Abstract
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.
| Original language | English |
|---|---|
| Pages (from-to) | 543-560.e9 |
| Journal | Developmental Cell |
| Volume | 57 |
| Issue number | 4 |
| DOIs | |
| State | Published - Feb 28 2022 |
| Externally published | Yes |
Funding
This work was funded by the US National Institutes of Health (NRSA postdoctoral fellowship 1F32GM136030-01 and MIRA 1R35GM131725) to R.S. and P.N.B. respectively; Deutsche Forschungsgemeinschaft (International Research Training Group 2403) to C.-W.H. and U.O.; the US National Science Foundation (Postdoctoral Research Fellowships in Biology Program grant no. IOS-2010686) to T.M.N.; USDA-NIFA 2021-67034-35139 to I.W.T.; the Helmholtz Association (Helmholtz-Einstein Berlin International School for Data Science) to A.H.C.V. and U.O.; a Burroughs Wellcome Fund Career Award, NFRF Exploration Grant, NSERC Discovery Grant, and CIHR Project Grant to L.G. S.Z. A.A. and G.S.; and by the Howard Hughes Medical Institute to P.N.B. as an Investigator. Work was performed by B.J.C. at the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, supported under contract no. DE-AC02-05CH11231. The authors thank Kook Hui Ryu and John Schiefelbein for advice on protoplast preparation, Nicolas Devos and Duke GCB for sequencing services, Megan Perkins Jacobs, Heather Belcher, Sarah Van Dierdonck, and Matthew Herbst for technical and other assistance, Jos? Maria Muino Acuna for scRNA-seq analysis support, Abdull J. Massri, Pablo Szekely, Cara Winter, Jazz Dickinson, David McClay, Zhongchi Liu, Jan Philipp Junker, and Gregory Wray for critical reading of early drafts. R.S. C.-W.H. T.M.N. B.J.C. P.N.B. and U.O. conceptualized the experiments. R.S. T.M.N. and I.W.T. generated the scRNA-seq data. R.S. C.-W.H. T.M.N. B.J.C. A.H.C.V. L.G. S.Z. A.A. and G.S. analyzed the data. R.S. performed confocal imaging. R.S. wrote the manuscript with input from all authors. G.S. P.N.B. and U.O. supervised the experiments and analyses. P.N.B. is a member of the Developmental Cell advisory board and is the co-founder and Chair of the Scientific Advisory Board of Hi Fidelity Genetics, a company that works on crop root growth. This work was funded by the US National Institutes of Health (NRSA postdoctoral fellowship 1F32GM136030-01 and MIRA 1R35GM131725 ) to R.S. and P.N.B., respectively; Deutsche Forschungsgemeinschaft (International Research Training Group 2403) to C.-W.H. and U.O.; the US National Science Foundation (Postdoctoral Research Fellowships in Biology Program grant no. IOS-2010686 ) to T.M.N.; USDA -NIFA 2021-67034-35139 to I.W.T.; the Helmholtz Association (Helmholtz-Einstein Berlin International School for Data Science) to A.H.C.V. and U.O.; a Burroughs Wellcome Fund Career Award, NFRF Exploration Grant, NSERC Discovery Grant, and CIHR Project Grant to L.G., S.Z., A.A., and G.S.; and by the Howard Hughes Medical Institute to P.N.B. as an Investigator. Work was performed by B.J.C. at the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, supported under contract no. DE-AC02-05CH11231 . The authors thank Kook Hui Ryu and John Schiefelbein for advice on protoplast preparation, Nicolas Devos and Duke GCB for sequencing services, Megan Perkins Jacobs, Heather Belcher, Sarah Van Dierdonck, and Matthew Herbst for technical and other assistance, José Maria Muino Acuna for scRNA-seq analysis support, Abdull J. Massri, Pablo Szekely, Cara Winter, Jazz Dickinson, David McClay, Zhongchi Liu, Jan Philipp Junker, and Gregory Wray for critical reading of early drafts.
Keywords
- Arabidopsis
- SCARECROW
- SHORTROOT
- cell fate
- development
- root
- scRNA-seq
- transcriptomics