July 19, 2019  |  

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

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

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.

Journal: Nature biotechnology
DOI: 10.1038/nbt.2432
Year: 2012

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