Proteomics

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Snapper: a high-sensitive algorithm to detect methylation motifs based on Oxford Nanopore reads

ABSTRACT: The Oxford Nanopore technology has a great potential for the analysis of genome methylation, including full-genome methylome profiling. However, there are certain issues while identifying methylation motif sequences caused by low sensitivity of the currently available motif enrichment algorithms. Here, we present Snapper, a new highly-sensitive approach to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper has shown higher enrichment sensitivity compared with the MEME tool coupled with Tombo or Nanodisco instruments, which was demonstrated on H. pylori strain J99 studied earlier using the PacBio technology. In addition, we used Snapper to characterize the total methylome of a new H.pylori strain A45. The analysis revealed the presence of at least 4 methylation sites that have not been described for H. pylori earlier. We experimentally confirmed a new CCAG-specific methyltransferase and indirectly inferred a new CCAAK-specific methyltransferase.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Helicobacter Pylori J99 (campylobacter Pylori J99)

SUBMITTER: Ivan Butenko  

LAB HEAD: Ivan Butenko

PROVIDER: PXD038899 | Pride | 2024-01-26

REPOSITORIES: Pride

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<h4>Motivation</h4>The Oxford Nanopore technology has a great potential for the analysis of methylated motifs in genomes, including whole-genome methylome profiling. However, we found that there are no methylation motifs detection algorithms, which would be sensitive enough and return deterministic results. Thus, the MEME suit does not extract all Helicobacter pylori methylation sites de novo even using the iterative approach implemented in the most up-to-date methylation analysis tool Nanodisco  ...[more]

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