Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

doi:10.1073/pnas.1515170112

	Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression
	Zhang, Jie; Liu, Yuan; Xia, En-Hua; Yao, Qiu-Yang; Liu, Xiang-Dong; Gao, Li-Zhi
	2015-12-15
发表期刊	PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷号	112 期号:50 页码:E7022-E7029
摘要	Polyploidy, or whole-genome duplication (WGD), serves as a key innovation in plant evolution and is an important genomic feature for all eukaryotes. Neopolyploids have to overcome difficulties in meiosis, genomic alterations, changes of gene expression, and epigenomic reorganization. However, the underlying mechanisms for these processes are poorly understood. One of the most interesting aspects is that genome doubling events increase the dosage of all genes. Unlike allopolyploids entangled by both hybridization and polyploidization, autopolyploids, especially artificial lines, in relatively uniform genetic background offer a model system to understand mechanisms of genome-dosage effects. To investigate DNA methylation effects in response to WGD rather than hybridization, we produced autotetraploid rice with its diploid donor, Oryza sativa ssp. indica cv. Aijiaonante, both of which were independently self-pollinated over 48 generations, and generated and compared their comprehensive transcriptomes, base pair-resolution methylomes, and siRNAomes. DNA methylation variation of transposable elements (TEs) was observed as widespread in autotetraploid rice, in which hypermethylation of class II DNA transposons was predominantly noted in CHG and CHH contexts. This was accompanied by changes of 24-nt siRNA abundance, indicating the role of the RNA-directed DNA methylation pathway. Our results showed that the increased methylation state of class II TEs may suppress the expression of neighboring genes in autotetraploid rice that has obtained double alleles, leading to no significant differences in transcriptome alterations for most genes from its diploid donor. Collectively, our findings suggest that chromosome doubling induces methylation variation in TEs that affect gene expression and may become a "genome shock" response factor to help neoautopolyploids adapt to genome-dosage effects.
关键词	Methylome Autotetraploid Rice Gene Expression Genome-dosage Effect Transposable Elements
DOI	10.1073/pnas.1515170112
收录类别	SCI
语种	英语
WOS记录号	WOS:000366404200025
引用统计	被引频次：125[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/25322
专题	中国西南野生生物种质资源库
推荐引用方式 GB/T 7714	Zhang, Jie,Liu, Yuan,Xia, En-Hua,et al. Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2015,112(50):E7022-E7029.
APA	Zhang, Jie,Liu, Yuan,Xia, En-Hua,Yao, Qiu-Yang,Liu, Xiang-Dong,&Gao, Li-Zhi.(2015).Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,112(50),E7022-E7029.
MLA	Zhang, Jie,et al."Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112.50(2015):E7022-E7029.

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