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.

中文翻译：

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突出的拓扑相关域区分了水稻和拟南芥中的整体染色质堆积。

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，已经报道了在模型双子叶植物拟南芥中的全基因组染色质填充分析^1-4。在千人规模上，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^1-4高度相关。令人惊讶的是，拓扑相关域（TADs），似乎是许多动物物种中基因组包装的普遍结构特征，在拟南芥基因组^1,2,4-6中并不突出。使用全基因组染色质构象捕获方法Hi-C（参考⁷），我们报告了另一种典型植物水稻的高分辨率染色质填充模式。与拟南芥相比，我们揭示了在染色体和局部水平上染色质组织的新结构特征，其中数千种不同的TAD覆盖了大约四分之一的水稻基因组。水稻TAD边界与常染色体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，尽管局部染色质堆积模式基本保持不变，但我们报道了遭受冷胁迫的水稻幼苗中的染色体解聚。在对两种植物物种的比较中已经发现的实质性变化表明，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。