title: Lower levels of transgene silencing in roots is associated with reduced DNA methylation levels at non-symmetrical sites but not at symmetrical sites.
abstract: Transgene transcripts were recently shown to accumulate at higher levels in roots, relative to leaves, of silenced-transgenic Nicotiana benthamiana plants and to be inversely related with the accumulation of small interfering RNAs (siRNAs), suggesting that RNA silencing is less active in roots than in leaves (Andika et al., 2005. Mol. Plant-Microbe Interact. 18: 194). Here we show that the lower transgene RNA silencing activity in roots was associated with lower transgene methylation levels at non-symmetrical CpNpN context but not at symmetrical CpG or CpNpG context in three sets of transformant plants with different exogenous genes. In contrast, such a difference between roots and leaves was not observed for the Tnt1 retrotransposon: no Tnt1 transcript was detected in roots or in leaves of N. benthamiana, while equal levels of Tnt1-derived siRNA accumulation and Tnt1 methylation were found. From our data and previously reported information, we suggest that roots have less of an activity that acts at the step of generation of siRNAs.
authors.affiliation: Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046, Japan.
authors.forename: Ida Bagus
authors.initials: IB
authors.lastname: Andika
authors.forename: Hideki
authors.initials: H
authors.lastname: Kondo
authors.forename: Muhammad Danial
authors.initials: MD
authors.lastname: Rahim
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Tamada
mesh_terms: D001665:Binding Sites; D018899:CpG Islands; D004247:DNA / Q000235:genetics; D019175:DNA Methylation; D020868:Gene Silencing; D017343:Genes, Plant; D049452:Green Fluorescent Proteins / Q000378:metabolism; D008957:Models, Genetic; D016366:Open Reading Frames; D018517:Plant Roots; D030821:Plants, Genetically Modified; D012313:RNA / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013447:Sulfites / Q000737:chemistry; D014026:Nicotiana / Q000235:genetics*; D019076:Transgenes
chemical_list: D034741:RNA, Small Interfering; D013447:Sulfites; D049452:Green Fluorescent Proteins; D012313:RNA; D004247:DNA