Pausing during the transcription of MDV-1 cDNA by Escherichia coli RNA polymerase was compared with pausing during the replication of MDV-1 RNA by Qβ replicase. MDV-1 RNA is able to form many strong hairpin structures, and Qβ replicase pauses after the synthesis of each [Mills et a1. (1978) Cell 15, 541-550]. Although the transcripts were virtually identical to MDV-1 RNA, the locations at which RNA polymerase paused were different and apparently were not related to sequences that can form hairpins. These results indicate that hairpin stability, per se, cannot be used to predict the occurrence of pausing during transcription.Four pauses that occur within a 5-nucleotide region were studied in detail. Insertions and deletions were made in the template DNA to determine the contribution made by the surrounding sequences to these pauses. The results indicate that some of the pauses require the presence of particular upstream sequences, while others are unaffected by the template modifications. Thus, there are at least two different transcriptional pausing mechanisms: one depends on the nature of upstream sequences, while the other is independent of upstream sequences.
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