CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize.
CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize.
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DOI：
10.1101/gr.146985.112
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发表时间：
2013-04
期刊：
影响因子：
7
通讯作者：
Dawe RK
中科院分区：
文献类型：
--
作者：
Gent JI;Ellis NA;Guo L;Harkess AE;Yao Y;Zhang X;Dawe RK
在多种植物、真菌和动物中，小rna介导的染色质结构调控是抑制不需要的遗传活性的重要手段。特别是在植物中，24-nt sirna在一个被称为rna定向DNA甲基化（RdDM）的过程中指导重复DNA的从头甲基化，无论是外源的还是内源的。新甲基化机制的许多组成部分最近已经被确定，包括多种RNA聚合酶，但触发甲基化的特定遗传特征仍然知之甚少。通过对玉米进行全基因组亚硫酸盐测序，我们发现靠近细胞基因的转座子（特别是在基因开始或结束的1kb范围内）与从头甲基化密切相关，24-nt sirna和CHH序列背景下的甲基化都证明了这一点。此外，我们发现转座子的主要类别表现出由邻近基因决定的CHH甲基化梯度。我们的研究结果进一步表明，玉米基因间染色质存在两种主要形式，根据与基因的接近程度来区分：一种形式以密集的CG和CHG甲基化和缺乏转录为标志，另一种形式以CHH甲基化和多种形式RNA聚合酶的活性为标志。后者的存在，我们称之为CHH岛，可能对细胞基因表达如何与大基因组中直接相邻的转座子抑制协调有影响，在转座子的环境中散布着复杂的基因组织。
Small RNA-mediated regulation of chromatin structure is an important means of suppressing unwanted genetic activity in diverse plants, fungi, and animals. In plants specifically, 24-nt siRNAs direct de novo methylation to repetitive DNA, both foreign and endogenous, in a process known as RNA-directed DNA methylation (RdDM). Many components of the de novo methylation machinery have been identified recently, including multiple RNA polymerases, but specific genetic features that trigger methylation remain poorly understood. By applying whole-genome bisulfite sequencing to maize, we found that transposons close to cellular genes (particularly within 1 kb of either a gene start or end) are strongly associated with de novo methylation, as evidenced both by 24-nt siRNAs and by methylation specifically in the CHH sequence context. In addition, we found that the major classes of transposons exhibited a gradient of CHH methylation determined by proximity to genes. Our results further indicate that intergenic chromatin in maize exists in two major forms that are distinguished based on proximity to genes—one form marked by dense CG and CHG methylation and lack of transcription, and one marked by CHH methylation and activity of multiple forms of RNA polymerase. The existence of the latter, which we call CHH islands, may have implications for how cellular gene expression could be coordinated with immediately adjacent transposon repression in a large genome with a complex organization of genes interspersed in a landscape of transposons.
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影响因子：
14.9
作者：
Gent JI;Dong Y;Jiang J;Dawe RK
通讯作者：
Dawe RK
影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
56.9
作者：
Erhard, Karl F., Jr.;Stonaker, Jennifer L.;Hollick, Jay B.
通讯作者：
Hollick, Jay B.
影响因子：
4.5
作者：
Burkhart KB;Guang S;Buckley BA;Wong L;Bochner AF;Kennedy S
通讯作者：
Kennedy S
DOI：
10.1038/nrg2719
发表时间：
2010-03
期刊：
Nature reviews. Genetics
影响因子：
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作者：
通讯作者：
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