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PMID: 19122662 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nature genetics ·Vol. 41 ·No. 2 ·2009-02-00 ·Pages 258-63

Jiao Y, Tausta SL, Gandotra N, Sun N, Liu T, Clay NK, Ceserani T, Chen M, Ma L, Holford M, Zhang HY, Zhao H, Deng XW, Nelson T

Abstract

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.

MeSH Terms
Atlases as Topic Base Sequence Body Patterning/genetics Cluster Analysis Gene Expression Profiling Gene Expression Regulation, Developmental Gene Expression Regulation, Plant Genes, Plant/physiology Models, Biological Oligonucleotide Array Sequence Analysis Organ Specificity/genetics Oryza/cytology,embryology,genetics,physiology Plant Components, Aerial/cytology,embryology,genetics,growth & development Seeds/cytology,genetics
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Jiao Yuling
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.
Tausta S Lori
Gandotra Neeru
Sun Ning
Liu Tie
Clay Nicole K
Ceserani Teresa
Chen Meiqin
Ma Ligeng
Holford Matthew
Zhang Hui-yong
Zhao Hongyu
Deng Xing-Wang
Nelson Timothy
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Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.282
Published
2009-02-00
Epub
2009-00-04
Pages
258-63
Language
English
Region
United States
NLM ID
9216904
Subset
IM
Databases
GEO
GSE13161
External Links
PubMed source DOI: 10.1038/ng.282 View journal details
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