Extensive Modulation of the Transcription Factor Transcriptome during Somatic Embryogenesis in Arabidopsis thaliana

Molecular mechanisms controlling plant totipotency are largely unknown and studies on somatic embryogenesis (SE), the process through which already differentiated cells reverse their developmental program and become embryogenic, provide a unique means for deciphering molecular mechanisms controlling developmental plasticity of somatic cells. Among various factors essential for embryogenic transition of somatic cells transcription factors (TFs), crucial regulators of genetic programs, are believed to play a central role. Herein, we used quantitative real-time polymerase chain reaction (qRT-PCR) to identify TF genes affected during SE induced by in vitro culture in Arabidopsis thaliana. Expression profiles of 1,880 TFs were evaluated in the highly embryogenic Col-0 accession and the non-embryogenic tanmei/emb2757 mutant. Our study revealed 729 TFs whose expression changes during the 10-days incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. The embryo-induction stage of SE occurring during the first 5 days of culture was associated with a robust and dramatic change of the TF transcriptome characterized by the drastic up-regulation of the expression of a great majority (over 80%) of the TFs active during embryogenic culture. In contrast to SE induction, the advanced stage of embryo formation showed attenuation and stabilization of transcript levels of many TFs. In total, 519 of the SE-modulated TFs were functionally annotated and transcripts related with plant development, phytohormones and stress responses were found to be most abundant. The involvement of selected TFs in SE was verified using T-DNA insertion lines and a significantly reduced embryogenic response was found for the majority of them. This study provides comprehensive data focused on the expression of TF genes during SE and suggests directions for further research on functional genomics of SE.

调控植物全能性的分子机制在很大程度上仍未明确；而体细胞胚发生（somatic embryogenesis, SE）——即已分化细胞逆转其发育程序并转变为胚性状态的过程——为解析体细胞发育可塑性的分子机制提供了独一无二的研究途径。在体细胞向胚性转变所需的各类关键因子中，作为基因程序核心调控因子的转录因子（transcription factors, TFs）被认为发挥核心作用。
本研究采用实时荧光定量聚合酶链式反应（quantitative real-time polymerase chain reaction, qRT-PCR），对离体培养诱导的拟南芥（Arabidopsis thaliana）体细胞胚发生过程中受影响的TF基因进行了筛选。我们对高胚性的哥伦比亚生态型Col-0以及非胚性的tanmei/emb2757突变体中的1880个TF基因的表达谱进行了评估。
研究共鉴定出729个在体细胞胚发生的10天培养周期内表达发生变化的TF基因；其中141个TF基因在胚性与非胚性培养物中的表达模式存在显著差异。体细胞胚发生的胚胎诱导阶段，即培养的前5天，伴随TF转录组的剧烈且显著变化，其特征为胚性培养物中80%以上的活跃TF基因的表达水平大幅上调。与胚胎诱导阶段不同，胚胎形成的后期阶段中多数TF的转录水平趋于衰减并趋于稳定。
本研究中共有519个受体细胞胚发生调控的TF基因获得了功能注释，其中与植物发育、植物激素及应激反应相关的转录本最为丰富。我们通过T-DNA插入突变体株系验证了部分筛选得到的TF基因在体细胞胚发生中的功能，结果显示多数突变体的胚发生能力显著降低。
本研究提供了体细胞胚发生过程中TF基因表达的系统性数据，并为体细胞胚发生功能基因组学的后续研究指明了方向。