Characterization of the SHR Regulatory Hub for Root Development

Abstract

SHORTROOT (SHR) is a well-studied transcription factor necessary for properArabidopsis root development. Decades of research have revealed roles for this important regulator in radial patterning, regulation of stem cell activity, lateral root formation, middle cortex development, and apoplastic barrier establishment. These diverse functions are likely mediated by interactions with other context-specific regulators. Yet, relatively few SHR interactors have been identified, and the interaction domains and joint regulatory targets have not been distinguished. Here we use proximity labeling to generate a cell type-specific dataset of SHR proximal proteins in the Arabidopsis root endodermis. This SHR proxiome contains proteins with known root- regulatory functions that up until now have not been linked to SHR, as well as regulatory factors that may shed light on the mechanisms behind the many functions of SHR. Analysis of single-cell RNA sequencing data enriches our understanding of the regulatory hub. We use single-cell RNA sequencing data to predict interaction domains and demonstrate a strategy for identifying SHR-specific and joint targets of regulation.