TY - JOUR T1 - Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors JF - Dev Cell Y1 - 2016 A1 - Sparks, E. E. A1 - Drapek, C. A1 - Gaudinier, A. A1 - Li, S. A1 - Ansariola, M. A1 - Shen, N. A1 - Hennacy, J. H. A1 - Zhang, J. A1 - Turco, G. A1 - Petricka, J. J. A1 - Foret, J. A1 - Hartemink, A. J. A1 - Gordan, R. A1 - Megraw, M. A1 - Brady, S. M. A1 - Benfey, P. N. KW - Arabidopsis Proteins/ genetics/ metabolism KW - Arabidopsis/ genetics/growth & development/ metabolism KW - Computer Simulation KW - Gene Expression Regulation, Plant KW - Gene Regulatory Networks KW - Genes, Plant KW - Genes, Reporter KW - Genes, Synthetic KW - Models, Genetic KW - Plant Roots/cytology/metabolism KW - Plants, Genetically Modified KW - Promoter Regions, Genetic KW - Repressor Proteins/genetics/metabolism KW - Trans-Activators/genetics/metabolism KW - Transcription Factors/ genetics/ metabolism KW - Two-Hybrid System Techniques AB -

Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT. The aggregate spatial expression of these regulators is not sufficient to predict transcriptional specificity. Instead, modeling, transcriptional reporters, and synthetic promoters support a mechanism whereby expression at the top of the SHORTROOT-SCARECROW cascade is established through opposing activities of activators and repressors.

VL - 39 SN - 1878-1551 (Electronic)1534-5807 (Linking) UR - https://doi.org/10.1016/j.devcel.2016.09.031 JO - Developmental cell ER - TY - JOUR T1 - The protein expression landscape of the Arabidopsis root. JF - Proc Natl Acad Sci U S A Y1 - 2012 A1 - Petricka, Jalean J A1 - Schauer, Monica A A1 - Megraw, Molly A1 - Breakfield, Natalie W A1 - Thompson, J Will A1 - Georgiev, Stoyan A1 - Soderblom, Erik J A1 - Ohler, Uwe A1 - Moseley, Martin Arthur A1 - Grossniklaus, Ueli A1 - Benfey, Philip N KW - Arabidopsis KW - Arabidopsis Proteins KW - Base Sequence KW - Chromatography, Liquid KW - DNA Primers KW - Gene Expression Profiling KW - Plant Roots KW - Plants, Genetically Modified KW - Protein Array Analysis KW - Protein Interaction Mapping KW - Proteome KW - Proteomics KW - RNA, Plant KW - Tandem Mass Spectrometry AB -

Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.

VL - 109 IS - 18 ER -