GATC sites where methylation changes over time correspond to a change in gene expression in a dam mutant. GATC sites where methylation changes over time correspond to a change in gene expression in a dam mutant. (A) IPD ratios of GATC sites with an FDR of <0.05 and involved in sialic acid catabolism across 5 days of incubation. The IPD ratio is the mean IPD of the sample at a specific position divided by the mean IPD of the control (dam mutant) at that same position. Therefore, an IPD ratio of 1 indicates that the means at that position are equal. The positions in the chromosome are shown in the legend (e.g., 3265636). (B) Transcript abundance fold change between WT and dam strains after 8 and 72 h of incubation in LB. Each bar represents an average of three biological replicates, and the error bars show the standard deviations. The dnaE strain is a negative control that is known not to be regulated through Dam methylation (and shows a fold change ratio of ~1). Note that transcription of nanA, whose promoter region does include GATC sites, does not change with the loss of Dam methylation, suggesting that other regulatory mechanisms are at play. Lacey L. Westphal et al. mSystems 2016; doi:10.1128/mSystems.00130-16