High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns

• Published in: Science (American Association for the Advancement of Science) 2007-11, Vol.318 (5851), p.801-806
• Main Authors: Brady, Siobhan M, Orlando, David A, Lee, Ji-Young, Wang, Jean Y, Koch, Jeremy, Dinneny, José R, Mace, Daniel, Ohler, Uwe, Benfey, Philip N
• Format: Article
• Language: English
• Subjects: Arabidopsis; Arabidopsis - cytology; Arabidopsis - genetics; Arabidopsis - growth & development; Auxins; Biological and medical sciences; Biosynthesis; Botany; Cell lines; Cell walls; Cells; Cellular biology; Datasets; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Genes; Green Fluorescent Proteins; Hair cells; Oligonucleotide Array Sequence Analysis; Plant growth. Development of the storage organs; Plant physiology and development; Plant Roots - cytology; Plant Roots - genetics; Plant Roots - growth & development; Stem cells; Vegetative apparatus, growth and morphogenesis. Senescence; Xylem
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.1146265

Transcriptional programs that regulate development are exquisitely controlled in space and time. Elucidating these programs that underlie development is essential to understanding the acquisition of cell and tissue identity. We present microarray expression profiles of a high-resolution set of developmental time points within a single Arabidopsis root and a comprehensive map of nearly all root cell types. These cell type-specific transcriptional signatures often predict previously unknown cellular functions. A computational pipeline identified dominant expression patterns that demonstrate transcriptional similarity between disparate cell types. Dominant expression patterns along the root's longitudinal axis do not strictly correlate with previously defined developmental zones, and in many cases, we observed expression fluctuation along this axis. Both robust co-regulation of gene expression and potential phasing of gene expression were identified between individual roots. Methods that combine these profiles demonstrate transcriptionally rich and complex programs that define Arabidopsis root development in both space and time.