MeStudio: crossing methylation and genomic features for comparative epigenomic analyses

Abstract

DNA methylation is one of the most relevant 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 epigenomics landscape of individuals and populations. Here, we present MeStudio, a pipeline which allows to analyse and combine genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDS) and noncoding sequences, including both intergenic sequences, and sequences upstream to CDS. We show the usage and performances of MeStudio on a set of single-molecule real time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti. MeStudio is freely available under an open source GPLv3 license at https://github.com/combogenomics/MeStudio

Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges

“…To extract DNA methylation information from sequencing data and directly quantify and compare the position of methylated sites with respect to genome-derived features (e.g., coding and non-coding regions), bioinformatic pipelines are needed. The position of methylated sites throughout the genome is of key importance when the interest is in understanding the role that epigenetic modifications have in gene expression control and phenotypic plasticity [68]. The integration of computational methods with experimental approaches is vital for predicting methylation motifs in prokaryotic genomes.…”

“…Tools have also been developed to analyze DNA methylation profiles on metagenomic data (https://github.com/hoonjeseong/Meta-epigenomics (accessed on 15 March 2024), but all of these computational packages do not offer the possibility of mapping methylated motifs with respect to annotated functional features of the genomes (e.g., coding sequences, promoters, or other relevant features or genomic positions). Our laboratory recently developed a pipeline (MeStudio [68]) for extracting DNA methylation information from SMRT sequencing data, allowing for the comparison of the position of methylated motifs with respect to the genome annotation. Report outputs can be used to compare the methylation status of DNA regions in different environmental contexts or to perform genome-wide comparisons of strains.…”

“…recently developed a pipeline (MeStudio [68]) for extracting DNA methylation information from SMRT sequencing data, allowing for the comparison of the position of methylated motifs with respect to the genome annotation. Report outputs can be used to compare the methylation status of DNA regions in different environmental contexts or to perform genome-wide comparisons of strains.…”

“…However, even this tool needs improvement, since we can measure the methylated bases not included in motifs only indirectly and the input from Nanopore ONT sequencing cannot be processed at the moment. Here, the MeStudio [68] workflow is shown. Starting from genome sequencing obtained by the SMRT sequencing technique and genome annotation file, the recurrent methylated DNA motifs identified are searched within the genome sequence(s).…”

“…Figure 2.An analysis of genome-wide DNA methylation data. Here, the MeStudio[68] workflow is shown. Starting from genome sequencing obtained by the SMRT sequencing technique and genome annotation file, the recurrent methylated DNA motifs identified are searched within the genome sequence(s).…”