title: The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs.
abstract: Transposable elements (TEs) are mobile fragments of DNA that are repressed in both plant and animal genomes through the epigenetic inheritance of repressed chromatin and expression states. The epigenetic silencing of TEs in plants is mediated by a process of RNA-directed DNA methylation (RdDM). Two pathways of RdDM have been identified: RNA Polymerase IV (Pol IV)-RdDM, which has been shown to be responsible for the de novo initiation, corrective reestablishment, and epigenetic maintenance of TE and/or transgene silencing; and RNA-dependent RNA Polymerase6 (RDR6)-RdDM, which was recently identified as necessary for maintaining repression for a few TEs. We have further characterized RDR6-RdDM using a genome-wide search to identify TEs that generate RDR6-dependent small interfering RNAs. We have determined that TEs only produce RDR6-dependent small interfering RNAs when transcriptionally active, and we have experimentally identified two TE subfamilies as direct targets of RDR6-RdDM. We used these TEs to test the function of RDR6-RdDM in assays for the de novo initiation, corrective reestablishment, and maintenance of TE silencing. We found that RDR6-RdDM plays no role in maintaining TE silencing. Rather, we found that RDR6 and Pol IV are two independent entry points into RdDM and epigenetic silencing that perform distinct functions in the silencing of TEs: Pol IV-RdDM functions to maintain TE silencing and to initiate silencing in an RNA Polymerase II expression-independent manner, while RDR6-RdDM functions to recognize active Polymerase II-derived TE mRNA transcripts to both trigger and correctively reestablish TE methylation and epigenetic silencing.
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA.
authors.forename: Saivageethi
authors.initials: S
authors.lastname: Nuthikattu
authors.forename: Andrea D
authors.initials: AD
authors.lastname: McCue
authors.forename: Kaushik
authors.initials: K
authors.lastname: Panda
authors.forename: Dalen
authors.initials: D
authors.lastname: Fultz
authors.forename: Christopher
authors.initials: C
authors.lastname: DeFraia
authors.forename: Erica N
authors.initials: EN
authors.lastname: Thomas
authors.forename: R Keith
authors.initials: RK
authors.lastname: Slotkin
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D020868:Gene Silencing; D018745:Genome, Plant / Q000235:genetics; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D030821:Plants, Genetically Modified; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D019076:Transgenes
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements; D018749:RNA, Plant; D034741:RNA, Small Interfering; D012319:RNA Polymerase II; C499181:RNA polymerase IV, Arabidopsis; C514575:RDR6 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase; D012321:DNA-Directed RNA Polymerases
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