Mapping DNA Methylation to Methyltransferases in Microbial Communities

Bøjer, Jeppe Støtt

4. term

Biotechnology, Master

2025

2025-08-06

55 pages

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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