title: Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice.
abstract: In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana) to a crop, rice (Oryza sativa), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants. To uncover such conserved N-regulatory network modules, we first generated an N-regulatory network based solely on rice transcriptome and gene interaction data. Next, we enhanced the network knowledge in the rice N-regulatory network using transcriptome and gene interaction data from Arabidopsis and new data from Arabidopsis and rice plants exposed to the same N treatment conditions. This cross-species network analysis uncovered a set of N-regulated transcription factors (TFs) predicted to target the same genes and network modules in both species. Supernode analysis of the TFs and their targets in these conserved network modules uncovered genes directly related to N use (e.g. N assimilation) and to other shared biological processes indirectly related to N. This cross-species network approach was validated with members of two TF families in the supernode network, BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTOR1-TGA and HYPERSENSITIVITY TO LOW PI-ELICITED PRIMARY ROOT SHORTENING1 (HRS1)/HRS1 Homolog family, which have recently been experimentally validated to mediate the N response in Arabidopsis.
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003 (M.O., S.S., M.S.K., G.M.C.); andInstituto de Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, C1428ADN Buenos Aires, Argentina (M.O.).
authors.forename: Mariana
authors.initials: M
authors.lastname: Obertello
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003 (M.O., S.S., M.S.K., G.M.C.); andInstituto de Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, C1428ADN Buenos Aires, Argentina (M.O.).
authors.forename: Stuti
authors.initials: S
authors.lastname: Shrivastava
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003 (M.O., S.S., M.S.K., G.M.C.); andInstituto de Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, C1428ADN Buenos Aires, Argentina (M.O.).
authors.forename: Manpreet S
authors.initials: MS
authors.lastname: Katari
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003 (M.O., S.S., M.S.K., G.M.C.); andInstituto de Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, C1428ADN Buenos Aires, Argentina (M.O.) gloria.coruzzi@nyu.edu.
authors.forename: Gloria M
authors.initials: GM
authors.lastname: Coruzzi
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D053263:Gene Regulatory Networks / Q000187:drug effects*; D008957:Models, Genetic; D009154:Mutation; D009584:Nitrogen / Q000378:metabolism / Q000494:pharmacology*; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D018520:Plant Shoots / Q000235:genetics / Q000378:metabolism; D030821:Plants, Genetically Modified; D011485:Protein Binding; D013045:Species Specificity; D014157:Transcription Factors / Q000145:classification / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D050976:Basic-Leucine Zipper Transcription Factors; C558731:HRS1 protein, Arabidopsis; D010940:Plant Proteins; D014157:Transcription Factors; D009584:Nitrogen