Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery.
Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery.
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DOI：
10.1101/gr.215186.116
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发表时间：
2017-07
期刊：
影响因子：
7
通讯作者：
Liu C
中科院分区：
文献类型：
--
作者：
Bi X;Cheng YJ;Hu B;Ma X;Wu R;Wang JW;Liu C
核空间不是一个同质的生化环境。许多研究表明，基因的转录活性与其在核空间中的位置有关。随着转录抑制染色质区域lamin-associated domains （LADs）的发现，染色质在核周围的非随机定位及其生物学相关性在动物中得到了广泛的研究。然而，目前尚不清楚植物中是否存在类似的染色质组织。在这里，使用限制性内切酶介导的染色质免疫沉淀策略，我们提出了在拟南芥细胞核外周区染色质非随机结构域组织的全基因组鉴定。我们表明，在各种组织中，染色体臂上10%-20%的区域锚定在核周围，这些区域在不同组织之间很大程度上重叠。与动物中的LADs不同，植物中已识别的结构域既不缺乏基因，也不富含A/ t。这些结构域富含沉默的蛋白质编码基因、转座元件基因和异色标记，它们共同定义了一个受抑制的环境。此外，这些结构域与我们的全基因组染色质相互作用数据集（Hi-C）密切相关，在很大程度上解释了Hi-C图谱上揭示的染色质区室的模式。此外，我们的研究结果揭示了调节转座元件沉默的不同DNA甲基化途径的空间间隔，其中位于核周围和内部的转座元件的CHH甲基化分别优先由CMT2和DRM甲基转移酶介导。综上所述，这些结果证明了拟南芥基因组在核空间中的功能分配。
The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonrandom positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme–mediated chromatin immunoprecipitation, we present genome-wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10%–20% of the regions on the chromosome arms are anchored at the nuclear periphery, and these regions largely overlap between different tissues. Unlike LADs in animals, the identified domains in plants are not gene-poor or A/T-rich. These domains are enriched with silenced protein-coding genes, transposable element genes, and heterochromatic marks, which collectively define a repressed environment. In addition, these domains strongly correlate with our genome-wide chromatin interaction data set (Hi-C) by largely explaining the patterns of chromatin compartments, revealed on Hi-C maps. Moreover, our results reveal a spatial compartment of different DNA methylation pathways that regulate silencing of transposable elements, where the CHH methylation of transposable elements located at the nuclear periphery and in the interior are preferentially mediated by CMT2 and DRM methyltransferases, respectively. Taken together, the results demonstrate functional partitioning of the Arabidopsis genome in the nuclear space.