Glycine max Transcriptome or Gene expression

Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposon mobility during plant developmental processes. Recently, the variation of DNA methylation has been described between wild type and DNA methylation-related mutants in Arabidopsis thaliana. However, the elaborate representation of soybean DNA methylomes remains lacking. Here, we described the epigenome maps of soybean root, stem, leaf, and cotyledon of developing seed at a single-base resolution. We confirmed the transcription start sites of genes using high-throughput sequencing and reported the DNA methylation patterns in gene and transposon regions. The correlation between gene expression and DNA methylation was revealed through transcriptome sequencing. We found CHH methylation may function in promotion of gene expression and ten cotyledon-preferred genes were identified CHH hypermethylated in cotyledon. Small RNA library sequencing showed that DNA methylation was enhanced by small RNAs not by strand-specific way, and the variation of DNA methylation between the organs was highly related with expression of small RNAs. Overall design: mRNA-Seq of roots, stems, leaves, and cotyledons of developing seeds

胞嘧啶甲基化（Cytosine methylation）是植物发育进程中动态调控基因表达与转座子活性的关键机制。此前已有研究针对拟南芥（Arabidopsis thaliana）野生型与DNA甲基化相关突变体的DNA甲基化变异展开报道，但目前仍缺乏大豆DNA甲基化组的精细表征。本研究以单碱基分辨率绘制了大豆发育种子的根、茎、叶及子叶的表观基因组图谱。研究团队通过高通量测序验证了基因的转录起始位点，明确了基因与转座子区域的DNA甲基化模式，并结合转录组测序分析，揭示了基因表达与DNA甲基化的相关性。本研究发现，CHH型甲基化（CHH methylation）可能具有促进基因表达的功能，并鉴定出10个在子叶中呈现CHH高甲基化的子叶偏好性基因。小RNA文库测序结果表明，DNA甲基化的增强由小RNA介导，且不依赖链特异性方式；不同器官间的DNA甲基化变异与小RNA的表达水平高度相关。实验整体设计：对发育种子的根、茎、叶及子叶进行mRNA测序（mRNA-Seq）。