A Gene Expression Map of Shoot Cell Types Reveals New Regulatory Mechanisms

Gene regulatory networks control development via cell type-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from its peripheral zone, making the whole shoot a ramifying system. Leaves then develop polarity patterns following initiation to form a planar shape. Here we provide a rigorous and comprehensive comparison of translating RNAs among SAM and leaf cell types. We used RNA sequencing to quantify gene expression in target cell types labeled for translating ribosome affinity purification to generate a cell type-specific translatome map covering representative vegetative stage SAM and leaf cell types. We show that many cell types have previously overlooked cellular functions, and provide evidence that some cell types, which previously had been considered to have limited similarity, utilize similar regulatory modules. Further experimental studies validated the importance of leaf cell type-specific cytokinin response in leaf polarity patterning. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals.