Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Identifieur interne : 004742 ( Main/Merge ); précédent : 004741; suivant : 004743Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Auteurs : Elena A. Vidal [Chili] ; Tomás C. Moyano [Chili] ; Gabriel Krouk [France, États-Unis] ; Manpreet S. Katari [États-Unis] ; Milos Tanurdzic [États-Unis, Australie] ; W Richard Mccombie [États-Unis] ; Gloria M. Coruzzi [États-Unis] ; Rodrigo A. Gutiérrez [Chili]Source :
- BMC Genomics [ 1471-2164 ] ; 2013.
Abstract
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
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.
Url:
DOI: 10.1186/1471-2164-14-701
PubMed: 24119003
PubMed Central: 3906980
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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</nlm:aff><country xml:lang="fr">Chili</country><wicri:regionArea>FONDAP Center for Genome Regulation. 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Vidal</name><affiliation wicri:level="1"><nlm:aff id="I1">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</nlm:aff><country xml:lang="fr">Chili</country><wicri:regionArea>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</wicri:regionArea><wicri:noRegion>Santiago 8331010</wicri:noRegion></affiliation></author><author><name sortKey="Moyano, Tomas C" sort="Moyano, Tomas C" uniqKey="Moyano T" first="Tomás C" last="Moyano">Tomás C. Moyano</name><affiliation wicri:level="1"><nlm:aff id="I1">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</nlm:aff><country xml:lang="fr">Chili</country><wicri:regionArea>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</wicri:regionArea><wicri:noRegion>Santiago 8331010</wicri:noRegion></affiliation></author><author><name sortKey="Krouk, Gabriel" sort="Krouk, Gabriel" uniqKey="Krouk G" first="Gabriel" last="Krouk">Gabriel Krouk</name><affiliation wicri:level="3"><nlm:aff id="I2">Biochimie et Physiologie Moléculaire des Plantes, UMR 5004 CNRS/INRA/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes-Claude Grignon, Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Biochimie et Physiologie Moléculaire des Plantes, UMR 5004 CNRS/INRA/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes-Claude Grignon, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Katari, Manpreet S" sort="Katari, Manpreet S" uniqKey="Katari M" first="Manpreet S" last="Katari">Manpreet S. Katari</name><affiliation wicri:level="2"><nlm:aff id="I3">Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Tanurdzic, Milos" sort="Tanurdzic, Milos" uniqKey="Tanurdzic M" first="Milos" last="Tanurdzic">Milos Tanurdzic</name><affiliation wicri:level="2"><nlm:aff id="I4">Cold Spring Harbor Laboratory, New York, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cold Spring Harbor Laboratory, New York</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I5">Present address: School of Biological Sciences, The University of Queensland, St Lucia, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Present address: School of Biological Sciences, The University of Queensland, St Lucia</wicri:regionArea><wicri:noRegion>St Lucia</wicri:noRegion></affiliation></author><author><name sortKey="Mccombie, W Richard" sort="Mccombie, W Richard" uniqKey="Mccombie W" first="W Richard" last="Mccombie">W Richard Mccombie</name><affiliation wicri:level="2"><nlm:aff id="I4">Cold Spring Harbor Laboratory, New York, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cold Spring Harbor Laboratory, New York</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Coruzzi, Gloria M" sort="Coruzzi, Gloria M" uniqKey="Coruzzi G" first="Gloria M" last="Coruzzi">Gloria M. Coruzzi</name><affiliation wicri:level="2"><nlm:aff id="I3">Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Gutierrez, Rodrigo A" sort="Gutierrez, Rodrigo A" uniqKey="Gutierrez R" first="Rodrigo A" last="Gutiérrez">Rodrigo A. Gutiérrez</name><affiliation wicri:level="1"><nlm:aff id="I1">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</nlm:aff><country xml:lang="fr">Chili</country><wicri:regionArea>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</wicri:regionArea><wicri:noRegion>Santiago 8331010</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>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.</p></sec><sec><title>Results</title><p>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 <italic>Arabidopsis thaliana</italic> 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.</p></sec><sec><title>Conclusions</title><p>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.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Crawford, Nm" uniqKey="Crawford N">NM Crawford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Redinbaugh, Mg" uniqKey="Redinbaugh M">MG Redinbaugh</name></author><author><name sortKey="Campbell, Wh" uniqKey="Campbell W">WH Campbell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stitt, M" uniqKey="Stitt M">M 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