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.
authors.affiliation: 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. gloria.coruzzi@nyu.edu.
authors.forename: Elena A
authors.initials: EA
authors.lastname: Vidal
authors.forename: Tomás C
authors.initials: TC
authors.lastname: Moyano
authors.forename: Gabriel
authors.initials: G
authors.lastname: Krouk
authors.forename: Manpreet S
authors.initials: MS
authors.lastname: Katari
authors.forename: Milos
authors.initials: M
authors.lastname: Tanurdzic
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Gloria M
authors.initials: GM
authors.lastname: Coruzzi
authors.forename: Rodrigo A
authors.initials: RA
authors.lastname: Gutiérrez
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation / Q000187:drug effects; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D009566:Nitrates / Q000494:pharmacology*; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics; D011061:Poly A / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D035683:MicroRNAs; D009566:Nitrates; D018749:RNA, Plant; D011061:Poly A