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

BMC Genomics

Research Article

Gabriel Krouk¹  Manpreet S Katari²  Gloria M Coruzzi²  W Richard McCombie³  Milos Tanurdzic⁴  Rodrigo A Gutiérrez⁵  Tomás C Moyano⁵  Elena A Vidal⁵ 

[1] Biochimie et Physiologie Moléculaire des Plantes, UMR 5004 CNRS/INRA/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes-Claude Grignon, Montpellier, France;Center for Genomics and Systems Biology, Department of Biology, New York University, 10003, New York, NY, USA;Center for Genomics and Systems Biology, Department of Biology, New York University, 10003, New York, NY, USA;Cold Spring Harbor Laboratory, New York, USA;Cold Spring Harbor Laboratory, New York, USA;School of Biological Sciences, The University of Queensland, St Lucia, Australia;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, 8331010, Santiago, Chile;

关键词: Arabidopsis;    Nitrate;    RNA-seq;    Roots;    MicroRNA;    Transcriptomics;   

DOI  :  10.1186/1471-2164-14-701

 received in 2013-02-05, accepted in 2013-06-10,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundNitrate 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.ResultsIn 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.ConclusionsSequencing 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.

【 授权许可】

Unknown   
© Vidal et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.