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Dynamics of gene expression in single root cells of A. thaliana

Ken Jean-Baptiste, José L McFaline-Figueroa, Cristina M Alexandre, Michael W Dorrity, Lauren Saunders, Kerry L Bubb, Cole Trapnell, Stanley Fields, Christine Queitsch, Josh Cuperus
Plant Cell 2019 March 28
Single-cell RNA-seq can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of cell lineages. Here, we apply this approach to A. thaliana root cells to capture gene expression in 3,121 root cells. We used Monocle 3, ordering single-cell transcriptomes in an unsupervised manner reconstructing single-cell developmental trajectories. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched across development, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. We assess and interpret changes in total RNA expression along developmental trajectories and show that trajectory branch points mark developmental decisions. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single-cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution.


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