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

Vidal, E. A., Moyano, T. C., Krouk, G., Katari, M. S., Tanurdzic, M., McCombie, W. R., Coruzzi, G. M., Gutierrez, R. A. (2013) Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics, 14. p. 701. ISSN 1471-2164

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URL: http://www.ncbi.nlm.nih.gov/pubmed/24119003
DOI: 10.1186/1471-2164-14-701

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.

Item Type: Paper
Subjects: organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
Investigative techniques and equipment > assays > next generation sequencing
Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:
Communities: CSHL labs > Martienssen lab
CSHL labs > McCombie lab
Depositing User: Matt Covey
Date Deposited: 22 Jan 2014 21:43
Last Modified: 22 Jan 2014 21:43
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29340

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