Scientists develop new technique to analyze the epigenetics of bacteria

By John Murphy, MDLinx
Published December 23, 2015

Key Takeaways

Scientists have developed a new technique to more precisely analyze bacterial populations in order to reveal changes in gene expression that drive virulence. This novel method could be a potent new tool to offset the growing challenge of antibiotic resistance by bacterial pathogens.

In the bacterial kingdom, the most prevalent modifications of DNA bases are in the form of methylations. Bacterial DNA methylation, beyond its participation in host defense, also plays important roles in the regulation of gene expression, virulence, and antibiotic resistance. However, the conventional method for studying bacterial methylomes relies on a population-level consensus that lacks the single-cell resolution required to observe epigenetic heterogeneity.

Using the existing single molecule, real-time (SMRT) sequencing method, the research team developed SMALR (single molecule modification analysis of long reads), which revealed distinct types of epigenetic heterogeneity. The team, which published their results in the journal Nature Communications, included researchers from Icahn School of Medicine at Mount Sinai and New York University Langone Medical Center in New York, and Brigham and Women’s Hospital of Harvard Medical School in Boston.

“We found that a typical clonal bacterial population that would otherwise be considered homogeneous using conventional techniques has epigenetically distinct subpopulations with different gene expression patterns," said senior author Gang Fang, PhD, Assistant Professor of Genetics and Genomics at the Icahn School of Medicine at Mount Sinai. “Given that phenotypic heterogeneity within a bacterial population can increase its advantage of survival under stress conditions such as antibiotic treatment, this new technique is quite promising for future treatment of bacterial pathogens as it enables de novo detection and characterization of epigenetic heterogeneity in a bacterial population.”

To put this new method to the test, the researchers studied seven bacterial strains. For Helicobacter pylori—a pathogenic bacterium that colonizes over 40% of the world population and is associated with gastric cancer—the team discovered that epigenetic heterogeneity can quickly emerge as a single cell divides, and different subpopulations with distinct methylation patterns have distinct gene expressions patterns. This may have contributed to the increasing rate of antibiotic resistance of H. pylori, the scientists suggest.

“The application of this new technique will enable a more comprehensive characterization of the functions of DNA methylation and their impact on bacterial physiology. Resolving nucleotide modifications at the single molecule, single nucleotide level, especially when integrated with other single molecule- or single cell-level data such as RNA and protein expression, will help resolve regulatory relationships that govern higher order phenotypes such as drug resistance,” said co-author Eric Schadt, PhD, Professor of Genomics at the Icahn School of Medicine at Mount Sinai. “The approach we developed can also be used to analyze DNA viruses and human mitochondrial DNA, both of which present significant epigenetic heterogeneity.”

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