CAREER: Dissecting the Environmentally Responsive Plant Epigenome

据预测，气候危机不仅会与更严重的非生物胁迫同时发生，而且还会改变作物适宜性的范围以及众多植物病原体的地理范围。因此，迫切需要通过育种开发更具抗逆性的农作物，以保障我们未来的粮食安全。植物应激防御途径的一个关键组成部分是表观基因组，它是各种结构特征的关键调节层，以环境线索依赖性方式控制遗传信息的解释。负责塑造动态植物表观基因组的建筑师是 DNA 结合蛋白，通常称为转录因子。它们充当能够改变表观基因组结构的蛋白质复合物的关键招募平台。该项目将利用新开发的高通量表观基因组分析平台来研究主MYC型螺旋-环-螺旋转录因子MYC2在塑造环境响应表观基因组中的作用。由于 MYC2 控制着植物防御网络的一个主要分支，因此预计对其功能的更好理解将提供重要的新见解，并有可能推动美国农业抗逆作物的开发。新开发的平台将提供给该领域的其他研究人员，从而广泛影响植物科学研究。对于改善育种工作同样重要的是培训下一代科学家并向他们介绍基因组学研究。表观基因组探索者课程将促进这一机会，学生可以深入研究动态植物表观基因组并发现令人兴奋的新信息。利用主转录因子的调节能力来改造具有增强抗逆能力的植物，有望减轻当前气候危机的负面影响。植物针对草食性昆虫和真菌的免疫反应由茉莉酸 (JA) 途径控制，其中 MYC2 作为其主要调节因子。对防御激素 JA 的感知直接控制以 MYC2 为中心的 JA 响应表观基因组的组成，从而控制其功能输出，其中包括 MYC2、各种转录共激活因子/阻遏因子和染色质调节因子。尽管其监管重要性显着，但对该监管模块的动态性质和功能仍然知之甚少。该项目的目标将揭示 MYC2 如何在模式植物拟南芥中建立 JA 响应表观基因组。通过利用新开发的 PHILO（植物高通量低输入）ChIP-seq 平台，将以 MYC2 为中心的 JA 响应表观基因组将得到全面研究，重点是 JA 诱导的增强子区域。 CRISPR/Cas9 促进的顺式调控变异也将用于揭示活跃 JA 信号传导过程中 MYC2 模块的一般原理。此外，通过升高温度扰乱 JA 响应表观基因组，将研究植物免疫途径和热形态发生途径之间未经探索但极其重要的串扰。总而言之，关于如何建立 JA 响应表观基因组以及如何操纵它所获得的知识将为创造新的植物品种以增强植物的抗逆能力铺平道路。所有项目成果都将通过长期公共数据和种质存储库的存放，向更广泛的研究界提供。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

The Climate Crisis is not only predicted to coincide with more severe episodes of abiotic stress, but it is also predicted to shift the range of crop suitability as well as the geographic range of numerous plant pathogens. As a result, there is an urgent need for the development of more stress-resilient crop plants through breeding to safeguard our future food security. A critical component of plant stress defense pathways is the epigenome which is a critical regulatory layer of various structural features that control the interpretation of the genetic information in an environmental cue-dependent manner. The architects responsible for shaping the dynamic plant epigenome are DNA-binding proteins, commonly known as transcription factors. They act as pivotal recruitment platforms for protein complexes capable of altering the structure of the epigenome. This project will use a newly developed high-throughput epigenome profiling platform to investigate the role of the master MYC-type helix-loop-helix transcription factor MYC2 in shaping the environmentally-responsive epigenome. Since MYC2 controls a major branch of the plant defense network, it is anticipated that a better understanding of its function will provide significant new insight with the potential to advance the development of resilient crops for U.S. agriculture. The newly developed platform will be made available to other researchers in the field thereby broadly impacting plant science research. Equally important to improve breeding efforts is training the next generation of scientists and introducing them to genomics-enabled research. This opportunity will be facilitated through the Epigenome Explorer course, where students can dive into the study of dynamic plant epigenomes and uncover thrilling new information. Harnessing the regulatory capabilities of master transcription factors to engineer plants with enhanced stress resilience holds great promise mitigating the negative impact of the current climate crisis. Plant immune responses against herbivorous insects and fungi are controlled by the jasmonic acid (JA) pathway with MYC2 as its master regulator. Perception of the defense hormone JA directly controls the composition and consequently the functional output of the MYC2-centric JA-responsive epigenome which comprises MYC2, various transcriptional co-activators/repressors, and chromatin regulators. Despite its significant regulatory importance, the dynamic nature and the functional repertoire of this regulatory module remains poorly understood. The goal of this project will shed light on how MYC2 establishes the JA-responsive epigenome in the model plant Arabidopsis thaliana. By utilizing the newly developed PHILO (Plant HIgh-throughput LOw input) ChIP-seq platform, the MYC2-centric JA-responsive epigenome will be comprehensively investigated with an emphasis on JA-induced enhancer regions. CRISPR/Cas9-facilated cis-regulatory variation will also be utilized to reveal general principles of the MYC2 module during active JA signaling. Moreover, by perturbing the JA-responsive epigenome with elevated temperature, an unexplored but immensely important crosstalk between a plant immune pathway and the thermomorphogenesis pathway will be studied. Taken together, the knowledge gained on how the JA-responsive epigenome is established and how it can be manipulated will pave the way for the creation of new plant varieties to enhance plant resilience to stresses. All project outcomes will be made available to the broader research community through deposition at long-term public data and germplasm repositories.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.