Year: 2019
Type: article
Abstract: Single cell RNA sequencing 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 Arabidopsis (Arabidopsis thaliana) root cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single cell developmental trajectories along pseudotime. 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 in early and late cells, 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.
Source: The Plant Cell
DOI: 10.1105/tpc.18.00785
Institution: University of Washington
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,934
Funders: National Science Foundation, University of Washington, Paul G. Allen Frontiers Group, National Institutes of Health, National Heart, Lung, and Blood Institute, National Institute of General Medical Sciences, National Institute of Diabetes and Digestive and Kidney Diseases, U.S. National Library of Medicine, Division of Molecular and Cellular Biosciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development
Awards: Pulmonary Macrophage Transplantation for Pulmonary Alveolar Proteinosis, Niche signals in HSC genesis, RESEARCH-PGR: Enhancer discovery and design in agriculturally important crop plants, G2718321779, Charting the regulatory topography of the cell differentiation landscape with single-cell RNA-Seq., G2913930052, G4218497036, University of Washington Center for Nuclear Organization and Function, University of Washington PhD Training in Big Data for Genomics and Neuroscience, Using the Plant Heat Stress Response to Probe Genome-wide Regulatory Landscapes for Functional Relevance, Cardiovascular Research Training Program, Toward a mechanistic understanding of genetic interactions
OpenAlex ID: W2929165397