Tian Caihuan, Zhang Xiaoni, He Jun, Yu Haopeng, Wang Ying, Shi Bihai, Han Yingying, Wang Guoxun, Feng Xiaoming, Zhang Cui, Wang Jin, Qi Jiyan, Yu Rong, Jiao Yuling
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China.
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, China College of Life Sciences, Capital Normal University, Beijing, China.
Mol Syst Biol. 2014 Oct 30;10(10):755. doi: 10.15252/msb.20145470.
Gene regulatory networks (GRNs) control development via cell type-specific gene expression and interactions between transcription factors (TFs) and regulatory promoter regions. Plant organ boundaries separate lateral organs from the apical meristem and harbor axillary meristems (AMs). AMs, as stem cell niches, make the shoot a ramifying system. Although AMs have important functions in plant development, our knowledge of organ boundary and AM formation remains rudimentary. Here, we generated a cellular-resolution genomewide gene expression map for low-abundance Arabidopsis thaliana organ boundary cells and constructed a genomewide protein-DNA interaction map focusing on genes affecting boundary and AM formation. The resulting GRN uncovers transcriptional signatures, predicts cellular functions, and identifies promoter hub regions that are bound by many TFs. Importantly, further experimental studies determined the regulatory effects of many TFs on their targets, identifying regulators and regulatory relationships in AM initiation. This systems biology approach thus enhances our understanding of a key developmental process.
基因调控网络（GRNs）通过细胞类型特异性基因表达以及转录因子（TFs）与调控启动子区域之间的相互作用来控制发育。植物器官边界将侧生器官与顶端分生组织分隔开，并容纳腋生分生组织（AMs）。AMs作为干细胞龛，使茎成为一个分支系统。尽管AMs在植物发育中具有重要功能，但我们对器官边界和AM形成的了解仍然很基础。在这里，我们为低丰度的拟南芥器官边界细胞生成了一个细胞分辨率的全基因组基因表达图谱，并构建了一个全基因组蛋白质-DNA相互作用图谱，重点关注影响边界和AM形成的基因。由此产生的GRN揭示了转录特征，预测了细胞功能，并确定了许多TFs结合的启动子枢纽区域。重要的是，进一步的实验研究确定了许多TFs对其靶标的调控作用，确定了AM起始中的调节因子和调控关系。因此，这种系统生物学方法增强了我们对一个关键发育过程的理解。
