Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation
Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation
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与活性基因相关的染色质环和异染色质塑造水稻基因组结构以进行转录调控
DOI：
10.1038/s41467-019-11535-9
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发表时间：
2019-08-13
影响因子：
16.6
通讯作者：
Li, Xingwang
中科院分区：
文献类型：
--
作者：
Zhao, Lun;Wang, Shuangqi;Li, Xingwang
深入了解高分辨率三维基因组组织及其对转录的影响在植物中仍然很难实现。在这里，使用长读ChIA-PET方法，我们映射H3 K4 me 3和RNA聚合酶II（RNAPII）相关的启动子-启动子相互作用和H3 K9 me 2标记的异染色质相互作用在水稻核苷酸/基因分辨率。染色质结构被分成不同的独立的空间相互作用模块，具有不同的转录潜力，并覆盖约82%的基因组。与非活性模块相比，活性模块具有更高密度的活性环基因，并贡献了水稻中大部分的转录活性。此外，启动子-启动子相互作用基因倾向于协同转录。相反，异染色质介导的环在染色质构型中形成相对稳定的结构域。此外，我们研究了遗传变异对染色质相互作用和转录的影响，并确定了eQTL和e-traits的遗传调控之间的空间相关性。因此，我们的研究结果揭示了水稻转录调控的层次和模块化的3D基因组结构。
Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- and RNA polymerase II (RNAPII)-associated promoter-promoter interactions and H3K9me2-marked heterochromatin interactions at nucleotide/gene resolution in rice. The chromatin architecture is separated into different independent spatial interacting modules with distinct transcriptional potential and covers approximately 82% of the genome. Compared to inactive modules, active modules possess the majority of active loop genes with higher density and contribute to most of the transcriptional activity in rice. In addition, promoter-promoter interacting genes tend to be transcribed cooperatively. In contrast, the heterochromatin-mediated loops form relative stable structure domains in chromatin configuration. Furthermore, we examine the impact of genetic variation on chromatin interactions and transcription and identify a spatial correlation between the genetic regulation of eQTLs and e-traits. Thus, our results reveal hierarchical and modular 3D genome architecture for transcriptional regulation in rice.