Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP

Abstract

Bacterial DNA methylation is involved in diverse cellular functions ranging from modulation of gene expression, DNA repair, and restriction-modification systems for defense against viruses and other foreign DNA. Methylome analysis determines sites within a bacterial chromosome that are methylated, revealing motifs that may be targeted by native restriction enzymes. Identification of these motifs is therefore critical to making an organism genetically tractable, where mimicking the methylome patterns in Escherichia coli allows plasmid DNA to be protected from restriction in the target organism and can therefore drastically enhance transformation efficiency. Oxford Nanopore Technologies (ONT) sequencing can detect methylated bases during sequencing, but software is needed to identify the corresponding methylated motifs within the data. Here, we develop MIJAMP (MIJAMP Is Just A MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONTs Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating false, under-, or overexplained motifs. MIJAMP can also report methylation data on a specific, user-defined motif. Using MIJAMP, we determined the methylated motifs both in a control strain (wild type E. coli) and in Picosynecococcus sp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available at https://code.ornl.gov/alexander-public/mijamp/.