Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

被引：17

作者：

Takahashi, Satoshi ^{[1
]}

Osabe, Kenji ^{[2
]}

Fukushima, Naoki ^{[3
]}

Takuno, Shohei ^{[4
]}

Miyaji, Naomi ^{[3
]}

Shimizu, Motoki ^{[5
]}

Takasaki-Yasuda, Takeshi ^{[3
]}

Suzuki, Yutaka ^{[6
]}

Dennis, Elizabeth S. ^{[7
,8
]}

Seki, Motoaki ^{[1
,9
,10
]}

Fujimoto, Ryo ^{[3
]}

机构：

[1] RIKEN, Ctr Sustainable Resource Sci, Yokohama, Kanagawa 2300045, Japan

[2] Grad Univ, Okinawa Inst Sci & Technol, Plant Epigenet Unit, Onna Son, Okinawa 9040495, Japan

[3] Kobe Univ, Grad Sch Agr Sci, Nada Ku, Kobe, Hyogo 6578501, Japan

[4] Grad Univ Adv Studies, SOKENDAI, Dept Evolutionary Studies Biosyst, Hayama, Kanagawa 2400193, Japan

[5] Iwate Biotechnol Res Ctr, Narita Kitakami, Iwate 0240003, Japan

[6] Univ Tokyo, Grad Sch Frontier Sci, Dept Computat Biol, Kashiwa, Chiba 2770882, Japan

[7] CSIRO Agr & Food, Canberra, ACT 2601, Australia

[8] Univ Technol Sydney, POB 123, Broadway, NSW 2007, Australia

[9] Japan Sci & Technol, Core Res Evolut Sci & Technol, Kawaguchi, Saitama 3320012, Japan

[10] RIKEN, Cluster Pioneering Res, Wako, Saitama 3510198, Japan

来源：

DNA RESEARCH | 2018年 / 25卷 / 05期

基金：

日本科学技术振兴机构;

关键词：

DNA methylation; histone H3 lysine 9 di-methylation; small RNA; epigenetic; Brassica; ARABIDOPSIS-THALIANA; EPIGENETIC VARIATION; PATTERNS; GENES; IDENTIFICATION; SEQUENCES; EPIGENOME;

D O I：

10.1093/dnares/dsy021

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Epigenetic gene regulation is crucial to plant life and can involve dynamic interactions between various histone modifications, DNA methylation, and small RNAs. Detailed analysis of epigenome information is anticipated to reveal how the DNA sequence of the genome is translated into the plant's phenotype. The aim of this study was to map the DNA methylation state at the whole genome level and to clarify the relationship between DNA methylation and transcription, small RNA expression, and histone H3 lysine 9 di-methylation (H3K9me2) in Brassica rapa. We performed whole genome bisulfite sequencing, small RNA sequencing, and chromatin immunoprecipitation sequencing using H3K9me2 antibody in a Chinese cabbage inbred line, RJKB-T24, and examined the impact of epigenetic states on transcription. Cytosine methylation in DNA was analysed in different sequence contexts (CG, CHG, and CHH) (where H could be A, C, or T) and position (promoter, exon, intron, terminator, interspersed repeat regions), and the H3K9me2 and 24 nucleotide small interfering RNAs (24nt-siRNA) were overlaid onto the B. rapa reference genome. The epigenome was compared with that of Arabidopsis thaliana and the relationship between the position of DNA methylation and gene expression, and the involvement of 24 nt siRNAs and H3K9me2 are discussed.

引用

页码：511 / 520

页数：10

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