Contribution of cis-regulatory elements in a plant's response to environmental stress

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Environmental stresses, such as high temperature, can negatively impact the growth and yield of many crops in the world. Rooted in the ground, plants have unique strategies for being more resilient to changes in their environment, a major part of which involves the reprograming of gene expression. The control of gene expression is achieved in part by complex interactions between transcription factors and cis-regulatory DNA elements, which are located either adjacent to (promoter elements), or at large distances from (distal regulatory elements) their target genes. While a number of key genes have been identified to confer high temperature tolerance, many studies trying to identify genetic variants associated with tolerance traits have identified variants located within cis-regulatory elements. Whereas the importance of distal cis-regulatory elements, such as enhancers, in gene regulation has been shown in many eukaryotic genomes, their impact on genome-wide and stress-specific transcriptional reprograming remains largely unknown in plants. The long-term objective of my research program is to determine the contribution of distal cis-regulatory elements to a plant's ability to respond to environmental stressors. As a first step, I will focus on a specific class of distal cis-regulatory elements, enhancers, in the context of high temperature stress in the staple food Asian rice (Oryza sativa). The specific objectives associated with the current proposal include: 1: Characterize the transcriptional activity of enhancers in response to high temperature stress in rice. 2: Study the different types of active enhancers in the rice genome under high temperature stress. 3: Identify candidate enhancers and their target genes using computational methods and functional validation. My research program will characterize the roles of distal cis-regulatory DNA elements and their interaction with target genes to understand how plant genomes reprogram gene expression under environmental stress. This knowledge will be key to predict and prioritize candidate regulatory targets for crop improvement. Indeed, providing resistance to environmental stress, has been a major goal of modern breeding approaches, especially in rice which is grown in regions largely impacted by high temperatures. The approaches used in these studies will generate biological insight and analytical capabilities that can be applied to other crop plants and other environmental stresses.