背景:体细胞胚发生(SE)举例说明了植物细胞独特的发育可塑性。监管过程,包括控制细胞转录组胚胎重编程的表观遗传修饰,刚刚开始被揭露。
结果:为了鉴定SE中组蛋白乙酰化调节表达的基因,我们分析了拟南芥外植体的整体转录组进行胚胎发生诱导,以响应组蛋白去乙酰化酶抑制剂的处理,曲古霉素A(TSA)。比较了TSA诱导的和生长素(2,4-二氯苯氧基乙酸;2,4-D)诱导的转录组。RNA-seq结果揭示了涉及广泛失调的TSA和生长素诱导的转录组反应的相似性,主要是镇压,大多数基因。在差异表达基因(DEGs)中,我们确定了SE的主调节因子(转录因子-TFs),参与生物合成的基因,信令,以及在吲哚-3-乙酸(IAA)生物合成中的生长素和NITRILS酶编码基因的极性运输。TSA上调的TF基因在生长素诱导的SE中具有重要功能,包括LEC1/LEC2,FUS3,AGL15,MYB118,PHB,PHV,PLTs,和WUS/WOX。TSA诱导的转录组也揭示了应激相关基因的广泛上调,包括与应激激素生物合成有关的那些。与转录组数据一致,TSA诱导的外植体积累水杨酸(SA)和脱落酸(ABA),提示组蛋白乙酰化(Hac)在SE诱导过程中调节应激激素相关反应中的作用。由于子叶外植体的正面大部分有助于SE诱导,我们还确定了对TSA治疗有反应的器官极性相关基因,包括AIL7/PLT7、RGE1、LBD18、40、HB32、CBF1和ULT2。相关突变体的分析支持极性相关基因在SE诱导中的作用。
结论:研究结果为破译控制植物体细胞胚胎发生转变的表观遗传网络提供了一步。
BACKGROUND: Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed.
RESULTS: To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction.
CONCLUSIONS: The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.