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

Elena A. Vidal; Tomás C. Moyano; Gabriel Krouk; Manpreet S. Katari; Milos Tanurdzic; W. R. McCombie; Gloria M. Coruzzi; Rodrigo A. Gutiérrez

doi:10.1186/1471-2164-14-701

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

Elena A. Vidal, Tomás C. Moyano, Gabriel Krouk, Manpreet S. Katari, Milos Tanurdzic, W. R. McCombie, Gloria M. Coruzzi, Rodrigo A. Gutiérrez

Biology and Genomics

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Article number	701
Journal	BMC Genomics
Volume	14
Issue number	1
DOIs	https://doi.org/10.1186/1471-2164-14-701
State	Published - Oct 11 2013

Keywords

Arabidopsis
MicroRNA
Nitrate
RNA-seq
Roots
Transcriptomics

ASJC Scopus subject areas

Biotechnology
Genetics

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10.1186/1471-2164-14-701

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@article{d3d346dcdbb64877b54fdcc6f7c2e18f,

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

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.",

keywords = "Arabidopsis, MicroRNA, Nitrate, RNA-seq, Roots, Transcriptomics",

author = "Vidal, {Elena A.} and Moyano, {Tom{\'a}s C.} and Gabriel Krouk and Katari, {Manpreet S.} and Milos Tanurdzic and McCombie, {W. R.} and Coruzzi, {Gloria M.} and Guti{\'e}rrez, {Rodrigo A.}",

note = "Funding Information: This work was supported by International Early Career Scientist program from Howard Hughes Medical Institute to R.A.G., Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation [15090007 to R.A.G.], Millennium Nucleus Center for Plant Functional Genomics [P10-062-F to R.A.G.], Fondo Nacional de Desarrollo Cient{\'i}fico y Tecnol{\'o}gico [1100698 to R.A.G.], Comisi{\'o}n Nacional de Investigaci{\'o}n Cient{\'i}fica y Tecnol{\'o}gica-ANR program [ANR-007 to R.A.G.], the National Institutes of Health [GM032877 to G.M.C.] and National Science Foundation [MCB-0929338 to G.M.C.], Agence Nationale de la Recherche [NitroNet: ANR 11 PDOC 020 01 to G.K.] and Centre National de la Recherche Scientifique [PEPS Bio math Info 2012–2013: SuperRegNet to G.K.]. E.A.V is supported by Proyecto de Inserci{\'o}n en la Academia (PSD74).",

year = "2013",

month = oct,

day = "11",

doi = "10.1186/1471-2164-14-701",

language = "English (US)",

volume = "14",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central Ltd.",

number = "1",

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TY - JOUR

T1 - Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots

AU - Vidal, Elena A.

AU - Moyano, Tomás C.

AU - Krouk, Gabriel

AU - Katari, Manpreet S.

AU - Tanurdzic, Milos

AU - McCombie, W. R.

AU - Coruzzi, Gloria M.

AU - Gutiérrez, Rodrigo A.

N1 - Funding Information: This work was supported by International Early Career Scientist program from Howard Hughes Medical Institute to R.A.G., Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation [15090007 to R.A.G.], Millennium Nucleus Center for Plant Functional Genomics [P10-062-F to R.A.G.], Fondo Nacional de Desarrollo Científico y Tecnológico [1100698 to R.A.G.], Comisión Nacional de Investigación Científica y Tecnológica-ANR program [ANR-007 to R.A.G.], the National Institutes of Health [GM032877 to G.M.C.] and National Science Foundation [MCB-0929338 to G.M.C.], Agence Nationale de la Recherche [NitroNet: ANR 11 PDOC 020 01 to G.K.] and Centre National de la Recherche Scientifique [PEPS Bio math Info 2012–2013: SuperRegNet to G.K.]. E.A.V is supported by Proyecto de Inserción en la Academia (PSD74).

PY - 2013/10/11

Y1 - 2013/10/11

N2 - 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.

AB - 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.

KW - Arabidopsis

KW - MicroRNA

KW - Nitrate

KW - RNA-seq

KW - Roots

KW - Transcriptomics

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JO - BMC Genomics

JF - BMC Genomics

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ER -

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

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