Figure 1.

Expression atlas for the experimental data of Jeong et al. [1] and Peter et al. [2]. The atlas was constructed using the Genewiz software [21]. DNA topoisomerase genes are underlined, and the replication origin and terminus are marked in bold. The outer circle (1) shows the change in expression of genes in response to supercoiling (log p values), where more negative values correspond to genes that are more significantly influenced by DNA relaxation; and circle (2) shows the correlation of these expression values with DNA supercoiling, where high absolute values correspond to gene-expression levels that show most correlation or anti-correlation with measured levels of DNA relaxation; both sets of data are from Peter et al. [2]. Shown in the next four circles (3-6) are the expression values of chosen experimental conditions from Jeong et al. [1]: (3) wild-type cells in rich medium (LB), (4) minimal medium (M9), (5) following 30 minutes of treatment with the gyrase inhibitor norfloxacin, and (6) cells carrying a mutation (GyrAD82G) in a gyrase gene, respectively. Circle (7) shows the location of protein coding sequences on the positive strand (CDS+), on the negative strand (CDS-), and the rRNA and tRNA genes. Circle (8) shows a running average of the absolute value of the nucleosomal position preference [22], and circle (9) the AT content (± 3 standard deviations from chromosomal average). Expression data from Jeong et al. [1] were centered and scaled. Circle (10) shows distance along the chromosome, in megabases (M), counting from the beginning of the GenBank sequence.