Examples of candidate regulatory unmethylated sites.

In all panels bar charts show the extent of DNA methylation (inter-pulse duration ratio) at the candidate regulatory unmethylated site (blue) and, for comparison, at the ten immediately flanking upstream and downstream motif instances (red). The sequence interval covered in each chart varies due to the density of motifs across the respective genomes. A) Unmethylated sites are present upstream of the Hpa operon in four Enterobacteria species. In 3 cases, the unmethylated site is at the orthologous GATC, in S. bongori, the unmethylated site is located ~100bp upstream of the conserved sites. B) Conserved unmethylated site upstream of a PadR transcriptional regulator in Arthrobacter species. C) Cluster of unmethylated sites upstream of transcriptional regulator and sugar degradation operon in Spirochaeta smaragdinae. D) Cluster of non- or weakly-methylated sites throughout a non-ribosomal peptide synthase operon.