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DNA replication and transcription are essential processes for cell growth and division. The polymerase complexes charged with these tasks share the same template and so there is a potential for conflict between the two. Studies both in vivo and in vitro indicate that RNA polymerase complexes can indeed arrest the progress of replication forks and that cell viability is endangered as a result. Stable ternary complexes formed at lesions in the template DNA or as a result of backtracking may be especially troublesome. Numerous processes have evolved to reduce conflict between replication and transcription and to rescue any replication forks that suffer damage when conflict does occur. In bacteria, these systems are so highly tuned and co-ordinated that cells normally suffer few problems even under conditions allowing rapid growth and therefore demanding both efficient chromosome duplication and high levels of gene expression. The threat to genome transmission and cell viability becomes apparent when this interplay is disrupted.