Methylome profiles to investigate gene regulation mediated by phase-variable DNA methyltransferases in serogroup B <i>Neisseria meningitidis</i>

<i>Neisseria meningitidis</i> serogroup B is a major cause of meningitis and septicemia. Here, we report PacBio HiFi single-molecule real-time (SMRT) methylomics data sets for strains MC58, B6116/77, and M0579. These strains encode the phase-variable DNA methyltransferases ModA11, ModA12, and ModD1, respectively, which are epigenetic regulators pivotal to meningococcal pathogenicity.