4.3 Article Proceedings Paper

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

期刊

CROP & PASTURE SCIENCE
卷 69, 期 1, 页码 107-120

出版社

CSIRO PUBLISHING
DOI: 10.1071/CP17394

关键词

epigenetics; fusarium wilt; gene expression; methylome; transposable elements

资金

  1. MEXT KAKENHI [221S0002]
  2. Open Partnership Joint Projects of JSPS Bilateral Joint Research Projects [14544567]
  3. RIKEN [2478002, 24113509, 15H05614]
  4. Japan Science and Technology Agency (JST) [Core Research for Evolutionary Science and Technology (CREST)] [JPMJCR13B4]
  5. Grants-in-Aid for Scientific Research [16H06279, 15H05614] Funding Source: KAKEN

向作者/读者索取更多资源

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.

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