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

Hasan Mehraj; Satoshi Takahashi; Naomi Miyaji; Ayasha Akter; Yutaka Suzuki; Motoaki Seki; Elizabeth S Dennis; Ryo Fujimoto

doi:10.3389/fpls.2021.659634

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

Front Plant Sci. 2021 Jun 7:12:659634. doi: 10.3389/fpls.2021.659634. eCollection 2021.

Authors

Hasan Mehraj¹, Satoshi Takahashi², Naomi Miyaji¹, Ayasha Akter^{1

3}, Yutaka Suzuki⁴, Motoaki Seki^{2

5

6}, Elizabeth S Dennis^{7

8}, Ryo Fujimoto¹

Affiliations

¹ Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
² RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
³ Department of Horticulture, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh, Bangladesh.
⁴ Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
⁵ RIKEN Cluster for Pioneering Research, Saitama, Japan.
⁶ Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
⁷ CSIRO Agriculture and Food, Canberra, ACT, Australia.
⁸ School of Life Sciences, Faculty of Science University of Technology, Sydney, NSW, Australia.

Abstract

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 Brassica rapa L. 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. H3K4me3- and H3K36me3-marked genes showed low tissue-specific gene expression, and 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 susceptible to changes by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. We showed that the presence of H3K36me3 marks was associated with different gene expression levels or tissue specificity between paralogous paired genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes.

Keywords: brassica; epigenetics; histone H3 lysine 36 tri-methylation; histone H3 lysine 4 tri-methylation; subfunctionalization.