Letter abstract
Nature Genetics 41, 258 - 263 (2009)
Published online: 4 January 2009 | doi:10.1038/ng.282
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies
Yuling Jiao1,3,4, S Lori Tausta1,4, Neeru Gandotra1,4, Ning Sun2,4, Tie Liu1,3,4, Nicole K Clay1,3, Teresa Ceserani1,3, Meiqin Chen1,3, Ligeng Ma1,3, Matthew Holford2, Hui-yong Zhang1,3, Hongyu Zhao2, Xing-Wang Deng1 & Timothy Nelson1
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.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA, and Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China.
- Center for Statistical Genomics and Proteomics, Yale University, New Haven, Connecticut 06520, USA.
- Present addresses: Division of Biology, California Institute of Technology, Pasadena, California 91125, USA (Y.J.); Biology Department, Stanford University, Stanford, California 94305, USA (T.L.); Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA (N.K.C.); Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada (T.C.); Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China (M.C.); National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China (L.M. and H.-Y.Z.).
- These authors contributed equally to this work.
Correspondence to: Timothy Nelson1 e-mail: timothy.nelson@yale.edu
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