Genome-wide systematic identification of methyltransferase recognition and modification patterns

Abstract

Genome-wide analysis of DNA methylation patterns using single molecule real-time DNA sequencing has boosted the number of publicly available methylomes. However, there is a lack of tools coupling methylation patterns and the corresponding methyltransferase genes. Here we demonstrate a high-throughput method for coupling methyltransferases with their respective motifs, using automated cloning and analysing the methyltransferases in vectors carrying a strain-specific cassette containing all potential target sites. To validate the method, we analyse the genomes of the thermophile Moorella thermoacetica and the mesophile Acetobacterium woodii, two acetogenic bacteria having substantially modified genomes with 12 methylation motifs and a total of 23 methyltransferase genes. Using our method, we characterize the 23 methyltransferases, assign motifs to the respective enzymes and verify activity for 11 of the 12 motifs.

Fig. 1

MetMap workflow. The box designated “automated” indicates the steps that were automated. The variance in the occurrence of motifs in the motif-cassette depends on the nature of the motifs; A motif including unspecific regions of 2–10 n’s (typical for Type I motifs) is present 12 times in the cassette, whereas motifs not including such regions is repeated 10 times

Fig. 2

Handling of the sequences. a mapping based selection of the sequences based upon the motif cassette; b 2nd round of mapping based selection based upon both the motif cassette and the gene coding for the methyltransferases; c analysing the grouped sequences though the ‘Modification and Motif_Analysis’ pipeline