Literature about putative epigenetic state changes in mammal sequences after cloning steps in Escherichia coli
E.coli strains that have dam or dcm methylases can methylate plasmid at adenines or cytosines respectively. See here — It is a NEB web page but has links to the cited references.

DH5α has both the methylases- dam+ dcm+ , BL21 is dam+ dcm− and ET12567 is dam− dcm−