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.

[1]  M. Gerstein,et al.  Design principles of molecular networks revealed by global comparisons and composite motifs , 2006, Genome Biology.

[2]  F. Coustry,et al.  The two activation domains of the CCAAT-binding factor CBF interact with the dTAFII110 component of the Drosophila TFIID complex. , 1998, The Biochemical journal.

[3]  Daniel L. Mace,et al.  A High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns , 2007, Science.

[4]  Robert B Goldberg,et al.  Arabidopsis LEAFY COTYLEDON1 Is Sufficient to Induce Embryo Development in Vegetative Cells , 1998, Cell.

[5]  S. S. Koh,et al.  Identification of novel universal housekeeping genes by statistical analysis of microarray data. , 2007, Journal of biochemistry and molecular biology.

[6]  Timothy Nelson,et al.  Laser microdissection of plant tissue: what you see is what you get. , 2006, Annual review of plant biology.

[7]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[8]  Mukesh Jain,et al.  Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa) , 2005, Functional & Integrative Genomics.

[9]  G. Churchill.  Fundamentals of experimental design for cDNA microarrays , 2002, Nature Genetics.

[10]  Da-Peng Zhang,et al.  The Mg-chelatase H subunit is an abscisic acid receptor , 2006, Nature.

[11]  J. Murray,et al.  Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. , 1998, Plant physiology.

[12]  J. Yazaki,et al.  Microarray analysis of brassinosteroids- and gibberellin-regulated gene expression in rice seedlings , 2004, Molecular Genetics and Genomics.

[13]  J. Summers,et al.  “What you see is what you get” , 2005 .

[14]  Nori Kurata,et al.  Identification and characterization of cytokinin-signalling gene families in rice. , 2006, Gene.

[15]  Jian Wang,et al.  A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. , 2005, Genome research.

[16]  S. L. Tausta,et al.  Plant cell types: reporting and sampling with new technologies. , 2008, Current opinion in plant biology.

[17]  C. Tonelli,et al.  Regulation of novel members of the Arabidopsis thaliana CCAAT-binding nuclear factor Y subunits. , 2002, Gene.

[18]  R. Hill,et al.  The RNA-binding protein FCA is an abscisic acid receptor , 2006, Nature.

[19]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[20]  L. Lukens,et al.  Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains. , 2006, The Plant journal : for cell and molecular biology.

[21]  T. Nelson,et al.  COTYLEDON VASCULAR PATTERN2–Mediated Inositol (1,4,5) Triphosphate Signal Transduction Is Essential for Closed Venation Patterns of Arabidopsis Foliar Organs , 2004, The Plant Cell Online.

[22]  Kazuo Shinozaki,et al.  Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) Function as Transcriptional Activators in Abscisic Acid Signaling Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.006130. , 2003, The Plant Cell Online.

[23]  J. Petricka,et al.  Arabidopsis Nucleolin Affects Plant Development and Patterning1[W][OA] , 2007, Plant Physiology.

[24]  Shoshi Kikuchi,et al.  Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. , 2004, Physiological genomics.

[25]  W. J. Lucas,et al.  Rice phloem thioredoxin h has the capacity to mediate its own cell-to-cell transport through plasmodesmata , 1998, Planta.

[26]  Ming Chen,et al.  The two-component signal system in rice (Oryza sativa L.): a genome-wide study of cytokinin signal perception and transduction. , 2007, Genomics.

[27]  Wei-Hua Wu,et al.  A G Protein-Coupled Receptor Is a Plasma Membrane Receptor for the Plant Hormone Abscisic Acid , 2007, Science.

[28]  C. Pál,et al.  The evolutionary dynamics of eukaryotic gene order , 2004, Nature Reviews Genetics.

[29]  D. Shasha,et al.  A Gene Expression Map of the Arabidopsis Root , 2003, Science.

[30]  T. Speed,et al.  GOstat: find statistically overrepresented Gene Ontologies within a group of genes. , 2004, Bioinformatics.