## 11 Conclusions  
Overall, we observe positive correlation between the temporal expression of global regulatory genes and their cognate regulons (see Figure 9) as well as between the regulons and couplons (see Figures 6-8) on the one hand, and positive correlations between the spatial organization of regulons and couplons (in terms of their genomic distribution patterns; see Figure 5) on the other. Taken together, these observations suggest that the expression of global regulators is coordinated with organization of target genes in the chromosome, lending support to the hypothesis that transcriptional regulation shapes the spatial organization of genes [104; 130]. The determinative impact of the regulons of NAPs and global TFs on spatial patterns of cognate RpoD couplons is apparently related to the fact that RpoD transcribes vast majority of the genes and so, tends to impose uniformity, whereas the effects of NAPs and global TFs regulating subsets of genes (as defined by the TRN) convey discreteness to the spatial couplon patterns (Figure 5A,C; Supplementary Figures S3 and S4). The alternative sigma factors are associated with particular functions [85] and also in this case, we see that the spatial impacts of the ASF regulons predominate (Figure 5B,D; Supplementary Figure S5). However, this does not explain why the regulon and couplon genes are organized in spatially defined clusters (see Figure 5 and Supplementary Figures S1-S5). While the relation of regulatory gene expression pattern to the temporal regulon (or couplon) patterns appears trivial, the question is how the expression pattern of a regulator (be it a NAP or sigma factor) is related to spatial organization of cognate regulons and couplons in genome. One relevant observation is the distinct organization of the NAP and TF genes with respect to their targets in genome, indicating that the main parameters defining the position of a TF in the network hierarchy are the number and chromosomal distances of the genes they regulate and their protein concentration gradients [130]. Another relevant observation is that regulatory genes form gradients diffusing from their sites of production [131; 132]. It is thus conceivable that the observed spatial patterns of regulons and couplons are selected to optimize the exposure of target genes to the gradients of diffusing regulators. Furthermore, recent observations that alterations of gene expression and phenotype can be induced by chromosomal position shift of a NAP gene, despite the maintenance of its natural expression pattern [105] and, that the effect of positional shift can be aggravated by altering the expression pattern of the NAP gene [107], support the proposal that the physical structure of chromosome is optimized by direct regulatory interactionsinvolving the NAPs and other DNA structuring proteins [133]. In this respect it is relevant, that the NAPs can distinctly modulate the chromosomal regional dynamics by inducing transient domain boundaries in the genome [134; 135]. Such adjustment would involve selection for efficient interactions between the growth phase-dependent concentration gradients of regulators and chromosomal domains by restricting the range of chromosome configurations within the available configuration space, delimited by various factors including macromolecular crowding, entropic repulsion, confinement-induced organisation and packing density of the DNA polymer. The spatiotemporal coupling between the _E. coli_ chromosomal gene order and expression, the spatial organization of transcriptional regulation on both chromosomal arms along the OriC-Ter axis [103; 104] the successive, growth phase-dependent activation of the OriC and Ter chromosomal ends [30; 103] and clustering of co-functional genes [136] are all consistent with this notion. Notably, dynamic 3D colocalization of co-regulated genes optimized by locally increasing concentration of transcription factors has been proposed to occur in yeast [137].