Scaffold attachment region structure

The DNA of a bacterial cell, such as Escherichia coli, is a circular double-stranded molecule often referred to as the bacterial chromosome. In E. coli this DNA molecule contains 4.6 million base pairs. The circular DNA is packaged into a region of the cell called the nucleoid (see Topic Al) where it is organized into 50 or so loops or domains that are bound to a central protein scaffold, attached to the cell membrane. Fig. la illustrates this organization, although only six loops are shown for clarity. Within this structure, the DNA is actually not a circular double-stranded DNA molecule such as that shown in Fig. lb but is negatively supercoiled, that is, it is twisted upon itself (Fig. lc) and is also complexed with several DNA-binding proteins, the most common of which are proteins HU, HLP-1 and H-NS. These are histone-like proteins (see below for a description of histones). 

Describe the general organization of a eukaryotic chromosome. What structural role do scaffold associated regions (SARs) or matrix attachment regions (MARs) play Where are genes primarily located relative to chromosome structure ... 

A highly compact structure can be isolated that contains a single, supercoiled DNA molecule and protein. This is the bacterial chromosome or nucleoid. Because removal of protein decreases the compactness of this structure, it is concluded that the protein acts as a scaffold to keep the nucleoid in a compact state by binding to specific regions of the DNA molecule. The nucleoid DNA is also attached to the cytoplasmic membrane. 

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