Beaulaurier, JohnZhang, Xue-SongZhu, ShijiaSebra, RobertRosenbluh, ChaggaiDeikus, GintarasShen, NanMunera, DianaWaldor, MatthewChess, AndrewBlaser, Martin J.Schadt, Eric E.Fang, Gang2015-08-032015Beaulaurier, J., X. Zhang, S. Zhu, R. Sebra, C. Rosenbluh, G. Deikus, N. Shen, et al. 2015. “Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.” Nature Communications 6 (1): 7438. doi:10.1038/ncomms8438. http://dx.doi.org/10.1038/ncomms8438.2041-1723http://nrs.harvard.edu/urn-3:HUL.InstRepos:17820663Beyond 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.en-USJournal Article2015-08-0310.1038/ncomms8438