Variety is the spice of life: engineering tools for visualizing transcriptional heterogeneity and its effect on cell differentiation in Arabidopsis

Abstract

Two genetically identical cells exposed to the same signals will have differences in gene expression. Despite this variability, multicellular development proceeds remarkably robustly in most cases. How and when variation on the cellular level manifests in multicellular coordination and organogenesis is not well understood. Cell-to-cell variation in gene expression can be highly detrimental and actively buffered out; however, in other contexts, it is crucial and actively amplified. For example, variation must be minimized to build organs with consistent size and shape, yet the initiation of organogenesis requires a subset of cells to take on a new fate, a process that often relies on small differences between cells. Aiming to uncover the manifestation of cell-to-cell variation in development, I built a series of serine integrase-based transcriptional recorders to visualize cell-to-cell variation, and then used these tools to analyze Arabidopsis stomatal development and root initiation. In addition, I helped engineer tissue-specific Integrase Erasers to study essential genes. Finally, I showed that the plant hormone auxin acts as a gene expression driver and coordinator in root initiation. Auxin triggers cell-to-cell expression variation by assigning some cells a root precursor fate, while at the same time ensures that these precursor cells are coordinated for robust root formation. My thesis has provided genetic tools for synthetic biologists to apply across applications, and has also demonstrated how the application of these tools can elucidate the role, manifestation, and management of variation in development.