title: A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.
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.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Yuling
authors.initials: Y
authors.lastname: Jiao
authors.forename: S Lori
authors.initials: SL
authors.lastname: Tausta
authors.forename: Neeru
authors.initials: N
authors.lastname: Gandotra
authors.forename: Ning
authors.initials: N
authors.lastname: Sun
authors.forename: Tie
authors.initials: T
authors.lastname: Liu
authors.forename: Nicole K
authors.initials: NK
authors.lastname: Clay
authors.forename: Teresa
authors.initials: T
authors.lastname: Ceserani
authors.forename: Meiqin
authors.initials: M
authors.lastname: Chen
authors.forename: Ligeng
authors.initials: L
authors.lastname: Ma
authors.forename: Matthew
authors.initials: M
authors.lastname: Holford
authors.forename: Hui-yong
authors.initials: HY
authors.lastname: Zhang
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.forename: Xing-Wang
authors.initials: XW
authors.lastname: Deng
authors.forename: Timothy
authors.initials: T
authors.lastname: Nelson
mesh_terms: D001271:Atlases as Topic; D001483:Base Sequence; D019521:Body Patterning / Q000235:genetics*; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000502:physiology; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000235:genetics; D012275:Oryza / Q000166:cytology* / Q000196:embryology / Q000235:genetics* / Q000502:physiology; D035261:Plant Components, Aerial / Q000166:cytology / Q000196:embryology / Q000235:genetics / Q000254:growth & development; D012639:Seeds / Q000166:cytology / Q000235:genetics