Repression Mediated Embryonic Paterning in Arabidopsis

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Plants begin their life with a very basic body plan consisting of a shoot at the top and a root at the bottom. These structures form in the embryo, and proper development of the shoot and root is controlled in large part by a plant hormone called auxin. Auxin is synthesized and transported throughout the embryo and therefore each cell must make a decision whether to respond or not respond to its presence. This project seeks to uncover the mechanisms used by cells to dampen the response to auxin, and the resulting gene expression and developmental changes that occur when this process is disrupted. As auxin is used to pattern organs throughout the life of the plant, these studies will be broadly applicable to plant development and will apply to the growth and patterning of commercially available crop plants. Reagents created from this work will also be used during outreach programs for the general public at the Mildred E. Mathias Botanical Garden as well as in undergraduate classrooms at the University of California Los Angeles.This project seeks to understand the relationship between two classes of transcription factors, the AUX/IAA and AUXIN RESPONSE FACTORS, during Arabidopsis embryo patterning. Specifically, the action of three AUX/IAAs (AUX/IAA8,9,31) and three ARFs (ARF1,2,9) that work with the co-repressor TOPLESS (TPL) to repress gene expression will be explored. Genome wide targets of AUX/IAA8 and ARF2 will be determined during embryogenesis using chromatin immunoprecipitation followed by deep sequencing. These targets will then be compared to the known targets of TPL to define a shared transcriptional network. RNA-seq in both aux/iaa8 and arf2 mutant backgrounds will be used to correlate gene expression changes with genome binding. The study will also document both the protein and mRNA accumulation patterns of all six of these genes and a characterization of a hextuple mutant will be carried out using well-characterized fluorescent reporters and in situ hybridizations. Finally, the biological function of the B3 repression motif found in ARF2 will be explored and an in planta repression assay will be used to determine the transcriptional activity of ARF2 at a cellular level. Taken together, these experiments will provide the field with one of the most complete characterizations of an AUX/IAA and ARF protein to date. As these proteins are used throughout development and are found in almost all plants, the results should be applicable to many studies on how plant hormones regulate development.