Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool

DNA methylation is one of the most observed epigenetic modifications. It is present in eukaryotes and prokaryotes and is related to several biological phenomena, including gene flow and adaptation to environmental conditions. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomic landscape of individuals and populations. Here, we present a pipeline named MeStudio, with the aim of analyzing and combining genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDSs) and noncoding sequences, including both intergenic sequences and sequences upstream of the CDS. We apply this novel tool, showing the usage and performance of MeStudio, on a set of single-molecule real-time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti.

Automated summary

DNA methylation is a commonly observed epigenetic modification found in both eukaryotes and prokaryotes, and it is implicated in various biological phenomena such as gene regulation and adaptation to the environment. Advances in third-generation sequencing technologies have enabled the direct detection of genome-wide methylation profiles, providing opportunities to understand and utilize the epigenomic landscape at the individual and population levels. Here, we introduce a pipeline called MeStudio, which analyzes and combines genome-wide methylation profiles with genomic features, allowing for the identification of DNA methylation in coding and noncoding sequences. We demonstrate the utility and performance of MeStudio using single-molecule real-time sequencing outputs from Sinorhizobium meliloti strains.