Fig. 3
From: Direct imaging of the circular chromosome in a live bacterium
DNA density mapping along the circular E. coli genome. a Schematic of the E. coli genome with two FROS markers at the left and right arms shown in b-e. The arrow indicates the direction of density mapping. b Example of a circular chromosome as indicated in A, with the HU-mYPet fluorescence intensity shown in grey scale (deconvolved image). Scale bar, 2 μm. c Local DNA density along the ridge line of single circular chromosomes plotted as a function of percentile distance from L3. Each line indicates a single chromosome. An example chromosome density is highlighted in black. Blue arrows indicate local maxima (peaks) and local minima (valleys) in this example curve. n = 82. d Average cumulative density function mapping the genomic coordinates to the contour coordinates along the ridge of the circular chromosome. Marks indicate the measured positions of the R3 locus and global minimum Imin, and the predicted positions of oriC and dif sites. Error bars indicate s.d. e Local DNA density plotted versus genomic coordinate in percentile distance along the ridge line from the predicted oriC sites, with mean values and positions of dif, L3 and R3 indicated. Dark and light shading indicates s.e.m and s.d. Inset: schematic illustrating the DNA density distribution along a typical circular E. coli chromosome as concluded from the blob analysis and contour density analysis. n = 292. f DNA density distribution of a second independent strain with Ori1/Ter3 labels, plotted as in panel e. Note that in this strain left and right arms can be distinguished less well due to symmetry (Fig. 1a). n = 74. g, h Distributions of local maxima (plotted upwards) and local minima (downwards) in the DNA intensity within individual chromosomes along the genomes from oriC to dif site. Bin size 5% of the genome length (230kbp). Local maxima and minima are identified as in c. ‘D’ denotes local DNA density. i DNA density distribution of a ΔmatP strain with Ori1/Ter3 labels, plotted as in panel e. j Example of a circular chromosome in a ΔmatP cell, with the HU-mYPet fluorescence intensity shown in grey scale (deconvolved image). Scale bar, 2 μm
