MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing
Crits-Christoph, A.; Kang, S. C.; Lee, H. H.; Ostrov, N.
Show abstract
Bacteria and archaea use restriction-modification (R-M) systems to distinguish self from foreign DNA by methylating their genomes with DNA methyltransferases with diverse sequence specificities, and these immunity systems often vary at the strain level. Identifying active methylation patterns and R-M systems can reveal barriers to the introduction of recombinant DNA or phage infection. Here, we present the computational MicrobeMod toolkit for identifying 5mC and 6mA methylation sequence motifs and R-M systems in bacterial genomes using nanopore sequencing of native DNA. We benchmark this approach on a set of reference E. coli strains expressing methyltransferases with known specificities. We then applied these analyses to 31 diverse bacterial and archaeal organisms to reveal the methylation patterns of strains with previously unexplored epigenetics, finding that prokaryotic 5-methylcytosine may be more common than previously reported. In summary, MicrobeMod can rapidly reveal new epigenetics within a prokaryotic genome sequenced with Oxford Nanopore R10.4.1 flow cells at sequencing depths as low as 10x and only requires native DNA. This toolkit can be used to advance fundamental knowledge of bacterial methylation and guide strategies to overcome R-M barriers of genetic tractability in non-model microbes.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Rapid Identification of Methylase Specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes 96%
- vRhyme enables binning of viral genomes from metagenomes 95%
- Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems 94%
Similar papers in this journal
- Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes 95%
- BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes 94%
- Illumina Complete Long Read Assay yields contiguous bacterial genomes from human gut metagenomes 94%
Similar papers in this journal
- Differential adenine methylation analysis reveals increased variability in 6mA in the absence of methyl-directed mismatch repair 96%
- REC protein family expansion by the emergence of a new signaling pathways 93%
- Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.