Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

Gang Fang, Diana Munera, David I Friedman, Anjali Mandlik, Michael C Chao, Onureena Banerjee, Zhixing Feng, Bojan Losic, Milind C Mahajan, Omar J Jabado, Gintaras Deikus, Tyson A Clark, Khai Luong, Iain A Murray, Brigid M Davis, Alona Keren-Paz, Andrew Chess, Richard J Roberts, Jonas Korlach, Steve W Turner, Vipin Kumar, Matthew K Waldor, Eric E Schadt

Single-molecule real-time (SMRT) DNA sequencing allows the systematic detection of chemical modifications such as methylation but has not previously been applied on a genome-wide scale. We used this approach to detect 49,311 putative 6-methyladenine (m6A) residues and 1,407 putative 5-methylcytosine (m5C) residues in the genome of a pathogenic Escherichia coli strain. We obtained strand-specific information for methylation sites and a quantitative assessment of the frequency of methylation at each modified position. We deduced the sequence motifs recognized by the methyltransferase enzymes present in this strain without prior knowledge of their specificity. Furthermore, we found that deletion of a phage-encoded methyltransferase-endonuclease (restriction-modification; RM) system induced global transcriptional changes and led to gene amplification, suggesting that the role of RM systems extends beyond protecting host genomes from foreign DNA.