CAREER: Dissecting the Environmentally Responsive Plant Epigenome

气候危机不仅预计将与更严重的非生物胁迫事件重合，而且预计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，迫切需要通过育种来发展更具抗逆性的作物，以保障我们未来的粮食安全。植物逆境防御途径的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设计师是DNA结合蛋白，通常被称为转录因子。它们是能够改变表观基因组结构的蛋白质复合体的关键招募平台。该项目将使用新开发的高通量表观基因组图谱平台来研究主控MYC型螺旋-环-螺旋转录因子MYC2在塑造环境响应的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，预计对其功能的更好了解将为推动美国农业弹性作物的发展提供重要的新见解。新开发的平台将向该领域的其他研究人员提供，从而对植物科学研究产生广泛影响。要改进育种工作，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。这一机会将通过表观基因组探索者课程来促进，在该课程中，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。利用主要转录因子的调节能力来设计具有增强抗逆性的植物，有望缓解当前气候危机的负面影响。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，MYC2是其主要调节因子。对防御激素JA的感知直接控制以MYC2为中心的JA反应表观基因组的组成，从而控制功能输出，该表观基因组包括MYC2、各种转录辅助激活/抑制因子和染色质调节因子。尽管它具有重要的监管意义，但人们对这个监管模块的动态性质和功能仍然知之甚少。该项目的目标将阐明MYC2如何在模式植物拟南芥中建立JA反应的表观基因组。通过利用新开发的FIRO(植物高通量低输入)芯片-SEQ平台，将全面研究以JA为中心的JA反应表观基因组，重点是JA诱导的增强子区域。CRISPR/Cas9促进的顺式调节变异也将被用来揭示活动JA信号过程中MYC2模块的一般原理。此外，通过用高温干扰JA反应的表观基因组，将研究植物免疫途径和热形态发生途径之间的一个未知但极其重要的串扰。综上所述，关于JA响应的表观基因组是如何建立的以及如何操纵它的知识将为创造新的植物品种以增强植物对逆境的适应能力铺平道路。所有项目成果将通过存放在长期公共数据和种质资源库提供给更广泛的研究社区。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.