Identification of plant enhancers using an in vitro transcription system

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Increasing world population as well as the challenges to productive agriculture caused by climate change call for improved, stress-resistant crops to satisfy the food needs of future generations. Improvements in domesticated plants can often be generated by variation in cis-regulatory sequences, such as enhancers, that regulate gene expression. While many studies have identified enhancers in animals and characterized their common features and mechanism of action, our knowledge of the elements in plant cells that regulate gene expression is still very limited. Few plant enhancers have been characterized to date. The identification of additional enhancers will increase our understanding of how they function for all plants, and make them available as tools for genetic engineering of crop plants to increase their yield and resistance to abiotic stress.In this study, I will use an approach termed “self-transcribing active regulatory region sequencing” (STARR-seq) in an in vitro transcription system derived from plant cells to identify and characterize enhancers in the genome of the model plant Arabidopsis thaliana. Motif searches and saturation mutagenesis analyses will help me to delineate functional sequences such as transcription factor binding sites within the newly discovered enhancers. Taken together, the identification of functional enhancers and the transcription factors that recognize them will lead to a better understanding of how plants develop, evolve and react to stimuli. This knowledge will guide future studies on crop improvement through editing of enhancers.