stationary phase. An increase in the number of MukB molecules could have influence on the processivity of the MukBEF complex as a DNA loop extruding factor resulting in larger or a greater number of the loops. Supercoiling can act in a concerted manner with DNA architectural proteins to reorganize the nucleoid. The overall supercoiling level decreases in the stationary phase, and supercoiling exhibits a different pattern at the regional level. Changes in supercoiling can alter the topological organization of the nucleoid. Furthermore, because a chromosomal region of high transcription activity forms a CID boundary, changes in transcription activity during different growth phases could alter the formation of CID boundaries, and thus the spatial organization of the nucleoid. It is possible that changes in CID boundaries observed in the stationary phase could be due to the high expression of a different set of genes in the stationary phase compared to the growth phase. Nucleoid structure and gene expression NAPs and gene expression The E. coli chromosome structure and gene expression appear to influence each other reciprocally. On the one hand, a correlation of a CID boundary with high transcription activity indicates that chromosome organization is driven by transcription. On the other hand, the 3D structure of DNA within nucleoid at every scale may be linked to gene expression. First, it has been shown that reorganization of the 3D architecture of the nucleoid in E. coli can dynamically modulate cellular transcription pattern. A mutant of HUa made the nucleoid very much condensed by increased positive superhelicity of the chromosomal DNA. Consequently, many genes were repressed, and many quiescent genes were expressed. Besides, there are many specific cases in which protein-mediated local architectural changes alter gene transcription. For example, the formation of rigid nucleoprotein filaments by H-NS blocks RNAP access to the promoter thus prevent gene transcription. Through gene silencing, H-NS acts as a global repressor preferentially inhibiting transcription of horizontally transferred genes. In another example, specific binding of HU at the gal operon facilitates the formation of a DNA loop that keeps the gal operon repressed in the absence of the inducer. The topologically distinct DNA micro-loop created by coherent bending of DNA by Fis at stable RNA promoters activates transcription. DNA bending by IHF differentially controls transcription from the two tandem promoters of the ilvGMEDA operon in E. coli. Specific topological changes by NAPs not only regulate gene transcription, but are