Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Copyright policy )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.
- SupAgro France
- University of Queensland Australia
- National Research Institute for Agriculture, Food and Environment France
- New York University United States
- The University of Queensland Australia
570, Arabidopsis, Nitrate, Genes, Plant, Plant Roots, 1311 Genetics, 13 Acción por el clima, nitrate, Gene Expression Regulation, Plant, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Transcriptomics, Gene Library, 580, 13 Climate Action, Nitrates, Base Sequence, Arabidopsis Proteins, Sequence Analysis, RNA, transcriptomique, 02 Hambre cero, Genetic Variation, High-Throughput Nucleotide Sequencing, MicroRNA, Roots, 02 Zero Hunger, racine, arabidopsis, MicroRNAs, RNA, Plant, 1305 Biotechnology, micro arn, RNA-seq, Poly A, Transcriptome, Biotechnology, Research Article
570, Arabidopsis, Nitrate, Genes, Plant, Plant Roots, 1311 Genetics, 13 Acción por el clima, nitrate, Gene Expression Regulation, Plant, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Transcriptomics, Gene Library, 580, 13 Climate Action, Nitrates, Base Sequence, Arabidopsis Proteins, Sequence Analysis, RNA, transcriptomique, 02 Hambre cero, Genetic Variation, High-Throughput Nucleotide Sequencing, MicroRNA, Roots, 02 Zero Hunger, racine, arabidopsis, MicroRNAs, RNA, Plant, 1305 Biotechnology, micro arn, RNA-seq, Poly A, Transcriptome, Biotechnology, Research Article
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