title: Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs.
abstract: Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA-dependent RNA polymerase 2 (RDR2) is a component of the RNA-directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA-seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, >6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2-sensitive and RDR2-resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant.
authors: Interdepartmental Plant Biology Program, Iowa State University, Ames, Iowa, USA.
authors: Yi
authors: Y
authors: Jia
authors: Damon R
authors: DR
authors: Lisch
authors: Kazuhiro
authors: K
authors: Ohtsu
authors: Michael J
authors: MJ
authors: Scanlon
authors: Daniel
authors: D
authors: Nettleton
authors: Patrick S
authors: PS
authors: Schnable
mesh_terms: D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D020029:Base Pairing / Q000235:genetics; D042002:Chromatin Assembly and Disassembly / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D015536:Down-Regulation / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D007834:Lasers; D018519:Meristem / Q000235:genetics; D042282:Microdissection; D009154:Mutation / Q000235:genetics; D018749:RNA, Plant / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase / Q000172:deficiency* / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements; D018749:RNA, Plant; D034741:RNA, Small Interfering; C519655:RDR2 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase