title: NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation.
abstract: RNA-directed DNA methylation (RdDM) is an RNAi-based mechanism for establishing transcriptional gene silencing in plants. The plant-specific RNA polymerases IV and V are required for the generation of 24-nucleotide (nt) siRNAs and for guiding sequence-specific DNA methylation by the siRNAs, respectively. However, unlike the extensively studied multisubunit Pol II, our current knowledge about Pol IV and Pol V is restricted to only the two largest subunits NRPD1a/NRPD1 and NRPD1b/NRPE1 and the one second-largest subunit NRPD2a. It is unclear whether other subunits may be required for the functioning of Pol IV and Pol V in RdDM. From a genetic screen for second-site suppressors of the DNA demethylase mutant ros1, we identified a new component (referred to as RDM2) as well as seven known components (NRPD1, NRPE1, NRPD2a, AGO4, HEN1, DRD1, and HDA6) of the RdDM pathway. The differential effects of the mutations on two mechanistically distinct transcriptional silencing reporters suggest that RDM2, NRPD1, NRPE1, NRPD2a, HEN1, and DRD1 function only in the siRNA-dependent pathway of transcriptional silencing, whereas HDA6 and AGO4 have roles in both siRNA-dependent and -independent pathways of transcriptional silencing. In the rdm2 mutants, DNA methylation and siRNA accumulation were reduced substantially at loci previously identified as endogenous targets of Pol IV and Pol V, including 5S rDNA, MEA-ISR, AtSN1, AtGP1, and AtMU1. The amino acid sequence of RDM2 is similar to that of RPB4 subunit of Pol II, but we show evidence that RDM2 has diverged significantly from RPB4 and cannot function in Pol II. An association of RDM2 with both NRPD1 and NRPE1 was observed by coimmunoprecipitation and coimmunolocalization assays. Our results show that RDM2/NRPD4/NRPE4 is a new component of the RdDM pathway in Arabidopsis and that it functions as part of Pol IV and Pol V.
authors.affiliation: Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA.
authors.forename: Xin-Jian
authors.initials: XJ
authors.lastname: He
authors.forename: Yi-Feng
authors.initials: YF
authors.lastname: Hsu
authors.forename: Olga
authors.initials: O
authors.lastname: Pontes
authors.forename: Jianhua
authors.initials: J
authors.lastname: Zhu
authors.forename: Jian
authors.initials: J
authors.lastname: Lu
authors.forename: Ray A
authors.initials: RA
authors.lastname: Bressan
authors.forename: Craig
authors.initials: C
authors.lastname: Pikaard
authors.forename: Co-Shine
authors.initials: CS
authors.lastname: Wang
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics / Q000502:physiology*; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017343:Genes, Plant; D008969:Molecular Sequence Data; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D010641:Phenotype; D030821:Plants, Genetically Modified; D021122:Protein Subunits; D034622:RNA Interference; D012319:RNA Polymerase II / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D009687:Nuclear Proteins; D021122:Protein Subunits; D018749:RNA, Plant; D034741:RNA, Small Interfering; C471271:ROS1 protein, Arabidopsis; D012319:RNA Polymerase II; C499181:RNA polymerase IV, Arabidopsis; D012321:DNA-Directed RNA Polymerases