A High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns

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.

[1]  D. Dubnau,et al.  Noise in Gene Expression Determines Cell Fate in Bacillus subtilis , 2007, Science.

[2]  Tom Beeckman,et al.  Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis , 2007, Development.

[3]  R. Green,et al.  Regulation of output from the plant circadian clock , 2007, The FEBS journal.

[4]  Jie Chen,et al.  A Complex Oscillating Network of Signaling Genes Underlies the Mouse Segmentation Clock , 2006, Science.

[5]  P. Benfey,et al.  Combining Expression and Comparative Evolutionary Analysis. The COBRA Gene Family[W][OA] , 2006, Plant Physiology.

[6]  P. Benfey,et al.  Whole-Genome Analysis of the SHORT-ROOT Developmental Pathway in Arabidopsis , 2006, PLoS biology.

[7]  Uwe Ohler,et al.  Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[8]  D. Inzé,et al.  Cell Cycle Progression in the Pericycle Is Not Sufficient for SOLITARY ROOT/IAA14-Mediated Lateral Root Initiation in Arabidopsis thalianaw⃞ , 2005, The Plant Cell Online.

[9]  L. Laplaze,et al.  GAL4-GFP enhancer trap lines for genetic manipulation of lateral root development in Arabidopsis thaliana. , 2005, Journal of experimental botany.

[10]  P. Benfey,et al.  Cell type–specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines , 2005, Nature Methods.

[11]  Tal Nawy,et al.  Transcriptional Profile of the Arabidopsis Root Quiescent Centerw⃞ , 2005, The Plant Cell Online.

[12]  E. Davidson,et al.  Gene regulatory networks for development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Wilhelm Gruissem,et al.  Global analysis of the core cell cycle regulators of Arabidopsis identifies novel genes, reveals multiple and highly specific profiles of expression and provides a coherent model for plant cell cycle control. , 2005, The Plant journal : for cell and molecular biology.

[14]  J. Celenza,et al.  The Arabidopsis ATR1 Myb Transcription Factor Controls Indolic Glucosinolate Homeostasis1 , 2005, Plant Physiology.

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

[16]  Ari Pekka Mähönen,et al.  APL regulates vascular tissue identity in Arabidopsis , 2003, Nature.

[17]  John D. Storey.  A direct approach to false discovery rates , 2002 .

[18]  D. Saslowsky,et al.  Localization of flavonoid enzymes in Arabidopsis roots. , 2001, The Plant journal : for cell and molecular biology.

[19]  E. Truernit,et al.  Cell-to-Cell and Long-Distance Trafficking of the Green Fluorescent Protein in the Phloem and Symplastic Unloading of the Protein into Sink Tissues , 1999, Plant Cell.

[20]  N. Smirnoff,et al.  Analysis of the root-hair morphogenesis transcriptome reveals the molecular identity of six genes with roles in root-hair development in Arabidopsis. , 2006, The Plant journal : for cell and molecular biology.

[21]  John J. Wyrick,et al.  Genome analysis Athena : a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences , 2005 .

[22]  Ziv Bar-Joseph,et al.  Clustering short time series gene expression data , 2005, ISMB.