Integrative analysis of reference epigenomes in 20 rice varieties
Integrative analysis of reference epigenomes in 20 rice varieties
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20个水稻品种参考表观基因组综合分析
DOI：
10.1038/s41467-020-16457-5
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发表时间：
2020-05-27
影响因子：
16.6
通讯作者：
Li, Xingwang
中科院分区：
文献类型：
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作者：
Zhao, Lun;Xie, Liang;Li, Xingwang
表观基因组修饰是转录调控的工具，但在水稻中仍然没有探索全面的参考表观基因组。在这里，我们开发了一个增强的染色质免疫沉淀（eChIP）的方法，为植物，并产生全基因组的五个组蛋白修饰和RNA聚合酶II占用它的剖析。通过整合染色质可及性，DNA甲基化，转录组数据集，我们构建了全面的表观基因组景观在不同组织中的20个代表性的水稻品种。大约81.8%的水稻基因组被注释了不同的表观基因组特性。使用开放的染色质和H3 K4 me 3标记的区域的启动子区域的细化提供了对转录调控的深入了解。我们确定了广泛的增强子样启动子与潜在的增强子功能的转录调控，通过染色质相互作用。活性和抑制性组蛋白修饰和预测的增强子在组织中变化很大，而非活性染色质状态相对稳定。总之，这些数据集构成了水稻功能元件注释的宝贵资源，并表明表观基因组信息在理解转录调控中的核心作用。各种水稻品种的综合表观基因组图谱仍然不可用。在这里，作者报告了eChIP的发展，作为常规植物ChIP-seq协议的快速和低投入升级，用于20个水稻品种的表观基因组分析，并注释了超过80%的基因组具有不同的表观基因组特性，用于转录调控。
Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach for plants, and generate genome-wide profiling of five histone modifications and RNA polymerase II occupancy with it. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we construct comprehensive epigenome landscapes across various tissues in 20 representative rice varieties. Approximately 81.8% of rice genomes are annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provides insight into transcriptional regulation. We identify extensive enhancer-like promoters with potential enhancer function on transcriptional regulation through chromatin interactions. Active and repressive histone modifications and the predicted enhancers vary largely across tissues, whereas inactive chromatin states are relatively stable. Together, these datasets constitute a valuable resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation. Comprehensive epigenomic maps of various rice varieties are still unavailable. Here, the authors report the development of eChIP as a fast and low-input upgrade of regular plant ChIP-seq protocol for epigenome analysis of 20 rice varieties and annotate over 80% of the genome with different epigenome properties for transcriptional regulation.