title: DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function.
abstract: Plant RNA silencing operates via RNA-directed DNA-methylation (RdDM) to repress transcription or by targeting mRNAs via posttranscriptional gene silencing (PTGS). These pathways rely on distinct Dicer-like (DCL) proteins that process double-stranded RNA (dsRNA) into small-interfering RNAs (siRNAs). Here, we explored the expression and subcellular localization of Arabidopsis thaliana DCL4. DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic protein, which also represents the ancestral form in plants. A longer DCL4 transcript isoform encoding a nuclear localization signal, DCL4NLS, is present in Arabidopsis, but DNA methylation normally suppresses its expression. Hypomethylation caused by mutation, developmental reprogramming, and biotic stress correlates with enhanced DCL4NLSexpression, while hypermethylation of a DCL4 transgene causes a reduction in DCL4NLSexpression. DCL4NLSfunctions in a noncanonical siRNA pathway, producing a unique set of 21-nucleotide-long "disiRNAs," for DCL4NLSisoform-dependent siRNAs, through the nuclear RdDM dsRNA synthesis pathway. disiRNAs originate mostly from transposable elements (TEs) and TE-overlapping/proximal genes, load into the PTGS effector ARGONAUTE1 (AGO1), and display a subtle effect on transcript accumulation together with overlapping 24-nucleotide siRNAs. We propose that, via PTGS, disiRNAs could help to tighten the expression of epigenetically activated TEs and genes using the methylation-state-responsive DCL4NLS.
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland voinneto@ethz.ch npumplin@ethz.ch.
authors.forename: Nathan
authors.identifier: 0000-0003-4492-5358
authors.initials: N
authors.lastname: Pumplin
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.
authors.forename: Alexis
authors.initials: A
authors.lastname: Sarazin
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.
authors.forename: Pauline E
authors.initials: PE
authors.lastname: Jullien
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.
authors.forename: Nicolas G
authors.identifier: 0000-0002-2161-7910
authors.initials: NG
authors.lastname: Bologna
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Oberlin
authors.affiliation: Department of Biology, ETH Zurich, 8092 Zurich, Switzerland voinneto@ethz.ch npumplin@ethz.ch.
authors.forename: Olivier
authors.initials: O
authors.lastname: Voinnet
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics / Q000378:metabolism; D043244:Ribonuclease III / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements; D020033:Protein Isoforms; D034741:RNA, Small Interfering; D012324:RNA-Dependent RNA Polymerase; C504982:DCL4 protein, Arabidopsis; D043244:Ribonuclease III