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Furuta Y, Namba-Fukuyo H, Shibata TF, Nishiyama T, Shigenobu S, Suzuki Y, Sugano S, Hasebe M, Kobayashi I. Methylome diversification through changes in DNA methyltransferase sequence specificity. PLoS Genet 2014; 10:e1004272. [PMID: 24722038 PMCID: PMC3983042 DOI: 10.1371/journal.pgen.1004272] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 02/13/2014] [Indexed: 12/20/2022] Open
Abstract
Epigenetic modifications such as DNA methylation have large effects on gene expression and genome maintenance. Helicobacter pylori, a human gastric pathogen, has a large number of DNA methyltransferase genes, with different strains having unique repertoires. Previous genome comparisons suggested that these methyltransferases often change DNA sequence specificity through domain movement--the movement between and within genes of coding sequences of target recognition domains. Using single-molecule real-time sequencing technology, which detects N6-methyladenines and N4-methylcytosines with single-base resolution, we studied methylated DNA sites throughout the H. pylori genome for several closely related strains. Overall, the methylome was highly variable among closely related strains. Hypermethylated regions were found, for example, in rpoB gene for RNA polymerase. We identified DNA sequence motifs for methylation and then assigned each of them to a specific homology group of the target recognition domains in the specificity-determining genes for Type I and other restriction-modification systems. These results supported proposed mechanisms for sequence-specificity changes in DNA methyltransferases. Knocking out one of the Type I specificity genes led to transcriptome changes, which suggested its role in gene expression. These results are consistent with the concept of evolution driven by DNA methylation, in which changes in the methylome lead to changes in the transcriptome and potentially to changes in phenotype, providing targets for natural or artificial selection.
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Affiliation(s)
- Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Hiroe Namba-Fukuyo
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | | | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
- * E-mail:
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