title: Arabidopsis RNASE THREE LIKE2 Modulates the Expression of Protein-Coding Genes via 24-Nucleotide Small Interfering RNA-Directed DNA Methylation.
abstract: RNaseIII enzymes catalyze the cleavage of double-stranded RNA (dsRNA) and have diverse functions in RNA maturation. Arabidopsis thaliana RNASE THREE LIKE2 (RTL2), which carries one RNaseIII and two dsRNA binding (DRB) domains, is a unique Arabidopsis RNaseIII enzyme resembling the budding yeast small interfering RNA (siRNA)-producing Dcr1 enzyme. Here, we show that RTL2 modulates the production of a subset of small RNAs and that this activity depends on both its RNaseIII and DRB domains. However, the mode of action of RTL2 differs from that of Dcr1. Whereas Dcr1 directly cleaves dsRNAs into 23-nucleotide siRNAs, RTL2 likely cleaves dsRNAs into longer molecules, which are subsequently processed into small RNAs by the DICER-LIKE enzymes. Depending on the dsRNA considered, RTL2-mediated maturation either improves (RTL2-dependent loci) or reduces (RTL2-sensitive loci) the production of small RNAs. Because the vast majority of RTL2-regulated loci correspond to transposons and intergenic regions producing 24-nucleotide siRNAs that guide DNA methylation, RTL2 depletion modifies DNA methylation in these regions. Nevertheless, 13% of RTL2-regulated loci correspond to protein-coding genes. We show that changes in 24-nucleotide siRNA levels also affect DNA methylation levels at such loci and inversely correlate with mRNA steady state levels, thus implicating RTL2 in the regulation of protein-coding gene expression.
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France.
authors.forename: Emilie
authors.identifier: http://orcid.org/0000-0002-4017-6436
authors.initials: E
authors.lastname: Elvira-Matelot
authors.affiliation: URGI, INRA, 78000 Versailles, France.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Hachet
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France.
authors.forename: Nahid
authors.identifier: http://orcid.org/0000-0002-4643-0642
authors.initials: N
authors.lastname: Shamandi
authors.affiliation: CNRS, UMR 5096, LGDP, 66860 Perpignan, France Université de Perpignan Via Domitia, UMR 5096, LGDP, 66860 Perpignan, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Comella
authors.affiliation: CNRS, UMR 5096, LGDP, 66860 Perpignan, France Université de Perpignan Via Domitia, UMR 5096, LGDP, 66860 Perpignan, France.
authors.forename: Julio
authors.identifier: http://orcid.org/0000-0002-2717-7995
authors.initials: J
authors.lastname: Sáez-Vásquez
authors.affiliation: URGI, INRA, 78000 Versailles, France.
authors.forename: Matthias
authors.initials: M
authors.lastname: Zytnicki
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France herve.vaucheret@versailles.inra.fr.
authors.forename: Hervé
authors.initials: H
authors.lastname: Vaucheret
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D017930:Genes, Reporter; D056426:Genetic Loci / Q000235:genetics; D018517:Plant Roots / Q000235:genetics / Q000502:physiology; D012330:RNA, Double-Stranded / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D012330:RNA, Double-Stranded; D012333:RNA, Messenger; D018749:RNA, Plant; D034741:RNA, Small Interfering; C527348:RTL2 protein, Arabidopsis; D043244:Ribonuclease III