title: Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.
abstract: 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.
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: John
authors.initials: J
authors.lastname: Beaulaurier
authors.affiliation: Department of Medicine, New York University School of Medicine, New York 10016, USA.
authors.forename: Xue-Song
authors.initials: XS
authors.lastname: Zhang
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: Shijia
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Sebra
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: Chaggai
authors.initials: C
authors.lastname: Rosenbluh
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: Gintaras
authors.initials: G
authors.lastname: Deikus
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: Nan
authors.initials: N
authors.lastname: Shen
authors.affiliation: Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Munera
authors.affiliation: Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Waldor
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Chess
authors.affiliation: Department of Medicine, New York University School of Medicine, New York 10016, USA.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Blaser
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: Eric E
authors.initials: EE
authors.lastname: Schadt
authors.affiliation: Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Fang
mesh_terms: D001483:Base Sequence; D016123:Campylobacter jejuni / Q000235:genetics; D016935:Caulobacter crescentus / Q000235:genetics; D055353:Chromohalobacter / Q000235:genetics; D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000378:metabolism*; D044127:Epigenesis, Genetic; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D045302:Geobacter / Q000235:genetics; D016480:Helicobacter pylori / Q000235:genetics; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D015254:DNA Modification Methylases