Figure 7. 3C analysis showed changes of DNA conformation around hox and nifJ operon on entry to microoxic condition and the impact of cyabrb2 deletion on DNA conformation.

(A and F) Schematic diagram of 3C analysis around hox operon (A) and nifJ operon (F). In the panels (A) and (F), the black horizontal arrow shows the location of the bait primer, and white horizontal arrows ((a) to (n) in hox operon (A) and (a’) to (t’) in nifJ operon (F)) indicate loci where the interaction frequency with bait were assayed. Vertical black arrowheads indicate the position of HindIII sites. ChIP-seq data of cyAbrB2 in the aerobic condition is displayed in the bottom, and cyAbrB2 binding regions are marked with shade. (B–E) The line plot showing the interaction frequency of each locus with hox fragment. Two of data sets are presented; (B) wildtype vs ∆cyabrb2 in aerobic condition, (C) wildtype vs ∆cyabrb2 in 1 hr of microoxic condition, (E) wildtype in aerobic vs 1 hr of microoxic condition, and (E) ∆cyabrb2 in aerobic vs 1 hr of microoxic condition are compared. (G–J) The line plot showing the interaction frequency of each locus with nifJ fragment. Two data sets are selected and presented; (G) wildtype vs ∆cyabrb2 in aerobic condition, (H) wildtype vs ∆cyabrb2 in 1 hr of microoxic condition, (I) wildtype in aerobic vs 1 hr of microoxic condition, and (J) ∆cyabrb2 in aerobic vs 1 hr of microoxic conditions are compared. The line plots indicate the average interaction frequency over the random ligation (n=3). Individual data are plotted as dots.

Figure 7—figure supplement 1. Dynamics of individual 3C scores.

Re-plotting of Figure 7 with the x-axis showing time (0, 1, 4 hr in microoxic conditions) and the y-axis showing the interaction frequency. Plots from the individual samples are connected by solid (wildtype) or dotty (∆cyabrb2) lines.

Figure 7—figure supplement 2. The validation of unidirectional primer sets for 3C assay is shown in Figure 7.

The 3C sample in this assay is the mixture of all 3C samples assayed in Figure 7.