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Title: Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community
Authors: Hiraoka, Satoshi
Okazaki, Yusuke
Anda, Mizue
Toyoda, Atsushi
Nakano, Shin-ichi
Iwasaki, Wataru
Author's alias: 平岡, 聡史
岡崎, 友輔
按田, 瑞恵
豊田, 敦
中野, 伸一
岩崎, 渉
Keywords: Environmental microbiology
Methylation analysis
Microbial ecology
Microbial genetics
Issue Date: 11-Jan-2019
Publisher: Springer Nature
Journal title: Nature Communications
Volume: 10
Thesis number: 159
Abstract: DNA methylation plays important roles in prokaryotes, and their genomic landscapes--prokaryotic epigenomes--have recently begun to be disclosed. However, our knowledge of prokaryotic methylation systems is focused on those of culturable microbes, which are rare in nature. Here, we used single-molecule real-time and circular consensus sequencing techniques to reveal the ‘metaepigenomes’ of a microbial community in the largest lake in Japan, Lake Biwa. We reconstructed 19 draft genomes from diverse bacterial and archaeal groups, most of which are yet to be cultured. The analysis of DNA chemical modifications in those genomes revealed 22 methylated motifs, nine of which were novel. We identified methyltransferase genes likely responsible for methylation of the novel motifs, and confirmed the catalytic specificities of four of them via transformation experiments using synthetic genes. Our study highlights metaepigenomics as a powerful approach for identification of the vast unexplored variety of prokaryotic DNA methylation systems in nature.
Rights: © The Author(s) 2019. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
DOI(Published Version): 10.1038/s41467-018-08103-y
PubMed ID: 30635580
Appears in Collections:Journal Articles

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