title: Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine.
abstract: Atrazine (ATR) is a pesticide widely used for controlling weeds for crop production. Crop contamination with ATR negatively affects crop growth and development. This study presents the first genome-wide single-base-resolution maps of DNA methylation in ATR-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between the ATR-exposed and ATR-free (control) rice. Most of DNA methyltransferases, histone methyltransferases and DNA demethylase were differentially regulated by ATR. We found more genes hypermethylated than those hypomethylated in the regions of upstream, genebody and downstream under ATR exposure. A stringent group of 674 genes (p < 0.05, two-fold change) with a strong preference of differential expression in ATR-exposed rice was identified. Some of the genes were identified in a subset of loss of function mutants defective in DNA methylation/demethylation. Provision of 5-azacytidine (AZA, inhibitor of DNA methylation) promoted the rice growth and reduced ATR content. By UPLC/Q-TOF-MS/MS, 8 degraded products and 9 conjugates of ATR in AZA-treated rice were characterized. Two of them has been newly identified in this study. Our data show that ATR-induced changes in DNA methylation marks are possibly involved in an epigenetic mechanism associated with activation of specific genes responsible for ATR degradation and detoxification.
authors.affiliation: Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.|Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Yi Chen
authors.initials: YC
authors.lastname: Lu
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Sheng Jun
authors.initials: SJ
authors.lastname: Feng
authors.affiliation: Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.|Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Jing Jing
authors.initials: JJ
authors.lastname: Zhang
authors.affiliation: Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.|Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Luo
authors.affiliation: State key laboratory of food science and technology, Jiangnan University, Wuxi 214122, China.
authors.forename: Shuang
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Yang
mesh_terms: D001280:Atrazine / Q000494:pharmacology*; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D063990:Gene Ontology; D018745:Genome, Plant; D012275:Oryza / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D010575:Pesticides / Q000494:pharmacology*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000187:drug effects
chemical_list: D018744:DNA, Plant; D010575:Pesticides; D010940:Plant Proteins; D001280:Atrazine