Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Year: 2013
Type: article
Abstract: BACKGROUND: Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out. RESULTS: In this work, we employed the Illumina high throughput sequencing technology to perform an integrated analysis of the poly-A + enriched and the small RNA fractions of the Arabidopsis thaliana root transcriptome in response to nitrate treatments. Our sequencing strategy identified new nitrate-regulated genes including 40 genes not represented in the ATH1 Affymetrix GeneChip, a novel nitrate-responsive antisense transcript and a new nitrate responsive miRNA/TARGET module consisting of a novel microRNA, miR5640 and its target, AtPPC3. CONCLUSIONS: Sequencing of small RNAs and mRNAs uncovered new genes, and enabled us to develop new hypotheses for nitrate regulation and coordination of carbon and nitrogen metabolism.
Source: BMC Genomics
Institutions: Pontificia Universidad Católica de Chile, Centre National de la Recherche Scientifique, Institut Agro Montpellier, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Institut des Sciences des Plantes de Montpellier, New York University, The University of Queensland, Cold Spring Harbor Laboratory
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $3,090
Funders: National Science Foundation, Agence Nationale de la Recherche, Centre National de la Recherche Scientifique, National Institutes of Health, Comisión Nacional de Investigación Científica y Tecnológica, National Institute of General Medical Sciences, Fondo Nacional de Desarrollo Científico y Tecnológico, Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias
Awards: G1897634215, G2117865532, Identification and modeling of molecular networks involved in Nitrate sensing in Arabidopsis., Arabidopsis 2010: Nitrogen Networks in Plants, G4800435524, G5574618443, G5665028823, G645334864, A systems approach to regulatory networks controlling N-assimilation, G8759663535, G9000046793
OpenAlex ID: W1990775762