FROM SINGLE CELLS TO ORGANS: CELL TYPE SPECIFIC TRANSCRIPTION AND SIGNALING FOR ROBUST PATTERNING AND GROWTH OF THE ARABIDOPSIS THALIANA SEPAL
Organ formation is a highly dynamic process that involves the coordinated initiation of organogenesis, outgrowth, and differentiation of many cell types. This requires highly regulated gene expression within individual cells, and across entire organs, and must remain robust to external perturbations. In this dissertation, I use the Arabidopsis thaliana sepal as a model to investigate robustness in gene expression and organ growth. In chapter 1, I explore the question of “what is a cell type?” The concept of a cell type has evolved with modern research methods like single cell RNA-sequencing and findings that differentiated cell de-differentiate and re-differentiate under the certain mechanical and/or transcriptional cues. Biological research continues to broaden our appreciation for the richness in diversity of cell types, intermediates, developmental trajectories, and plasticity across multicellular organisms. In chapter 2, I delve deeper into the field of cell type biology by dissecting a 1 kilobase enhancer sequence that confers cell type specific expression to giant cells. This occurs through the combinatorial action of three transcription factor classes – DOFs, class IV HD-ZIPs, and class II TCPs - none of which individually has giant cell specific expression. Rather, TCPs activate expression throughout the entire epidermis, HD-ZIPs enhance expression levels in the giant cells, and DOFs decrease expression enough to suppress expression in the small cells, but not in giant cells. In chapter 3, I use single cell RNA-seq and spatial transcriptomics to identify key cell types young flower buds in wild-type and in the mutant drmy1, which has lost robust sepal initiation and outgrowth. I detect upregulation in brassinosteroid (BR) signaling in drmy1, particularly in meristematic and epidermal cell types. Using chemical treatments and BR mutants, I demonstrate that increasing or decreasing brassinosteroid signaling has differential effects on different sepals of the same flower bud. My work reveals the importance of cell type specificity in gene expression and signaling for development. Cells must integrate multiple transcription factors in a combinatorial fashion to generate cell type specific gene expression patterns, and in turn, organ development requires specific levels and patterns of various transcriptional networks to achieve proper growth patterns.