Unraveling transcriptional subnetworks of Arabidopsis ground tissue

Duke University, Durham NC

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Abstract

DESCRIPTION (provided by applicant): The objectives for this training period are to: 1) develop and apply experimental and computational skills to whole genome technologies to investigate asymmetric cell division, 2) identify and describe transcriptional programs utilizing high resolution, global expression data and new techniques, 3) gain an understanding of the biological function of transcriptional programs in the cells of plant ground tissue assisted by a novel high-throughput method. To accomplish these objectives I plan to utilize the model plant Arabidopsis thaliana as a system to study the transcriptional circuitry underlying cellular instruction and response within ground tissue. To reach the first objective I will be trained in the Benfey lab to perform and analyze microarrays as well as chromatin immunoprecipitation followed microarray (ChlP-chip) to obtain comprehensive transcriptional targets of an uncharacterized transcription factor (TF) with a demonstrated role in asymmetric cell division in the Arabidopsis root. To achieve the second objective I will use robust spatiotemporal co-expression clusters of a high-resolution, cell-type specific data set generated from Fluorescence Activated Cell Sorting (FACS) technology pioneered in the lab. I will be trained to perform chromatin immunoprecipitation followed by quantitative PCR (ChlP-qPCR) to identify direct targets of ground tissue specific TFs within these clusters. To attain the third objective I will develop genetic and molecular resources of genes within the transcriptional subnetworks of the previous objectives. Facilitated by the 'rootarray', a high-throughput confocal imaging platform of the Benfey lab, I will assay phenotypes and characterize the biological functions of the transcription factors and their targets in the cellular specification, development, and stress responses of the ground tissue. The skills and resources I will obtain from this proposal will provide the training and tools required for my career and future research in systems biology on the transcriptional circuitry underlying plant cell and tissue development and function. Public Health Relevance: Asymmetric cell division, mechanisms of cellular development and response, and transcriptional networks functioning in the tissue studied in this proposal are common to all eukaryotic organisms. As these mechanisms have been found to be involved in cancer and human disease, knowledge of the informational pathways in model organisms that instruct specific cells to carry out tissue function and response is thus broadly applicable and relevant to those of humans.