State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.
Université Paris Saclay, GQE-Le Moulon, Gif-sur-Yvette, 91190, France.
Physiol Plant. 2023 Mar;175(2):e13892. doi: 10.1111/ppl.13892.
Elucidating regulators, including transcription factors (TFs) and RNA-binding proteins (RBPs), underlying gene transcriptional and post-transcriptional co-regulatory network is key to understand plant cold responses. Previous studies were mainly conducted on single species, and whether the regulators are conserved across different species remains elusive. Here, we selected three species that diverged at the early evolution of rosids (~99-113 million years ago), performed cold-responsive phylotranscriptome experiments, and integrated chromatin immunoprecipitation- and DNA affinity purification-sequencing (ChIP/DAP-seq) analysis to explore cold-responsive regulators and their regulatory networks. First, we detected over 10,000 cold-induced differentially expressed genes (DEGs) and alternative splicing genes (DASGs) in each species. Among the DEGs, a set of TFs and RBPs were conserved in rosid cold response. Compared to TFs, RBPs displayed a delayed cold-responsive pattern, implying a hierarchical regulation of DEGs and DASGs. By integrating DEGs and DASGs, we identified 259 overlapping DE-DASG orthogroups (closely-related homologs) that were cold-regulated at both transcriptional and post-transcriptional levels in all three studied species. Notably, pathway analysis on each of the DEGs, DASGs, and DE-DASGs in the three species showed a common enrichment connected to the circadian rhythm. Evidently, 226 cold-responsive genes were directly targeted by at least two circadian rhythm components (CCA1, LHY, RV4, RVE7, and RVE8). Finally, we revealed an ancient hierarchy of cold-responsive regulatory networks at transcriptional and post-transcriptional levels launched by circadian components in rosids. Altogether, this study sheds light on conserved regulators underlying cold-responsive regulatory networks across rosid species, despite a long evolutionary history after their divergence.
阐明基因转录和转录后协同调控网络的调控因子（转录因子（TFs）和 RNA 结合蛋白（RBPs））是理解植物冷响应的关键。以前的研究主要在单一物种中进行，调控因子是否在不同物种中保守仍不清楚。在这里，我们选择了三个在蔷薇科早期进化（~99-113 百万年前）中分化的物种，进行了冷响应的系统发生转录组实验，并整合了染色质免疫沉淀和 DNA 亲和力纯化测序（ChIP/DAP-seq）分析，以探索冷响应调控因子及其调控网络。首先，我们在每个物种中检测到了超过 10000 个冷诱导的差异表达基因（DEGs）和可变剪接基因（DASGs）。在 DEGs 中，一组 TFs 和 RBPs 在蔷薇科的冷反应中是保守的。与 TFs 相比，RBPs 表现出延迟的冷响应模式，这表明 DEGs 和 DASGs 的层次调节。通过整合 DEGs 和 DASGs，我们鉴定了 259 个重叠的 DE-DASG 同源物（密切相关的同源物），它们在所有三种研究的物种中都在转录和转录后水平上受到冷调控。值得注意的是，对三种物种中的每一种 DEGs、DASGs 和 DE-DASGs 的通路分析都显示出与昼夜节律连接的共同富集。显然，226 个冷响应基因直接被至少两个昼夜节律成分（CCA1、LHY、RV4、RVE7 和 RVE8）靶向。最后，我们揭示了蔷薇科中，由昼夜节律成分在转录和转录后水平上启动的冷响应调控网络的古老层次结构。总之，这项研究揭示了在蔷薇科物种中，冷响应调控网络背后的保守调控因子，尽管在它们分化后的漫长进化历史中仍然存在。
