cis-Element- and Transcriptome-Based Screening of Root Hair-Specific Genes and Their Functional Characterization in Arabidopsis

• Published in: Plant physiology (Bethesda) Vol. 150; no. 3; pp. 1459 - 1473
• Main Authors: Won, Su-Kyung, Lee, Yong-Ju, Lee, Ha-Yeon, Heo, Yoon-Kyung, Cho, Misuk, Cho, Hyung-Taeg
• Format: Journal Article
• Language: English
• Published: Rockville, MD American Society of Plant Biologists 01.07.2009
• Subjects: Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - metabolism; Arabidopsis Proteins - chemistry; Arabidopsis Proteins - genetics; Arabidopsis Proteins - physiology; Biological and medical sciences; Cell walls; Consensus Sequence; Epidermal cells; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; Genes; Genetic screening; Genomics - methods; Hair cells; Morphogenesis; Oligonucleotide Array Sequence Analysis; Phenotype; Plant cells; Plant physiology and development; Plant roots; Plant Roots - genetics; Plant Roots - growth & development; Plants; Plants, Genetically Modified - metabolism; Response Elements; Root hairs; Systems Biology, Molecular Biology, and Gene Regulation; Arabidopsis thaliana; Screening; Gene; Root; Plant physiology; Cruciferae; Dicotyledones; Angiospermae; Root hair; Transcriptome; Spermatophyta; Experimental plant
• ISSN: 0032-0889; 1532-2548; 1532-2548
• DOI: 10.1104/pp.109.140905

Understanding the cellular differentiation of multicellular organisms requires the characterization of genes whose expression is modulated in a cell type-specific manner. The Arabidopsis (Arabidopsis thaliana) root hair cell is one model for studying cellular differentiation. In this study, root hair cell-specific genes were screened by a series of in silico and experimental filtration procedures. This process included genome-wide screening for genes with a root hair-specific cis-element in their promoters, filtering root-specific genes from the root hair-specific cis-element-containing genes, further filtering of genes that were suppressed in root hair-defective plant lines, and experimental confirmation by promoter assay. These procedures revealed 19 root hair-specific genes, including many protein kinases and cell wall-related genes, most of which have not been characterized thus far. Functional analyses of these root hair-specific genes with loss-of-function mutants and overexpressing transformants revealed that they play roles in hair growth and morphogenesis. This study demonstrates that a defined cis-element can serve as a filter to screen certain cell type-specific genes and implicates many new root hair-specific genes in root hair development.