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Significance The significance of this work lies in the application of innovative analytical, sequencing, and computational tools to discover a novel epigenetic regulatory mechanism. Here, we discovered that phosphorothioate (PT) DNA modifications are maintained at a constant density in a genome in part by DNA shape-driven target site selection. While structurally similar GAAC, GTTC, and GATC motifs are all modified by PT-catalyzing proteins, methylation of G6m ATC by Dam methyltransferase blocks PT modification of GATC and shifts PTs to the other two sites inSalmonella enterica , maintaining a constant number of PTs in the genome.

Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria