## 6 Spatiotemporal Organization of Transcription in Genome  
Previous explorations of chromosomal gene organisation revealed the gene copy number effects on gene expression, with higher expression levels characteristic of locations close to the chromosomal replication origin due to multiple rounds of replication initiation [99; 100]. These positional effects were interpreted as basic differences in the \"expressivity\" potential of different chromosomal locations, rather than unique features of translocated genes. Other studies proposed that organization of genes in bacterial genome is explained by selective pressure driving the clustering of essential genes on the leading strand and thus, suggested that gene essentiality, not expressivity, is the determinative  
Figure 4: Relationship between DNA topology and the thermodynamic stability of transcribed sequences. (**A**). High-resolution agarose gel-electrophoresis of DNA plasmids isolated from exponentially growing wild-type and _rpoZ_ mutant cells. More negatively supercoiled topoisomers migrate faster in the gel. Note the relaxation of DNA in _rpoZ_ mutant. (**B**). Comparison of the DNA thermodynamic stability of promoter sequence context in wild type and _rpoZ_ mutant cells. Position of transcription start site (TSS) is indicated by 0. Average DNA GC-content of the promoter sequence context for all genes (black curve). Average DNA GC-content of genes up-regulated in wild-type and _rpoZ_ mutant cells during exponential phase is indicated by red and blue curves, respectively (data from [39]). (**C**). High-resolution agarose gel-electrophoresis of plasmids isolated from exponentially growing (expo) and stationary (stat) _E. coli_ CSH50 cells. Note the relaxation of DNA in stationary phase. (**D**). Comparison of the DNA thermodynamic stability of promoter sequence context in exponentially growing (expo) and stationary (stat) _E. coli_ CSH50 cells. The TSS position is indicated by 0. Average DNA GC-content of the promoter sequence context for all genes (black curve). Average DNA GC-content of genes up-regulated in exponentially growing and stationary cells is indicated by red and blue curves, respectively. factor of chromosomal gene organisation. Still another explanation of spatial gene clustering did not take into account their function but rather their persistence, i.e., their presence either in the majority, or in the minority of the organisms [101; 102]. However, pivotal for understanding the relationship between chromosomal gene organization and gene activity was the discovery of coupling between the highly conserved spatial order of major regulatory genes along the chromosomal OriC-Ter axis and the temporal order of their expression during the bacterial growth cycle (i.e., during the period from inoculation of the \"overnight\" culture in fresh growth medium through the exponential growth to stationary phase) [103; 104; 30; 100]. In other words, it became apparent that the major factor organizing the important regulatory genes spatially along the OriC-Ter axis of the chromosome is the temporal requirement of their products during the bacterial growth cycle. Furthermore, this temporal expression pattern was linked to a putative growth phase-dependent OriC-Ter gradient of negative superhelicity thus coupling the gene expression to the metabolic state of the cell. So far, the existence of this superhelicity gradient could not be experimentally demonstrated. However, the importance of gene order along the chromosomal OriC-Ter axis has been supported by genetic studies demonstrating that chromosomal position shifts of regulatory genes lead to rewiring of the genetic network as well as alterations of both the growth phase-dependent DNA supercoil dynamics and the bacterial phenotype [105; 106; 107]. Furthermore, the chromosomal gene order appears to underlie the spatial organization of function in genome. In particular, it was observed that anabolic genes are enriched around the OriC-end and catabolic genes around the Ter-end of the _E. coli_ chromosome [108].