Genome-Wide Analysis of DNA Methylation in Soybean
Genome-Wide Analysis of DNA Methylation in Soybean作者机构：State Key Lab of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049 China
出 版 物：《Molecular Plant》 (分子植物（英文版）)
年 卷 期：2013年第6卷第6期
页 面：1961-1974页
核心收录：
学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种]
基 金：973 project National Natural Science Foundation of China Transgenic Research Project
主 题：soybean DNA methylation, differentially methylated regions, organs.
摘 要：Cytosine methylation is an important mechanism for dynamical regulation of gene expression and trans- posable element （TE） mobility during plant developmental processes. Here, we identified the transcription start sites of genes using high-throughput sequencing and then analyzed the DNA methylation status in soybean roots, stems, leaves, and cotyledons of developing seeds at single-base resolution. Profiling of DNA methylation in different organs revealed 2162 differentially methylated regions among organs, and a portion of hypomethylated regions were correlated with high expression of neighboring genes. Because of the different distribution of class I TEs （retrotransposons） and class II TEs （DNA transposons）, the promoters of the lowest-expressed genes showed higher levels of CG and CHG methyla- tion but a lower level of CHH methylation. We further found that the CHH methylation level of class II TEs was higher than class I TEs, possibly due to the presence of more smRNAs in class II TEs. In cotyledons of developing seeds, smRNA abundance was roughly positively correlated with hypermethylated regions but negatively related to hypomethylated regions. These studies provide significant insights into the complicated interplays among DNA methylation, smRNA abundance, TE distribution, and gene expression in soybean.
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