Transcription through a simple DNA repeat blocks replication elongation

The influence of d(G)n·d(C)n repeats on plasmid replica-tion in Escherichia coli cells was analyzed using electro-phoretic analysis of replication intermediates. These repeats impeded the replication fork in a length-and orientation-dependent manner. Unexpectedly, the replication arrest relied primarily on the repeats’ transcription. When the d(C)n sequence served as the transcriptional template, both transcription and replication were blocked. This was true for transcrip-tion driven by either bacterial or phage RNA poly-merases. We hypothesize that the replication fork halts after it encounters a stalled ternary complex of the RNA polymerase, the DNA template and the r(G)n transcript. This constitutes a novel mechanism for the regulation of replication elongation. The effects of this mechanism on repeat length polymorphism and genome rearrangements are discussed