A global view of RNA-protein interactions reveals novel root hair cell fate regulators

The Arabidopsis thaliana root epidermis is comprised of two cell types, hair and nonhair cells, which differentiate from the same precursor. Although the transcriptional programs regulating these events are well studied, post-transcriptional factors functioning in this cell fate decision are mostly unknown. Here, we globally identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei. This analysis reveals distinct structural and protein binding patterns across both transcriptomes, allowing identification of differential RNA binding protein (RBP) recognition sites. Using these sequences, we identify two RBPs that regulate hair cell development. Specifically, we find that SERRATE functions in a microRNA-dependent manner to inhibit hair cell fate, while also terminating growth of root hairs mostly independent of microRNA biogenesis. Additionally, we show that GLYCINE-RICH PROTEIN 8 promotes hair cell fate while alleviating phosphate starvation stress. In total, this global analysis reveals novel post-transcriptional regulators of plant root epidermal cell fate. Plant root hair cells function in water and nutrient uptake. Foley et al. characterize global RNA-protein interactions and RNA secondary structure in Arabidopsis root hair and non-hair cell nuclei using protein-interaction-profile sequencing. The dataset uncovers cell type-specific RNA secondary structure, RBP binding patterns, and RBP regulators of hair cell fate.