Open Access Highly Accessed Research article

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots

Elena A Vidal1, Tomás C Moyano1, Gabriel Krouk23, Manpreet S Katari3, Milos Tanurdzic45, W Richard McCombie4, Gloria M Coruzzi3* and Rodrigo A Gutiérrez1*

Author Affiliations

1 FONDAP Center for Genome Regulation. Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile

2 Biochimie et Physiologie Moléculaire des Plantes, UMR 5004 CNRS/INRA/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes-Claude Grignon, Montpellier, France

3 Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA

4 Cold Spring Harbor Laboratory, New York, USA

5 Present address: School of Biological Sciences, The University of Queensland, St Lucia, Australia

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BMC Genomics 2013, 14:701  doi:10.1186/1471-2164-14-701

Published: 11 October 2013



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.


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.


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.

Arabidopsis; Nitrate; RNA-seq; Roots; MicroRNA; Transcriptomics