Adaptation inception: implanting epigenetic memories of cold stress in cereals

极端天气的频率、强度和持续时间的变化是气候变化的后果，对农业环境构成挑战。可悲的是，对植物对环境变化的适应机制的有限理解限制了我们为这些后果做准备的能力。温带植物通过调整它们的物候来适应低温，是适应研究的有用系统。未驯化的短柱花是研究冷适应的一个强大的谷物模型，因为它自然生长在冰冻频繁的环境中，表现出一系列春化要求，并且正如我们的实验室首次证明的那样，可以在冷驯化后提高其耐寒能力。我们的长期目标是理解和操纵谷物对环境胁迫的反应中基于染色质的调控机制，以减轻它们对生产发展的影响。最近的工作不仅涉及到转录调控，还涉及到记录特定的逆境记忆，这些记忆可以在以前受到挑战的植物中触发更强、更快的细胞反应。因此，我们假设表观基因组的动态调整是启动植物对不断变化的环境的反应并支持适应的关键调控机制。目标1和目标2将通过分别确定组蛋白修饰和DNA甲基化的变化来表征冷驯化的稻瘟病菌染色质状态。这些目标将使全基因组能够欣赏与低温波动相关的染色质标记。Aim 2还将质疑B.disachyon的从头DNA甲基化途径在寒冷反应中的输入。这一目标将把从头甲基化途径与植物记录和响应低温事件的能力联系起来，该途径与胁迫诱导基因座的表观遗传记忆形成有关。在目标3中，我们希望通过植入对寒冷暴露的人工记忆来设计具有增强耐寒性的谷物。在这里，我们建议通过在B.disachyon中部署基于CRISPR的工具来设计在AIMS 1和2中观察到的启动染色质记忆状态。这一新方法将允许植物在不首先暴露于限制生长的触发因素的情况下为压力做好准备。重要的是，目标3将测试在作物中编辑表观基因组以增强逆境恢复能力的可行性。总之，拟议的工作将为植物染色质动态响应环境线索提供新的见解。使用CRISPR工具重塑染色质将促进谷类作物的改良，并进一步推动关于使用非传统育种方法的辩论。因此，我们的工作将转化为强大的作物生产系统、可持续的粮食安全和更低的价格。最后，它将提供能够创建、评估和管理表观遗传和编辑技术衍生的农产品的HQP。

Changes in the frequency, intensity and duration of weather extremes are consequences of climate change and impose challenges to agroenvironments. Sadly, the limited understanding of plants' adaptive mechanisms to changing environments restrains our ability to prepare for these consequences. Temperate plants persist by adjusting their phenology to low temperatures and are useful systems for adaptation studies. The undomesticated Brachypodium distachyon is a powerful cereal model to study cold adaptation because it naturally grows in environments where freezing spells are frequent, displays a range of vernalization requirements and as our lab first demonstrated, can increase its freezing tolerance capacity upon cold acclimation. Our long-term goal is to understand and manipulate chromatin-based regulatory mechanisms involved in cereal responses to environmental stresses to mitigate their impact on productive development. Recent work implicates chromatin-based mechanisms not only in transcriptional regulation but also in recording specific memories of stresses that can trigger stronger, more rapid cellular responses in previously challenged plants. We thus hypothesize that dynamic tuning of epigenomes is a key regulatory mechanism that primes plant responses to changing environments and supports adaptation. Aims 1 and 2 will characterize chromatin states of cold-acclimated B. distachyon by respectively identifying changes in histone modifications and DNA methylation. These aims will allow a genome-wide appreciation of chromatin marks associated with low temperature fluctuations. Aim 2 will also query the input of B. distachyon's de novo DNA methylation pathway in cold responses. This aim will link the de novo methylation pathway, which is implicated in epigenetic memory formation at stress-induced loci, to the plant's capacity to record and respond to low temperature events. With aim 3, we hope to engineer cereals with enhanced cold tolerance by implanting artificial memories of cold exposure. Here, we propose to engineer the primed chromatin memory states observed in aims 1 and 2 by deploying CRISPR-based tools in B. distachyon. This novel approach will allow plants to be primed for stress without first being exposed to growth-limiting triggers. Importantly, aim 3 will test the feasibility of epigenome editing in crops to enhance stress resilience. Together, the work proposed will provide novel insights on plant chromatin dynamics in response to environmental cues. The use of CRISPR tools to reshape chromatin will galvanize cereal crop improvement and further inform the debate on the use of non-traditional breeding approaches. Our work will thus translate to robust crop production systems, sustainable food security and lower prices. Finally, it will provide HQP capable of creating, assessing and regulating agricultural products derived from epigenetic and editing technologies.