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Differential expression networks and inheritance patterns of long non-coding RNAs in castor bean seeds.
Plant J. 2018 07; 95(2):324-340.PJ

Abstract

Long non-coding RNAs (lncRNAs) serve as versatile regulators of plant growth and development. The potential functions and inheritance patterns of lncRNAs, as well as the epigenetic regulation of lncRNA itself, remain largely uncharacterized in plant seeds, especially in the persistent endosperm of the dicotyledons. In this study, we investigated diverse RNA-seq data and catalogued 5356 lncRNAs in castor bean seeds. A small fraction of lncRNAs were transcribed from the same direction as the promoters of protein-coding genes (PCgenes) and exhibited strongly coordinated expression with the nearby PCgene. Co-expression analysis with weighted gene co-expression network analysis (WGCNA) showed these lncRNAs to be involved in differential transcription networks between the embryo and endosperm in the early developing seed. Genomic DNA methylation analyses revealed that the expression level of lncRNAs was tightly linked to DNA methylation and that endosperm hypomethylation could promote the expression of linked lncRNAs. Intriguingly, upon hybridization, most lncRNAs with divergent genome sequences between two parents could be reconciled and were expressed according to their parental genome contribution; however, some deviation in the expression of allelic lncRNAs was observed and found to be partially dependent on parental effects. In triploid endosperm, the expression of most lncRNAs was not dosage sensitive, as only 20 lncRNAs had balanced dosage. Our findings not only demonstrate that lncRNAs play potential roles in regulating the development of castor bean endosperm and embryo, but also provide novel insights into the parental effects, allelic expression and epigenetic regulation of lncRNAs in dicotyledonous seeds.

Authors+Show Affiliations

Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China.Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China. Graduate University of the Chinese Academy of Sciences, Beijing, 100049, China.Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China. Graduate University of the Chinese Academy of Sciences, Beijing, 100049, China.Guangzhou Gene denovo Biotechnology, Guangzhou, 510006, China.Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China.Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China. Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

29738104

Citation

Xu, Wei, et al. "Differential Expression Networks and Inheritance Patterns of Long Non-coding RNAs in Castor Bean Seeds." The Plant Journal : for Cell and Molecular Biology, vol. 95, no. 2, 2018, pp. 324-340.
Xu W, Yang T, Wang B, et al. Differential expression networks and inheritance patterns of long non-coding RNAs in castor bean seeds. Plant J. 2018;95(2):324-340.
Xu, W., Yang, T., Wang, B., Han, B., Zhou, H., Wang, Y., Li, D. Z., & Liu, A. (2018). Differential expression networks and inheritance patterns of long non-coding RNAs in castor bean seeds. The Plant Journal : for Cell and Molecular Biology, 95(2), 324-340. https://doi.org/10.1111/tpj.13953
Xu W, et al. Differential Expression Networks and Inheritance Patterns of Long Non-coding RNAs in Castor Bean Seeds. Plant J. 2018;95(2):324-340. PubMed PMID: 29738104.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Differential expression networks and inheritance patterns of long non-coding RNAs in castor bean seeds. AU - Xu,Wei, AU - Yang,Tianquan, AU - Wang,Bin, AU - Han,Bing, AU - Zhou,Huangkai, AU - Wang,Yue, AU - Li,De-Zhu, AU - Liu,Aizhong, Y1 - 2018/05/31/ PY - 2017/12/01/received PY - 2018/03/19/revised PY - 2018/04/25/accepted PY - 2018/5/9/pubmed PY - 2019/6/4/medline PY - 2018/5/9/entrez KW - DNA methylation KW - allelic expression KW - castor bean KW - dicotyledonous seeds KW - endosperm development KW - expression networks KW - genomic imprinting KW - inheritance patterns KW - long non-coding RNAs KW - weighted gene co-expression network analysis SP - 324 EP - 340 JF - The Plant journal : for cell and molecular biology JO - Plant J VL - 95 IS - 2 N2 - Long non-coding RNAs (lncRNAs) serve as versatile regulators of plant growth and development. The potential functions and inheritance patterns of lncRNAs, as well as the epigenetic regulation of lncRNA itself, remain largely uncharacterized in plant seeds, especially in the persistent endosperm of the dicotyledons. In this study, we investigated diverse RNA-seq data and catalogued 5356 lncRNAs in castor bean seeds. A small fraction of lncRNAs were transcribed from the same direction as the promoters of protein-coding genes (PCgenes) and exhibited strongly coordinated expression with the nearby PCgene. Co-expression analysis with weighted gene co-expression network analysis (WGCNA) showed these lncRNAs to be involved in differential transcription networks between the embryo and endosperm in the early developing seed. Genomic DNA methylation analyses revealed that the expression level of lncRNAs was tightly linked to DNA methylation and that endosperm hypomethylation could promote the expression of linked lncRNAs. Intriguingly, upon hybridization, most lncRNAs with divergent genome sequences between two parents could be reconciled and were expressed according to their parental genome contribution; however, some deviation in the expression of allelic lncRNAs was observed and found to be partially dependent on parental effects. In triploid endosperm, the expression of most lncRNAs was not dosage sensitive, as only 20 lncRNAs had balanced dosage. Our findings not only demonstrate that lncRNAs play potential roles in regulating the development of castor bean endosperm and embryo, but also provide novel insights into the parental effects, allelic expression and epigenetic regulation of lncRNAs in dicotyledonous seeds. SN - 1365-313X UR - https://www.unboundmedicine.com/medline/citation/29738104/Differential_expression_networks_and_inheritance_patterns_of_long_non_coding_RNAs_in_castor_bean_seeds_ L2 - https://doi.org/10.1111/tpj.13953 DB - PRIME DP - Unbound Medicine ER -