CAREER: Dissecting the Environmentally Responsive Plant Epigenome

据预测，气候危机不仅与更严重的非生物胁迫事件相吻合，而且还将改变作物适宜性的范围以及许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能力的作物，以保障我们未来的粮食安全。植物逆境防御途径的一个重要组成部分是表观基因组，它是各种结构特征的关键调控层，以环境线索依赖的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。它们作为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。该项目将使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MYC 2在塑造环境响应表观基因组中的作用。由于MYC 2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，并有可能促进美国农业中弹性作物的发展。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。提高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。这个机会将通过表观基因组探索者课程，在那里学生可以深入到动态植物表观基因组的研究和发现激动人心的新信息促进。利用主转录因子的调节能力来工程化具有增强的压力适应能力的植物，这对减轻当前气候危机的负面影响具有很大的希望。植物对食草性昆虫和真菌的免疫反应是由茉莉酸（JA）途径控制的，MYC 2是其主要调节因子。防御激素JA的感知直接控制组成，并因此控制MYC 2-中心JA-响应表观基因组的功能输出，所述表观基因组包括MYC 2、各种转录共激活子/抑制子和染色质调节子。尽管其重要的监管重要性，这个监管模块的动态性质和功能库仍然知之甚少。该项目的目标将阐明MYC 2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（Plant High-throughput LOw input）ChIP-seq平台，将全面研究以MYC 2为中心的JA响应表观基因组，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MYC 2模块在活性JA信号传导期间的一般原理。此外，通过用升高的温度扰动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的未探索但非常重要的串扰。总之，关于JA响应表观基因组如何建立以及如何操纵的知识将为创造新的植物品种铺平道路，以增强植物对压力的抵抗力。所有项目成果将通过长期公共数据和种质资源库的存放提供给更广泛的研究界。该奖项反映了NSF的法定使命，并通过使用基金会的知识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.