title: Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses.
abstract: Long non-protein coding RNAs (npcRNA) represent an emerging class of riboregulators, which either act directly in this long form or are processed to shorter miRNA and siRNA. Genome-wide bioinformatic analysis of full-length cDNA databases identified 76 Arabidopsis npcRNAs. Fourteen npcRNAs were antisense to protein-coding mRNAs, suggesting cis-regulatory roles. Numerous 24-nt siRNA matched to five different npcRNAs, suggesting that these npcRNAs are precursors of this type of siRNA. Expression analyses of the 76 npcRNAs identified a novel npcRNA that accumulates in a dcl1 mutant but does not appear to produce trans-acting siRNA or miRNA. Additionally, another npcRNA was the precursor of miR869 and shown to be up-regulated in dcl4 but not in dcl1 mutants, indicative of a young miRNA gene. Abiotic stress altered the accumulation of 22 npcRNAs among the 76, a fraction significantly higher than that observed for the RNA binding protein-coding fraction of the transcriptome. Overexpression analyses in Arabidopsis identified two npcRNAs as regulators of root growth during salt stress and leaf morphology, respectively. Hence, together with small RNAs, long npcRNAs encompass a sensitive component of the transcriptome that have diverse roles during growth and differentiation.
authors.affiliation: Institut des Sciences du Végétal (ISV), CNRS, 91198 Gif-sur-Yvette, France.
authors.forename: Besma
authors.initials: B
authors.lastname: Ben Amor
authors.forename: Sonia
authors.initials: S
authors.lastname: Wirth
authors.forename: Francisco
authors.initials: F
authors.lastname: Merchan
authors.forename: Philippe
authors.initials: P
authors.lastname: Laporte
authors.forename: Yves
authors.initials: Y
authors.lastname: d'Aubenton-Carafa
authors.forename: Judith
authors.initials: J
authors.lastname: Hirsch
authors.forename: Alexis
authors.initials: A
authors.lastname: Maizel
authors.forename: Allison
authors.initials: A
authors.lastname: Mallory
authors.forename: Antoine
authors.initials: A
authors.lastname: Lucas
authors.forename: Jean Marc
authors.initials: JM
authors.lastname: Deragon
authors.forename: Herve
authors.initials: H
authors.lastname: Vaucheret
authors.forename: Claude
authors.initials: C
authors.lastname: Thermes
authors.forename: Martin
authors.initials: M
authors.lastname: Crespi
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics; D001483:Base Sequence; D018797:Cell Cycle Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D030821:Plants, Genetically Modified; D012322:RNA Precursors / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D043244:Ribonuclease III / Q000235:genetics; D012260:Ribonucleases / Q000235:genetics; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D018797:Cell Cycle Proteins; D035683:MicroRNAs; D012322:RNA Precursors; D018749:RNA, Plant; D034741:RNA, Small Interfering; D022661:RNA, Untranslated; C504982:DCL4 protein, Arabidopsis; D012260:Ribonucleases; C402383:DCL1 protein, Arabidopsis; D043244:Ribonuclease III