Conserved local hypomethylation control during the bacterial cell cycle and by superimposed environmental cues

Heritable DNA methylation imprints occur in most genomes and underlie genetic variability in humans. The mechanism and consequences of establishing and propagating local hypomethylation through consecutive rounds of DNA replication and intermittent cell division cycles are poorly understood. Our genome-wide and site-specific methyl-N6-adenine (m6A-) analyses reveal a conserved local hypomethylation mechanism in two a-proteobacterial model systems. We show that MucR, a DNA-binding protein that uses an ancestral zinc-finger fold to control expression of virulence and cell cycle genes, competes with the cell cycle-regulated adenine-methyltransferase CcrM for target sites in S-phase, but not in G1-phase. Constitutive expression of CcrM or heterologous methylases during the cell cycle homogenizes m6A patterns even when MucR is present and controls transcription. We also find that environmental responses can impose methylation remodelling at certain sites, while the conserved cell cycle circuitry imposes systemic constraints on when local hypomethylation is instated. Overall design: 4 ChIPseq samples in synchronized C. crescentus cells, SMRT methylation profiles of Wild type and ?mucR1 ?mucR2 cells, 6 RECseq samples in Wildtype C. crescentus, E. coli, S. meliloti, V. cholera El Tor and in mucR1 mutants of C. crescentus and S. meliloti.