title: Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium.
abstract: We report genome-wide single-base resolution maps of methylated cytosines and transcriptome change in Cd-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between Cd-exposed and Cd-free rice genomes. There are 2320 non-redundant differentially methylated regions detected in the genome. RNA sequencing revealed 2092 DNA methylation-modified genes differentially expressed under Cd exposure. More genes were found hypermethylated than those hypomethylated in CG, CHH and CHG (where H is A, C or T) contexts in upstream, gene body and downstream regions. Many of the genes were involved in stress response, metal transport and transcription factors. Most of the DNA methylation-modified genes were transcriptionally altered under Cd stress. A subset of loss of function mutants defective in DNA methylation and histone modification activities was used to identify transcript abundance of selected genes. Compared with wide type, mutation of MET1 and DRM2 resulted in general lower transcript levels of the genes under Cd stress. Transcripts of OsIRO2, OsPR1b and Os09g02214 in drm2 were significantly reduced. A commonly used DNA methylation inhibitor 5-azacytidine was employed to investigate whether DNA demethylation affected physiological consequences. 5-azacytidine provision decreased general DNA methylation levels of selected genes, but promoted growth of rice seedlings and Cd accumulation in rice plant.
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: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Xue Song
authors.initials: XS
authors.lastname: Liu
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Tao
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Shang Kun
authors.initials: SK
authors.lastname: Tan
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Shan Shan
authors.initials: SS
authors.lastname: Chu
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Youko
authors.initials: Y
authors.lastname: Oono
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Xian Duo
authors.initials: XD
authors.lastname: Zhang
authors.affiliation: Institute of Food Safety and Quality, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Zhi Min
authors.initials: ZM
authors.lastname: Yang
mesh_terms: D002104:Cadmium / Q000494:pharmacology*; D019175:DNA Methylation / Q000187:drug effects*; D017343:Genes, Plant / Q000187:drug effects / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D012275:Oryza / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D016133:Polymerase Chain Reaction; D018749:RNA, Plant / Q000235:genetics / Q000502:physiology; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000187:drug effects*
chemical_list: D018749:RNA, Plant; D002104:Cadmium
keywords: DNA methylation; Oryza sativa; bisulfite-sequencing; cadmium; transcriptome