Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids
Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids
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DOI：
10.1105/tpc.109.072041
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发表时间：
2010-01-01
期刊：
影响因子：
11.6
通讯作者：
Deng, Xing-Wang
中科院分区：
文献类型：
--
作者：
He, Guangming;Zhu, Xiaopeng;Deng, Xing-Wang
杂种优势亲本杂种中转录组和表观基因组的行为具有重要意义。在这里，我们报告了两个水稻 (Oryza sativa) 亚种及其互杂杂交体的表观基因组、mRNA 和小 RNA 转录组的高度集成图谱。我们发现基因活性与 DNA 甲基化以及转录区域的活性和抑制性组蛋白修饰相关。差异表观遗传修饰与杂种和亲本系之间转录水平的变化相关。观察到互杂种中基因表达和表观遗传修饰的独特模式。通过对序列数据中的单核苷酸多态性进行分析，我们观察到互杂杂种中表观遗传修饰或基因表达的等位基因偏差与其在亲本系中的差异具有高度相关性。不同小RNA大小类别的丰度在亲本之间存在差异，并且在相互杂交中下调的小RNA多于上调的小RNA。总之，我们的数据揭示了杂种优势水稻杂交转录和表观遗传趋势的全面概述，并为水稻界提供了有用的资源。
The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here, we report highly integrated maps of the epigenome, mRNA, and small RNA transcriptomes of two rice ( Oryza sativa) subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents, and more small RNAs were downregulated than upregulated in the reciprocal hybrids. Together, our data reveal a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses and provide a useful resource for the rice community.