Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L.

Mr Hasan Mehraj1, Dr Satoshi Takahashi2, Dr Yutaka  Suzuki3, Dr Motoaki Seki2,4,5, Dr Elizabeth S.  Dennis6,7, Dr Ryo  Fujimoto1 

1Kobe University, Nada-Ku, Kobe, Japan,
2RIKEN Center for Sustainable Resource Science, Yokohama, Japan,
3Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan, 4RIKEN Cluster for Pioneering Research, Saitama, Japan,
5Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan,
6CSIRO Agriculture and Food, Canberra, Australia,
7School of Life Sciences, Faculty of Science, University of Technology, Sydney, Australia

Brassica rapa L. is an important agricultural crop that includes many important vegetables such as Chinese cabbage, pak choi, turnip etc. B. rapa has experienced whole-genome triplication that generates three subgenomes (LF, MF1, and MF2). Covalent modifications of histone proteins act as epigenetic regulators of gene expression. We report the distribution of two active histone marks (H3K4me3 and H3K36me3) in 14-day leaves in two lines of B. rapa by chromatin immunoprecipitation sequencing. Both lines were enriched with H3K4me3 and H3K36me3 marks at the transcription start site, and the transcription level of a gene was associated with the level of H3K4me3 and H3K36me3. The expression of H3K4me3- and H3K36me3-marked genes had a low level of tissue specificity. Genes with both H3K4me3 and H3K36me3 had a high level of expression and were constitutively expressed. Bivalent active and repressive histone modifications such as H3K4me3 and H3K27me3 marks or antagonistic coexistence of H3K36me3 and H3K27me3 marks were observed in some genes. Expression may be influenced by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. The presence of H3K36me3 marks but not H3K4me3 marks was associated with different levels of gene expression or tissue specificity between paralogous pairs of genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes.

Keywords: histone H3 lysine 4 tri-methylation, histone H3 lysine 36 tri-methylation, epigenetics, subfunctionalization, Brassica

Correspondence: Ryo Fujimoto [leo@people.kobe-u.ac.jp]


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