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Cheng K, Xu Y, Yang C, Ouellette L, Niu L, Zhou X, Chu L, Zhuang F, Liu J, Wu H, Charron JB, Luo M. Histone tales: lysine methylation, a protagonist in Arabidopsis development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:793-807. [PMID: 31560751 DOI: 10.1093/jxb/erz435] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/17/2019] [Indexed: 05/20/2023]
Abstract
Histone methylation plays a fundamental role in the epigenetic regulation of gene expression driven by developmental and environmental cues in plants, including Arabidopsis. Histone methyltransferases and demethylases act as 'writers' and 'erasers' of methylation at lysine and/or arginine residues of core histones, respectively. A third group of proteins, the 'readers', recognize and interpret the methylation marks. Emerging evidence confirms the crucial roles of histone methylation in multiple biological processes throughout the plant life cycle. In this review, we summarize the regulatory mechanisms of lysine methylation, especially at histone H3 tails, and focus on the recent advances regarding the roles of lysine methylation in Arabidopsis development, from seed performance to reproductive development, and in callus formation.
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Affiliation(s)
- Kai Cheng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Luc Ouellette
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Longjian Niu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xiaochen Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liutian Chu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhuang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Liu
- Institute for Food and Bioresource Engineering, Department of Energy and Resources Engineering and BIC-ESAT, College of Engineering, Peking University, Beijing, China
| | - Hualing Wu
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, Guangdong, China
| | - Jean-Benoit Charron
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Ming Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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Ré DA, Cambiagno DA, Arce AL, Tomassi AH, Giustozzi M, Casati P, Ariel FD, Manavella PA. CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants. MOLECULAR PLANT 2020; 13:72-87. [PMID: 31606467 DOI: 10.1016/j.molp.2019.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
CURLY LEAF (CLF) encodes the methyltransferase subunit of the Polycomb Repressor Complex 2 (PRC2), which regulates the expression of target genes through H3K27 trimethylation. We isolated a new CLF mutant allele (clf-78) using a genetic screen designed to identify microRNA (miRNA) deficient mutants. CLF mutant plants showed impaired miRNA activity caused by increased ubiquitination and enhanced degradation of ARGONAUTE 1 (AGO1) in specific tissues. Such CLF-mediated AGO1 regulation was evident when plants were exposed to UV radiation, which caused increased susceptibility of clf mutants to some UV-induced responses. Furthermore, we showed that CLF directly regulates FBW2, which in turn triggers AGO1 degradation in the clf mutants. Interestingly, AGO1 bound to a target appeared particularly prone to degradation in the mutant plants, a process that was exacerbated when the complex bound a non-cleavable target. Thus, prolonged AGO1-target interaction seems to favor AGO1 degradation, suggesting that non-cleavable miRNA targets may overcome translation inhibition by modulating AGO1 stability in plants.
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Affiliation(s)
- Delfina A Ré
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Ariel H Tomassi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Marisol Giustozzi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Rosario, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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Zheng C, Ye M, Sang M, Wu R. A Regulatory Network for miR156-SPL Module in Arabidopsis thaliana. Int J Mol Sci 2019; 20:ijms20246166. [PMID: 31817723 PMCID: PMC6940959 DOI: 10.3390/ijms20246166] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Vegetative phase changes in plants describes the transition between juvenile and adult phases of vegetative growth before flowering. It is one of the most fundamental mechanisms for plants to sense developmental signals, presenting a complex process involving many still-unknown determinants. Several studies in annual and perennial plants have identified the conservative roles of miR156 and its targets, SBP/SPL genes, in guiding the switch of plant growth from juvenile to adult phases. Here, we review recent progress in understanding the regulation of miR156 expression and how miR156-SPLs mediated plant age affect other processes in Arabidopsis. Powerful high-throughput sequencing techniques have provided rich data to systematically study the regulatory mechanisms of miR156 regulation network. From this data, we draw an expanded miR156-regulated network that links plant developmental transition and other fundamental biological processes, gaining novel and broad insight into the molecular mechanisms of plant-age-related processes in Arabidopsis.
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Affiliation(s)
- Chenfei Zheng
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (M.Y.); (M.S.)
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (M.Y.); (M.S.)
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (M.Y.); (M.S.)
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (M.Y.); (M.S.)
- Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
- Correspondence: ; Tel.: +86-10-6322-6264
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Ruta V, Longo C, Boccaccini A, Madia VN, Saccoliti F, Tudino V, Di Santo R, Lorrai R, Dello Ioio R, Sabatini S, Costi R, Costantino P, Vittorioso P. Inhibition of Polycomb Repressive Complex 2 activity reduces trimethylation of H3K27 and affects development in Arabidopsis seedlings. BMC PLANT BIOLOGY 2019; 19:429. [PMID: 31619182 PMCID: PMC6796367 DOI: 10.1186/s12870-019-2057-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 09/26/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Polycomb repressive complex 2 (PRC2) is an epigenetic transcriptional repression system, whose catalytic subunit (ENHANCER OF ZESTE HOMOLOG 2, EZH2 in animals) is responsible for trimethylating histone H3 at lysine 27 (H3K27me3). In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. RESULTS We show here that the 1,5-bis (3-bromo-4-methoxyphenyl)penta-1,4-dien-3-one compound (RDS 3434), previously reported as an EZH2 inhibitor in human leukemia cells, is active on the Arabidopsis catalytic subunit of PRC2, since treatment with the drug reduces the total amount of H3K27me3 in a dose-dependent fashion. Consistently, we show that the expression level of two PRC2 targets is significantly increased following treatment with the RDS 3434 compound. Finally, we show that impairment of H3K27 trimethylation in Arabidopsis seeds and seedlings affects both seed germination and root growth. CONCLUSIONS Our results provide a useful tool for the plant community in investigating how PRC2 affects transcriptional control in plant development.
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Affiliation(s)
- Veronica Ruta
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Chiara Longo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alessandra Boccaccini
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Valentina Noemi Madia
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Chimica e Tecnologie del Farmaco, Dipartimento di Eccellenza 2018-2022, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Saccoliti
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Chimica e Tecnologie del Farmaco, Dipartimento di Eccellenza 2018-2022, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Valeria Tudino
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Chimica e Tecnologie del Farmaco, Dipartimento di Eccellenza 2018-2022, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Roberto Di Santo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Chimica e Tecnologie del Farmaco, Dipartimento di Eccellenza 2018-2022, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Riccardo Lorrai
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Sabrina Sabatini
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Roberta Costi
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Chimica e Tecnologie del Farmaco, Dipartimento di Eccellenza 2018-2022, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Paolo Costantino
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Paola Vittorioso
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Hou N, Cao Y, Li F, Yuan W, Bian H, Wang J, Zhu M, Han N. Epigenetic regulation of miR396 expression by SWR1-C and the effect of miR396 on leaf growth and developmental phase transition in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5217-5229. [PMID: 31198943 PMCID: PMC6793462 DOI: 10.1093/jxb/erz285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 05/31/2019] [Indexed: 05/20/2023]
Abstract
In this study, we investigated the regulatory function of miR396 in the phase transition in Arabidopsis thaliana. Using AtMIR396a/b knockout mutants generated through clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-directed genome editing, we showed that miR396 negatively regulates the leaf size and vegetative phase transition, and the first leaf with abaxial trichomes appeared earlier in the mir396ab double mutant than in the wild type (WT) and was significantly delayed in miR396 overexpression lines. Moreover, mir396ab exhibited early flowering, whereas 35S:MIR396a/b and cib4-1 delayed flowering, and the flowering time was negatively correlated with FT gene expression. Furthermore, in arp6 and pie1 mutants, which are deficient in the ATP-dependent chromatin remodeling complex (SWR1-C), miR396 expression was significantly repressed. Compared with the WT, reduced H2A.Z deposit and stronger relative nucleosome occupancy in the promoter region of MIR396a was found in the arp6 mutant, indicating that SWR1-C contributes to the transcriptional activation of MIR396a via nucleosome dynamics. In addition, miR396 displayed specific spatio-temporal expression patterns in the leaf, which was altered in arp6 and pie1, and therefore affected the transcript levels of CIB4 and FT in these mutants. We propose that miR396 is not only a marker of cell differentiation, but also an age signal for leaf development and phase change. Meanwhile, SWR1-C-mediated epigenetic regulation contributes to the age-dependent enhancement of miR396 expression and differential miR396 accumulation among leaves.
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Affiliation(s)
- Ning Hou
- Key Lab for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yanli Cao
- Key Lab for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fengyun Li
- Key Lab for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weiyi Yuan
- Key Lab for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongwu Bian
- Key Lab for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junhui Wang
- Key Lab for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Muyuan Zhu
- Key Lab for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ning Han
- Key Lab for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Correspondence:
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Xing L, Li Y, Qi S, Zhang C, Ma W, Zuo X, Liang J, Gao C, Jia P, Shah K, Zhang D, An N, Zhao C, Han M, Zhao J. Comparative RNA-Sequencing and DNA Methylation Analyses of Apple (Malus domestica Borkh.) Buds with Diverse Flowering Capabilities Reveal Novel Insights into the Regulatory Mechanisms of Flower Bud Formation. PLANT & CELL PHYSIOLOGY 2019; 60:1702-1721. [PMID: 31077318 DOI: 10.1093/pcp/pcz080] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
In plants, DNA methylation (i.e. chromatin modification) is important for various biological processes, including growth, development and flowering. Because 'Fuji' apple trees are alternate bearing and have a long ripening period and poor-quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4% and 23.7% of the CG, CHG and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that nonexpressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g. SOC1, AP1 and SPLs) and some transcription factor genes (e.g. GATA, bHLH, bZIP and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.
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Affiliation(s)
- Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Siyan Qi
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chenguang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xiya Zuo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jiayan Liang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Pen Jia
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kamran Shah
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Juan Zhao
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
- College of Mechanical and Electronic Engineering, Northwest A & F University, Yangling, Shaanxi, P. R. China
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Chen Q, Xu X, Xu D, Zhang H, Zhang C, Li G. WRKY18 and WRKY53 Coordinate with HISTONE ACETYLTRANSFERASE1 to Regulate Rapid Responses to Sugar. PLANT PHYSIOLOGY 2019; 180:2212-2226. [PMID: 31182557 PMCID: PMC6670108 DOI: 10.1104/pp.19.00511] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/01/2019] [Indexed: 05/18/2023]
Abstract
Sugars provide a source of energy; they also function as signaling molecules that regulate gene expression, affect metabolism, and alter growth in plants. Rapid responses to sugar signaling and metabolism are essential for optimal growth and fitness, but the regulatory mechanisms underlying these are largely unknown. In this study, we found that the rapid induction of sugar responses in Arabidopsis (Arabidopsis thaliana) requires the W-box cis-elements in the promoter region of GLC 6-PHOSPHATE/PHOSPHATE TRANSLOCATOR2, a well-studied sugar response marker gene. The transcription factors WRKY18 and WRKY53 directly bind to the W-Box cis-elements in the promoter region of sugar response genes and activate their expression. In addition, HISTONE ACETYLTRANSFERASE 1 (HAC1) is recruited to the WRKY18 and WRKY53 complex that resides on the promoters. In this complex, HAC1 facilitates the acetylation of histone 3 Lys 27 (H3K27ac) on the sugar-responsive genes. Taken together, our findings demonstrate a mechanism by which sugar regulates chromatin modification and gene expression, thus helping plants to adjust their growth in response to environmental changes.
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Affiliation(s)
- Qingshuai Chen
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiyu Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Di Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Haisen Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Cankui Zhang
- Department of Agronomy, Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
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Role for the shoot apical meristem in the specification of juvenile leaf identity in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:10168-10177. [PMID: 31023887 DOI: 10.1073/pnas.1817853116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extent to which the shoot apical meristem (SAM) controls developmental decisions, rather than interpreting them, is a longstanding issue in plant development. Previous work suggests that vegetative phase change is regulated by signals intrinsic and extrinsic to the SAM, but the relative importance of these signals for this process is unknown. We investigated this question by examining the effect of meristem-deficient mutations on vegetative phase change and on the expression of key regulators of this process, miR156 and its targets, SPL transcription factors. We found that the precocious phenotypes of meristem-deficient mutants are a consequence of reduced miR156 accumulation. Tissue-specific manipulation of miR156 levels revealed that the SAM functions as an essential pool of miR156 early in shoot development, but that its effect on leaf identity declines with age. We also found that SPL genes control meristem size by repressing WUSCHEL expression via a novel genetic pathway.
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Wang J, Mei J, Ren G. Plant microRNAs: Biogenesis, Homeostasis, and Degradation. FRONTIERS IN PLANT SCIENCE 2019; 10:360. [PMID: 30972093 PMCID: PMC6445950 DOI: 10.3389/fpls.2019.00360] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/07/2019] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs), a class of endogenous, tiny, non-coding RNAs, are master regulators of gene expression among most eukaryotes. Intracellular miRNA abundance is regulated under multiple levels of control including transcription, processing, RNA modification, RNA-induced silencing complex (RISC) assembly, miRNA-target interaction, and turnover. In this review, we summarize our current understanding of the molecular components and mechanisms that influence miRNA biogenesis, homeostasis, and degradation in plants. We also make comparisons with findings from other organisms where necessary.
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Affiliation(s)
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs. Genes (Basel) 2019; 10:genes10030210. [PMID: 30871088 PMCID: PMC6470504 DOI: 10.3390/genes10030210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/22/2019] [Accepted: 03/06/2019] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.
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61
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Chen Y, Zheng Q, Jia X, Chen K, Wang Y, Wu T, Xu X, Han Z, Zhang Z, Zhang X. MdGGT1 Impacts Apple miR156 Precursor Levels via Ontogenetic Changes in Subcellular Glutathione Homeostasis. FRONTIERS IN PLANT SCIENCE 2019; 10:994. [PMID: 31417600 PMCID: PMC6684775 DOI: 10.3389/fpls.2019.00994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/16/2019] [Indexed: 05/03/2023]
Abstract
UNLABELLED The vegetative phase change in flowering plants is controlled by microRNA156 (miR156) under transcriptional regulation. However, the developmental signals upstream of miR156 are not well understood. The glutathione/glutathione disulfide (GSH/GSSG) ratios and GSH levels decline significantly during phase change, which is consistent with miR156 expression in apple (Malus domestica Borkh.). Here, we found that the content of protein conjugated glutathione was remarkably higher in chloroplasts and nuclei of adult than juvenile phase apple hybrids. The decrease in miR156 expression was most relevant to the activities of serine acetyltransferase (SAT) and soluble γ-glutamyl transpeptidase (GGT), and the expressions of MdGGT1 or MdSATs. Transgenic apples over-expressing MdMIR156 or miR156-mimetic (MIM156) did not alter MdGGT1 expression or the soluble GGT activity. Inhibition of GGT activity with serine-borate complex or acivicin led to significant reduction in GSH content, the GSH/GSSG ratio, and the expressions of MdMIR156a5, MdMIR156a12, and miR156. Depletion of GSH with diethyl maleate without altering GGT activity caused a dramatic decrease in the expression of MdMIR156a5, MdMIR156a12, and miR156. Manipulating GGT activity and GSH homeostasis by transgenic over-expressing or RNAi MdGGT1 increased or decreased MdMIR156a5 and MdMIR156a12 levels, respectively. These data provided novel evidence that MdGGT1 participates in transcriptional level of transcription regulation of miR156 precursors during ontogenesis. HIGHLIGHTS - MdGGT1 affects thiol redox status and indirectly participates in the regulation of miR156 expression during vegetative phase change.
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Affiliation(s)
- Yakun Chen
- College of Horticulture, China Agricultural University, Beijing, China
| | - Qingbo Zheng
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaolin Jia
- College of Horticulture, China Agricultural University, Beijing, China
| | - Keqin Chen
- Horticulture College, Shenyang Agricultural University, Liaoning, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhihong Zhang
- Horticulture College, Shenyang Agricultural University, Liaoning, China
- *Correspondence: Zhihong Zhang,
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
- Xinzhong Zhang,
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62
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Shu J, Chen C, Thapa RK, Bian S, Nguyen V, Yu K, Yuan Z, Liu J, Kohalmi SE, Li C, Cui Y. Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings. PLANT DIRECT 2019; 3:e00100. [PMID: 31245749 PMCID: PMC6508855 DOI: 10.1002/pld3.100] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/14/2018] [Accepted: 11/19/2018] [Indexed: 05/25/2023]
Abstract
The Polycomb Group (PcG) proteins form two protein complexes, PcG Repressive Complex 1 (PRC1) and PRC2, which are key epigenetic regulators in eukaryotes. PRC2 represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 (H3K27me3). In Arabidopsis (Arabidopsis thaliana), CURLY LEAF (CLF) and SWINGER (SWN) are two major H3K27 methyltransferases and core components of PRC2, playing essential roles in plant growth and development. Despite their importance, genome-wide binding profiles of CLF and SWN have not been determined and compared yet. In this study, we generated transgenic lines expressing GFP-tagged CLF/SWN under their respective native promoters and used them for ChIP-seq analyses to profile the genome-wide distributions of CLF and SWN in Arabidopsis seedlings. We also profiled and compared the global H3K27me3 levels in wild-type (WT) and PcG mutants (clf, swn, and clf swn). Our data show that CLF and SWN bind to almost the same set of genes, except that SWN has a few hundred more targets. Two short DNA sequences, the GAGA-like and Telo-box-like motifs, were found enriched in the CLF and SWN binding regions. The H3K27me3 levels in clf, but not in swn, were markedly reduced compared with WT; and the mark was undetectable in the clf swn double mutant. Further, we profiled the transcriptomes in clf, swn, and clf swn, and compared that with WT. Thus this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC2 in plant growth and development.
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Affiliation(s)
- Jie Shu
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
- Department of BiologyWestern UniversityLondonOntarioCanada
| | - Chen Chen
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
- Department of BiologyWestern UniversityLondonOntarioCanada
| | - Raj Kumar Thapa
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
- Department of BiologyWestern UniversityLondonOntarioCanada
| | - Shaomin Bian
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
- College of Plant ScienceJilin UniversityChangchunChina
| | - Vi Nguyen
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
| | - Kangfu Yu
- Harrow Research and Development CentreAgriculture and Agri‐Food CanadaHarrowOntarioCanada
| | - Ze‐Chun Yuan
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
| | - Jun Liu
- Guangdong Academy of Agricultural SciencesGuangzhouChina
| | | | - Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Yuhai Cui
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonOntarioCanada
- Department of BiologyWestern UniversityLondonOntarioCanada
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63
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Sun L, Song G, Guo W, Wang W, Zhao H, Gao T, Lv Q, Yang X, Xu F, Dong Y, Pu L. Dynamic Changes in Genome-Wide Histone3 Lysine27 Trimethylation and Gene Expression of Soybean Roots in Response to Salt Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:1031. [PMID: 31552061 PMCID: PMC6746917 DOI: 10.3389/fpls.2019.01031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/23/2019] [Indexed: 05/14/2023]
Abstract
Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. Eight thousand seven hundred ninety eight soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.
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Affiliation(s)
- Lei Sun
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Guangshu Song
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weixuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Tingting Gao
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Qingxue Lv
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Xue Yang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingshan Dong
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
- *Correspondence: Yingshan Dong, ; Li Pu,
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yingshan Dong, ; Li Pu,
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64
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Sarvepalli K, Nath U. CIN-TCP transcription factors: Transiting cell proliferation in plants. IUBMB Life 2018; 70:718-731. [PMID: 29934986 DOI: 10.1002/iub.1874] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022]
Abstract
Leaves are the most conspicuous planar organs in plants, designed for efficient capture of sunlight and its conversion to energy that is channeled into sustaining the entire biosphere. How a few founder cells derived from the shoot apical meristem give rise to diverse leaf forms has interested naturalists and developmental biologists alike. At the heart of leaf morphogenesis lie two simple cellular processes, division and expansion, that are spatially and temporally segregated in a developing leaf. In leaves of dicot model species, cell division occurs predominantly at the base, concomitant with the expansion and differentiation of cells at the tip of the lamina that drives increase in leaf surface area. The timing of the transition from one cell fate (division) to the other (expansion) within a growing leaf lamina is a critical determinant of final leaf shape, size, complexity and flatness. The TCP proteins, unique to plant kingdom, are sequence-specific DNA-binding transcription factors that control several developmental and physiological traits. A sub-group of class II TCPs, called CINCINNATA-like TCPs (CIN-TCPs henceforth), are key regulators of the timing of the transition from division to expansion in dicot leaves. The current review highlights recent advances in our understanding of how the pattern of CIN-TCP activity is translated to the dynamic spatio-temporal control of cell-fate transition through the transactivation of cell-cycle regulators, growth-repressing microRNAs, and interactions with the chromatin remodeling machinery to modulate phytohormone responses. Unravelling how environmental inputs influence CIN-TCP-mediated growth control is a challenge for future studies. © 2018 IUBMB Life, 70(8):718-731, 2018.
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Affiliation(s)
- Kavitha Sarvepalli
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Utpal Nath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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65
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Sun Q, Qiao J, Zhang S, He S, Shi Y, Yuan Y, Zhang X, Cai Y. Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development. PeerJ 2018; 6:e4945. [PMID: 29915693 PMCID: PMC6004305 DOI: 10.7717/peerj.4945] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/18/2018] [Indexed: 12/20/2022] Open
Abstract
Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages.
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Affiliation(s)
- Quan Sun
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China.,Chongqing University of Posts and Telecommunications, College of Bioinformation, ChongQing, China
| | - Jing Qiao
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Sai Zhang
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Shibin He
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Yuzhen Shi
- Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Youlu Yuan
- Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiao Zhang
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China.,Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Yingfan Cai
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
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66
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Dotto M, Gómez MS, Soto MS, Casati P. UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2018; 41:1394-1406. [PMID: 29447428 DOI: 10.1111/pce.13166] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/31/2018] [Accepted: 01/31/2018] [Indexed: 05/18/2023]
Abstract
UV-B is a high-energy component of the solar radiation perceived by the plant and induces a number of modifications in plant growth and development, including changes in flowering time. However, the molecular mechanisms underlying these changes are largely unknown. In the present work, we demonstrate that Arabidopsis plants grown under white light supplemented with UV-B show a delay in flowering time, and this developmental reprogramming is mediated by the UVR8 photoreceptor. Using a combination of gene expression analyses and UV-B irradiation of different flowering mutants, we gained insight into the pathways involved in the observed flowering time delay in UV-B-exposed Arabidopsis plants. We provide evidence that UV-B light downregulates the expression of MSI1 and CLF, two of the components of the polycomb repressive complex 2, which in consequence drives a decrease in H3K27me3 histone methylation of MIR156 and FLC genes. Modification in the expression of several flowering time genes as a consequence of the decrease in the polycomb repressive complex 2 activity was also determined. UV-B exposure of flowering mutants supports the involvement of this complex in the observed delay in flowering time, mostly through the age pathway.
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Affiliation(s)
- Marcela Dotto
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Santa Fe, 2000, Argentina
| | - María Sol Gómez
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Santa Fe, 2000, Argentina
| | - María Soledad Soto
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Santa Fe, 2000, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Santa Fe, 2000, Argentina
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67
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Carter B, Bishop B, Ho KK, Huang R, Jia W, Zhang H, Pascuzzi PE, Deal RB, Ogas J. The Chromatin Remodelers PKL and PIE1 Act in an Epigenetic Pathway That Determines H3K27me3 Homeostasis in Arabidopsis. THE PLANT CELL 2018; 30:1337-1352. [PMID: 29802212 PMCID: PMC6048792 DOI: 10.1105/tpc.17.00867] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 05/07/2018] [Accepted: 05/24/2018] [Indexed: 05/20/2023]
Abstract
Selective, tissue-specific gene expression is facilitated by the epigenetic modification H3K27me3 (trimethylation of lysine 27 on histone H3) in plants and animals. Much remains to be learned about how H3K27me3-enriched chromatin states are constructed and maintained. Here, we identify a genetic interaction in Arabidopsis thaliana between the chromodomain helicase DNA binding chromatin remodeler PICKLE (PKL), which promotes H3K27me3 enrichment, and the SWR1-family remodeler PHOTOPERIOD INDEPENDENT EARLY FLOWERING1 (PIE1), which incorporates the histone variant H2A.Z. Chromatin immunoprecipitation-sequencing and RNA-sequencing reveal that PKL, PIE1, and the H3K27 methyltransferase CURLY LEAF act in a common gene expression pathway and are required for H3K27me3 levels genome-wide. Additionally, H3K27me3-enriched genes are largely a subset of H2A.Z-enriched genes, further supporting the functional linkage between these marks. We also found that recombinant PKL acts as a prenucleosome maturation factor, indicating that it promotes retention of H3K27me3. These data support the existence of an epigenetic pathway in which PIE1 promotes H2A.Z, which in turn promotes H3K27me3 deposition. After deposition, PKL promotes retention of H3K27me3 after DNA replication and/or transcription. Our analyses thus reveal roles for H2A.Z and ATP-dependent remodelers in construction and maintenance of H3K27me3-enriched chromatin in plants.
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Affiliation(s)
- Benjamin Carter
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Brett Bishop
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Kwok Ki Ho
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Ru Huang
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Wei Jia
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Pete E Pascuzzi
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Libraries, Purdue University, West Lafayette, Indiana 47907
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
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68
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Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana. PLoS Genet 2018; 14:e1007337. [PMID: 29672610 PMCID: PMC5929574 DOI: 10.1371/journal.pgen.1007337] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 05/01/2018] [Accepted: 03/27/2018] [Indexed: 12/17/2022] Open
Abstract
Vegetative phase change is regulated by a decrease in the abundance of the miRNAs, miR156 and miR157, and the resulting increase in the expression of their targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. To determine how miR156/miR157 specify the quantitative and qualitative changes in leaf morphology that occur during vegetative phase change, we measured their abundance in successive leaves and characterized the phenotype of mutations in different MIR156 and MIR157 genes. miR156/miR157 decline rapidly between leaf 1&2 and leaf 3 and decrease more slowly after this point. The amount of miR156/miR157 in leaves 1&2 greatly exceeds the threshold required to specify their identity. Subsequent leaves have relatively low levels of miR156/miR157 and are sensitive to small changes in their abundance. In these later-formed leaves, the amount of miR156/miR157 is close to the threshold required to specify juvenile vs. adult identity; a relatively small decrease in the abundance of miR156/157 in these leaves produces a disproportionately large increase in SPL proteins and a significant change in leaf morphology. miR157 is more abundant than miR156 but has a smaller effect on shoot morphology and SPL gene expression than miR156. This may be attributable to the inefficiency with which miR157 is loaded onto AGO1, as well as to the presence of an extra nucleotide at the 5' end of miR157 that is mis-paired in the miR157:SPL13 duplex. miR156 represses different targets by different mechanisms: it regulates SPL9 by a combination of transcript cleavage and translational repression and regulates SPL13 primarily by translational repression. Our results offer a molecular explanation for the changes in leaf morphology that occur during shoot development in Arabidopsis and provide new insights into the mechanism by which miR156 and miR157 regulate gene expression. Leaves produced at different stages in the development of an Arabidopsis shoot vary predictably in shape and size. Previous studies have shown that this phenomenon is regulated by variation in the abundance of the miRNAs, miR156 and miR157, but how miR156/miR157 produce the changes in leaf morphology that occur during shoot development is not understood. To answer this question, we measured the abundance of miR156/miR157 and their SPL targets in successive leaf primordia, and characterized the effect of variation in the abundance of miR156/miR157 on leaf morphology and the abundance of SPL transcripts and SPL proteins. miR156/miR157 are present at very high levels in the first two rosette leaves, where they act as buffers to stabilize leaf identity. They are present at lower and steadily declining levels in subsequent leaves, where they act to modulate leaf morphogenesis. In these later-formed leaves, a small decrease in the abundance of miR156/miR157 produces a disproportionately large increase in SPL activity, primarily as a result of the increased translation of SPL transcripts. Our results provide a new view of vegetative phase change in Arabidopsis and the mechanism by which miR156 and miR157 regulate this process.
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69
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Dhami N, Tissue DT, Cazzonelli CI. Leaf-age dependent response of carotenoid accumulation to elevated CO 2 in Arabidopsis. Arch Biochem Biophys 2018; 647:67-75. [PMID: 29604257 DOI: 10.1016/j.abb.2018.03.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 03/07/2018] [Accepted: 03/26/2018] [Indexed: 01/06/2023]
Abstract
Carotenoids contribute to photosynthesis, photoprotection, phytohormone and apocarotenoid biosynthesis in plants. Carotenoid-derived metabolites control plant growth, development and signalling processes and their accumulation can depend upon changes in the environment. Elevated carbon dioxide (eCO2) often enhances carbon assimilation, early growth patterns and overall plant biomass, and may increase carotenoid accumulation due to higher levels of precursors from isoprenoid biosynthesis. Variable effects of eCO2 on carotenoid accumulation in leaves have been observed for different plant species. Here, we determined whether the variable response of carotenoids to eCO2 was potentially a function of leaf age and the impact of eCO2 on leaf development by growing Arabidopsis in ambient CO2 (400 ppm) and eCO2 (800 ppm). eCO2 increased plant leaf number, rosette area, biomass, seed yield and net photosynthesis. In addition, eCO2 increased carotenoid content by 10-20% in younger emerging leaves, but not in older mature leaves. Older leaves contained approximately 60% less total carotenoids compared to younger leaves. The age-dependent effect on carotenoid content was observed for cotyledon, juvenile and adult phase leaves. We conclude that younger leaves utilize additional carbon from enhanced photosynthesis in eCO2 to increase carotenoid content, yet older leaves have less capacity to store additional carbon into carotenoids.
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Affiliation(s)
- Namraj Dhami
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Christopher I Cazzonelli
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
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70
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Negishi K, Endo M, Abe M, Araki T. SODIUM POTASSIUM ROOT DEFECTIVE1 regulates FLOWERING LOCUS T expression via the microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module in response to potassium conditions. PLANT & CELL PHYSIOLOGY 2018; 59:404-413. [PMID: 29253219 DOI: 10.1093/pcp/pcx199] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/09/2017] [Indexed: 06/07/2023]
Abstract
To determine flowering time, plants perceive multiple environmental stimuli and integrate these signals in the regulation of a florigen gene, FLOWERING LOCUS T (FT). It has been known that nutrient availability affects flowering time in both laboratories and fields. Nitrogen (N), phosphorus (P) and potassium (K) are the three major macronutrients which are important for plant growth and development. Although N and P stimuli can alter the expression of regulators of FT including microRNA156 (miR156) and miR156-targeted transcription factors of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family, how K+ conditions affect flowering is still unclear. We focused on SODIUM POTASSUIM ROOT DEFECTIVE1 (NaKR1) whose mutant plants showed Na+ and K+ overaccumulation and late flowering. It was reported that NaKR1 is involved in the phloem transport of FT protein. Here we report that NaKR1 is also required for the promotion of FT expression in long-day conditions. NaKR1 affects the accumulation of miR156 and SPL3 expression, suggesting that NaKR1 regulates FT expression in part through the miR156-SPL3 module. The late-flowering phenotype of the nakr1-1 mutant was partially suppressed under low K+ conditions, and miR156 abundance and SPL3 expression in the nakr1-1 mutant and, to a lesser extent, in wild-type plants responded to K+ conditions. Taken together, our findings suggest that the miR156-SPL3 module mediates regulation of FT expression by NaKR1 in response to K+ conditions. Finally, we propose a model in which NaKR1 plays dual roles in regulation of flowering, one in the regulation of florigen production, the other in that of florigen transport.
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Affiliation(s)
- Katsuya Negishi
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501 Japan
| | - Motomu Endo
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501 Japan
| | - Mitsutomo Abe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Takashi Araki
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501 Japan
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Xu M, Leichty AR, Hu T, Poethig RS. H2A.Z promotes the transcription of MIR156A and MIR156C in Arabidopsis by facilitating the deposition of H3K4me3. Development 2018; 145:dev.152868. [PMID: 29361556 DOI: 10.1242/dev.152868] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 12/20/2017] [Indexed: 01/19/2023]
Abstract
Vegetative phase change in Arabidopsis thaliana is mediated by a decrease in the level of MIR156A and MIR156C, resulting in an increase in the expression of their targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes. Changes in chromatin structure are required for the downregulation of MIR156A and MIR156C, but whether chromatin structure contributes to their initial elevated expression is unknown. We found that mutations in components of the SWR1 complex (ARP6, SEF) and in genes encoding H2A.Z (HTA9 and HTA11) reduce the expression of MIR156A and MIR156C, and accelerate vegetative phase change, indicating that H2A.Z promotes juvenile vegetative identity. However, arp6 and sef did not accelerate the temporal decline in miR156, and the downregulation of MIR156A and MIR156C was not accompanied by significant change in the level of H2A.Z at these loci. We conclude that H2A.Z contributes to the high expression of MIR156A/MIR156C early in shoot development, but does not regulate the timing of vegetative phase change. Our results also suggest that H2A.Z promotes the expression of MIR156A/MIR156C by facilitating the deposition of H3K4me3, rather than by decreasing nucleosome occupancy.
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Affiliation(s)
- Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aaron R Leichty
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Buendía-Monreal M, Gillmor CS. The Times They Are A-Changin': Heterochrony in Plant Development and Evolution. FRONTIERS IN PLANT SCIENCE 2018; 9:1349. [PMID: 30283473 PMCID: PMC6157392 DOI: 10.3389/fpls.2018.01349] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 08/27/2018] [Indexed: 05/16/2023]
Abstract
Alterations in the timing of developmental programs during evolution, that lead to changes in the shape, or size of organs, are known as heterochrony. Heterochrony has been widely studied in animals, but has often been neglected in plants. During plant evolution, heterochronic shifts have played a key role in the origin and diversification of leaves, roots, flowers, and fruits. Heterochrony that results in a juvenile or simpler outcome is known as paedomorphosis, while an adult or more complex outcome is called peramorphosis. Mechanisms that alter developmental timing at the cellular level affect cell proliferation or differentiation, while those acting at the tissue or organismal level change endogenous aging pathways, morphogen signaling, and metabolism. We believe that wider consideration of heterochrony in the context of evolution will contribute to a better understanding of plant development.
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Xu Y, Zhang L, Wu G. Epigenetic Regulation of Juvenile-to-Adult Transition in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1048. [PMID: 30079076 PMCID: PMC6063087 DOI: 10.3389/fpls.2018.01048] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/28/2018] [Indexed: 05/02/2023]
Abstract
Epigenetic regulation is referred to as changes in gene function that do not involve changes in the DNA sequence, it is usually accomplished by DNA methylation, histone modifications (repressive marks such as H3K9me, H3K27me, H2Aub, or active marks such as H3K4me, H3K36me, H3Ac), and chromatin remodeling (nucleosome composition, occupancy, and location). In plants, the shoot apex produces different lateral organs during development to give rise to distinguishable phases of a juvenile, an adult and a reproductive phase after embryogenesis. The juvenile-to-adult transition is a key developmental event in plant life cycle, and it is regulated by a decrease in the expression of a conserved microRNA-miR156/157, and a corresponding increase in the expression of its target genes encoding a set of plant specific SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) proteins. Recent work has revealed that the miR156/157-SPL pathway is the master regulator of juvenile-to-adult transition in plants, and genes in this pathway are subjected to epigenetic regulation, such as DNA methylation, histone modifications, and chromatin remodeling. In this review, we summarized the recent progress in understanding the epigenetic regulation of the miR156/157-SPL pathway during juvenile-to-adult transition and bring forward some perspectives of future research in this field.
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Affiliation(s)
- Yunmin Xu
- State Key Laboratory of Subtropical Silviculture, School of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Lu Zhang
- State Key Laboratory of Subtropical Silviculture, School of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Gang Wu
- State Key Laboratory of Subtropical Silviculture, School of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
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74
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Chomicki G, Coiro M, Renner SS. Evolution and ecology of plant architecture: integrating insights from the fossil record, extant morphology, developmental genetics and phylogenies. ANNALS OF BOTANY 2017; 120:855-891. [PMID: 29165551 PMCID: PMC5710528 DOI: 10.1093/aob/mcx113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 10/03/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND In contrast to most animals, plants have an indeterminate body plan, which allows them to add new body parts during their lifetime. A plant's realized modular construction is the result of exogenous constraints and endogenous processes. This review focuses on endogenous processes that shape plant architectures and their evolution. SCOPE The phylogenetic distribution of plant growth forms across the phylogeny implies that body architectures have originated and been lost repeatedly, being shaped by a limited set of genetic pathways. We (1) synthesize concepts of plant architecture, so far captured in 23 models; (2) extend them to the fossil record; (3) summarize what is known about their developmental genetics; (4) use a phylogenetic approach in several groups to infer how plant architecture has changed and by which intermediate steps; and (5) discuss which macroecological factors may constrain the geographic and ecological distribution of plant architectures. CONCLUSIONS Dichotomously branching Paleozoic plants already encompassed a considerable diversity of growth forms, here captured in 12 new architectural models. Plotting the frequency of branching types through time based on an analysis of 58 927 land plant fossils revealed a decrease in dichotomous branching throughout the Devonian and Carboniferous, mirrored by an increase in other branching types including axillary branching. We suggest that the evolution of seed plant megaphyllous leaves enabling axillary branching contributed to the demise of dichotomous architectures. The developmental-genetic bases for key architectural traits underlying sympodial vs. monopodial branching, rhythmic vs. continuous growth, and axillary branching and its localization are becoming well understood, while the molecular basis of dichotomous branching and plagiotropy remains elusive. Three phylogenetic case studies of architecture evolution in conifers, Aloe and monocaulous arborescent vascular plants reveal relationships between architectural models and show that some are labile in given groups, whereas others are widely conserved, apparently shaped by ecological factors, such as intercepted sunlight, temperature, humidity and seasonality.
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Affiliation(s)
- Guillaume Chomicki
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Munich, Germany
| | - Mario Coiro
- Institute of Systematic Botany, University of Zürich, Zürich, Switzerland
| | - Susanne S Renner
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Munich, Germany
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Control of chrysanthemum flowering through integration with an aging pathway. Nat Commun 2017; 8:829. [PMID: 29018260 PMCID: PMC5635119 DOI: 10.1038/s41467-017-00812-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 07/24/2017] [Indexed: 12/04/2022] Open
Abstract
Age, as a threshold of floral competence acquisition, prevents precocious flowering when there is insufficient biomass, and ensures flowering independent of environmental conditions; however, the underlying regulatory mechanisms are largely unknown. In this study, silencing the expression of a nuclear factor gene, CmNF-YB8, from the short day plant chrysanthemum (Chrysanthemum morifolium), results in precocious transition from juvenile to adult, as well as early flowering, regardless of day length conditions. The expression of SQUAMOSA PROMOTER BINDING-LIKE (SPL) family members, SPL3, SPL5, and SPL9, is upregulated in CmNF-YB8-RNAi plants, while expression of the microRNA, cmo-MIR156, is downregulated. In addition, CmNF-YB8 is shown to bind to the promoter of the cmo-MIR156 gene. Ectopic expression of cmo-miR156, using a virus-based microRNA expression system, restores the early flowering phenotype caused by CmNF-YB8 silencing. These results show that CmNF-YB8 influences flowering time through directly regulating the expression of cmo-MIR156 in the aging pathway. The mechanisms by which plant age regulates flowering remain incompletely understood. Here the authors show that age dependent regulation of SPL transcription factors by miR156 influence flowering via control of NF-YB8 expression in Chrysanthemum.
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76
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Guo C, Xu Y, Shi M, Lai Y, Wu X, Wang H, Zhu Z, Poethig RS, Wu G. Repression of miR156 by miR159 Regulates the Timing of the Juvenile-to-Adult Transition in Arabidopsis. THE PLANT CELL 2017; 29:1293-1304. [PMID: 28536099 PMCID: PMC5502449 DOI: 10.1105/tpc.16.00975] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/07/2017] [Accepted: 05/23/2017] [Indexed: 05/18/2023]
Abstract
Temporally regulated microRNAs have been identified as master regulators of developmental timing in both animals and plants. In plants, vegetative development is regulated by a temporal decrease in miR156 level, but how this decreased expression is initiated and then maintained during shoot development remains elusive. Here, we show that miR159 is required for the correct timing of vegetative development in Arabidopsis thaliana Loss of miR159 increases miR156 level throughout shoot development and delays vegetative development, whereas overexpression of miR159 slightly accelerated vegetative development. The repression of miR156 by miR159 is predominantly mediated by MYB33, an R2R3 MYB domain transcription factor targeted by miR159. Loss of MYB33 led to subtle precocious vegetative phase change phenotypes in spite of the significant downregulation of miR156. MYB33 simultaneously promotes the transcription of MIR156A and MIR156C, as well as their target, SPL9, by directly binding to the promoters of these three genes. Rather than acting as major players in vegetative phase change in Arabidopsis, our results suggest that miR159 and MYB33 function as modifiers of vegetative phase change; i.e., miR159 facilitates vegetative phase change by repressing MYB33 expression, thus preventing MYB33 from hyperactivating miR156 expression throughout shoot development to ensure correct timing of the juvenile-to-adult transition in Arabidopsis.
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Affiliation(s)
- Changkui Guo
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yunmin Xu
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Min Shi
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yongmin Lai
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Xi Wu
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Huasen Wang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Zhujun Zhu
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Gang Wu
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
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Yang R, Zheng Z, Chen Q, Yang L, Huang H, Miki D, Wu W, Zeng L, Liu J, Zhou JX, Ogas J, Zhu JK, He XJ, Zhang H. The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci. Genome Biol 2017; 18:103. [PMID: 28569170 PMCID: PMC5452414 DOI: 10.1186/s13059-017-1226-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/03/2017] [Indexed: 11/27/2022] Open
Abstract
Background The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana. Results Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter. Mutation of PKL results in DNA methylation changes at more than half of the loci that are targeted by RNA-directed DNA methylation (RdDM). A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the pkl mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the pkl mutant are positively correlated with changes in 24-nt siRNA levels. In addition, PKL is required for the accumulation of Pol V-dependent transcripts and for the positioning of Pol V-stabilized nucleosomes at several tested loci, indicating that RNA polymerase V-related functions are impaired in the pkl mutant. Conclusions PKL is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the pkl mutant are correlated with changes in the non-coding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions, PKL may be required to create a chromatin environment that influences non-coding RNA production, DNA methylation, and transcriptional silencing. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1226-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rong Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Zhimin Zheng
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Qing Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lan Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Wenwu Wu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Liang Zeng
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Jun Liu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China.
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Nguyen STT, Greaves T, McCurdy DW. Heteroblastic Development of Transfer Cells Is Controlled by the microRNA miR156/SPL Module. PLANT PHYSIOLOGY 2017; 173:1676-1691. [PMID: 28082719 PMCID: PMC5338675 DOI: 10.1104/pp.16.01741] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/10/2017] [Indexed: 05/08/2023]
Abstract
We report that wall ingrowth deposition in phloem parenchyma (PP) transfer cells (TCs) in leaf veins of Arabidopsis (Arabidopsis thaliana) represents a novel trait of heteroblasty. Development of PP TCs involves extensive deposition of wall ingrowths adjacent to cells of the sieve element/companion cell complex. These PP TCs potentially facilitate phloem loading by enhancing efflux of symplasmic Suc for subsequent active uptake into cells of the sieve element/companion cell complex. PP TCs with extensive wall ingrowths are ubiquitous in mature cotyledons and juvenile leaves, but dramatically less so in mature adult leaves, an observation consistent with PP TC development reflecting vegetative phase change (VPC) in Arabidopsis. Consistent with this conclusion, the abundance of PP TCs with extensive wall ingrowths varied across rosette development in three ecotypes displaying differing durations of juvenile phase, and extensive deposition of wall ingrowths was observed in rejuvenated leaves following prolonged defoliation. PP TC development across juvenile, transition, and adult leaves correlated positively with levels of miR156, a major regulator of VPC in plants, and corresponding changes in wall ingrowth deposition were observed when miR156 was overexpressed or its activity suppressed by target mimicry. Analysis of plants carrying miR156-resistant forms of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes showed that wall ingrowth deposition was increased in SPL9-group but not SPL3-group genes, indicating that SPL9-group genes may function as negative regulators of wall ingrowth deposition in PP TCs. Collectively, our results point to wall ingrowth deposition in PP TCs being under control of the genetic program regulating VPC.
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Affiliation(s)
- Suong T T Nguyen
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Teighan Greaves
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - David W McCurdy
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
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Park J, Oh DH, Dassanayake M, Nguyen KT, Ogas J, Choi G, Sun TP. Gibberellin Signaling Requires Chromatin Remodeler PICKLE to Promote Vegetative Growth and Phase Transitions. PLANT PHYSIOLOGY 2017; 173:1463-1474. [PMID: 28057895 PMCID: PMC5291033 DOI: 10.1104/pp.16.01471] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/27/2016] [Indexed: 05/20/2023]
Abstract
PICKLE (PKL) is an ATP-dependent chromodomain-helicase-DNA-binding domain (CHD3) chromatin remodeling enzyme in Arabidopsis (Arabidopsis thaliana). Previous studies showed that PKL promotes embryonic-to-vegetative transition by inhibiting expression of seed-specific genes during seed germination. The pkl mutants display a low penetrance of the "pickle root" phenotype, with a thick and green primary root that retains embryonic characteristics. The penetrance of this pickle root phenotype in pkl is dramatically increased in gibberellin (GA)-deficient conditions. At adult stages, the pkl mutants are semidwarfs with delayed flowering time, which resemble reduced GA-signaling mutants. These findings suggest that PKL may play a positive role in regulating GA signaling. A recent biochemical analysis further showed that PKL and GA signaling repressors DELLAs antagonistically regulate hypocotyl cell elongation genes by direct protein-protein interaction. To elucidate further the role of PKL in GA signaling and plant development, we studied the genetic interaction between PKL and DELLAs using the hextuple mutant containing pkl and della pentuple (dP) mutations. Here, we show that PKL is required for most of GA-promoted developmental processes, including vegetative growth such as hypocotyl, leaf, and inflorescence stem elongation, and phase transitions such as juvenile-to-adult leaf and vegetative-to-reproductive phase. The removal of all DELLA functions (in the dP background) cannot rescue these phenotypes in pkl RNA-sequencing analysis using the ga1 (a GA-deficient mutant), pkl, and the ga1 pkl double mutant further shows that expression of 80% of GA-responsive genes in seedlings is PKL dependent, including genes that function in cell elongation, cell division, and phase transitions. These results indicate that the CHD3 chromatin remodeler PKL is required for regulating gene expression during most of GA-regulated developmental processes.
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Affiliation(s)
- Jeongmoo Park
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Dong-Ha Oh
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Maheshi Dassanayake
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Khoa Thi Nguyen
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Joe Ogas
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Giltsu Choi
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.);
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.);
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
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Li J, Wang Z, Hu Y, Cao Y, Ma L. Polycomb Group Proteins RING1A and RING1B Regulate the Vegetative Phase Transition in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:867. [PMID: 28596781 PMCID: PMC5443144 DOI: 10.3389/fpls.2017.00867] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/09/2017] [Indexed: 05/18/2023]
Abstract
Polycomb group (PcG) protein-mediated gene silencing is a major regulatory mechanism in higher eukaryotes that affects gene expression at the transcriptional level. Here, we report that two conserved homologous PcG proteins, RING1A and RING1B (RING1A/B), are required for global H2A monoubiquitination (H2Aub) in Arabidopsis. The mutation of RING1A/B increased the expression of members of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family and caused an early vegetative phase transition. The early vegetative phase transition observed in ring1a ring1b double mutant plants was dependent on an SPL family gene, and the H2Aub status of the chromatin at SPL locus was dependent on RING1A/B. Moreover, mutation in RING1A/B affected the miRNA156a-mediated vegetative phase transition, and RING1A/B and the AGO7-miR390-TAS3 pathway were found to additively regulate this transition in Arabidopsis. Together, our results demonstrate that RING1A/B regulates the vegetative phase transition in Arabidopsis through the repression of SPL family genes.
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82
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Brunner AM, Varkonyi-Gasic E, Jones RC. Phase Change and Phenology in Trees. COMPARATIVE AND EVOLUTIONARY GENOMICS OF ANGIOSPERM TREES 2017. [DOI: 10.1007/7397_2016_30] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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83
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Hyun Y, Richter R, Coupland G. Competence to Flower: Age-Controlled Sensitivity to Environmental Cues. PLANT PHYSIOLOGY 2017; 173:36-46. [PMID: 27920161 PMCID: PMC5210750 DOI: 10.1104/pp.16.01523] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/05/2016] [Indexed: 05/18/2023]
Abstract
miR156 and SPL transcription factors play various roles in conferring competence to flower in plants.
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Affiliation(s)
- Youbong Hyun
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - René Richter
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
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Xiao J, Lee US, Wagner D. Tug of war: adding and removing histone lysine methylation in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:41-53. [PMID: 27614255 DOI: 10.1016/j.pbi.2016.08.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/11/2016] [Accepted: 08/24/2016] [Indexed: 05/17/2023]
Abstract
Histone lysine methylation plays a fundamental role in the epigenetic regulation of gene expression in multicellular eukaryotes, including plants. It shapes plant developmental and growth programs as well as responses to the environment. The methylation status of certain amino-acids, in particular of the histone 3 (H3) lysine tails, is dynamically controlled by opposite acting histone methyltransferase 'writers' and histone demethylase 'erasers'. The methylation status is interpreted by a third set of proteins, the histone modification 'readers', which specifically bind to a methylated amino-acid on the H3 tail. Histone methylation writers, readers, and erasers themselves are regulated by intrinsic or extrinsic stimuli; this forms a feedback loop that contributes to development and environmental adaptation in Arabidopsis and other plants. Recent studies have expanded our knowledge regarding the biological roles and dynamic regulation of histone methylation. In this review, we will discuss recent advances in understanding the regulation and roles of histone methylation in plants and animals.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Un-Sa Lee
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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85
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Xu Y, Guo C, Zhou B, Li C, Wang H, Zheng B, Ding H, Zhu Z, Peragine A, Cui Y, Poethig S, Wu G. Regulation of Vegetative Phase Change by SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA. PLANT PHYSIOLOGY 2016; 172:2416-2428. [PMID: 27803189 PMCID: PMC5129735 DOI: 10.1104/pp.16.01588] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/30/2016] [Indexed: 05/05/2023]
Abstract
Plants progress from a juvenile vegetative phase of development to an adult vegetative phase of development before they enter the reproductive phase. miR156 has been shown to be the master regulator of the juvenile-to-adult transition in plants. However, the mechanism of how miR156 is transcriptionally regulated still remains elusive. In a forward genetic screen, we identified that a mutation in the SWI2/SNF2 chromatin remodeling ATPase BRAHMA (BRM) exhibited an accelerated vegetative phase change phenotype by reducing the expression of miR156, which in turn caused a corresponding increase in the levels of SQUAMOSA PROMOTER BINDING PROTEIN LIKE genes. BRM regulates miR156 expression by directly binding to the MIR156A promoter. Mutations in BRM not only increased occupancy of the -2 and +1 nucleosomes proximal to the transcription start site at the MIR156A locus but also the levels of trimethylated histone H3 at Lys 27. The precocious phenotype of brm mutant was partially suppressed by a second mutation in SWINGER (SWN), but not by a mutation in CURLEY LEAF, both of which are key components of the Polycomb Group Repressive Complex 2 in plants. Our results indicate that BRM and SWN act antagonistically at the nucleosome level to fine-tune the temporal expression of miR156 to regulate vegetative phase change in Arabidopsis.
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Affiliation(s)
- Yunmin Xu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Changkui Guo
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Bingying Zhou
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Chenlong Li
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Huasen Wang
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Ben Zheng
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Han Ding
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Zhujun Zhu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Angela Peragine
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Yuhai Cui
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Scott Poethig
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Gang Wu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.);
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
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86
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Xu M, Hu T, Zhao J, Park MY, Earley KW, Wu G, Yang L, Poethig RS. Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006263. [PMID: 27541584 PMCID: PMC4991793 DOI: 10.1371/journal.pgen.1006263] [Citation(s) in RCA: 323] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/27/2016] [Indexed: 01/18/2023] Open
Abstract
Correct developmental timing is essential for plant fitness and reproductive success. Two important transitions in shoot development-the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition-are mediated by a group of genes targeted by miR156, SQUAMOSA PROMOTER BINDING PROTEIN (SBP) genes. To determine the developmental functions of these genes in Arabidopsis thaliana, we characterized their expression patterns, and their gain-of-function and loss-of-function phenotypes. Our results reveal that SBP-LIKE (SPL) genes in Arabidopsis can be divided into three functionally distinct groups: 1) SPL2, SPL9, SPL10, SPL11, SPL13 and SPL15 contribute to both the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition, with SPL9, SP13 and SPL15 being more important for these processes than SPL2, SPL10 and SPL11; 2) SPL3, SPL4 and SPL5 do not play a major role in vegetative phase change or floral induction, but promote the floral meristem identity transition; 3) SPL6 does not have a major function in shoot morphogenesis, but may be important for certain physiological processes. We also found that miR156-regulated SPL genes repress adventitious root development, providing an explanation for the observation that the capacity for adventitious root production declines as the shoot ages. miR156 is expressed at very high levels in young seedlings, and declines in abundance as the shoot develops. It completely blocks the expression of its SPL targets in the first two leaves of the rosette, and represses these genes to different degrees at later stages of development, primarily by promoting their translational repression. These results provide a framework for future studies of this multifunctional family of transcription factors, and offer new insights into the role of miR156 in Arabidopsis development.
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Affiliation(s)
- Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jianfei Zhao
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mee-Yeon Park
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Keith W. Earley
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gang Wu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Li Yang
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - R. Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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87
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Tian Y, Cai L, Tian Y, Tu Y, Qiu H, Xie G, Huang D, Zheng R, Zhang W. miR156a Mimic Represses the Epithelial-Mesenchymal Transition of Human Nasopharyngeal Cancer Cells by Targeting Junctional Adhesion Molecule A. PLoS One 2016; 11:e0157686. [PMID: 27341697 PMCID: PMC4920421 DOI: 10.1371/journal.pone.0157686] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/02/2016] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) have been documented as having an important role in the development of cancer. Broccoli is very popular in large groups of the population and has anticancer properties. Junctional adhesion molecule A (JAMA) is preferentially concentrated at tight junctions and influences cell morphology and migration. Epithelial-mesenchymal transition (EMT) is a developmental program associated with cancer progression and metastasis. In this study we aimed to investigate the role of miRNAs from broccoli in human nasopharyngeal cancer (NPC). We demonstrated that a total of 84 conserved miRNAs and 184 putative novel miRNAs were found in broccoli by sequencing technology. Among these, miR156a was expressed the most. In addition, synthetic miR156a mimic inhibited the EMT of NPC cells in vitro. Furthermore, it was confirmed that JAMA was the target of miR156a mimic as validated by 3' UTR luciferase reporter assays and western blotting. Knockdown of JAMA was consistent with the effects of miR156a mimic on the EMT of NPC, and the up-regulation of JAMA could partially restore EMT repressed by miR156a mimic. In conclusion, these results indicate that the miR156a mimic inhibits the EMT of NPC cells by targeting the 3' UTR of JAMA. These miRNA profiles of broccoli provide a fundamental basis for further research. Moreover, the discovery of miR156a may have clinical implications for the treatment of patients with NPC.
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Affiliation(s)
- Yunhong Tian
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Longmei Cai
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Yunming Tian
- Huizhou Municipal Central Hospital, Huizhou, Guangdong Province, People’s Republic of China
| | - Yinuo Tu
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Huizhi Qiu
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Guofeng Xie
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Donglan Huang
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Ronghui Zheng
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong Province, People’s Republic of China
- * E-mail: (WZ); (RZ)
| | - Weijun Zhang
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong Province, People’s Republic of China
- * E-mail: (WZ); (RZ)
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88
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Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. Dev Cell 2016; 37:254-66. [PMID: 27134142 DOI: 10.1016/j.devcel.2016.04.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/16/2016] [Accepted: 04/01/2016] [Indexed: 01/06/2023]
Abstract
Flowering is initiated in response to environmental and internal cues that are integrated at the shoot apical meristem (SAM). We show that SPL15 coordinates the basal floral promotion pathways required for flowering of Arabidopsis in non-inductive environments. SPL15 directly activates transcription of the floral regulators FUL and miR172b in the SAM during floral induction, whereas its paralog SPL9 is expressed later on the flanks of the SAM. The capacity of SPL15 to promote flowering is regulated by age through miR156, which targets SPL15 mRNA, and gibberellin (GA), which releases SPL15 from DELLAs. Furthermore, SPL15 and the MADS-box protein SOC1 cooperate to promote transcription of their target genes. SPL15 recruits RNAPII and MED18, a Mediator complex component, in a GA-dependent manner, while SOC1 facilitates active chromatin formation with the histone demethylase REF6. Thus, we present a molecular basis for assimilation of flowering signals and transcriptional control at the SAM during flowering.
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89
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Cross-Talk Between Sporophyte and Gametophyte Generations Is Promoted by CHD3 Chromatin Remodelers in Arabidopsis thaliana. Genetics 2016; 203:817-29. [PMID: 27075727 DOI: 10.1534/genetics.115.180141] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 03/27/2016] [Indexed: 11/18/2022] Open
Abstract
Angiosperm reproduction requires the integrated development of multiple tissues with different genotypes. To achieve successful fertilization, the haploid female gametophytes and diploid ovary must coordinate their development, after which the male gametes must navigate through the maternal sporophytic tissues to reach the female gametes. After fertilization, seed development requires coordinated development of the maternal diploid integuments, the triploid endosperm, and the diploid zygote. Transcription and signaling factors contribute to communication between these tissues, and roles for epigenetic regulation have been described for some of these processes. Here we identify a broad role for CHD3 chromatin remodelers in Arabidopsis thaliana reproductive development. Plants lacking the CHD3 remodeler, PICKLE, exhibit various reproductive defects including abnormal development of the integuments, female gametophyte, and pollen tube, as well as delayed progression of ovule and embryo development. Genetic analyses demonstrate that these phenotypes result from loss of PICKLE in the maternal sporophyte. The paralogous gene PICKLE RELATED 2 is preferentially expressed in the endosperm and acts antagonistically with respect to PICKLE in the seed: loss of PICKLE RELATED 2 suppresses the large seed phenotype of pickle seeds. Surprisingly, the alteration of seed size in pickle plants is sufficient to determine the expression of embryonic traits in the seedling primary root. These findings establish an important role for CHD3 remodelers in plant reproduction and highlight how the epigenetic status of one tissue can impact the development of genetically distinct tissues.
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