Journal
DEVELOPMENTAL CELL
Volume 57, Issue 4, Pages 543-+Publisher
CELL PRESS
DOI: 10.1016/j.devcel.2022.01.008
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Funding
- US National Institutes of Health [1F32GM136030-01, MIRA 1R35GM131725]
- Deutsche Forschungsgemeinschaft [2403]
- US National Science Foundation (Postdoctoral Research Fellowships in Biology Program) [IOS-2010686]
- USDA-NIFA [2021-67034-35139]
- Helmholtz Association (Helmholtz-Einstein Berlin International School for Data Science)
- Burroughs Wellcome Fund Career Award
- NFRF Exploration Grant
- NSERC Discovery Grant
- CIHR Project Grant
- Howard Hughes Medical Insti-tute
- US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility [DE-AC02-05CH11231]
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This study constructed a comprehensive atlas at single-cell resolution to investigate the gene expression dynamics and transcriptional regulators during Arabidopsis root development. The results revealed tissue trans-differentiation and provided insights into cell identity determination and organ development regulation.
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.
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