Mapping DNA Methylation to Methyltransferases in Microbial Communities
Author
Bøjer, Jeppe Støtt
Term
4. term
Education
Publication year
2025
Pages
55
Abstract
Across all domains of life, the genetic code is overlaid with epigenetic modifications that ex-tend beyond the primary nucleotide sequence. The most common and nearly universal mech-anism of epigenetic signaling is DNA methylation. In bacteria, it modulates a range of biologi-cal processes, including host defense mechanisms, cell cycle regulation, gene expression, and virulence. This modification is facilitated by DNA methyltransferases, which dictate the methylation patterns of bacterial genomes in a motif-specific manner, often differing among species and strains. Recent technological advances in Nanopore sequencing now enable the direct detection of DNA methylation from a standard sequencing run. Despite this, only a few efforts have been made to utilize ONT methylation calls for methylation motif discovery in bac-teria, but none which scales or extends motif discovery to metagenome sequencing of micro-bial communities. To address this, we developed Nanomotif, a fast, scalable, bioinformatic tool for identification and utilization of methylation motifs in metagenomic samples. The MTa-se-linker submodule of Nanomotif replaces existing manual and non-scalable methods with a modern, user-friendly bioinformatics tool that pairs methylation motifs to their cognate DNA methyltransferases. In the era of metagenomics, tools like this are essential for faster epige-netic profiling across entire microbial communities. Motif-methyltransferase pairs not only help circumvent restriction-modification barriers but also open new avenues to explore the func-tional roles of methylation and its implications for microbial physiology and ecology.
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