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Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.

TitleSingle-molecule sequencing detection of N6-methyladenine in microbial reference materials.
Publication TypeJournal Article
Year of Publication2019
AuthorsMcIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE
JournalNat Commun
Volume10
Issue1
Pagination579
Date Published2019 Feb 04
ISSN2041-1723
Abstract

The DNA base modification N6-methyladenine (mA) is involved in many pathways related to the survival of bacteria and their interactions with hosts. Nanopore sequencing offers a new, portable method to detect base modifications. Here, we show that a neural network can improve mA detection at trained sequence contexts compared to previously published methods using deviations between measured and expected current values as each adenine travels through a pore. The model, implemented as the mCaller software package, can be extended to detect known or confirm suspected methyltransferase target motifs based on predictions of methylation at untrained contexts. We use PacBio, Oxford Nanopore, methylated DNA immunoprecipitation sequencing (MeDIP-seq), and whole-genome bisulfite sequencing data to generate and orthogonally validate methylomes for eight microbial reference species. These well-characterized microbial references can serve as controls in the development and evaluation of future methods for the identification of base modifications from single-molecule sequencing data.

DOI10.1038/s41467-019-08289-9
Alternate JournalNat Commun
PubMed ID30718479
PubMed Central IDPMC6362088
Grant ListR01 MH117406 / MH / NIMH NIH HHS / United States