3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments
3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments
复制标题
由局部 A/B 区室确定的大型植物基因组的 3D 染色质结构。
DOI：
10.1016/j.molp.2017.11.005
复制
发表时间：
2017-12-04
期刊：
影响因子：
27.5
通讯作者：
Zhong, Silin
中科院分区：
文献类型：
--
作者：
Dong, Pengfei;Tu, Xiaoyu;Zhong, Silin
基因组的空间组织在基因表达的调控中起着重要作用。然而，动物基因组的核心结构特征，例如拓扑相关域（TAD）和染色质环，在极其紧凑的拟南芥基因组中并不突出。在这项研究中，我们检查了基因组大小为 0.4 至 2.4 Gb 的玉米、番茄、高粱、谷子和水稻的染色质结构及其 DNA 甲基化、组蛋白修饰、可及染色质和基因表达。我们发现这些植物基因组可以分为类似哺乳动物的 A/B 区室。在更高的分辨率下，这些植物的染色体可以进一步划分为反映其常染色质、异染色质和多梳状态的局部 A/B 区室。所有这些植物中的染色质都被组织成在物种间不保守的结构域。它们与果蝇区室结构域相似，并根据其转录活性和表观遗传特征分为活性型、多梳型、抑制型和中间型，结构域边界与局部 A/B 区室连接处重叠。在大型玉米和番茄基因组中，我们观察到广泛的染色质环。然而，与在 TAD 边界富集的哺乳动物染色质环不同，植物染色质环通常形成于抑制域之外的基因岛之间，并且与活性区室密切相关。我们的研究表明植物具有复杂而独特的 3D 染色质结构，需要进一步研究以阐明其生物学功能。
The spatial organization of the genome plays an important role in the regulation of gene expression. However, the core structural features of animal genomes, such as topologically associated domains (TADs) and chromatin loops, are not prominent in the extremely compact Arabidopsis genome. In this study, we examine the chromatin architecture, as well as their DNA methylation, histone modifications, accessible chromatin, and gene expression, of maize, tomato, sorghum, foxtail millet, and rice with genome sizes ranging from 0.4 to 2.4 Gb. We found that these plant genomes can be divided into mammalian-like A/B compartments. At higher resolution, the chromosomes of these plants can be further partitioned to local A/B compartments that reflect their euchromatin, heterochromatin, and polycomb status. Chromatins in all these plants are organized into domains that are not conserved across species. They show similarity to the Drosophila compartment domains, and are clustered into active, polycomb, repressive, and intermediate types based on their transcriptional activities and epigenetic signatures, with domain border overlaps with the local A/B compartment junctions. In the large maize and tomato genomes, we observed extensive chromatin loops. However, unlike the mammalian chromatin loops that are enriched at the TAD border, plant chromatin loops are often formed between gene islands outside the repressive domains and are closely associated with active compartments. Our study indicates that plants have complex and unique 3D chromatin architectures, which require further study to elucidate their biological functions.