Single-molecule sequencing technology assists microbial DNA methylation study

Researchers sequenced 230 diverse archaeal and bacterial genomes to learn more about the roles DNA methylation plays in prokaryotes. 

The epigenome of a cell is the collected set of changes made to specific bases in its genomic DNA that affect how the genome is actually used and results from chemical modification (usually methylation.) Uncovering the breadth of the planet's microbial epigenomic diversity can help researchers better understand the biology of microbes that play a role in the global nutrient cycles, as well as revealing genomic regulatory systems that could be useful for energy and environment applications.

DNA methylation, the most common epigenetic change, is a process eukaryotes use to regulate gene expression, for example, keeping certain genes from turning on. Though prokaryotes (bacteria and archaea) are also known to have methylated DNA, the roles this process might play in these single cell organisms is less well understood.

To learn more, a team including researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), relied on single-molecule, real-time (SMRT) sequencing at the DOE JGI and Pacific Biosciences to reveal DNA methylation patterns in 230 bacterial and archaeal genomes.

They found evidence of DNA methylation in 215 microbes (93 percent of those sequenced). While many DNA methylating enzymes are part of restriction modification systems, consistent with their known role in defense against phages and viruses, the findings suggest that a substantial number of others may be involved in genome regulation, and have a more crucial role in prokaryotic physiology and biology than had been previously suspected.