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

Vidal, Elena A., Moyano, Tomás C., Krouk, Gabriel, Katari, Manpreet S., Tanurdzic, Milos, McCombie, W. Richard, Coruzzi, Gloria M. and Gutierrez, Rodrigo A. (2013) Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics, 14 1: 701.1-701.15. doi:10.1186/1471-2164-14-701


Author Vidal, Elena A.
Moyano, Tomás C.
Krouk, Gabriel
Katari, Manpreet S.
Tanurdzic, Milos
McCombie, W. Richard
Coruzzi, Gloria M.
Gutierrez, Rodrigo A.
Title Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Formatted title
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2013-10-11
Sub-type Article (original research)
DOI 10.1186/1471-2164-14-701
Open Access Status DOI
Volume 14
Issue 1
Start page 701.1
End page 701.15
Total pages 15
Place of publication London, United Kingdom
Publisher BioMed Central
Subject 1305 Biotechnology
1311 Genetics
Formatted 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. 
Keyword Arabidopsis
MicroRNA
Nitrate
RNA-seq
Roots
Transcriptomics
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Biological Sciences Publications
 
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