In vivo evidence for back and forth oscillations of the transcription elongation complex

We have used a combination of DNA and RNA footprinting experiments to analy ze the structural rearrangements experienced by a transcription elongation complex that was halted ill vivo by a protein readblock, We show that the c omplex readblocked within an (ATC/TAG)(n), sequence is in a dynamic equilib rium between upstream- and downstream-translocated conformers. By increasin g the strength of the putative RNA-DNA hybrid, the ternary complex is readi ly trapped in the downstream-translocated conformation, where the melted DN A region is limited to 8 bp, The shift of the equilibrium towards the downs tream location is also achieved by introducing within the 5' end of the mes sage an RNA sequence that can pair with a segment of the transcript in the vicinity of the halted ternary complex. Our results demonstrate that within certain template DNA sequences, the back and forth oscillations of the ter nary complex actually occur in a multipolymerase system and inside the cell . Furthermore, the cis-acting effect of the upstream RNA sequence underscor es an important phenomenon in gene regulation where a transcript may regula te its own elongation.