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Nanopore detection of bacterial DNA base modifications

By Alexa B.R. McIntyre, Noah Alexander, Aaron S. Burton, Sarah Castro-Wallace, Charles Y. Chiu, Kristen K. John, Sarah E. Stahl, Sheng Li, Christopher E. Mason

Posted 13 Apr 2017
bioRxiv DOI: 10.1101/127100 (published DOI: 10.1038/s41467-019-08289-9)

The common bacterial base modification N6-methyladenine (m6A) is involved in many pathways related to an organism's ability to survive and interact with its environment. Recent research has shown that nanopore sequencing can detect m5C with per-read accuracy of upwards of 80% but m6A with significantly lower accuracy. Here we use a binary classifier to improve m6A classification by marking adenines as methylated or unmethylated based on differences between measured and expected current values as each adenine travels through the nanopore. We also illustrate the importance of read quality for base modification detection and compare to PacBio methylation calls. With recent demonstrations of nanopore sequencing in Antarctica and onboard the International Space Station, the ability to reliably characterize m6A presents an opportunity to further examine the role of methylation in bacterial adaptation to extreme environments.

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