title: Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development.
abstract: Seed development is an important process of reproductive development and consists of embryo and endosperm development; both comprise several key processes. To determine and investigate the functions of the dynamic DNA methylome during seed development, we profiled the DNA methylation genome wide in a series of developmental stages of rice (Oryza sativa) embryo and endosperm by methylcytosine immunoprecipitation followed by Illumina sequencing. The results showed that embryo is hypermethylated predominantly around non-transposable element (TE) genes, short DNA-TEs, and short interspersed TEs compared with endosperm, and non-TE genes have the most diverse methylation status across seed development. In addition, lowly expressed genes are significantly enriched in hypermethylated genes, but not vice versa, confirming the crucial role of DNA methylation in suppressing gene transcription. Further analysis revealed the significantly decreased methylation at early developing stages (from 2 to 3 d after pollination), indicating a predominant role of demethylation during early endosperm development and that genes with a consistent negative correlation between DNA methylation change and expression change may be potentially directly regulated by DNA methylation. Interestingly, comparative analysis of the DNA methylation profiles revealed that both rice indica and japonica subspecies showed robust fluctuant profiles of DNA methylation levels in embryo and endosperm across seed development, with the highest methylation level at 6 d after pollination (2 d after pollination of endosperm in japonica as well), indicating that a complex and finely controlled methylation pattern is closely associated with seed development regulation. The systemic characterization of the dynamic DNA methylome in developing rice seeds will help us understand the effects and mechanism of epigenetic regulation in seed development.
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Mei-Qing
authors.initials: MQ
authors.lastname: Xing
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Yi-Jing
authors.initials: YJ
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Shi-Rong
authors.identifier: http://orcid.org/0000-0003-2594-3198
authors.initials: SR
authors.lastname: Zhou
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Wen-Yan
authors.initials: WY
authors.lastname: Hu
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Xue-Ting
authors.initials: XT
authors.lastname: Wu
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Ya-Jin
authors.initials: YJ
authors.lastname: Ye
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Xiao-Xia
authors.initials: XX
authors.lastname: Wu
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Yun-Ping
authors.initials: YP
authors.lastname: Xiao
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
authors.forename: Xuan
authors.initials: X
authors.lastname: Li
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.) hwxue@sibs.ac.cn.
authors.forename: Hong-Wei
authors.identifier: http://orcid.org/0000-0002-7641-5320
authors.initials: HW
authors.lastname: Xue
mesh_terms: D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics; D056625:Endosperm / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010940:Plant Proteins / Q000235:genetics; D012639:Seeds / Q000235:genetics* / Q000254:growth & development
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins