title: 5' to 3' mRNA Decay Contributes to the Regulation of Arabidopsis Seed Germination by Dormancy.
abstract: The regulation of plant gene expression, necessary for development and adaptive responses, relies not only on RNA transcription but also on messenger RNA (mRNA) fate. To understand whether seed germination relies on the degradation of specific subsets of mRNA, we investigated whether the 5' to 3' RNA decay machinery participated in the regulation of this process. Arabidopsis (Arabidopsis thaliana) seeds ofexoribonuclease4(xrn4) andvaricose(vcs) mutants displayed distinct dormancy phenotypes. Transcriptome analysisof xrn4-5andvcs-8mutant seeds allowed us to identify genes that are likely to play a role in the control of germination. Study of 5' untranslated region features of these transcripts revealed that specific motifs, secondary energy, and GC content could play a role in their degradation by XRN4 and VCS, and Gene Ontology clustering revealed novel actors of seed dormancy and germination. Several specific transcripts identified as being putative targets of XRN4 and VCS in seeds (PECTIN LYASE-LIKE,ASPARTYL PROTEASE,DWD-HYPERSENSITIVE-TO-ABA3, andYELLOW STRIPE-LIKE5) were further studied by reverse genetics, and their functional roles in the germination process were confirmed by mutant analysis. These findings suggest that completion of germination and its regulation by dormancy also depend on the degradation of specific subsets of mRNA.
authors.affiliation: Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.).|Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and.|Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.).
authors.forename: Isabelle
authors.initials: I
authors.lastname: Basbouss-Serhal
authors.affiliation: Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.).|Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and.|Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.).
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Pateyron
authors.affiliation: Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.).|Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and.|Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.).
authors.forename: Françoise
authors.initials: F
authors.lastname: Cochet
authors.affiliation: Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.).|Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and.|Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.).
authors.forename: Juliette
authors.identifier: 0000-0003-0433-6102
authors.initials: J
authors.lastname: Leymarie
authors.affiliation: Sorbonne Universités, UPMC Université Paris 06, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., F.C., J.L., C.B.); christophe.bailly@upmc.fr.|Institute of Plant Sciences Paris Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France (S.P.); and christophe.bailly@upmc.fr.|Institute of Plant Sciences Paris Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France (S.P.) christophe.bailly@upmc.fr.
authors.forename: Christophe
authors.identifier: 0000-0002-5878-9249
authors.initials: C
authors.lastname: Bailly
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000040:Abscisic Acid / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D016000:Cluster Analysis; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018525:Germination / Q000235:genetics*; D009154:Mutation; D059372:Nucleotide Motifs / Q000235:genetics; D057445:Plant Dormancy / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000235:genetics* / Q000254:growth & development
chemical_list: D020121:5' Untranslated Regions; D029681:Arabidopsis Proteins; D010940:Plant Proteins; D012333:RNA, Messenger; C483689:VARICOSE protein, Arabidopsis; C418137:Xrn1 protein, plant; D000040:Abscisic Acid; D005095:Exoribonucleases