CAREER: Investigating the dynamic interplay between DNA methylation and bacterial evolution

Epigenetics refers to heritable changes in the genome that alter gene expression and chromosome structure without altering the underlying DNA sequence. These changes can come in the form of DNA methylation, which are small chemical additions to the DNA, or in chromosome-associated proteins which package the DNA into organized structures. While the role of epigenetics in organisms such as plants, animals, and fungi is well established, its evolutionary significance in bacteria remains poorly understood. Recent observations suggest that the proteins bacteria use to organize their DNA and respond to stress may interact with DNA methylation, pointing to a previously unrecognized link between epigenetics and adaptation. By examining the interplay between these molecular processes over time, this research will advance foundational knowledge of genome evolution and the principles governing how bacteria respond to environmental challenges. This project utilizes cutting-edge DNA sequencing technologies, machine learning algorithms, and high-performance computing to identify methylation targets and will contribute to the progress of science by developing new experimental and computational approaches for studying genome structure and evolution in microbes. It also integrates research and education by engaging undergraduate students in discovery-driven learning at the intersection of microbiology, genomics, and data science, helping to build a skilled workforce in bioinformatics and biotechnology. DNA methylation is a widespread but poorly understood feature of bacterial genomes, with potential to influence gene regulation, phenotypic plasticity, and evolutionary dynamics. Despite its prevalence, the role of epigenetic modifications in bacterial evolution remains largely unexplored. This project seeks to investigate the bidirectional relationship between DNA methylation and evolutionary change by combining experimental evolution, synthetic biology, and genomic analyses. Specifically, it will (1) reconstruct evolved mutations in nucleoid-associated proteins identified through long-term evolution experiments to determine their effects on the methylome, gene expression, and organismal fitness, and (2) engineer heterologous DNA methylation systems into Escherichia coli to assess how novel methylation patterns influence evolutionary trajectories. Together, these approaches will establish a generalizable framework for studying bacterial epigenetics in an evolutionary context. The anticipated outcomes include new insights into how DNA methylation contributes to gene regulation, adaptation, and genome evolution, thereby expanding evolutionary understanding to incorporate epigenetic mechanisms. Experiments will also produce libraries of E. coli with novel methylation systems creating a resource that may enable genetics in previously untractable systems. In parallel, the project will advance bioinformatics literacy through the development of a course-based undergraduate research experience (CURE) that engages biology and data-science students in analyzing microbial genomic data and discovering novel DNA methylation systems though single-molecule DNA sequencing and bioinformatics. Producing new insights into epigenetic variation across the bacterial tree of life, while training students in interdisciplinary, data-intensive approaches central to modern biology. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria. NSF Award ID: 2540620 | Program: 01002627DB NSF RESEARCH & RELATED ACTIVIT,01003031DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: Megan Behringer | Institution: Vanderbilt University, NASHVILLE, TN | Award Amount: $1,032,370 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2540620 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2540620.html