A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

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The functions of the plant body rely on interactions among distinct and nonequivalent cell types. The comparison of transcriptomes from different cell types should expose the transcriptional networks that underlie cellular attributes and contributions. Using laser microdissection and microarray profiling, we have produced a cell type transcriptome atlas that includes 40 cell types from rice (Oryza sativa) shoot, root and germinating seed at several developmental stages, providing patterns of cell specificity for individual genes and gene classes. Cell type comparisons uncovered previously unrecognized properties, including cell-specific promoter motifs and coexpressed cognate binding factor candidates, interaction partner candidates and hormone response centers. We inferred developmental regulatory hierarchies of gene expression in specific cell types by comparison of several stages within root, shoot and embryo.

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Figure 1: Global patterns of cellular gene expression.
Figure 2: Cell-specific transcripts and selected metabolic pathways.
Figure 3: Cellular distributions of transcripts from selected hormone-related genes.
Figure 4: Identification of candidate cis and trans transcriptional control cognate partners on the basis of cellular coexpression.

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Gene Expression Omnibus


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We thank N. Li for valuable database advice and assistance and P. Wu (Zhejiang University) for the rice root micrograph in Figure 3. This work was supported by US National Science Foundation Plant Genome Program grant DBI-0325821 to T.N., X.-W.D. and H.Z. T.L. and M.C. were supported in part by Peking-Yale Monsanto Fellowships.

Author information

T.N., X.-W.D. and H.Z. conceived and oversaw the research. S.L.T., N.G. and T.L. performed cell isolations, RNA isolations and informatic analysis. Y.J., H.Z. and L.M. performed microarray hybridizations and informatic analysis. T.C., N.K.C. and M.C. performed cell and RNA isolations. N.S. designed and performed statistical methods for data processing and analysis. M.H. designed and implemented the atlas database and analytical tools. T.N. prepared the manuscript, with assistance from all coauthors.

Note: Supplementary information is available on the Nature Genetics website.

Correspondence to Timothy Nelson.

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Supplementary Methods, Supplementary Figures 1–6 and Supplementary Tables 1–4 (PDF 2128 kb)

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