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

Nat Genet. 2009 Feb;41(2):258-63. doi: 10.1038/ng.282. Epub 2009 Jan 4.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

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*
  • Oryza / embryology
  • Oryza / genetics*
  • Oryza / physiology
  • Plant Components, Aerial / cytology
  • Plant Components, Aerial / embryology
  • Plant Components, Aerial / genetics
  • Plant Components, Aerial / growth & development
  • Seeds / cytology
  • Seeds / genetics

Associated data

  • GEO/GSE13161