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4 January 2018 Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa
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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.

© CSIRO 2018
Satoshi Takahashi, Naoki Fukushima, Kenji Osabe, Etsuko Itabashi, Motoki Shimizu, Naomi Miyaji, Takeshi Takasaki-Yasuda, Yutaka Suzuki, Motoaki Seki, and Ryo Fujimoto "Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa," Crop and Pasture Science 69(1), 107-120, (4 January 2018).
Received: 9 December 2016; Accepted: 1 November 2017; Published: 4 January 2018

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