Integration of stress-regulated transcription, mRNA turnover and translation in plants

植物在高度可变的环境中茁壮成长，因为它们能够响应环境因素（包括光、温度、氧气、湿度和养分供应）来调节生长和繁殖。当环境条件不理想时，例如在干旱或洪水期间，植物会打开或关闭其基因的一个子集，以控制细胞代谢和调整发育。这种转换所涉及的分子过程还没有很好的理解。 该项目将使用高分辨率基因组技术，包括为本研究开发的技术，来定义模式植物拟南芥中基因网络的协调调节，这些基因网络在低氧胁迫下发挥作用，低氧胁迫是一种与洪水相关的条件。研究结果将使人们更好地了解植物如何有效地感知和应对短时间的低氧和洪水。跨基因活动多个步骤的遗传资源、方法和数据集将是植物生物学家宝贵的社区资源。该研究将在西班牙裔服务机构进行，博士后，研究生和本科生研究人员将接受生物学和生物信息学的跨学科培训。学员还将获得教学和指导经验，并将参与科学传播。该项目将为一所西班牙裔社区大学的生物学课程开发一个实验室模块，并让本科生和五年级学生参与与农业相关的令人兴奋的实践研究。植物对外部刺激的反应范围从细胞代谢的快速时间变化到发育的季节性调整。 这些变化是由多个步骤的基因表达的上下切换引起的，包括转录，mRNA降解和翻译。该项目将研究低氧激活基因转录快速跟踪mRNA翻译，限制其破坏的假设。该研究将重点关注在低氧胁迫下促进转录或促进mRNA周转的特定类型的蛋白质。一套基因组学数据集-包括染色质可及性，转录，mRNA降解和翻译效率的测量-将通过预测建模进行收集和分析，以获得植物如何响应低氧条件的综合系统级视图。

Plants thrive in highly variable environments because of their ability to modulate growth and reproduction in response to environmental factors including light, temperature, oxygen, moisture, and nutrient availability. When environmental conditions are sub-optimal, for example during a drought or flood, plant switch on or off a subset of their genes to control cellular metabolism and adjust development. The molecular processes involved in this switching are not well-understood. This project will use high-resolution genomic technologies, including ones developed for this study, to define the coordinated regulation of networks of genes in the model plant Arabidopsis thaliana that function under low oxygen stress, a condition associated with flooding. The results will provide a greater understanding of how plants sense and respond effectively to short periods of low oxygen and floods. The genetic resources, methods and datasets spanning multiple steps of gene activity will be a valuable community resource for plant biologists. The research will be carried out at a Hispanic Serving institution where postdoctoral, graduate, and undergraduate researchers will receive interdisciplinary training in biology and bioinformatics. Trainees will also gain experience in teaching and mentoring, and will participate in science communication. The project will develop a lab module for a biology course at a Hispanic-serving community college and engage undergraduates and 5th graders in exciting hands-on research related to agriculture.Plant responses to external stimuli range from rapid temporal changes in cellular metabolism to seasonal adjustments in development. These changes are induced by toggling up and down of gene expression at multiple steps, including transcription, mRNA decay, and translation. This project will examine the hypothesis that low oxygen-activated gene transcription fast-tracks mRNAs for translation, limiting their destruction. The study will focus on specific classes of proteins that promote transcription under low oxygen stress or facilitate the turnover of mRNAs. A suite of genomics datasets--including measurements of chromatin accessibility, transcription, mRNA degradation, and translation efficiency--will be collected and analyzed by predictive modeling to obtain an integrated, systems-level view of how plants respond to low-oxygen conditions.