The remote control of transcription, DNA looping and DNA compaction

mRNA synthesis can be controlled at some distance from the start of transcription in eukaryotes and prokaryotes. It is generally assumed that the distal elements of the transcriptional machinery directly interact with the proximal elements, forcing the DNA to bend in a loop. DNA loop formation and transcription can be affected by the distance between the sites, their helical positioning, their orientation, their concentration (responsible for a cis- or a trans-effect of the DNA sequences), and DNA compaction in chromatin. The corresponding in vitro and in vivo situations have been critically examined for a number of systems, mostly prokaryotic.