دورية أكاديمية
Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development.
| العنوان: | Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development. |
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| المؤلفون: | Xing MQ; 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.)., Zhang YJ; 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.)., Zhou SR; 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.)., Hu WY; 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.)., Wu XT; 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.)., Ye YJ; 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.)., Wu XX; 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.)., Xiao YP; 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.)., Li X; 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.)., Xue HW; 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. |
| المصدر: | Plant physiology [Plant Physiol] 2015 Aug; Vol. 168 (4), pp. 1417-32. Date of Electronic Publication: 2015 Jul 05. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Society of Plant Biologists Country of Publication: United States NLM ID: 0401224 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1532-2548 (Electronic) Linking ISSN: 00320889 NLM ISO Abbreviation: Plant Physiol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Original Publication: Lancaster, Pa., American Society of Plant Physiologists. |
| مواضيع طبية MeSH: | DNA Methylation* , Gene Expression Profiling* , Gene Expression Regulation, Developmental* , Gene Expression Regulation, Plant*, Oryza/*genetics , Seeds/*genetics, DNA Transposable Elements/genetics ; Endosperm/genetics ; Endosperm/growth & development ; Gene Ontology ; Genes, Plant/genetics ; Genome, Plant/genetics ; Oryza/growth & development ; Plant Proteins/genetics ; Seeds/growth & development |
| مستخلص: | 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. (© 2015 American Society of Plant Biologists. All Rights Reserved.) |
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| سلسلة جزيئية: | GEO GSE11966; GSE27856; GSE57615; GSE57706 |
| المشرفين على المادة: | 0 (DNA Transposable Elements) 0 (Plant Proteins) |
| تواريخ الأحداث: | Date Created: 20150707 Date Completed: 20160511 Latest Revision: 20181113 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC4528747 |
| DOI: | 10.1104/pp.15.00414 |
| PMID: | 26145151 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1532-2548 |
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| DOI: | 10.1104/pp.15.00414 |