strain of topA, the gene encoding Topo I, survives only because of the presence of suppressor mutations in the genes encoding DNA gyrase. These mutations result in reduced gyrase activity, suggesting that excess negative supercoiling due to the absence of Topo I is compensated by reduced negative supercoiling activity of DNA gyrase. Topo III is dispensable in E. coli and is not known to have any role in supercoiling in E. coli. The primary function of Topo IV is to resolve sister chromosomes. However, it has been shown to also contribute to the steady-state level of negative supercoiling by relaxing negative supercoiling together with Topo I. Transcription A twin supercoiling domain model proposed by Liu and Wang argued that unwinding of DNA double helix during transcription induces supercoiling in DNA as shown in. According to their model, transcribing RNA polymerase (RNAP) sliding along DNA forces the DNA to rotate on its helical axis. A hindrance in the free rotation of DNA might arise due to a topological constraint, causing the DNA in front of RNAP to become over-twisted (positively supercoiled) and the DNA behind RNAP would become under-twisted (negatively supercoiled). It has been found that a topological constraint is not needed because RNAP generates sufficient torque that causes supercoiling even in a linear DNA template. If DNA is already negatively supercoiled, this action relaxes existing negative supercoils before causing a buildup of positive supercoils ahead of RNAP and introduces more negative supercoils behind RNAP. In principle, DNA gyrase and Topo I should remove excess positive and negative supercoils respectively but if the RNAP elongation rate exceeds the turnover of the two enzymes, transcription contributes to the steady-state level of supercoiling. Control of supercoiling by NAPs In the eukaryotic chromatin, DNA is rarely present in the free supercoiled form because nucleosomes restrain almost all negative supercoiling through tight binding of DNA to histones. Similarly, in E. coli, nucleoprotein complexes formed by NAPs restrain half of the supercoiling density of the nucleoid. In other words, if a NAP dissociates from a nucleoprotein complex, the DNA would adopt the free, plectonemic form. DNA binding of HU, Fis, and H-NS has been experimentally shown to restrain negative supercoiling in a relaxed but topologically constrained DNA. They can do so either by changing the helical pitch of DNA or generating toroidal writhes by DNA bending and wrapping. Alternatively, NAPs can preferentially bind to and stabilize