Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.
Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.
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DOI：
10.1093/dnares/dsy021
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发表时间：
2018-10-01
期刊：
影响因子：
--
通讯作者：
Fujimoto R
中科院分区：
文献类型：
--
作者：
Takahashi S;Osabe K;Fukushima N;Takuno S;Miyaji N;Shimizu M;Takasaki-Yasuda T;Suzuki Y;Dennis ES;Seki M;Fujimoto R
表观遗传基因调控对植物生命至关重要，并且可以涉及各种组蛋白修饰、DNA甲基化和小RNA之间的动态相互作用。对表观基因组信息的详细分析有望揭示基因组的DNA序列是如何翻译成植物的表型的。本研究的目的是在全基因组水平上绘制芜菁DNA甲基化状态，并阐明DNA甲基化与转录、小RNA表达和组蛋白H3赖氨酸9二甲基化（H3 K9 me 2）之间的关系。我们进行了全基因组亚硫酸氢盐测序，小RNA测序，染色质免疫沉淀测序使用H3 K9 me 2抗体在大白菜自交系，RJKB-T24，并检查表观遗传状态对转录的影响。在不同的序列背景（CG、CHG和CHH）（其中H可以是A、C或T）和位置（启动子、外显子、内含子、终止子、散布重复区）中分析DNA中的胞嘧啶甲基化，并且将H3 K9 me 2和24个核苷酸的小干扰RNA（24 nt-siRNA）覆盖在B上。rapa参考基因组。比较了表观基因组与拟南芥表观基因组的差异，讨论了DNA甲基化位点与基因表达的关系，以及24 nt siRNA和H3 K9 me 2的参与。
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 (24 nt-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.
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DOI：
10.1038/nrm4043
发表时间：
2015-09
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Du J;Johnson LM;Jacobsen SE;Patel DJ
通讯作者：
Patel DJ
影响因子：
12.3
作者：
Niederhuth CE;Bewick AJ;Ji L;Alabady MS;Kim KD;Li Q;Rohr NA;Rambani A;Burke JM;Udall JA;Egesi C;Schmutz J;Grimwood J;Jackson SA;Springer NM;Schmitz RJ
通讯作者：
Schmitz RJ
影响因子：
64.5
作者：
Kawakatsu T;Huang SC;Jupe F;Sasaki E;Schmitz RJ;Urich MA;Castanon R;Nery JR;Barragan C;He Y;Chen H;Dubin M;Lee CR;Wang C;Bemm F;Becker C;O'Neil R;O'Malley RC;Quarless DX;1001 Genomes Consortium;Schork NJ;Weigel D;Nordborg M;Ecker JR
通讯作者：
Ecker JR
影响因子：
5.1
作者：
Fujimoto, Ryo;Sasaki, Taku;Nishio, Takeshi
通讯作者：
Nishio, Takeshi
影响因子：
64.8
作者：
Jackson, JP;Lindroth, AM;Jacobsen, SE
通讯作者：
Jacobsen, SE