters of SV40 late transcription.

CV1 cells were made permeable by treatment with lysolecithin and incubated in a transcription mixture containing ribonucleoside triphosphates including ATP or GTP 32P-labeled either in the alpha or beta position. 5'-terminal cap structures (7mGpgamma pbeta palpha X) on newly synthesized RNA were analyzed by digestion with nuclease P1 or with ribonuclease T2/bacterial alkaline phosphatase. Cap structures obtained after labeling with alpha-32P-GTP show that the 32P is found only adjacent to the 7mG residue (i.e., in the gamma position) and adjacent to the penultimate Gm or G nucleotide (i.e., in the alpha position). Analysis of RNA synthesized in the presence of beta-32P-ATP, however, shows GpppA cap structures which are labeled only in the beta position. In the presence of beta-32-p-GTP, only GpppG structures are labeled; these findings exclude the hypothesis that caps are synthesized from GTP and a monophosphate 5'-terminal RNA molecule. The results imply that the initial transcripts are used for cap formation, which indicates that the large majority (if not all) of capping sites correspond to initiation sites for transcription. In cells infected with wild-types SV40 the distribution of virus-specific caps is similar when labeled either with beta-32P-ATP or with alpha-32P-GTP or with 32p-phosphate. Thus, evidence is presented that heterogeneity of the cap structures in late SV40 is a consequence of independent initiation events and not of processing of a primary transcript followed by capping of the 5' ends generated.