Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis
Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis
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DOI：
10.1038/s41477-017-0005-9
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发表时间：
2017-09-01
期刊：
影响因子：
18
通讯作者：
Weigel, Detlef
中科院分区：
文献类型：
--
作者：
Liu, Chang;Cheng, Ying-Juan;Weigel, Detlef
基因组的非随机三维组织对于许多细胞过程至关重要。最近，已经报道了在模式双子叶植物拟南芥（Arabidopsis thaliana）中全基因组染色质包装的分析（1-4）。在大规模的调查中，A.拟南芥染色质相互作用网络与一系列基因组和表观基因组特征高度相关（1-4）。令人惊讶的是，拓扑相关结构域（TADs），这似乎是一个普遍的结构特征的基因组包装在许多动物物种，是不突出的A。拟南芥基因组（1，2，4 -6）。使用全基因组染色质构象捕获方法Hi-C（参考文献（7）），我们报告了另一种模式植物水稻的高分辨率染色质包装模式。我们揭示了新的结构特征的染色质组织在染色体和局部水平相比，A。thaliana，具有数千个不同的TADs，覆盖了大约四分之一的水稻基因组。水稻TAD边界与常染色质表观遗传标记和活性基因表达相关，并富含可被植物特异性TCP蛋白识别的序列基序。此外，我们报告染色体解凝聚水稻幼苗经历冷胁迫，尽管当地的染色质包装模式基本保持不变。在比较两种植物物种时已经发现的大量变异表明，植物中的染色质组织可能比多细胞动物中的染色质组织更多样化。
The non-random three-dimensional organization of genomes is critical for many cellular processes. Recently, analyses of genome-wide chromatin packing in the model dicot plant Arabidopsis thaliana have been reported(1-4). At a kilobase scale, the A. thaliana chromatin interaction network is highly correlated with a range of genomic and epigenomic features(1-4). Surprisingly, topologically associated domains (TADs), which appear to be a prevalent structural feature of genome packing in many animal species, are not prominent in the A. thaliana genome(1,2,4-6). Using a genome-wide chromatin conformation capture approach, Hi-C (ref. (7)), we report high-resolution chromatin packing patterns of another model plant, rice. We unveil new structural features of chromatin organization at both chromosomal and local levels compared to A. thaliana, with thousands of distinct TADs that cover about a quarter of the rice genome. The rice TAD boundaries are associated with euchromatic epigenetic marks and active gene expression, and enriched with a sequence motif that can be recognized by plant-specific TCP proteins. In addition, we report chromosome decondensation in rice seedlings undergoing cold stress, despite local chromatin packing patterns remaining largely unchanged. The substantial variation found already in a comparison of two plant species suggests that chromatin organization in plants might be more diverse than in multicellular animals.