Methylome diversification through changes in DNA methyltransferase sequence specificity.
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.
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.
Yoshikazu
Y
Furuta
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan.
Hiroe
H
Namba-Fukuyo
National Institute for Basic Biology, Okazaki, Japan.
Tomoko F
TF
Shibata
Advanced Science Research Center, Kanazawa University, Kanazawa, Japan.
Tomoaki
T
Nishiyama
National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan.
Shuji
S
Shigenobu
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan.
Yutaka
Y
Suzuki
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan.
Sumio
S
Sugano
National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan.
Mitsuyasu
M
Hasebe
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.
Ichizo
I
Kobayashi
D001483:Base Sequence; D019175:DNA Methylation / Q000235:genetics*; D015254:DNA Modification Methylases / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D016480:Helicobacter pylori / Q000235:genetics*; D059372:Nucleotide Motifs / Q000235:genetics; D059467:Transcriptome / Q000235:genetics
D015254:DNA Modification Methylases