Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression
文献类型：期刊论文
| 作者 | Zhang, Jie; Liu, Yuan ; Xia, En-Hua; Yao, Qiu-Yang; Liu, Xiang-Dong; Gao, Li-Zhi
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| 刊名 | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
 |
| 出版日期 | 2015-12-15 |
| 卷号 | 112期号:50页码:E7022-E7029 |
| 关键词 | methylome autotetraploid rice gene expression genome-dosage effect transposable elements |
| 英文摘要 | 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. |
| 类目[WOS] | Multidisciplinary Sciences |
| 研究领域[WOS] | Science & Technology - Other Topics |
| 关键词[WOS] | BASE RESOLUTION MAPS ; DNA METHYLATION ; CYTOSINE METHYLATION ; ARABIDOPSIS-THALIANA ; SMALL RNA ; EVOLUTIONARY CONSEQUENCES ; SECONDARY METABOLITES ; GENOME ; PLANTS ; HYBRIDIZATION |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000366404200025 |
| 源URL | [http://ir.kib.ac.cn/handle/151853/25322]  |
| 专题 | 昆明植物研究所_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. |
入库方式： OAI收割
来源：昆明植物研究所
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