title: Spatial transcriptomes of iron-deficient and cadmium-stressed rice.
abstract: Although the genes involved in metal homeostasis have been investigated over the past few decades, many genes related to metal homeostasis remain uncharacterized, and a comprehensive analysis of the expression of these genes is required. In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed Oryza sativa (rice) using laser microdissection and microarray analysis. Roots of Fe-deficient and Cd-stressed rice were separated into the vascular bundle, cortex, and epidermis plus exodermis. In addition, vascular bundles from new and old leaves at the lowest node, which are important for metal distribution, were analyzed separately. The spatial expression patterns were distinct in each tissue type. Fe deficiency and Cd stress also had significant effects on the transcriptomes, although these were less pronounced than the spatial effects. Genes encoding transporters involved in metal homeostasis, proteins associated with heavy metal detoxification, and phytohormone-related proteins were comprehensively investigated. Additionally, cis motifs involved in the regulation of these diverse expression changes in various tissue types were predicted. The spatial transcriptomes presented here provide novel insight into the molecular mechanisms of metal homeostasis.
authors.affiliation: Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Ogo
authors.affiliation: Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Kakei
authors.affiliation: Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
authors.forename: Reiko Nakanishi
authors.initials: RN
authors.lastname: Itai
authors.affiliation: Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.|Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-machi, Ishikawa, 921-8836, Japan.
authors.forename: Takanori
authors.initials: T
authors.lastname: Kobayashi
authors.affiliation: Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Nakanishi
authors.affiliation: Laboratory of Plant Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Laboratory of Plant Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan.
authors.forename: Mikio
authors.initials: M
authors.lastname: Nakazono
authors.affiliation: Departments of Global Agricultural Sciences and Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.|Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-machi, Ishikawa, 921-8836, Japan.
authors.forename: Naoko K
authors.initials: NK
authors.lastname: Nishizawa
mesh_terms: D001483:Base Sequence; D001692:Biological Transport / Q000187:drug effects / Q000235:genetics; D002104:Cadmium / Q000378:metabolism / Q000633:toxicity*; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D053263:Gene Regulatory Networks / Q000235:genetics; D017343:Genes, Plant; D006706:Homeostasis / Q000187:drug effects / Q000235:genetics; D000090463:Iron Deficiencies; D061346:Laser Capture Microdissection; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000187:drug effects / Q000235:genetics; D012275:Oryza / Q000187:drug effects / Q000235:genetics* / Q000502:physiology*; D010937:Plant Growth Regulators / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics / Q000502:physiology; D011401:Promoter Regions, Genetic / Q000235:genetics; D017262:Siderophores / Q000378:metabolism; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics*; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*; D015854:Up-Regulation / Q000187:drug effects / Q000235:genetics
chemical_list: D010937:Plant Growth Regulators; D010940:Plant Proteins; D017262:Siderophores; D002104:Cadmium
keywords: Oryza sativa (rice); cadmium (Cd); iron (Fe); laser microdissection; transcriptome