Escherichia coli Epigenome sequencing and assembly

In this study we have used Pacific Bioscience single molecule real-time (SMRT) long read sequencing to characterise the complete epigenome (genome and methylome) of 95JB1. Our analysis of the methylome of 95JB1 and a second isolate, 95NR1, identified hemimethylation of a novel motif (5'-CTGCm6AG-3') in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethalyted in the 95JB1, including at least 180 potential promoter regions that could explain regulatory differences between the strains. We identified a Type IIG methyltransferase encoded in both genomes in association with three additional genes in an operon-like arrangement. IS1203 mediated disruption of this operon in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the enormous potential of SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.