Bacterial epigenomics: Epigenetics in the age of population genomics

Poyin Chen, D. J.Darwin Bandoy, Bart C. Weimer

Research output: Chapter in Book/Report/Conference proceedingChapter


Genome methylation in bacteria is an area of intense interest because it has broad implications for bacteriophage resistance, replication, genomic diversity via replication fidelity, response to stress, gene expression regulation, and virulence. Increasing interest in bacterial DNA modification is coming about with investigation of host/microbe interactions and the microbiome association and coevolution with the host organism. Since the recognition of DNA methylation being important in Escherichia coli and bacteriophage resistance using restriction/modification systems, more than 43,600 restriction enzymes have been cataloged in more than 3600 different bacteria. While DNA sequencing methods have made great advances there is a dearth of method advances to examine these modifications in situ. However, the large increase in whole genome sequences has led to advances in defining the modification status of single genomes as well as mining new restriction enzymes, methyltransferases, and modification motifs. These advances provide the basis for the study of pan-epigenomes, population-scale comparisons among pangenomes to link replication fidelity and methylation status along with mutational analysis of mutLS. Newer DNA sequencing methods that include SMRT and nanopore sequencing will aid the detection of DNA modifications on the everincreasing whole genome and metagenome sequences that are being produced. As more sequences become available, larger analyses are being done to provide insight into the role and guidance of bacterial DNA modification to bacterial survival and physiology.

Original languageEnglish (US)
Title of host publicationThe Pangenome
Subtitle of host publicationDiversity, Dynamics and Evolution of Genomes
PublisherSpringer International Publishing
Number of pages20
ISBN (Electronic)9783030382810
ISBN (Print)9783030382803
StatePublished - Jun 22 2020


  • Direct RNA sequencing
  • Gene expression
  • Population bacterial genomics
  • Whole genome sequencing

ASJC Scopus subject areas

  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Mathematics(all)
  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)


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