In the bacterial world, methylated adenine and cytosine residues are most commonly associated with restriction-modification systems that provide a defense mechanism against invading foreign genomes. In addition, some forms of them also play important roles in the regulation of cell cycle, gene expression, virulence, and antibiotic resistance. Efficient and high resolution profiling of bacterial methylation events has not been possible until the recent advent of Single Molecule Real-Time sequencing (SMRTseq) technique that can detect N6-methyladenine (6mA) and 4-methylcytosine (4mC) residues, the two major types of methylation in the bacterial world, in addition to 5-methylcytosine (5mC). This technique enabled us to characterize one of the first whole-genome bacterial methylomes, the entire set of methylations, at single- nucleotide resolution. A fast growing number of bacteria are being characterized, revealing unexpected degrees of complexity and diversity in bacterial methylomes. However, existing methods using SMRTseq data mainly carried out at population levels cannot resolve epigenetic heterogeneity that often exists in a single population and empowers bacteria to better adapt to changing conditions. Also, SMRTseq has its own limitations that call for combinations with other existing complementary techniques. Last but not least, previous studies have mostly focused on gene-specific mechanisms of methylation-mediated regulation of gene expression, which only account for a very small fraction of global changes of gene expression induced by epigenetic perturbations. Motivated by both the unique advantages of SMRTseq and these emerging challenges, we propose to develop novel methods for multiscale detection and integrative functional characterization of bacterial DNA methylation. The novel methods will combine innovative developments across multiple disciplines: hybrid sequencing design, multi-dimensional molecular profiling, statistics and systems biology. They will enable the better understanding of the mechanisms and dynamics of epigenetic heterogeneity in different types of bacteria, and advance the integration of epigenetic variations into a systems biology framework for bacteria. We will apply these methods to study a diverse collection of bacteria with different methylome complexity, methylation-related phenotypes and clinical significance. We will also implement all the methods developed over the project period in an integrated program for the broader research community. The impact will not be restricted to current research on bacterial methylomes, but also to bacterial research in which DNA methylations are assumed to be independent of the biological processes of interest, partly due to the lack of techniques and tools. These include some that have important clinical relevance: virulence, antibiotic resistance and persistence that are causing critical health crisis

Public Health Relevance

Many bacteria are causal pathogens for infectious diseases with strong abilities to develop drug resistance, bypass immune system and adapt to different host environments, while other commensal bacteria play important roles at the interface of host metabolism and the immune system. We aim to develop methods that enable the multiscale detection of epigenetic variations in bacteria, integrative study of their regulatory functions, towards the discovery of novel mechanisms involved in the development of antibiotic resistance/persistence and their responses to diverse environmental and host conditions.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM114472-05
Application #
9774127
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Gaillard, Shawn R
Project Start
2015-09-08
Project End
2020-08-31
Budget Start
2019-09-01
Budget End
2020-08-31
Support Year
5
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Icahn School of Medicine at Mount Sinai
Department
Genetics
Type
Schools of Medicine
DUNS #
078861598
City
New York
State
NY
Country
United States
Zip Code
10029
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Beaulaurier, John; Zhu, Shijia; Deikus, Gintaras et al. (2018) Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nat Biotechnol 36:61-69
Zhu, Shijia; Fang, Gang (2018) MatrixEpistasis: ultrafast, exhaustive epistasis scan for quantitative traits with covariate adjustment. Bioinformatics 34:2341-2348
Wu, Tao P; Wang, Tao; Seetin, Matthew G et al. (2016) DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature 532:329-33
Topol, Aaron; Zhu, Shijia; Hartley, Brigham J et al. (2016) Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Rep 15:1024-1036
Chao, Michael C; Zhu, Shijia; Kimura, Satoshi et al. (2015) A Cytosine Methyltransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen [corrected]. PLoS Genet 11:e1005666
Beaulaurier, John; Zhang, Xue-Song; Zhu, Shijia et al. (2015) Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nat Commun 6:7438