title: Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting.
abstract: Posttranscriptional RNA silencing of many endogenous transcripts, viruses, and transgenes involves the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 (RDR6/DCL4)-dependent short interfering RNA (siRNA) biogenesis pathway. Arabidopsis thaliana contains several families of trans-acting siRNAs (tasiRNAs) that form in 21-nucleotide phased arrays through the RDR6/DCL4-dependent pathway and that negatively regulate target transcripts. Using deep sequencing technology and computational approaches, the phasing patterns of known tasiRNAs and tasiRNA-like loci from across the Arabidopsis genome were analyzed in wild-type plants and silencing-defective mutants. Several gene transcripts were found to be routed through the RDR6/DCL4-dependent pathway after initial targeting by one or multiple miRNAs or tasiRNAs, the most conspicuous example of which was an expanding clade of genes encoding pentatricopeptide repeat (PPR) proteins. Interestingly, phylogenetic analysis using Populus trichocarpa revealed evidence for small RNA-mediated regulatory mechanisms within a similarly expanded group of PPR genes. We suggest that posttranscriptional silencing mechanisms operate on an evolutionary scale to buffer the effects of rapidly expanding gene families.
authors.affiliation: Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.
authors.forename: Miya D
authors.initials: MD
authors.lastname: Howell
authors.forename: Noah
authors.initials: N
authors.lastname: Fahlgren
authors.forename: Elisabeth J
authors.initials: EJ
authors.lastname: Chapman
authors.forename: Jason S
authors.initials: JS
authors.lastname: Cumbie
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Sullivan
authors.forename: Scott A
authors.initials: SA
authors.lastname: Givan
authors.forename: Kristin D
authors.initials: KD
authors.lastname: Kasschau
authors.forename: James C
authors.initials: JC
authors.lastname: Carrington
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D001483:Base Sequence; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009711:Nucleotides; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism*; D012324:RNA-Dependent RNA Polymerase / Q000378:metabolism*; D043244:Ribonuclease III; D012260:Ribonucleases / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D035683:MicroRNAs; D009711:Nucleotides; D012333:RNA, Messenger; D034741:RNA, Small Interfering; C514575:RDR6 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase; C504982:DCL4 protein, Arabidopsis; D012260:Ribonucleases; D043244:Ribonuclease III