title: Analysis of target sequences of DDM1s in Brassica rapa by MSAP.
abstract: DNA methylation is an important epigenetic modification regulating gene expression and transposon silencing. Although epigenetic regulation is involved in some agricultural traits, there has been relatively little research on epigenetic modifications of genes in Brassica rapa, which includes many important vegetables. In B. rapa, orthologs of DDM1, a chromatin remodeling factor required for maintenance of DNA methylation, have been characterized and DNA hypomethylated knock-down plants by RNAi (ddm1-RNAi plants) have been generated. In this study, we investigated differences of DNA methylation status at the genome-wide level between a wild-type (WT) plant and a ddm1-RNAi plant by methylation-sensitive amplification polymorphism (MSAP) analysis. MSAP analysis detected changes of DNA methylation of many repetitive sequences in the ddm1-RNAi plant. Search for body methylated regions in the WT plant revealed no difference in gene body methylation levels between the WT plant and the ddm1-RNAi plant. These results indicate that repetitive sequences are preferentially methylated by DDM1 genes in B. rapa.
authors.affiliation: Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi, 981-8555, Japan.
authors.forename: Taku
authors.initials: T
authors.lastname: Sasaki
authors.forename: Ryo
authors.initials: R
authors.lastname: Fujimoto
authors.forename: Sachie
authors.initials: S
authors.lastname: Kishitani
authors.forename: Takeshi
authors.initials: T
authors.lastname: Nishio
mesh_terms: D001483:Base Sequence; D015139:Blotting, Southern; D029741:Brassica rapa / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D010940:Plant Proteins / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods*; D011110:Polymorphism, Genetic; D034622:RNA Interference; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D010940:Plant Proteins