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Authors: Beaulaurier, John and Zhang, Xue-Song and Zhu, Shijia and Sebra, Robert and Rosenbluh, Chaggai and Deikus, Gintaras and Shen, Nan and Munera, Diana and Waldor, Matthew K and Chess, Andrew and Blaser, Martin J and Schadt, Eric E and Fang, Gang

Beyond its role in host defense, bacterial DNA methylation also plays important roles in the regulation of gene expression, virulence and antibiotic resistance. Bacterial cells in a clonal population can generate epigenetic heterogeneity to increase population-level phenotypic plasticity. Single molecule, real-time (SMRT) sequencing enables the detection of N6-methyladenine and N4-methylcytosine, two major types of DNA modifications comprising the bacterial methylome. However, existing SMRT sequencing-based methods for studying bacterial methylomes rely on a population-level consensus that lacks the single-cell resolution required to observe epigenetic heterogeneity. Here, we present SMALR (single-molecule modification analysis of long reads), a novel framework for single molecule-level detection and phasing of DNA methylation. Using seven bacterial strains, we show that SMALR yields significantly improved resolution and reveals distinct types of epigenetic heterogeneity. SMALR is a powerful new tool that enables de novo detection of epigenetic heterogeneity and empowers investigation of its functions in bacterial populations.

Journal: Nature communications
DOI: 10.1038/ncomms8438
Year: 2015

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