Gene regulation from sites near and far

Although regulation of gene expression from distant sites would seem to have many advantages, this strategy is utilized far more frequently in eukaryotic cells than in prokaryotic cells. The inherent flexibility of DNA allows factors bound to distant regulatory sites to interact with transcription initiation factors or RNA polymerase components at the promoter of the regulated gene. Regulatory domains that are closely linked to the promoter lose this spatial flexibility, and must lie within a defined region in the vicinity of the promoter. The major drawback to regulation of gene expression from distant sites is that any gene with a promoter located within the effective radius of the regulatory factor will respond to its control. Thus, promoters of independently regulated genes must be separated by ample amounts of nonspecific DNA. Prokaryotic cells may have evolved to favor regulation of transcription from closely linked sites because this mechanism allows them to eliminate excess DNA, which may in turn enable them to achieve rapid growth in an energy-limited environment.