A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.
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.
Jiao
Yuling
Y
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.
Tausta
S Lori
SL
Gandotra
Neeru
N
Sun
Ning
N
Liu
Tie
T
Clay
Nicole K
NK
Ceserani
Teresa
T
Chen
Meiqin
M
Ma
Ligeng
L
Holford
Matthew
M
Zhang
Hui-yong
HY
Zhao
Hongyu
H
Deng
Xing-Wang
XW
Nelson
Timothy
T
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