nucleoid

The nucleoid (meaning nucleus-like) is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. The chromosome of a typical prokaryote is circular, and its length is very large compared to the cell dimensions, so it needs to be compacted in order to fit. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. Instead, the nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. Genome length varies widely (generally a few Mbp within a prokaryote phylum), and a cell may contain multiple copies of its genome.

Though the structure of a bacterial nucleoid has not yet been characterized in high resolution, key features have been researched in Escherichia coli as a model organism. In E. coli, the chromosomal DNA is on average negatively supercoiled and folded into plectonemic loops, which are confined to different physical regions and rarely diffuse into each other. These loops spatially organize into megabase-sized regions called macrodomains, within which DNA sites frequently interact, but between which interactions are rare. The condensed and spatially organized DNA forms a helical ellipsoid that is radially confined in the cell. The 3D structure of the DNA in the nucleoid appears to vary depending on conditions and is linked to gene expression so that the nucleoid architecture and gene transcription are tightly interdependent, influencing each other reciprocally.