Abstract：
The plant hormone abscisic acid (ABA) regulates essential processes in plant development and responsiveness to abiotic and biotic stresses. ABA perception triggers a post-translational signaling cascade that elicits the ABA gene regulatory network (GRN), encompassing hundreds of transcription factors (TFs) and thousands of transcribed genes. To further our knowledge of this GRN, we performed an RNA-seq time series experiment consisting of 14 time points in the 16 h following a one-time ABA treatment of 5-week-old Arabidopsis rosettes. During this time course, ABA rapidly changed transcription levels of 7151 genes, which were partitioned into 44 coexpressed modules that carry out diverse biological functions. We integrated our time-series data with publicly available TF-binding site data, motif data, and RNA-seq data of plants inhibited in translation, and predicted (i) which TFs regulate the different coexpression clusters, (ii) which TFs contribute the most to target gene amplitude, (iii) timing of engagement of different TFs in the ABA GRN, and (iv) hierarchical position of TFs and their targets in the multi-tiered ABA GRN. The ABA GRN was found to be highly interconnected and regulated at different amplitudes and timing by a wide variety of TFs, of which the bZIP family was most prominent, and upregulation of genes encompassed more TFs than downregulation. We validated our network models in silico with additional public TF-binding site data and transcription data of selected TF mutants. Finally, using a drought assay we found that the Trihelix TF GT3a is likely an ABA-induced positive regulator of drought tolerance.
摘要：
植物激素脱落酸（ABA）调节植物发育中的基本过程以及对非生物和生物胁迫的反应性。ABA感知触发翻译后信号级联，引发ABA基因调控网络（GRN），包含数百个转录因子（TFs）和数千个转录基因。为了进一步了解这个GRN，我们进行了RNA-seq时间序列实验，包括对5周龄拟南芥玫瑰花进行一次性ABA处理后的16小时内的14个时间点。在这段时间里，ABA迅速改变7151个基因的转录水平,它们被分成44个共同表达的模块，这些模块执行不同的生物学功能。我们将我们的时间序列数据与公开的TF结合位点数据进行了整合，主题数据，和RNA-seq数据的植物在翻译中被抑制，并预测(I)哪些TFs调控不同的共表达簇，(Ii)哪些TFs对靶基因振幅贡献最大，(iii)不同TFs参与ABAGRN的时机，（iv）TFs及其靶标在多层ABAGRN中的分层位置。ABAGRN被发现是高度相互关联的，并且在不同的幅度和时间被各种各样的TFs调节，其中bZIP家族最为突出，基因的上调比下调涵盖更多的TFs。我们使用其他公共TF结合位点数据和所选TF突变体的转录数据在计算机上验证了我们的网络模型。最后,使用干旱测定，我们发现TrihelixTFGT3a可能是ABA诱导的耐旱性正调节剂。
