Figure 6. Sigma factors are excluded from cyAbrB2 binding regions.

(A and B) Anti-co-occurrence of cyAbrB2 binding regions and sigma factors. Mosaic plots of cyAbrB2 binding regions and SigE peaks (A) or SigA binding peaks (B) are shown. Odds and p-values were calculated by Fisher’s exact test. (C) Snapshots of ChIP-seq data for CyAabrB2, SigE, and SigA at the nifJ region (top) and hox region (bottom). ChIP-seq data for cyAbrB2, SigE, and SigA under aerobic and dark microoxic conditions are overlayed. ChIP-seq data of cyAbrB2 under aerobic and microoxic conditions are colored blue and pink, respectively. ChIP-seq data for SigE and SigA are shown in solid lines (aerobic conditions) and the area charts (microoxic conditions). The positions of transcription start sites (TSSs) were obtained from a previous study (Kopf et al., 2014) and indicated by vertical dotted lines. Open triangles indicate peak summits under aerobic conditions, and solid triangles indicate peak summits under microoxic conditions.

Figure 6—figure supplement 1. Changes of SigE and SigA distribution on the entry to the microoxic condition.

(A) Venn diagram showing the number of peaks of SigE (left) and SigA (right) in aerobic (L + O₂) and dark microoxic (D − O₂) conditions. (B) Scatter plot showing changes in the binding signal of SigE and SigA by 1 hr cultivation under microoxic conditions. The binding signal of each 100 bp window is plotted.

Figure 6—figure supplement 2. Reproducibility of ChIP-seq data of SigA and SigE, compared with the previous study (Kariyazono and Osanai, 2022).

(Top) Venn diagrams show the overlapping of peaks called in this study and the previous study. (Bottom) Scatter plot comparing ChIP binding signals of SigA and SigE peaks commonly called in present and previous studies. Plots boxed by dashed lines are peaks called only in the present or previous study.