Figure 4.

Discernment of an in vivo methylation profile in E. coli. A; Overlap between sites of Dcm methylation and StuI cleavage. Dcm methylation and StuI cleavage sites are shown on top. The two overlaps between Dcm methylation (blue box) and StuI cleavage (red text) both block cleavage. B; The de novo optical map contig of MG1655 dcm⁺ strain of E. coli, assembled from 469 StuI maps. Outer red circle indicates the size of the contigs, individual restriction fragments are denoted with alternating colors and grey lines. The origin of the optical map does not coincide with the start of the published sequence, because the optical map was assembled de novo. C; A representative section (~430 kb) of the de novo StuI optical map contig of dcm⁺ E. coli. Alternating color blocks represent individual restriction fragments with their respective sizes (in kb) marked above the blocks. D; Comparison of in silico StuI map to de novo (C) Dcm⁺ E. coli optical map contig. StuI cleavage sites are represented as vertical bars. Red bars indicate cleavage sites observed in the de novo map. StuI sites overlapping with Dcm methylation (absent in the optical map) are shown as a blue vertical bar with a blue circle. Below are two examples of local sequence showing overlap between DNA cleavage and methylation sites and one example of local sequence showing no overlap.