title: Discriminative gene co-expression network analysis uncovers novel modules involved in the formation of phosphate deficiency-induced root hairs in Arabidopsis.
abstract: Cell fate and differentiation in the Arabidopsis root epidermis are genetically defined but remain plastic to environmental signals such as limited availability of inorganic phosphate (Pi). Root hairs of Pi-deficient plants are more frequent and longer than those of plants grown under Pi-replete conditions. To dissect genes involved in Pi deficiency-induced root hair morphogenesis, we constructed a co-expression network of Pi-responsive genes against a customized database that was assembled from experiments in which differentially expressed genes that encode proteins with validated functions in root hair development were over-represented. To further filter out less relevant genes, we combined this procedure with a search for common cis-regulatory elements in the promoters of the selected genes. In addition to well-described players and processes such as auxin signalling and modifications of primary cell walls, we discovered several novel aspects in the biology of root hairs induced by Pi deficiency, including cell cycle control, putative plastid-to-nucleus signalling, pathogen defence, reprogramming of cell wall-related carbohydrate metabolism, and chromatin remodelling. This approach allows the discovery of novel of aspects of a biological process from transcriptional profiles with high sensitivity and accuracy.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Jorge E
authors.initials: JE
authors.lastname: Salazar-Henao
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Wen-Dar
authors.initials: WD
authors.lastname: Lin
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.|Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan.|Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schmidt
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000648:ultrastructure; D029681:Arabidopsis Proteins / Q000235:genetics / Q000502:physiology*; D002467:Cell Nucleus / Q000378:metabolism; D022081:Cell Surface Extensions / Q000648:ultrastructure; D002473:Cell Wall / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly / Q000187:drug effects; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D005961:Glucosinolates / Q000096:biosynthesis; D007210:Indoleacetic Acids; D009024:Morphogenesis; D010710:Phosphates / Q000494:pharmacology*; D019441:Plant Epidermis / Q000648:ultrastructure*; D018517:Plant Roots / Q000648:ultrastructure*; D018087:Plastids / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D005961:Glucosinolates; D007210:Indoleacetic Acids; D010710:Phosphates