Crop and Pasture Science Crop and Pasture Science Society
Plant sciences, sustainable farming systems and food quality
RESEARCH ARTICLE

Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa

Satoshi Takahashi A H , Naoki Fukushima B H , Kenji Osabe C H , Etsuko Itabashi D , Motoki Shimizu E , Naomi Miyaji B , Takeshi Takasaki-Yasuda B , Yutaka Suzuki F , Motoaki Seki A G and Ryo Fujimoto B I
+ Author Affiliations
- Author Affiliations

A RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

B Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.

C Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.

D Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.

E Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan.

F Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.

G Core Research for Evolutional Science and Technology, Japan Science and Technology, Kawaguchi, Saitama 332-0012, Japan.

H These authors equally contributed to this work.

I Corresponding author. Email: leo@people.kobe-u.ac.jp

Crop and Pasture Science 69(1) 107-120 https://doi.org/10.1071/CP17394
Submitted: 9 December 2016  Accepted: 24 November 2017   Published: 4 January 2018

Abstract

DNA methylation is an epigenetic gene regulatory mechanism that plays an essential role in gene expression, transposon silencing, genome imprinting and plant development. We investigated the influence of DNA methylation on gene expression in Brassica rapa L., to understand whether epigenetic differences exist between inbred lines. Genome-wide DNA methylation was analysed by methylated DNA immunoprecipitation sequencing (MeDIP-seq) of 14-day-old first and second leaves from two inbred lines of Chinese cabbage, one susceptible and one resistant to fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans. MACS (model-based analysis for ChIP-seq) identified DNA methylation peaks in genic regions including 2 kb upstream, exon, intron and 2 kb downstream. More than 65% of genes showed similar patterns of DNA methylation in the genic regions in the two inbred lines. DNA methylation states of the two inbred lines were compared with their transcriptome. Genes having DNA methylation in the intron and in the 200 bp upstream and downstream regions were associated with a lower expression level in both lines. A small number of genes showed a negative correlation between differences in DNA methylation levels and differences in transcriptional levels in the two inbred lines, suggesting that DNA methylation in these genes results in transcriptional suppression.

Additional keywords: epigenetics, fusarium wilt, gene expression, methylome, transposable elements.


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