other forms of the underwound DNA such as cruciform structures and branched plectonemes. Fis has been reported to organize branched plectonemes through its binding to cross-over regions and HU preferentially binds to cruciform structures. NAPs also regulate DNA supercoiling indirectly. Fis can modulate supercoiling by repressing the transcription of the genes encoding DNA gyrase. There is genetic evidence to suggest that HU controls supercoiling levels by stimulating DNA gyrase and reducing the activity of Topo I. In support of the genetic studies, HU was shown to stimulate DNA gyrase-catalyzed decatenation of DNA in vitro. It is unclear mechanistically how HU modulates the activities of the gyrase and Topo I. HU might physically interact with DNA gyrase and Topo I or DNA organization activities of HU such as DNA bending may facilitate or inhibit the action of DNA gyrase and Topo I respectively. Plectonemic supercoils organize into multiple topological domains One of the striking features of the nucleoid is that plectonemic supercoils are organized into multiple topological domains. In other words, a single cut in one domain will only relax that domain and not the others. A topological domain forms because of a supercoiling-diffusion barrier. Independent studies employing different methods have reported that the topological domains are variable in size ranging from 10 to 400 kb. A random placement of barriers commonly observed in these studies seems to explain the wide variability in the size of domains. Although identities of domain barriers remain to be established, possible mechanisms responsible for the formation of the barriers include: (i) A domain barrier could form when a protein with an ability to restrain supercoils simultaneously binds to two distinct sites on the chromosome forming a topologically isolated DNA loop or domain. It has been experimentally demonstrated that protein-mediated looping in supercoiled DNA can create a topological domain. NAPs such as H-NS and Fis are potential candidates, based on their DNA looping abilities and the distribution of their binding sites. (ii) Bacterial interspersed mosaic elements (BIMEs) also appear as potential candidates for domain barriers. BIMEs are palindromic repeats sequences that are usually found between genes. A BIME has been shown to impede diffusion of supercoiling in a synthetically designed topological cassette inserted in the E. coli chromosome. There are ~600 BIMEs distributed across the genome, possibly dividing the chromosome into 600 topological domains. (iii) Barriers could also result from the attachment of DNA to the