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Deng Z, Liu Y, Zhou H. Distinct roles of CD244 expression in cancer diagnosis and prognosis: A pan-cancer analysis. Heliyon 2024; 10:e28928. [PMID: 38633624 PMCID: PMC11021915 DOI: 10.1016/j.heliyon.2024.e28928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
The abnormal expression of tumor associated genes in pan-cancer is closely related to the clinicopathological features of distinct cancer types. Thus, identifying the role of specific genes in pan-cancer is needed for developing effective anti-cancer strategies. However, the function of CD244 in pan-cancer has not been fully understood. In this study, we explored the CD244 expression profile across 33 tumor types based on The Cancer Genome Atlas project, the Gene Expression Omnibus database, and other bioinformatics tools. We found down-regulated expression levels in seven tumor types and up-regulated expression levels in two tumor types. We subsequently explored the relationship between survival rate and CD244 expression, and found the positive relationship in patients with adrenocortical carcinoma (ACC), head and neck squamous cell carcinoma (HNSC), skin cutaneous melanoma (SKCM), and uterine corpus endometrial carcinoma (UCEC). We further investigated the association between CD244 expression and tumor-infiltrating immune cells, and discovered their positive correlation in different tumors. We found that CD244 expression level was higher in normal samples than in UCEC samples, and was positively associated with CD8+ T cells infiltrating. The mutation status, promoter methylation, CD244-related molecules and signaling pathways were also employed to study the potential function of CD244 in tumor initiation and progression. Our study offers a comprehensive overview of CD244 in human tumors, revealing CD244 as a potential prognostic biomarker and immunotherapeutic target in cancers.
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Affiliation(s)
- Zhenzhen Deng
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yuanhong Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Haiyan Zhou
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, China
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2
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Yow AG, Laosuntisuk K, Young RA, Doherty CJ, Gillitt N, Perkins-Veazie P, Jenny Xiang QY, Iorizzo M. Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple. Sci Rep 2023; 13:18890. [PMID: 37919298 PMCID: PMC10622448 DOI: 10.1038/s41598-023-45722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
Pineapple originates from tropical regions in South America and is therefore significantly impacted by cold stress. Periodic cold events in the equatorial regions where pineapple is grown may induce early flowering, also known as precocious flowering, resulting in monetary losses due to small fruit size and the need to make multiple passes for harvesting a single field. Currently, pineapple is one of the most important tropical fruits in the world in terms of consumption, and production losses caused by weather can have major impacts on worldwide exportation potential and economics. To further our understanding of and identify mechanisms for low-temperature tolerance in pineapple, and to identify the relationship between low-temperature stress and flowering time, we report here a transcriptomic analysis of two pineapple genotypes in response to low-temperature stress. Using meristem tissue collected from precocious flowering-susceptible MD2 and precocious flowering-tolerant Dole-17, we performed pairwise comparisons and weighted gene co-expression network analysis (WGCNA) to identify cold stress, genotype, and floral organ development-specific modules. Dole-17 had a greater increase in expression of genes that confer cold tolerance. The results suggested that low temperature stress in Dole-17 plants induces transcriptional changes to adapt and maintain homeostasis. Comparative transcriptomic analysis revealed differences in cuticular wax biosynthesis, carbohydrate accumulation, and vernalization-related gene expression between genotypes. Cold stress induced changes in ethylene and abscisic acid-mediated pathways differentially between genotypes, suggesting that MD2 may be more susceptible to hormone-mediated early flowering. The differentially expressed genes and module hub genes identified in this study are potential candidates for engineering cold tolerance in pineapple to develop new varieties capable of maintaining normal reproduction cycles under cold stress. In addition, a total of 461 core genes involved in the development of reproductive tissues in pineapple were also identified in this study. This research provides an important genomic resource for understanding molecular networks underlying cold stress response and how cold stress affects flowering time in pineapple.
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Affiliation(s)
- Ashley G Yow
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
- Plants for Human Health Institute, North Carolina State University, Kannapolis, 28081, USA
| | - Kanjana Laosuntisuk
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Roberto A Young
- Research Department of Dole, Standard Fruit de Honduras, Zona Mazapan, 31101, La Ceiba, Honduras
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Penelope Perkins-Veazie
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
- Plants for Human Health Institute, North Carolina State University, Kannapolis, 28081, USA
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Massimo Iorizzo
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA.
- Plants for Human Health Institute, North Carolina State University, Kannapolis, 28081, USA.
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3
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Hu M, Xi Z, Wang J. Epigenetic Regulation of Subgenomic Gene Expression in Allotetraploid Brassica napus. PLANTS (BASEL, SWITZERLAND) 2023; 12:2608. [PMID: 37514223 PMCID: PMC10383903 DOI: 10.3390/plants12142608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/03/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
Abstract
The allotetraploid Brasscia napus has now been extensively utilized to reveal the genetic processes involved in hybridization and polyploidization. Here, transcriptome, WGBS, and Chip-Seq sequencing data were obtained to explore the regulatory consequences of DNA methylation and histone modifications on gene expression in B. napus. When compared with diploid parents, the expression levels of 14,266 (about 32%) and 17,054 (about 30%) genes were altered in the An and Cn subgenomes, respectively, and a total of 4982 DEGs were identified in B. napus. Genes with high or no expression in diploid parents often shifted to medium or low expression in B. napus. The number of genes with elevated methylation levels in gene promoters and gene body regions has increased in An and Cn subgenomes. The peak number of H3K4me3 modification increased, while the peak number of H3K27ac and H3K27me3 decreased in An and Cn subgenomes, and more genes that maintained parental histone modifications were identified in Cn subgenome. The differential multiples of DEGs in B. napus were positively correlated with DNA methylation levels in promoters and the gene body, and the differential multiples of these DEGs were also affected by the degree of variation in DNA methylation levels. Further analysis revealed that about 99% of DEGs were of DNA methylation, and about 68% of DEGs were modified by at least two types of DNA methylation and H3K4me3, H3K27ac, and H3K27me3 histone modifications. These results demonstrate that DNA methylation is crucial for gene expression regulation, and different epigenetic modifications have an essential function in regulating the differential expression of genes in B. napus.
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Affiliation(s)
- Meimei Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zengde Xi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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4
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Wang X, Yuan D, Liu Y, Liang Y, He J, Yang X, Hang R, Jia H, Mo B, Tian F, Chen X, Liu L. INDETERMINATE1 autonomously regulates phosphate homeostasis upstream of the miR399-ZmPHO2 signaling module in maize. THE PLANT CELL 2023; 35:2208-2231. [PMID: 36943781 PMCID: PMC10226601 DOI: 10.1093/plcell/koad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 05/30/2023]
Abstract
The macronutrient phosphorus is essential for plant growth and development. Plants have evolved multiple strategies to increase the efficiency of phosphate (Pi) acquisition to protect themselves from Pi starvation. However, the crosstalk between Pi homeostasis and plant development remains to be explored. Here, we report that overexpressing microRNA399 (miR399) in maize (Zea mays) is associated with premature senescence after pollination. Knockout of ZmPHO2 (Phosphate 2), a miR399 target, resulted in a similar premature senescence phenotype. Strikingly, we discovered that INDETERMINATE1 (ID1), a floral transition regulator, inhibits the transcription of ZmMIR399 genes by directly binding to their promoters, alleviating the repression of ZmPHO2 by miR399 and ultimately contributing to the maintenance of Pi homeostasis in maize. Unlike ZmMIR399 genes, whose expression is induced by Pi deficiency, ID1 expression was independent of the external inorganic orthophosphate status, indicating that ID1 is an autonomous regulator of Pi homeostasis. Furthermore, we show that ZmPHO2 was under selection during maize domestication and cultivation, resulting in a more sensitive response to Pi starvation in temperate maize than in tropical maize. Our study reveals a direct functional link between Pi-deprivation sensing by the miR399-ZmPHO2 regulatory module and plant developmental regulation by ID1.
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Affiliation(s)
- Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Dan Yuan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yanchun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Juan He
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Runlai Hang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hong Jia
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
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5
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Drozda A, Kurpisz B, Guan Y, Arasimowicz-Jelonek M, Plich J, Jagodzik P, Kuźnicki D, Floryszak-Wieczorek J. Insights into the expression of DNA (de)methylation genes responsive to nitric oxide signaling in potato resistance to late blight disease. FRONTIERS IN PLANT SCIENCE 2022; 13:1033699. [PMID: 36618647 PMCID: PMC9815718 DOI: 10.3389/fpls.2022.1033699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Our previous study concerning the pathogen-induced biphasic pattern of nitric oxide (NO) burst revealed that the decline phase and a low level of NO, due to S-nitrosoglutathione reductase (GSNOR) activity, might be decisive in the upregulation of stress-sensitive genes via histone H3/H4 methylation in potato leaves inoculated with avr P. infestans. The present study refers to the NO-related impact on genes regulating DNA (de)methylation, being in dialog with histone methylation. The excessive amounts of NO after the pathogen or GSNO treatment forced the transient upregulation of histone SUVH4 methylation and DNA hypermethylation. Then the diminished NO bioavailability reduced the SUVH4-mediated suppressive H3K9me2 mark on the R3a gene promoter and enhanced its transcription. However, we found that the R3a gene is likely to be controlled by the RdDM methylation pathway. The data revealed the time-dependent downregulation of the DCL3, AGO4, and miR482e genes, exerting upregulation of the targeted R3a gene correlated with ROS1 overexpression. Based on these results, we postulate that the biphasic waves of NO burst in response to the pathogen appear crucial in establishing potato resistance to late blight through the RdDM pathway controlling R gene expression.
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Affiliation(s)
- Andżelika Drozda
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Poznań, Poland
| | - Barbara Kurpisz
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Poznań, Poland
| | - Yufeng Guan
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Poznań, Poland
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | | | - Jarosław Plich
- Plant Breeding and Acclimatization Institute - National Research Institute, Młochów, Poland
| | - Przemysław Jagodzik
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Daniel Kuźnicki
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Poznań, Poland
| | - Jolanta Floryszak-Wieczorek
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Poznań, Poland
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6
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Guo Y, Jia MA, Li S, Li F. Geminiviruses boost active DNA demethylation for counter-defense. Trends Microbiol 2022; 30:1121-1124. [PMID: 35249803 DOI: 10.1016/j.tim.2022.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 01/13/2023]
Abstract
DNA methylation regulates gene expression under abiotic and biotic stresses. Recently, Gui et al. discovered that geminiviruses subverted DNA methylation-mediated defense through boosting the active DNA demethylation mediated by host DNA glycosylases to promote viral virulence. Their findings reveal a distinctive counter-defense strategy exploited by invading pathogens to achieve successful infection.
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Affiliation(s)
- Yushuang Guo
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, 550081, China
| | - Meng-Ao Jia
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, 550081, China
| | - Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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7
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Niu C, Jiang L, Cao F, Liu C, Guo J, Zhang Z, Yue Q, Hou N, Liu Z, Li X, Tahir MM, He J, Li Z, Li C, Ma F, Guan Q. Methylation of a MITE insertion in the MdRFNR1-1 promoter is positively associated with its allelic expression in apple in response to drought stress. THE PLANT CELL 2022; 34:3983-4006. [PMID: 35897144 PMCID: PMC9520589 DOI: 10.1093/plcell/koac220] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are widely distributed in the plant genome and can be methylated. However, whether DNA methylation of MITEs is associated with induced allelic expression and drought tolerance is unclear. Here, we identified the drought-inducible MdRFNR1 (root-type ferredoxin-NADP+ oxidoreductase) gene in apple (Malus domestica). MdRFNR1 plays a positive role in drought tolerance by regulating the redox system, including increasing NADP+ accumulation and catalase and peroxidase activities and decreasing NADPH levels. Sequence analysis identified a MITE insertion (MITE-MdRF1) in the promoter of MdRFNR1-1 but not the MdRFNR1-2 allele. MdRFNR1-1 but not MdRFNR1-2 expression was significantly induced by drought stress, which was positively associated with the MITE-MdRF1 insertion and its DNA methylation. The methylated MITE-MdRF1 is recognized by the transcriptional anti-silencing factors MdSUVH1 and MdSUVH3, which recruit the DNAJ domain-containing proteins MdDNAJ1, MdDNAJ2, and MdDNAJ5, thereby activating MdRFNR1-1 expression under drought stress. Finally, we showed that MdSUVH1 and MdDNAJ1 are positive regulators of drought tolerance. These findings illustrate the molecular roles of methylated MITE-MdRF1 (which is recognized by the MdSUVH-MdDNAJ complex) in induced MdRFNR1-1 expression as well as the drought response of apple and shed light on the molecular mechanisms of natural variation in perennial trees.
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Affiliation(s)
| | | | | | - Chen Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zitong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Qianyu Yue
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zeyuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
- College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Muhammad Mobeen Tahir
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
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Hu H, Du J. Structure and mechanism of histone methylation dynamics in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102211. [PMID: 35452951 DOI: 10.1016/j.pbi.2022.102211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Histone methylation plays a central role in regulating chromatin state and gene expression in Arabidopsis and is involved in a variety of physiological and developmental processes. Dynamic regulation of histone methylation relies on both histone methyltransferase "writer" and histone demethylases "eraser" proteins. In this review, we focus on the four major histone methylation modifications in Arabidopsis H3, H3K4, H3K9, H3K27, and H3K36, and summarize current knowledge of the dynamic regulation of these modifications, with an emphasis on the biochemical and structural perspectives of histone methyltransferases and demethylases.
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Affiliation(s)
- Hongmiao Hu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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9
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DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nat Commun 2022; 13:1335. [PMID: 35288562 PMCID: PMC8921224 DOI: 10.1038/s41467-022-28940-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/16/2022] [Indexed: 12/17/2022] Open
Abstract
A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, our understanding of the extent of involvement of this epigenetic mark in genome-wide gene regulation and plant developmental control is incomplete. Here, we knock out all five known DNA methyltransferases in Arabidopsis, generating DNA methylation-free plants. This quintuple mutant exhibits a suite of developmental defects, unequivocally demonstrating that DNA methylation is essential for multiple aspects of plant development. We show that CG methylation and non-CG methylation are required for a plethora of biological processes, including pavement cell shape, endoreduplication, cell death, flowering, trichome morphology, vasculature and meristem development, and root cell fate determination. Moreover, we find that DNA methylation has a strong dose-dependent effect on gene expression and repression of transposable elements. Taken together, our results demonstrate that DNA methylation is dispensable for Arabidopsis survival but essential for the proper regulation of multiple biological processes. Our understanding of the extent of involvement of DNA methylation in genome-wide gene regulation and plant developmental control is incomplete. Here, the authors knock out all five known DNA methyltransferases and show the developmental and gene expression changes in the DNA methylation-free Arabidopsis plants.
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10
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Xu Q, Wu L, Luo Z, Zhang M, Lai J, Li L, Springer NM, Li Q. DNA demethylation affects imprinted gene expression in maize endosperm. Genome Biol 2022; 23:77. [PMID: 35264226 PMCID: PMC8905802 DOI: 10.1186/s13059-022-02641-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/23/2022] [Indexed: 11/28/2022] Open
Abstract
Background DNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown. Results We analyze loss-of-function mutants of two major genes encoding DNA demethylases. No significant change in DNA methylation has been detected in these mutants. However, we detect increased DNA methylation levels in the mutants around genes and some transposons. The increase in DNA methylation is accompanied by alteration in gene expression, with a tendency to show downregulation, especially for the genes that are preferentially expressed in endosperm. Imprinted expression of both maternally and paternally expressed genes changes in F1 hybrid with the mutant as female and the wild-type as male parental line, but not in the reciprocal hybrid. This alteration in gene expression is accompanied by allele-specific DNA methylation differences, suggesting that removal of DNA methylation of the maternal allele is required for the proper expression of these imprinted genes. Finally, we demonstrate that hypermethylation in the double mutant is associated with reduced binding of transcription factor to its target, and altered gene expression. Conclusions Our results suggest that active removal of DNA methylation is important for transcription factor binding and proper gene expression in maize endosperm.
Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02641-x.
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Affiliation(s)
- Qiang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Leiming Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixiang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, China.
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11
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Wang L, Zheng K, Zeng L, Xu D, Zhu T, Yin Y, Zhan H, Wu Y, Yang DL. Reinforcement of CHH methylation through RNA-directed DNA methylation ensures sexual reproduction in rice. PLANT PHYSIOLOGY 2022; 188:1189-1209. [PMID: 34791444 PMCID: PMC8825330 DOI: 10.1093/plphys/kiab531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/15/2021] [Indexed: 05/23/2023]
Abstract
DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. Although the mechanism of RdDM has been well studied in Arabidopsis (Arabidopsis thaliana), most mutations in RdDM genes cause no remarkable developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 (OsRDR2) in rice (Oryza sativa). Mutation in OsRDR2 abolished the accumulation of 24-nt small interfering RNAs, and consequently substantially decreased genome-wide CHH (H = A, C, or T) methylation. Moreover, male and female reproductive development was disturbed, which led to sterility in osrdr2 mutants. We discovered that OsRDR2-dependent DNA methylation may regulate the expression of multiple key genes involved in stamen development, meiosis, and pollen viability. In wild-type (WT) plants but not in osrdr2 mutants, genome-wide CHH methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of CHH methylation in reproductive organs of the WT was mainly explained by the enhancement of RdDM activity, which includes OsRDR2 activity. Our results, which revealed a global increase in CHH methylation through enhancement of RdDM activity in reproductive organs, suggest a crucial role for OsRDR2 in the sexual reproduction of rice.
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Affiliation(s)
- Lili Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kezhi Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Longjun Zeng
- Yichun Academy of Science, Yichun 336000, Jiangxi Province, China
| | - Dachao Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianxin Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yumeng Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Huadong Zhan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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12
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Wang S, Xie H, Mao F, Wang H, Wang S, Chen Z, Zhang Y, Xu Z, Xing J, Cui Z, Gao X, Jin H, Hua J, Xiong B, Wu Y. N 4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana. Genome Biol 2022; 23:5. [PMID: 34980211 PMCID: PMC8722123 DOI: 10.1186/s13059-021-02578-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Direct analogs of chemically modified bases that carry important epigenetic information, such as 5-methylcytosine (m5C)/5-methyldeoxycytosine (5mC), 5-hydroxymethylcytosine (hm5C)/5-hydroxymethyldeoxycytosine (5hmC), and N6-methyladenosine (m6A)/N6-methyldeoxyadenosine (6mA), are detected in both RNA and DNA, respectively. The modified base N4-acetylcytosine (ac4C) is well studied in RNAs, but its presence and epigenetic roles in cellular DNA have not been explored. RESULTS Here, we demonstrate the existence of N4-acetyldeoxycytosine (4acC) in genomic DNA of Arabidopsis with multiple detection methods. Genome-wide profiling of 4acC modification reveals that 4acC peaks are mostly distributed in euchromatin regions and present in nearly half of the expressed protein-coding genes in Arabidopsis. 4acC is mainly located around transcription start sites and positively correlates with gene expression levels. Imbalance of 5mC does not directly affect 4acC modification. We also characterize the associations of 4acC with 5mC and histone modifications that cooperatively regulate gene expression. Moreover, 4acC is also detected in genomic DNA of rice, maize, mouse, and human by mass spectrometry. CONCLUSIONS Our findings reveal 4acC as a hitherto unknown DNA modification in higher eukaryotes. We identify potential interactions of this mark with other epigenetic marks in gene expression regulation.
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Affiliation(s)
- Shuai Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Hairong Xie
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Fei Mao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Shu Wang
- Jiangbei New Area Biopharmaceutical Public Service Platform Co., Ltd., Nanjing, China
| | - Zhenglin Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Yuxia Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Zhihui Xu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Jinming Xing
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Zhaokang Cui
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiquan Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Hongmei Jin
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jian Hua
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, USA
| | - Bo Xiong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
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13
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Sun C, Li D, Gao Z, Gao L, Shang L, Wang M, Qiao J, Ding S, Li C, Geisler M, Jiang D, Qi Y, Qian Q. OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:118-134. [PMID: 34726825 DOI: 10.1111/jipb.13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root (PR) absorbs mineral nutrients and provides mechanical support; however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4 (OsRLR4), osrlr4-1 and osrlr4-2 with longer PR, and three OsRLR4 overexpression lines, OE-OsRLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung (WT/HY), were identified. OsRLR4 is one of five members of the PRAF subfamily of the regulator chromosome condensation 1 (RCC1) family. Phylogenetic analysis of OsRLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. OsRLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that OsRLR4 functions directly upstream of the auxin transporter OsAUX1. Moreover, OsRLR4 interacts with the TRITHORAX-like protein OsTrx1 to promote H3K4me3 deposition at the OsAUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding.
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Affiliation(s)
- Chendong Sun
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Lin'an Hangzhou, 311300, China
| | - Dongming Li
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Lei Gao
- College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Lianguang Shang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Mei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiyue Qiao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Dean Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
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14
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Hu M, Li M, Wang J. Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors. Genes (Basel) 2021; 12:genes12121848. [PMID: 34946800 PMCID: PMC8701781 DOI: 10.3390/genes12121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.
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Affiliation(s)
- Meimei Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
- Correspondence:
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15
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Miao W, Dai J, Wang Y, Wang Q, Lu C, La Y, Niu J, Tan F, Zhou S, Wu Y, Chen H, La H. Roles of IDM3 and SDJ1/2/3 in Establishment and/or Maintenance of DNA Methylation in Arabidopsis. PLANT & CELL PHYSIOLOGY 2021; 62:1409-1422. [PMID: 34185870 DOI: 10.1093/pcp/pcab091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Previous studies had demonstrated that in Arabidopsis, IDM3 is involved in ROS1-mediated DNA demethylation pathway, and SUVH-SDJ complex functions as a DNA methylation reader complex for enhancing gene transcription, which presumably recruits ROS1 to the promoters of target genes for DNA demethylation. Here, our analyses, however, showed that the IDM3 and SDJ1/2/3, the components of the SUVH-SDJ complex, are implicated in establishing and/or maintaining DNA methylation as well through DDR (DRD1-DMS3-RDM1) complex. idm3-3 or sdj1/2/3 mutations led to genome-wide DNA hypomethylation, and both mutants shared a large number of common hypo-DMRs (Differentially Methylated Regions) with rdm1-4 and dms3-4, suggesting that IDM3 and SDJ1/2/3 help establish and/or maintain DNA methylation, mediated by RdDM pathway, at a subset of genomic regions largely through DDR complex. IDM3 is able to strongly interact with RDM1 and DMS3, but weakly with SDJ1 and SDJ3; SDJ1 and SDJ3 is capable of interacting separately with RDM1 and DMS3. Furthermore, comparisons of DNA methylation features in idm3-3 and sdj1/2/3 indicated that idm3-3 and sdj1/2/3 mutations make differential impacts on DNA methylation levels and patterns on a genome-wide scale, indicating that they are targeted to quite distinct genomic regions for aiding in DNA methylation. Further analyses on ChIP-seq data demonstrated that RDM1, DMS3 and NRPE1 are enriched in IDM3- and SDJ1/2/3-targted regions. Altogether, our results provide clear demonstration that IDM3 and SDJ1/2/3 play a part in establishing and/or maintaining DNA methylation of a group of genomic regions, through the DDR complex.
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Affiliation(s)
- Wei Miao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jie Dai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yutong Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chong Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yumei La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jiayu Niu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Feng Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shaoxia Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Huhui Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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16
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Abstract
Here, Parent et al. investigated the re-establishment of silencing in embryos using Arabidopsis. They demonstrate that small RNAs, along with asymmetric DNA methylation, direct the histone H3 lysine 9 dimethylation during Arabidopsis thaliana embryonic development, and this de novo silencing mechanism depends on the catalytic domain of SUVH9, a Su(Var)3-9 homolog thought to be catalytically inactive. Epigenetic reprogramming occurs during gametogenesis as well as during embryogenesis to reset the genome for early development. In flowering plants, many heterochromatic marks are maintained in sperm, but asymmetric DNA methylation is mostly lost. Asymmetric DNA methylation is dependent on small RNA but the re-establishment of silencing in embryo is not well understood. Here we demonstrate that small RNAs direct the histone H3 lysine 9 dimethylation during Arabidopsis thaliana embryonic development, together with asymmetric DNA methylation. This de novo silencing mechanism depends on the catalytic domain of SUVH9, a Su(Var)3-9 homolog thought to be catalytically inactive.
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17
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Liu T, Yang J, Liu S, Zhao Y, Zhou J, Jin Y, Huang L, Yuan Y. Regulation of chlorogenic acid, flavonoid, and iridoid biosynthesis by histone H3K4 and H3K9 methylation in Lonicera japonica. Mol Biol Rep 2020; 47:9301-9311. [PMID: 33190199 PMCID: PMC7666716 DOI: 10.1007/s11033-020-05990-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/06/2020] [Indexed: 01/23/2023]
Abstract
Lonicera japonica is used in Chinese herbal medicines with a wide spectrum of pharmacological properties associated with chlorogenic acid, flavonoid and iridoid. The biosynthesis of these compounds could be affected by genetic inheritance and epigenetic modification. However, the mechanisms that regulate the expression of genes involved in the biosynthesis of these compounds are rarely known. The results of qRT-PCR showed that the biosynthesis gene expression of these compounds was related to histone H3K4 and H3K9 methylation levels. These active compounds content of L. japonica were measured by UPLC-MS/MS. H3K4me3 showed a positive correlation with chlorogenic acid and loganic acid content, and H3K9me positively correlated with luteolin content. The correlation between histone methylation levels and the levels of luteolin and loganic acid in L. japonica from different producing areas validate the regulatory role of histone methylation in biosynthesis of bioactive compounds. Our study demonstrated a potential regulatory network of H3K9/H3K4 methylation to gene expression and content of secondary metabolites, and provided a basis for understanding the mechanism underlying the variation of major bioactive compounds in L. japonica.
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Affiliation(s)
- Tianrui Liu
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
| | - Jian Yang
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
| | - Shuang Liu
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
| | - Yuyang Zhao
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
| | - Junhui Zhou
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
| | - Yan Jin
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
| | - Luqi Huang
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
| | - Yuan Yuan
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
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18
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Ning YQ, Liu N, Lan KK, Su YN, Li L, Chen S, He XJ. DREAM complex suppresses DNA methylation maintenance genes and precludes DNA hypermethylation. NATURE PLANTS 2020; 6:942-956. [PMID: 32661276 DOI: 10.1038/s41477-020-0710-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/27/2020] [Indexed: 05/27/2023]
Abstract
The DNA methyltransferases MET1 and CMT3 are known to be responsible for maintenance of DNA methylation at symmetric CG and CHG sites, respectively, in Arabidopsis thaliana. However, it is unknown how the expression of methyltransferase genes is regulated in different cell states and whether change in expression affects DNA methylation at the whole-genome level. Using a reverse genetic screen, we identified TCX5, a tesmin/TSO1-like CXC domain-containing protein, and demonstrated that it is a transcriptional repressor of genes required for maintenance of DNA methylation, which include MET1, CMT3, DDM1, KYP and VIMs. TCX5 functions redundantly with its paralogue TCX6 in repressing the expression of these genes. In the tcx5 tcx6 double mutant, expression of these genes is markedly increased, thereby leading to markedly increased DNA methylation at CHG sites and, to a lesser extent, at CG sites at the whole-genome level. Furthermore, our whole-genome DNA methylation analysis indicated that the CG and CHG methylation level is lower in differentiated quiescent cells than in dividing cells in the wild type but is comparable in the tcx5/6 mutant, suggesting that TCX5/6 are required for maintenance of the difference in DNA methylation between the two cell types. We identified TCX5/6-containing multi-subunit complexes, which are known as DREAM in other eukaryotes, and demonstrated that the Arabidopsis DREAM components function as a whole to preclude DNA hypermethylation. Given that the DREAM complexes are conserved from plants to animals, the preclusion of DNA hypermethylation by DREAM complexes may represent a conserved mechanism in eukaryotes.
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Affiliation(s)
- Yong-Qiang Ning
- National Institute of Biological Sciences, Beijing, China
- The College of Life Sciences, Northwest University, Xi'an, China
| | - Na Liu
- National Institute of Biological Sciences, Beijing, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ke-Ke Lan
- National Institute of Biological Sciences, Beijing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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19
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Tan LM, Liu R, Gu BW, Zhang CJ, Luo J, Guo J, Wang Y, Chen L, Du X, Li S, Shao CR, Su YN, Cai XW, Lin RN, Li L, Chen S, Du J, He XJ. Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis. THE PLANT CELL 2020; 32:2178-2195. [PMID: 32358072 PMCID: PMC7346560 DOI: 10.1105/tpc.19.00944] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 05/07/2023]
Abstract
Chromatin remodeling and histone modifications are important for development and floral transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of Imitation Switch (ISWI) chromatin-remodeling complexes in Arabidopsis (Arabidopsis thaliana). We found that AT-RICH INTERACTING DOMAIN5 (ARID5), a subunit of a plant-specific ISWI complex, can regulate development and floral transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral transition.
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Affiliation(s)
- Lian-Mei Tan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Rui Liu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Bo-Wen Gu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Cui-Jun Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jinyan Luo
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jing Guo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yuhua Wang
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Lixian Chen
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Du
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Sisi Li
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Chang-Rong Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jiamu Du
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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20
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Xu L, Yuan K, Yuan M, Meng X, Chen M, Wu J, Li J, Qi Y. Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements. MOLECULAR PLANT 2020; 13:851-863. [PMID: 32087371 DOI: 10.1016/j.molp.2020.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 05/24/2023]
Abstract
Tillering is a major determinant of rice plant architecture and grain yield. Here, we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologs of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable elements (TEs) including miniature inverted-repeat TEs (MITEs). Interestingly, many genes are regulated either positively or negatively by TE methylation. Among them, OsMIR156d and OsMIR156j, which promote rice tillering, are repressed by CHH methylation at two MITEs in the promoters. By contrast, D14, which suppresses rice tillering, is activated by CHH methylation at an MITE in its downstream. Our findings reveal regulation of rice tillering by RNA-directed DNA methylation at MITEs and provide potential targets for agronomic trait enhancement through epigenome editing.
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Affiliation(s)
- Le Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kun Yuan
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Yuan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiangbing Meng
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiayang Li
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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21
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Chen DH, Qiu HL, Huang Y, Zhang L, Si JP. Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum. BMC PLANT BIOLOGY 2020; 20:40. [PMID: 31992218 PMCID: PMC6986063 DOI: 10.1186/s12870-020-2244-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/13/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Dendrobium catenatum, as a precious Chinese herbal medicine, is an epiphytic orchid plant, which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases, which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown. RESULTS In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris. We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su (var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually displayed wide but distinguished expressions in different tissues and organs. Finally, environmental stresses examination showed the expressions of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 are closely associated with drought-recovery treatment, the expression of DcSUVH5a, DcATXR5a and DcSUVR14a are significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock. CONCLUSIONS This study systematically identifies and classifies SDG genes in orchid plant D. catenatum, indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchids.
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Affiliation(s)
- Dong-Hong Chen
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
| | - Han-Lin Qiu
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Yong Huang
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, 410128, China
| | - Lei Zhang
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Jin-Ping Si
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
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22
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Yang Y, Tang K, Datsenka TU, Liu W, Lv S, Lang Z, Wang X, Gao J, Wang W, Nie W, Chu Z, Zhang H, Handa AK, Zhu JK, Zhang H. Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1224-1242. [PMID: 30652405 DOI: 10.1111/jipb.12778] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/14/2019] [Indexed: 05/05/2023]
Abstract
DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. To date, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here, we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR-Cas9 gene editing, we generated slmet1 mutants and observed severe developmental defects with a frame-shift mutation, including small and curly leaves, defective inflorescence, and parthenocarpy. In leaf tissues, mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole-genome scale, leading to a disturbed transcriptome including ectopic expression of many RIN target genes such as ACC2 in leaf tissues, which are normally expressed in fruits. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture. Meanwhile, tissue culture induces non-CG hypomethylation, which occurs more frequently at gene regions than at TE regions. Our results depict SlMET1- and tissue culture-dependent tomato DNA methylomes, and that SlMET1 is required for maintaining a normal transcriptome and normal development of tomato.
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Affiliation(s)
- Yu Yang
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Kai Tang
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
| | - Tatsiana U Datsenka
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
| | - Wenshan Liu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Suhui Lv
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xingang Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
| | - Jinghui Gao
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Wei Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Chenshan Plant Science Research Center, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Wenfeng Nie
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Chenshan Plant Science Research Center, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Avtar K Handa
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai 200032, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai 200032, China
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23
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Tvorogova VE, Krasnoperova EY, Kudriashov AA, Kuznetsova KA, Potsenkovskaya EA, Fedorova YA, Lutova LA. Transcriptomic analysis of Medicago truncatula calli with MtWOX9-1 overexpression. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- V. E. Tvorogova
- St. Petersburg State University, Department of Genetics and Biotechnology
| | - E. Y. Krasnoperova
- St. Petersburg State University, Department of Genetics and Biotechnology
| | - A. A. Kudriashov
- St. Petersburg State University, Department of Genetics and Biotechnology
| | - K. A. Kuznetsova
- St. Petersburg State University, Department of Genetics and Biotechnology
| | | | - Y. A. Fedorova
- St. Petersburg State University, Department of Genetics and Biotechnology
| | - L. A. Lutova
- St. Petersburg State University, Department of Genetics and Biotechnology
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24
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Miao W, Dai J, La Y, Lu C, Zhang J, Hong X, Zhou S, Wang Q, Wang X, Rui Q, Tan F, La H. Characterization and fine mapping of Arabidopsis RLL3, a locus required for DNA demethylation pathway. Mol Genet Genomics 2019; 295:81-93. [PMID: 31486938 DOI: 10.1007/s00438-019-01605-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/13/2019] [Indexed: 01/06/2023]
Abstract
DNA methylation pattern is found to be established by the combined actions of DNA methylation and demethylation. Compared to the DNA methylation pathway, DNA demethylation pathway, however, remains largely unknown. To better understand the DNA demethylation pathway, we performed genetic screening for Arabidopsis mutants with increased genomic DNA methylation levels through a 2 × 35S:LUC (LUC, luciferase) reporter system. A mutant with reduced LUC luminescence was identified by such a system, therefore named rll3-1 (for reduced LUC luminescence 3-1). The rll3-1 mutant exhibited pleiotropic developmental defects, such as delayed bolting as well as flowering, more branches, etc. By map-based cloning approach, rll3 locus that contains a single nuclear recessive mutation as revealed by the genetic analysis was mapped to a region between molecular markers CL102_B1 M1 and CL102_B3M1, which are located in bacterial artificial chromosome (BAC) clones F9P14 and F12K11, respectively, on chromosome 1. Chop-PCR analysis indicated that a total of seven tested loci displayed elevated DNA methylation levels. Whole-genome bisulfite sequencing further revealed 1536 loci exhibiting increased DNA methylation levels relative to Col-LUC control, among which there are 507 such loci overlapping between the rll3-1 and ros1-7 mutants, suggestive of a functional association between RLL3 and REPRESSOR OF SILENCING 1 (ROS1). Further investigations demonstrated that the expression levels of a few genes (like ROS1, IDM1, etc.), which are involved in DNA demethylation pathway, remained unchanged in the rll3-1 mutant, indicating that the increased DNA methylation levels in rll3-1 mutant are not attributable to downregulation of such genes. Taken together, our studies provide a demonstration of the involvement of RLL3 in the DNA demethylation pathway.
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Affiliation(s)
- Wei Miao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jie Dai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yumei La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chong Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jianzhen Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xinyue Hong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaoxia Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiangyu Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qi Rui
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Feng Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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25
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Kawakatsu T, Ecker JR. Diversity and dynamics of DNA methylation: epigenomic resources and tools for crop breeding. BREEDING SCIENCE 2019; 69:191-204. [PMID: 31481828 PMCID: PMC6711733 DOI: 10.1270/jsbbs.19005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/18/2019] [Indexed: 05/17/2023]
Abstract
DNA methylation is an epigenetic modification that can affect gene expression and transposable element (TE) activities. Because cytosine DNA methylation patterns are inherited through both mitotic and meiotic cell divisions, differences in these patterns can contribute to phenotypic variability. Advances in high-throughput sequencing technologies have enabled the generation of abundant DNA sequence data. Integrated analyses of genome-wide gene expression patterns and DNA methylation patterns have revealed the underlying mechanisms and functions of DNA methylation. Moreover, associations between DNA methylation and agronomic traits have also been uncovered. The resulting information may be useful for future applications of natural epigenomic variation, for crop breeding. Additionally, artificial epigenome editing may be an attractive new plant breeding technique for generating novel varieties with improved agronomic traits.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
1-2 Owashi Tsukuba, Ibaraki 305-8634,
Japan
- Corresponding author (e-mail: )
| | - Joseph R. Ecker
- Howard Hughes Medical Institute,
10010 North Torrey Pines Road, La Jolla, CA 92037,
USA
- The Salk Institute for Biological Studies,
10010 North Torrey Pines Road, La Jolla, CA 92037,
USA
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26
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Harris CJ, Scheibe M, Wongpalee SP, Liu W, Cornett EM, Vaughan RM, Li X, Chen W, Xue Y, Zhong Z, Yen L, Barshop WD, Rayatpisheh S, Gallego-Bartolome J, Groth M, Wang Z, Wohlschlegel JA, Du J, Rothbart SB, Butter F, Jacobsen SE. A DNA methylation reader complex that enhances gene transcription. Science 2019; 362:1182-1186. [PMID: 30523112 DOI: 10.1126/science.aar7854] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 09/07/2018] [Accepted: 10/31/2018] [Indexed: 12/14/2022]
Abstract
DNA methylation generally functions as a repressive transcriptional signal, but it is also known to activate gene expression. In either case, the downstream factors remain largely unknown. By using comparative interactomics, we isolated proteins in Arabidopsis thaliana that associate with methylated DNA. Two SU(VAR)3-9 homologs, the transcriptional antisilencing factor SUVH1, and SUVH3, were among the methyl reader candidates. SUVH1 and SUVH3 bound methylated DNA in vitro, were associated with euchromatic methylation in vivo, and formed a complex with two DNAJ domain-containing homologs, DNAJ1 and DNAJ2. Ectopic recruitment of DNAJ1 enhanced gene transcription in plants, yeast, and mammals. Thus, the SUVH proteins bind to methylated DNA and recruit the DNAJ proteins to enhance proximal gene expression, thereby counteracting the repressive effects of transposon insertion near genes.
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Affiliation(s)
- C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Marion Scheibe
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Somsakul Pop Wongpalee
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Wanlu Liu
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Evan M Cornett
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Robert M Vaughan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Xueqin Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Wei Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Yan Xue
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Linda Yen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shima Rayatpisheh
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Javier Gallego-Bartolome
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Martin Groth
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.,Institute of Oceanography, Minjiang University, 350108 Fuzhou, China
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jiamu Du
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany.
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA. .,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
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27
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Xiao X, Zhang J, Li T, Fu X, Satheesh V, Niu Q, Lang Z, Zhu JK, Lei M. A group of SUVH methyl-DNA binding proteins regulate expression of the DNA demethylase ROS1 in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:110-119. [PMID: 30589237 DOI: 10.1111/jipb.12768] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/25/2018] [Indexed: 05/22/2023]
Abstract
DNA methylation is typically regarded as a repressive epigenetic marker for gene expression. Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence (MEMS) in the promoter of the DNA demethylase gene ROS1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS1 expression. How DNA methylation in the MEMS region promotes ROS1 expression is not known. Here, we show that several Su(var)3-9 homologs (SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS. Mutations in the SUVHs lead to decreased ROS1 expression, causing DNA hypermethylation at more than 1,000 genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation.
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Affiliation(s)
- Xinlong Xiao
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jieqiong Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Li
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingfeng Niu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette 47907, USA
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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28
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Zhao QQ, Lin RN, Li L, Chen S, He XJ. A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:120-139. [PMID: 30589221 DOI: 10.1111/jipb.12767] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 05/29/2023]
Abstract
Although the mechanism of DNA methylation-mediated gene silencing is extensively studied, relatively little is known about how promoter methylated genes are protected from transcriptional silencing. SUVH1, an Arabidopsis Su(var)3-9 homolog, was previously shown to be required for the expression of a few promoter methylated genes. By chromatin immunoprecipitation combined with sequencing, we demonstrate that SUVH1 binds to methylated genomic loci targeted by RNA-directed DNA methylation. SUVH1 and its homolog SUVH3 function partially redundantly and interact with three DNAJ domain-containing homologs, SDJ1, SDJ2, and SDJ3, thus forming a complex which we named SUVH-SDJ. The SUVH-SDJ complex components are co-localized in a large number of methylated promoters and are required for the expression of a subset of promoter methylated genes. We demonstrate that the SUVH-SDJ complex components have transcriptional activation activity. SUVH1 and SUVH3 function synergistically with SDJ1, SDJ2, and SDJ3 and are required for plant viability. This study reveals how the SUVH-SDJ complex protects promoter methylated genes from transcriptional silencing and suggests that the transcriptional activation of promoter methylated genes mediated by the SUVH-SDJ complex may play a critical role in plant growth and development.
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Affiliation(s)
- Qiang-Qiang Zhao
- National Institute of Biological Sciences, Beijing 102206, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China
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29
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Gong Z. A SUVH-DNAJ/SDJ protein complex activates the expression of promoter-methylated genes in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:90-92. [PMID: 30637989 DOI: 10.1111/jipb.12777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 11/01/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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30
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Manfredini F, Romero AE, Pedroso I, Paccanaro A, Sumner S, Brown MJF. Neurogenomic Signatures of Successes and Failures in Life-History Transitions in a Key Insect Pollinator. Genome Biol Evol 2017; 9:3059-3072. [PMID: 29087523 PMCID: PMC5714134 DOI: 10.1093/gbe/evx220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2017] [Indexed: 12/22/2022] Open
Abstract
Life-history transitions require major reprogramming at the behavioral and physiological level. Mating and reproductive maturation are known to trigger changes in gene transcription in reproductive tissues in a wide range of organisms, but we understand little about the molecular consequences of a failure to mate or become reproductively mature, and it is not clear to what extent these processes trigger neural as well as physiological changes. In this study, we examined the molecular processes underpinning the behavioral changes that accompany the major life-history transitions in a key pollinator, the bumblebee Bombus terrestris. We compared neuro-transcription in queens that succeeded or failed in switching from virgin and immature states, to mated and reproductively mature states. Both successes and failures were associated with distinct molecular profiles, illustrating how development during adulthood triggers distinct molecular profiles within a single caste of a eusocial insect. Failures in both mating and reproductive maturation were explained by a general up-regulation of brain gene transcription. We identified 21 genes that were highly connected in a gene coexpression network analysis: nine genes are involved in neural processes and four are regulators of gene expression. This suggests that negotiating life-history transitions involves significant neural processing and reprogramming, and not just changes in physiology. These findings provide novel insights into basic life-history transitions of an insect. Failure to mate or to become reproductively mature is an overlooked component of variation in natural systems, despite its prevalence in many sexually reproducing organisms, and deserves deeper investigation in the future.
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Affiliation(s)
- Fabio Manfredini
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Alfonso E Romero
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Inti Pedroso
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alberto Paccanaro
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Seirian Sumner
- School of Biological Sciences, University of Bristol, United Kingdom
- Present address: Centre for Biodiversity & Environment Research, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
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31
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Adamkova K, Yi YJ, Petr J, Zalmanova T, Hoskova K, Jelinkova P, Moravec J, Kralickova M, Sutovsky M, Sutovsky P, Nevoral J. SIRT1-dependent modulation of methylation and acetylation of histone H3 on lysine 9 (H3K9) in the zygotic pronuclei improves porcine embryo development. J Anim Sci Biotechnol 2017; 8:83. [PMID: 29118980 PMCID: PMC5664433 DOI: 10.1186/s40104-017-0214-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/25/2017] [Indexed: 12/31/2022] Open
Abstract
Background The histone code is an established epigenetic regulator of early embryonic development in mammals. The lysine residue K9 of histone H3 (H3K9) is a prime target of SIRT1, a member of NAD+-dependent histone deacetylase family of enzymes targeting both histone and non-histone substrates. At present, little is known about SIRT1-modulation of H3K9 in zygotic pronuclei and its association with the success of preimplantation embryo development. Therefore, we evaluated the effect of SIRT1 activity on H3K9 methylation and acetylation in porcine zygotes and the significance of H3K9 modifications for early embryonic development. Results Our results show that SIRT1 activators resveratrol and BML-278 increased H3K9 methylation and suppressed H3K9 acetylation in both the paternal and maternal pronucleus. Inversely, SIRT1 inhibitors nicotinamide and sirtinol suppressed methylation and increased acetylation of pronuclear H3K9. Evaluation of early embryonic development confirmed positive effect of selective SIRT1 activation on blastocyst formation rate (5.2 ± 2.9% versus 32.9 ± 8.1% in vehicle control and BML-278 group, respectively; P ≤ 0.05). Stimulation of SIRT1 activity coincided with fluorometric signal intensity of ooplasmic ubiquitin ligase MDM2, a known substrate of SIRT1 and known limiting factor of epigenome remodeling. Conclusions We conclude that SIRT1 modulates zygotic histone code, obviously through direct deacetylation and via non-histone targets resulting in increased H3K9me3. These changes in zygotes lead to more successful pre-implantation embryonic development and, indeed, the specific SIRT1 activation due to BML-278 is beneficial for in vitro embryo production and blastocyst achievement.
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Affiliation(s)
- Katerina Adamkova
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic
| | - Young-Joo Yi
- Division of Biotechnology, Safety, Environment and Life Science Institute, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, 54596 South Korea
| | - Jaroslav Petr
- Institute of Animal Science, 10-Uhrineves, Prague, Czech Republic
| | - Tereza Zalmanova
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic.,Institute of Animal Science, 10-Uhrineves, Prague, Czech Republic
| | - Kristyna Hoskova
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic.,Institute of Animal Science, 10-Uhrineves, Prague, Czech Republic
| | - Pavla Jelinkova
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic
| | - Jiri Moravec
- Proteomic Laboratory, Biomedical Center of Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Milena Kralickova
- Laboratory of Reproductive Medicine of Biomedical Center, Charles University, Pilsen, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Miriam Sutovsky
- Division of Animal Science, University of Missouri, Columbia, MO USA
| | - Peter Sutovsky
- Division of Animal Science, University of Missouri, Columbia, MO USA.,Departments of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO USA
| | - Jan Nevoral
- Department of Veterinary Sciences, Faculty of Agriculture, Food and Natural Resources, Czech University of Life Sciences Prague, 6-Suchdol, Prague, Czech Republic.,Laboratory of Reproductive Medicine of Biomedical Center, Charles University, Pilsen, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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32
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Li D, Palanca AMS, Won SY, Gao L, Feng Y, Vashisht AA, Liu L, Zhao Y, Liu X, Wu X, Li S, Le B, Kim YJ, Yang G, Li S, Liu J, Wohlschlegel JA, Guo H, Mo B, Chen X, Law JA. The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status. eLife 2017; 6. [PMID: 28452714 PMCID: PMC5462541 DOI: 10.7554/elife.19893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 04/24/2017] [Indexed: 12/23/2022] Open
Abstract
DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing. DOI:http://dx.doi.org/10.7554/eLife.19893.001
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Affiliation(s)
- Dongming Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,School of Life Sciences, Lanzhou University, Lanzhou, China.,State Key Laboratory of Plant Cell and Chromosome Engineering, Hebei Collaboration Innovation Center for Cell Signaling, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Ana Marie S Palanca
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - So Youn Won
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Ying Feng
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,State Key Laboratory of Protein and Plant Gene research, College of Life Sciences, Peking University, Beijing, China
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, United States
| | - Li Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Xigang Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,State Key Laboratory of Plant Cell and Chromosome Engineering, Hebei Collaboration Innovation Center for Cell Signaling, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Xiuyun Wu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,Laboratory of Molecular Biology and Protein Science, Laboratory of the Ministry of Education, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Brandon Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Yun Ju Kim
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Guodong Yang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Shengben Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Jinyuan Liu
- Laboratory of Molecular Biology and Protein Science, Laboratory of the Ministry of Education, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, United States
| | - Hongwei Guo
- State Key Laboratory of Protein and Plant Gene research, College of Life Sciences, Peking University, Beijing, China
| | - Beixin Mo
- College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,Howard Hughes Medical Institute, University of California, Riverside, United States
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
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33
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Yang Y, La H, Tang K, Miki D, Yang L, Wang B, Duan CG, Nie W, Wang X, Wang S, Pan Y, Tran EJ, An L, Zhang H, Zhu JK. SAC3B, a central component of the mRNA export complex TREX-2, is required for prevention of epigenetic gene silencing in Arabidopsis. Nucleic Acids Res 2016; 45:181-197. [PMID: 27672037 PMCID: PMC5224508 DOI: 10.1093/nar/gkw850] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 12/17/2022] Open
Abstract
Epigenetic regulation is important for organismal development and response to the environment. Alteration in epigenetic status has been known mostly from the perspective of enzymatic actions of DNA methylation and/or histone modifications. In a genetic screen for cellular factors involved in preventing epigenetic silencing, we isolated an Arabidopsis mutant defective in SAC3B, a component of the conserved TREX-2 complex that couples mRNA transcription with nuleo-cytoplasmic export. Arabidopsis SAC3B dysfunction causes gene silencing at transgenic and endogenous loci, accompanied by elevation in the repressive histone mark H3K9me2 and by reduction in RNA polymerase Pol II occupancy. SAC3B dysfunction does not alter promoter DNA methylation level of the transgene d35S::LUC, although the DNA demethylase ROS1 is also required for d35S::LUC anti-silencing. THP1 and NUA were identified as SAC3B-associated proteins whose mutations also caused d35S::LUC silencing. RNA-DNA hybrid exists at the repressed loci but is unrelated to gene suppression by the sac3b mutation. Genome-wide analyses demonstrated minor but clear involvement of SAC3B in regulating siRNAs and DNA methylation, particularly at a group of TAS and TAS-like loci. Together our results revealed not only a critical role of mRNA-export factors in transcriptional anti-silencing but also the contribution of SAC3B in shaping plant epigenetic landscapes.
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Affiliation(s)
- Yu Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Honggui La
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.,Department of Biochemistry and Molecular Biology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Lan Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Bangshing Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Cheng-Guo Duan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Wenfeng Nie
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Xingang Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Siwen Wang
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | - Yufeng Pan
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China .,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China .,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
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34
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Jing Y, Sun H, Yuan W, Wang Y, Li Q, Liu Y, Li Y, Qian W. SUVH2 and SUVH9 Couple Two Essential Steps for Transcriptional Gene Silencing in Arabidopsis. MOLECULAR PLANT 2016; 9:1156-1167. [PMID: 27216319 DOI: 10.1016/j.molp.2016.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/07/2016] [Accepted: 05/15/2016] [Indexed: 05/18/2023]
Abstract
In Arabidopsis, an RNA-directed DNA methylation pathway (RdDM) is responsible for de novo establishment of DNA methylation and contributes to transcriptional gene silencing. Recently, the microrchidia (MORC)-type ATPases were shown to play essential roles in enforcing transcriptional gene silencing of a subset of genes and transposons by regulating the formation of higher-order chromatin architecture. However, how MORC proteins cooperate with the RdDM pathway components to regulate gene expression remains largely unclear. In this study, SUVH9 and MORC6 were identified from a screening of suppressors of idm1, which is a mutant defective in active DNA demethylation. SUVH9 and MORC6 are required for silencing of two reporter genes and some endogenous genes without enhancing DNA methylation levels. SUVH9, one of SU(VAR)3-9 homologs involved in RdDM, directly interacts with MORC6 and its two close homologs, MORC1 and MORC2. Similar to MORC6, SUVH9 and its homolog SUVH2 are required for heterochromatin condensation and formation of 3D chromatin architecture at SDC and Solo-LTR loci. We propose that SUVH2 and SUVH9 bind to the methylated DNA and facilitate the recruitment of a chromatin-remodeling complex to the target loci in association with MORC proteins.
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Affiliation(s)
- Yuqing Jing
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Han Sun
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Yuan
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Qi Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yannan Liu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.
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