also involved in other processes such as DNA replication initiation, recombination, and transposition. In contrast to specific gene regulation, how higher-order chromosome structure and its dynamics influences gene expression globally at the molecular level remains to be worked out. DNA supercoiling and gene expression A two-way interconnectedness exists between DNA supercoiling and gene transcription. Negative supercoiling of the promoter region can stimulate transcription by facilitating the promoter melting and by increasing the DNA binding affinity of a protein regulator. Stochastic bursts of transcription appear to be a general characteristic of highly expressed genes, and supercoiling levels of the DNA template contributes to transcriptional bursting. According to the twin supercoiling domain model, transcription of a gene can influence transcription of other nearby genes through a supercoiling relay. One such example is the activation of the leu-500 promoter. Supercoiling not only mediates gene-specific changes, but it also mediates large-scale changes in gene expression. Topological organization of the nucleoid could allow independent expression of supercoiling-sensitive genes in different topological domains. A genome-scale map of unrestrained supercoiling showed that genomic regions have different steady-state supercoiling densities, indicating that the level of supercoiling differs in individual topological domains. As a result, a change in supercoiling can result in domain-specific gene expression, depending on the level of supercoiling in each domain. The effect of supercoiling on gene expression can be mediated by NAPs that directly or indirectly influence supercoiling. The effect of HU on gene expression appears to involve a change in supercoiling and perhaps a higher-order DNA organization. A positive correlation between DNA gyrase binding and upregulation of the genes caused by the absence of HU suggests that changes in supercoiling are responsible for differential expression. HU was also found to be responsible for a positional effect on gene expression by insulating transcriptional units by constraining transcription-induced supercoiling. Point mutations in HUa dramatically changed the gene expression profile of E. coli, altering its morphology, physiology, and metabolism. As a result, the mutant strain was more invasive of mammalian cells. This dramatic effect was concomitant with nucleoid compaction and increased positive supercoiling. The mutant protein was an octamer, in contrast to the wild-type dimer. It wraps DNA on its surface in a right-handed manner, restraining positive supercoils as opposed to wild-type HU. These studies show that amino acid substitutions in HU can have a dramatic effect on nucleoid structure, that in turn results in significant phenotypic