Figure 2. Population-averaged biochemical methods based on locus-locus collision frequencies.

As in Figure 1, a summary of techniques (left) used to probe the spatial organization of bacterial chromosomes, with example discoveries (right). (a) λ Int recombination. Recombination between attP and attB sites causes the disruption of a reporter gene lacZ and creation of two new attL and attR sites. The direction of recombination is controlled by Int and Xis protein. The schematic of the E. coli genome shows oriC and ter as a red dot and a blue line, respectively. The left and right arms of the chromosome are colored green and orange. Four macrodomains: Ori, Ter, Left and Right are shown as thick opaque red, blue, green and orange lines, respectively. Two additional unstructured regions are shown as fuzzy green and orange lines. (b) γσ Res recombination. The slithering of supercoiled plectoneme brings γσ res sites (blue and orange squares or circles) together for synapsis, and subsequent excision of intervening DNA (red). The γσ Res system has shown that high levels of transcription (blue arrows) inhibits supercoil diffusion (black circles with arrowheads, preventing synapsis between flanking loci. (c) Genome-wide chromosome conformation capture assays (5C and Hi-C) have revealed the architecture of the C. crescentus chromosome. A Hi-C heat map uses colors to indicate the frequency of interactions between locus pairs across the genome. The main diagonal captures interactions within chromosomal arms (black dashed line) and the opposite diagonal indicates interactions between arms (grey dashed lines). The Hi-C map also indicates (see zoomed region) the presence of chromosomal interaction domains (CID) (orange triangles). A plectoneme-free region (blue) formed through high gene expression at domain boundaries spatially insulates DNA in flanking domains (green and red).