title: Genomic DNA Methylation Analyses Reveal the Distinct Profiles in Castor Bean Seeds with Persistent Endosperms.
abstract: Investigations of genomic DNA methylation in seeds have been restricted to a few model plants. The endosperm genomic DNA hypomethylation has been identified in angiosperm, but it is difficult to dissect the mechanism of how this hypomethylation is established and maintained because endosperm is ephemeral and disappears with seed development in most dicots. Castor bean (Ricinus communis), unlike Arabidopsis (Arabidopsis thaliana), endosperm is persistent throughout seed development, providing an excellent model in which to dissect the mechanism of endosperm genomic hypomethylation in dicots. We characterized the DNA methylation-related genes encoding DNA methyltransferases and demethylases and analyzed their expression profiles in different tissues. We examined genomic methylation including CG, CHG, and CHH contexts in endosperm and embryo tissues using bisulfite sequencing and revealed that the CHH methylation extent in endosperm and embryo was, unexpectedly, substantially higher than in previously studied plants, irrespective of the CHH percentage in their genomes. In particular, we found that the endosperm exhibited a global reduction in CG and CHG methylation extents relative to the embryo, markedly switching global gene expression. However, CHH methylation occurring in endosperm did not exhibit a significant reduction. Combining with the expression of 24-nucleotide small interfering RNAs (siRNAs) mapped within transposable element (TE) regions and genes involved in the RNA-directed DNA methylation pathway, we demonstrate that the 24-nucleotide siRNAs played a critical role in maintaining CHH methylation and repressing the activation of TEs in persistent endosperm development. This study discovered a novel genomic DNA methylation pattern and proposes the potential mechanism occurring in dicot seeds with persistent endosperm.
authors.affiliation: Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.).
authors.forename: Wei
authors.identifier: 0000-0003-0581-7872
authors.initials: W
authors.lastname: Xu
authors.affiliation: Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.).
authors.forename: Tianquan
authors.initials: T
authors.lastname: Yang
authors.affiliation: Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.).
authors.forename: Xue
authors.initials: X
authors.lastname: Dong
authors.affiliation: Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.).
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
authors.affiliation: Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.) liuaizhong@mail.kib.ac.cn.
authors.forename: Aizhong
authors.identifier: 0000-0002-3197-5535
authors.initials: A
authors.lastname: Liu
mesh_terms: D002367:Ricinus communis / Q000196:embryology* / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D056625:Endosperm / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D008780:Methyltransferases / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D018749:RNA, Plant; D008780:Methyltransferases