Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

被引：434

作者：

He, Guangming ^{[1
,2
,3
]}

Zhu, Xiaopeng ^{[4
]}

Elling, Axel A. ^{[3
]}

Chen, Liangbi ^{[5
]}

Wang, Xiangfeng ^{[1
,3
]}

Guo, Lan ^{[1
,2
]}

Liang, Manzhong ^{[5
]}

He, Hang ^{[1
,3
]}

Zhang, Huiyong ^{[2
]}

Chen, Fangfang ^{[2
]}

Qi, Yijun ^{[2
]}

Chen, Runsheng ^{[4
]}

Deng, Xing-Wang ^{[1
,2
,3
]}

机构：

[1] Peking Univ, Peking Yale Joint Ctr Plant Mol Genet & Agrobiote, Natl Lab Prot Engn & Plant Genet Engn, Coll Life Sci, Beijing 100871, Peoples R China

[2] Natl Inst Biol Sci, Beijing 102206, Peoples R China

[3] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA

[4] Chinese Acad Sci, Inst Biophys, Beijing 100101, Peoples R China

[5] Hunan Normal Univ, Dept Bot, Coll Life Sci, Changsha 410081, Peoples R China

来源：

PLANT CELL | 2010年 / 22卷 / 01期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

GENOME-WIDE; NATURAL VARIATION; GENE-EXPRESSION; DNA METHYLATION; SMALL RNAS; ARABIDOPSIS-THALIANA; TILING MICROARRAYS; DRAFT SEQUENCE; CHROMATIN; MAIZE;

D O I：

10.1105/tpc.109.072041

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：17 / 33

页数：17

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