101
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Liu J, Hu X, Qin P, Prasad K, Hu Y, Xu L. The WOX11-LBD16 Pathway Promotes Pluripotency Acquisition in Callus Cells During De Novo Shoot Regeneration in Tissue Culture. PLANT & CELL PHYSIOLOGY 2018; 59:734-743. [PMID: 29361138 DOI: 10.1093/pcp/pcy010] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/08/2018] [Indexed: 05/04/2023]
Abstract
De novo shoot regeneration in tissue culture undergoes at least two phases. Explants are first cultured on auxin-rich callus-inducing medium (CIM) to produce a group of pluripotent cells termed callus; the callus is then transferred to cytokinin rich shoot-inducing medium (SIM) to promote the formation of shoot progenitor cells, from which adventitious shoots may differentiate. Here, we show that the Arabidopsis thaliana transcription factor gene LATERAL ORGAN BOUNDARIES DOMAIN16 (LBD16) is involved in pluripotency acquisition in callus cells. LBD16, which is activated by WUSCHEL RELATED HOMEOBOX11 (WOX11), is specifically expressed in the newly formed callus on CIM and its expression decreases quickly when callus is moved to SIM. Blocking the WOX11-LBD16 pathway results in the loss of pluripotency in callus cultured on CIM, leading to shooting defects on SIM. Further analysis showed that LBD16 may function in the establishment of the root primordium-like identity in the newly formed callus, indicating that the root primordium-like identity is the cellular nature of pluripotency in callus cells. Additionally, LBD16 promotes cell division during callus initiation. Our study clarified that the WOX11-LBD16 pathway promotes pluripotency acquisition in callus cells.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Xiaomei Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Peng Qin
- Department of Instrument Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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102
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Lee K, Seo PJ. Dynamic Epigenetic Changes during Plant Regeneration. TRENDS IN PLANT SCIENCE 2018; 23:235-247. [PMID: 29338924 DOI: 10.1016/j.tplants.2017.11.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 05/18/2023]
Abstract
Plants have the remarkable ability to drive cellular dedifferentiation and regeneration. Changes in epigenetic landscapes accompany the cell fate transition. Notably, modifications of chromatin structure occur primarily during callus formation via an in vitro tissue culture process and, thus, pluripotent callus cells have unique epigenetic signatures. Here, we highlight the latest progress in epigenetic regulation of callus formation in plants, which addresses fundamental questions related to cell fate changes and pluripotency establishment. Global and local modifications of chromatin structure underlie callus formation, and the combination and sequence of epigenetic modifications further shape intricate cell fate changes. This review illustrates how a series of chromatin marks change dynamically during callus formation and their biological relevance in plant regeneration.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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103
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Horstman A, Bemer M, Boutilier K. A transcriptional view on somatic embryogenesis. ACTA ACUST UNITED AC 2017; 4:201-216. [PMID: 29299323 PMCID: PMC5743784 DOI: 10.1002/reg2.91] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/15/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Abstract
Somatic embryogenesis is a form of induced plant cell totipotency where embryos develop from somatic or vegetative cells in the absence of fertilization. Somatic embryogenesis can be induced in vitro by exposing explants to stress or growth regulator treatments. Molecular genetics studies have also shown that ectopic expression of specific embryo‐ and meristem‐expressed transcription factors or loss of certain chromatin‐modifying proteins induces spontaneous somatic embryogenesis. We begin this review with a general description of the major developmental events that define plant somatic embryogenesis and then focus on the transcriptional regulation of this process in the model plant Arabidopsis thaliana (arabidopsis). We describe the different somatic embryogenesis systems developed for arabidopsis and discuss the roles of transcription factors and chromatin modifications in this process. We describe how these somatic embryogenesis factors are interconnected and how their pathways converge at the level of hormones. Furthermore, the similarities between the developmental pathways in hormone‐ and transcription‐factor‐induced tissue culture systems are reviewed in the light of our recent findings on the somatic embryo‐inducing transcription factor BABY BOOM.
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Affiliation(s)
- Anneke Horstman
- Bioscience Wageningen University and Research Wageningen The Netherlands.,Laboratory of Molecular Biology Wageningen University and Research Wageningen The Netherlands
| | - Marian Bemer
- Laboratory of Molecular Biology Wageningen University and Research Wageningen The Netherlands
| | - Kim Boutilier
- Bioscience Wageningen University and Research Wageningen The Netherlands
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104
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Lee K, Park OS, Seo PJ. Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal 2017; 10:10/507/eaan0316. [PMID: 29184030 DOI: 10.1126/scisignal.aan0316] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular dedifferentiation, the transition of differentiated somatic cells to pluripotent stem cells, ensures developmental plasticity and contributes to wound healing in plants. Wounding induces cells to form a mass of unorganized pluripotent cells called callus at the wound site. Explanted cells can also form callus tissues in vitro. Reversible cellular differentiation-dedifferentiation processes in higher eukaryotes are controlled mainly by chromatin modifications. We demonstrate that ARABIDOPSIS TRITHORAX-RELATED 2 (ATXR2), a histone lysine methyltransferase that promotes the accumulation of histone H3 proteins that are trimethylated on lysine 36 (H3K36me3) during callus formation, promotes early stages of cellular dedifferentiation through activation of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes. The LBD genes of Arabidopsis thaliana are activated during cellular dedifferentiation to enhance the formation of callus. Leaf explants from Arabidopsis atxr2 mutants exhibited a reduced ability to form callus and a substantial reduction in LBD gene expression. ATXR2 bound to the promoters of LBD genes and was required for the deposition of H3K36me3 at these promoters. ATXR2 was recruited to LBD promoters by the transcription factors AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19. Leaf explants from arf7-1arf19-2 double mutants were defective in callus formation and showed reduced H3K36me3 accumulation at LBD promoters. Genetic analysis provided further support that ARF7 and ARF19 were required for the ability of ATXR2 to promote the expression of LBD genes. These observations indicate that the ATXR2-ARF-LBD axis is key for the epigenetic regulation of callus formation in Arabidopsis.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ok-Sun Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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105
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Huang Y, Chen DH, Liu BY, Shen WH, Ruan Y. Conservation and diversification of polycomb repressive complex 2 (PRC2) proteins in the green lineage. Brief Funct Genomics 2017; 16:106-119. [PMID: 27032420 DOI: 10.1093/bfgp/elw007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polycomb group (PcG) proteins are key epigenetic regulators of gene expression in animals and plants. They act in multiprotein complexes, of which the best characterized is the polycomb repressive complex 2 (PRC2), which catalyses the trimethylation of histone H3 at lysine 27 (H3K27me3) at chromatin targets. In Arabidopsis thaliana, PRC2 proteins are involved in the regulation of diverse developmental processes, including cell fate determination, vegetative growth and development, flowering time control and embryogenesis. Here, we systematically analysed the evolutionary conservation and diversification of PRC2 components in lower and higher plants. We searched for and identified PRC2 homologues from the sequenced genomes of several green lineage species, from the unicellular green alga Ostreococcus lucimarinus to more complicated angiosperms. We found that some PRC2 core components, e.g. E(z), ESC/FIE and MSI/p55, are ancient and have multiplied coincidently with multicellular evolution. For one component, some members are newly formed, especially in the Cruciferae. During evolution, higher plants underwent copy number multiplication of various PRC2 components, which occurred independently for each component, without any obvious co-amplification of PRC2 members. Among the amplified members, usually one was well-conserved and the others were more diversified. Gene amplification occurred at different times for different PcG members during green lineage evolution. Certain PRC2 core components or members of them were highly conserved. Our study provides an insight into the evolutionary conservation and diversification of PcG proteins and may guide future functional characterization of these important epigenetic regulators in plants other than Arabidopsis.
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Affiliation(s)
- Yong Huang
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | - Dong-Hong Chen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | - Bo-Yu Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, China
| | - Wen-Hui Shen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Institut de Biologie Moléculaire Des Plantes Du CNRS, Université de Strasbourg, 12 Rue Du Général Zimmer, Strasbourg Cedex, France
| | - Ying Ruan
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China.,Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, China
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106
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Ikeuchi M, Iwase A, Rymen B, Lambolez A, Kojima M, Takebayashi Y, Heyman J, Watanabe S, Seo M, De Veylder L, Sakakibara H, Sugimoto K. Wounding Triggers Callus Formation via Dynamic Hormonal and Transcriptional Changes. PLANT PHYSIOLOGY 2017; 175:1158-1174. [PMID: 28904073 PMCID: PMC5664475 DOI: 10.1104/pp.17.01035] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/08/2017] [Indexed: 05/18/2023]
Abstract
Wounding is a primary trigger of organ regeneration, but how wound stress reactivates cell proliferation and promotes cellular reprogramming remains elusive. In this study, we combined transcriptome analysis with quantitative hormonal analysis to investigate how wounding induces callus formation in Arabidopsis (Arabidopsis thaliana). Our time course RNA-seq analysis revealed that wounding induces dynamic transcriptional changes, starting from rapid stress responses followed by the activation of metabolic processes and protein synthesis and subsequent activation of cell cycle regulators. Gene ontology analyses further uncovered that wounding modifies the expression of hormone biosynthesis and response genes, and quantitative analysis of endogenous plant hormones revealed accumulation of cytokinin prior to callus formation. Mutants defective in cytokinin synthesis and signaling display reduced efficiency in callus formation, indicating that de novo synthesis of cytokinin is critical for wound-induced callus formation. We further demonstrate that type-B ARABIDOPSIS RESPONSE REGULATOR-mediated cytokinin signaling regulates the expression of CYCLIN D3;1 (CYCD3;1) and that mutations in CYCD3;1 and its homologs CYCD3;2 and 3 cause defects in callus formation. In addition to these hormone-mediated changes, our transcriptome data uncovered that wounding activates multiple developmental regulators, and we found novel roles of ETHYLENE RESPONSE FACTOR 115 and PLETHORA3 (PLT3), PLT5, and PLT7 in callus generation. All together, these results provide novel mechanistic insights into how wounding reactivates cell proliferation during callus formation.
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Affiliation(s)
- Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Bart Rymen
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Alice Lambolez
- Ecole Normale Supérieure of Paris, Paris cedex 05 75230, France
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Shunsuke Watanabe
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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107
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Hu B, Zhang G, Liu W, Shi J, Wang H, Qi M, Li J, Qin P, Ruan Y, Huang H, Zhang Y, Xu L. Divergent regeneration-competent cells adopt a common mechanism for callus initiation in angiosperms. ACTA ACUST UNITED AC 2017; 4:132-139. [PMID: 28975033 PMCID: PMC5617900 DOI: 10.1002/reg2.82] [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: 11/04/2016] [Revised: 06/13/2017] [Accepted: 06/14/2017] [Indexed: 12/22/2022]
Abstract
In tissue culture, the formation of callus from detached explants is a key step in plant regeneration; however, the regenerative abilities in different species are variable. While nearly all parts of organs of the dicot Arabidopsis thaliana are ready for callus formation, mature regions of organs in monocot rice (Oryza sativa) and other cereals are extremely unresponsive to tissue culture. Whether there is a common molecular mechanism beyond these different regenerative phenomena is unclear. Here we show that the Arabidopsis and rice use different regeneration‐competent cells to initiate callus, whereas the cells all adopt WUSCHEL‐RELATED HOMEOBOX 11 (WOX11) and WOX5 during cell fate transition. Different from Arabidopsis which maintains regeneration‐competent cells in mature organs, rice exhausts those cells during organ maturation, resulting in regenerative inability in mature organs. Our study not only explains this old perplexity in agricultural biotechnology, but also provides common molecular markers for tissue culture of different angiosperm species.
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Affiliation(s)
- Bo Hu
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China.,Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization Hunan Agricultural University Changsha Hunan 410128 China
| | - Guifang Zhang
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China.,University of Chinese Academy of Sciences 19A Yuquan Road Changsha Beijing 100049 China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China
| | - Jianmin Shi
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China.,College of Life and Environment Sciences Shanghai Normal University Shanghai 200234 China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China
| | - Meifang Qi
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China.,University of Chinese Academy of Sciences 19A Yuquan Road Changsha Beijing 100049 China
| | - Jiqin Li
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China
| | - Peng Qin
- Department of Instrument Science and Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Ying Ruan
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization Hunan Agricultural University Changsha Hunan 410128 China
| | - Hai Huang
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China.,University of Chinese Academy of Sciences 19A Yuquan Road Changsha Beijing 100049 China
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108
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Sheng L, Hu X, Du Y, Zhang G, Huang H, Scheres B, Xu L. Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture. Development 2017; 144:3126-3133. [PMID: 28743799 PMCID: PMC5611959 DOI: 10.1242/dev.152132] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/19/2017] [Indexed: 12/30/2022]
Abstract
Lateral roots (LRs), which originate from the growing root, and adventitious roots (ARs), which are formed from non-root organs, are the main contributors to the post-embryonic root system in Arabidopsis. However, our knowledge of how formation of the root system is altered in response to diverse inductive cues is limited. Here, we show that WOX11 contributes to root system plasticity. When seedlings are grown vertically on medium, WOX11 is not expressed in LR founder cells. During AR initiation, WOX11 is expressed in AR founder cells and activates LBD16. LBD16 also functions in LR formation and is activated in that context by ARF7/19 and not by WOX11. This indicates that divergent initial processes that lead to ARs and LRs may converge on a similar mechanism for primordium development. Furthermore, we demonstrated that when plants are grown in soil or upon wounding on medium, the primary root is able to produce both WOX11-mediated and non-WOX11-mediated roots. The discovery of WOX11-mediated root-derived roots reveals a previously uncharacterized pathway that confers plasticity during the generation of root system architecture in response to different inductive cues. Summary: Root system development can respond flexibly to developmental and environmental cues by utilizing WOX11-mediated and non-WOX11-mediated pathways, which converge on a common mechanism for primordium development involving LBD16.
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Affiliation(s)
- Lihong Sheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xiaomei Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yujuan Du
- Plant Developmental Biology Group, Wageningen University Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guifang Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hai Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Ben Scheres
- Plant Developmental Biology Group, Wageningen University Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China .,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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109
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Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1020008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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110
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Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem. Sci Rep 2017; 7:3370. [PMID: 28611454 PMCID: PMC5469831 DOI: 10.1038/s41598-017-03665-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/02/2017] [Indexed: 01/10/2023] Open
Abstract
Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigated the biological relevance of H3K4me3 and H3K27me3 in secondary xylem development using ChIP-seq and their association with transcript levels among other histone modifications in woody and herbaceous models. In developing secondary xylem of the woody model Eucalyptus grandis, H3K4me3 and H3K27me3 genomic spans were distinctly associated with xylogenesis-related processes, with (late) lignification pathways enriched for putative bivalent domains, but not early secondary cell wall polysaccharide deposition. H3K27me3-occupied genes, of which 753 (~31%) are novel targets, were enriched for transcriptional regulation and flower development and had significant preferential expression in roots. Linear regression models of the ChIP-seq profiles predicted ~50% of transcript abundance measured with strand-specific RNA-seq, confirmed in a parallel analysis in Arabidopsis where integration of seven additional histone modifications each contributed smaller proportions of unique information to the predictive models. This study uncovers the biological importance of histone modification antagonism and genomic span in xylogenesis and quantifies for the first time the relative correlations of histone modifications with transcript abundance in plants.
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111
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Shafiq S, Chen C, Yang J, Cheng L, Ma F, Widemann E, Sun Q. DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice. MOLECULAR PLANT 2017; 10:821-833. [PMID: 28412545 DOI: 10.1016/j.molp.2017.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/02/2017] [Accepted: 04/03/2017] [Indexed: 05/21/2023]
Abstract
R-loop structures (RNA:DNA hybrids) have important functions in many biological processes, including transcriptional regulation and genome instability among diverse organisms. DNA topoisomerase 1 (TOP1), an essential manipulator of DNA topology during RNA transcription and DNA replication processes, can prevent R-loop accumulation by removing the positive and negative DNA supercoiling that is made by RNA polymerases during transcription. TOP1 is required for plant development, but little is known about its function in preventing co-transcriptional R-loop accumulation in various biological processes in plants. Here we show that knockdown of OsTOP1 strongly affects rice development, causing defects in root architecture and gravitropism, which are the consequences of misregulation of auxin signaling and transporter genes. We found that R-loops are naturally formed at rice auxin-related gene loci, and overaccumulate when OsTOP1 is knocked down or OsTOP1 protein activity is inhibited. OsTOP1 therefore sets the accurate expression levels of auxin-related genes by preventing the overaccumulation of inherent R-loops. Our data reveal R-loops as important factors in polar auxin transport and plant root development, and highlight that OsTOP1 functions as a key to link transcriptional R-loops with plant hormone signaling, provide new insights into transcriptional regulation of hormone signaling in plants.
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Affiliation(s)
- Sarfraz Shafiq
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Permanent affiliation: Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Cheng
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fei Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Emilie Widemann
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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112
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Nakamura M, Hennig L. Inheritance of vernalization memory at FLOWERING LOCUS C during plant regeneration. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2813-2819. [PMID: 28498984 PMCID: PMC5853441 DOI: 10.1093/jxb/erx154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/20/2017] [Indexed: 05/30/2023]
Abstract
Specific gene states can be transmitted to subsequent cell generations through mitosis involving particular chromatin (epigenetic) states. During reproduction of plants and animals, however, most epigenetic states are reset to allow development to start anew. Flowering is one of the critical developmental steps by which plants acquire their reproductive capacity. This phase transition is controlled by environmental signals and autonomous regulation. The FLOWERING LOCUS C (FLC) gene is a flowering repressor that is epigenetically silenced after long-term exposure to cold, ensuring flowering in the spring season. In Arabidopsis thaliana, epigenetically silenced FLC expression is reset during sexual reproduction. Plants have a remarkable potential to regenerate from somatic cells. However, little is known about whether the regeneration process is similar to sexual reproduction in terms of affecting chromatin states. Here, we tested whether FLC silencing is reset during in vitro regeneration. Transcriptional repression and high H3K27me3 at FLC were both stably transmitted, resulting in early flowering in regenerated shoots. Thus, the silenced epigenetic state of FLC is reset only during sexual reproduction and not during in vitro regeneration. In contrast, the active epigenetic state of FLC was only partially maintained through in vitro reproduction, suggesting that regeneration causes stochastic FLC silencing.
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Affiliation(s)
- Miyuki Nakamura
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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113
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Xiao J, Jin R, Wagner D. Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome Biol 2017; 18:88. [PMID: 28490341 PMCID: PMC5425979 DOI: 10.1186/s13059-017-1228-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Run Jin
- 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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114
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Zhang TQ, Lian H, Zhou CM, Xu L, Jiao Y, Wang JW. A Two-Step Model for de Novo Activation of WUSCHEL during Plant Shoot Regeneration. THE PLANT CELL 2017; 29:1073-1087. [PMID: 28389585 PMCID: PMC5466026 DOI: 10.1105/tpc.16.00863] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/17/2017] [Accepted: 04/05/2017] [Indexed: 05/18/2023]
Abstract
Plant cells are totipotent and competent to regenerate from differentiated organs. It has been known for six decades that cytokinin-rich medium induces shoot regeneration from callus cells. However, the underlying molecular mechanism remains elusive. The homeodomain transcription factor WUSCHEL (WUS) is essential for de novo establishment of the shoot stem cell niche in Arabidopsis thaliana We found that WUS-positive (WUS+) cells mark the shoot progenitor region during regeneration. A cytokinin-rich environment initially promotes the removal of the repressive histone mark H3K27me3 at the WUS locus in a cell cycle-dependent manner. Subsequently, the B-type ARABIDOPSIS RESPONSE REGULATORs (ARRs) ARR1, ARR2, ARR10, and ARR12, which function as transcriptional activators in the cytokinin signaling pathway, spatially activate WUS expression through binding with microRNA165/6-targeted HD-ZIP III transcription factors. Thus, our results provide important insights into the molecular framework for cytokinin-directed shoot regeneration and reveal a two-step mechanism for de novo activation of WUS.
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Affiliation(s)
- Tian-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, P.R. China
- University of Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Heng Lian
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, P.R. China
| | - Chuan-Miao Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, P.R. China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, P.R. China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- National Center for Plant Gene Research, Beijing 100101, P.R. China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, P.R. China
- ShanghaiTech University, Shanghai 200031, P.R. China
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115
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Li D, Liu J, Liu W, Li G, Yang Z, Qin P, Xu L. The ISWI remodeler in plants: protein complexes, biochemical functions, and developmental roles. Chromosoma 2017; 126:365-373. [PMID: 28213686 DOI: 10.1007/s00412-017-0626-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/15/2017] [Accepted: 01/26/2017] [Indexed: 12/01/2022]
Abstract
Imitation Switch (ISWI) is a member of the ATP-dependent chromatin remodeling factor family, whose members move or restructure nucleosomes using energy derived from ATP hydrolysis. ISWI proteins are conserved in eukaryotes and usually form complexes with DDT (DNA-binding homeobox and different transcription factors)-domain proteins. Here, we review recent research on ISWI in the model plant Arabidopsis thaliana (AtISWI). AtISWI forms complexes with AtDDT-domain proteins, many of which have domain structures that differ from those of DDT-domain proteins in yeast and animals. This might suggest that plant ISWI complexes have unique roles. In vivo studies have shown that AtISWI is involved in the formation of the evenly spaced pattern of nucleosome arrangement in gene bodies-this pattern is associated with high transcriptional levels of genes. In addition, AtISWI and the AtDDT-domain protein RINGLET (RLT) are involved in many developmental processes in A. thaliana, including meristem fate transition and organ formation. Studies on the functions of AtISWI may shed light on how chromatin remodeling functions in plants and also provide new information about the evolution of ISWI remodeling complexes in eukaryotes.
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Affiliation(s)
- Dongjie Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.,College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jie Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guang Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhongnan Yang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Peng Qin
- Department of Instrumentation Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
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116
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Rosspopoff O, Chelysheva L, Saffar J, Lecorgne L, Gey D, Caillieux E, Colot V, Roudier F, Hilson P, Berthomé R, Da Costa M, Rech P. Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development. Development 2017; 144:1187-1200. [PMID: 28174250 DOI: 10.1242/dev.142570] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/26/2017] [Indexed: 02/01/2023]
Abstract
To understand how the identity of an organ can be switched, we studied the transformation of lateral root primordia (LRP) into shoot meristems in Arabidopsis root segments. In this system, the cytokinin-induced conversion does not involve the formation of callus-like structures. Detailed analysis showed that the conversion sequence starts with a mitotic pause and is concomitant with the differential expression of regulators of root and shoot development. The conversion requires the presence of apical stem cells, and only LRP at stages VI or VII can be switched. It is engaged as soon as cell divisions resume because their position and orientation differ in the converting organ compared with the undisturbed emerging LRP. By alternating auxin and cytokinin treatments, we showed that the root and shoot organogenetic programs are remarkably plastic, as the status of the same plant stem cell niche can be reversed repeatedly within a set developmental window. Thus, the networks at play in the meristem of a root can morph in the span of a couple of cell division cycles into those of a shoot, and back, through transdifferentiation.
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Affiliation(s)
- Olga Rosspopoff
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France.,Sorbonne Universités, UPCM Université Paris 06, UFR 927, Paris F-75005, France
| | - Liudmila Chelysheva
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France
| | - Julie Saffar
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France.,Université Paris-Diderot, Sorbonne Paris Cité, Paris F-75205, France
| | - Lena Lecorgne
- Sorbonne Universités, UPCM Université Paris 06, UFR 927, Paris F-75005, France
| | - Delphine Gey
- Muséum d'Histoire Naturelle, UMS 2700, OMSI, Paris F-75231, France
| | - Erwann Caillieux
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Paris F-75005, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Paris F-75005, France
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Paris F-75005, France
| | - Pierre Hilson
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France
| | - Richard Berthomé
- LIPM, Université de Toulouse, INRA, CNRS, INPT, Castanet-Tolosan F-31126, France.,CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR2594, Castanet-Tolosan 31326, France.,Plant Genomics Research Unit, UMR INRA 1165 - CNRS 8114 - UEVE, 2, CP5708, Evry Cedex 91057, France
| | - Marco Da Costa
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France .,Sorbonne Universités, UPCM Université Paris 06, UFR 927, Paris F-75005, France
| | - Philippe Rech
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France .,Sorbonne Universités, UPCM Université Paris 06, UFR 927, Paris F-75005, France
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117
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Birnbaum KD, Roudier F. Epigenetic memory and cell fate reprogramming in plants. ACTA ACUST UNITED AC 2017; 4:15-20. [PMID: 28316791 PMCID: PMC5350078 DOI: 10.1002/reg2.73] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 12/30/2022]
Abstract
Plants have a high intrinsic capacity to regenerate from adult tissues, with the ability to reprogram adult cell fates. In contrast, epigenetic mechanisms have the potential to stabilize cell identity and maintain tissue organization. The question is whether epigenetic memory creates a barrier to reprogramming that needs to be erased or circumvented in plant regeneration. Early evidence suggests that, while chromatin dynamics impact gene expression in the meristem, a lasting constraint on cell fate is not established until late stages of plant cell differentiation. It is not yet clear whether the plasticity of plant cells arises from the ability of cells to erase identity memory or to deploy cells that may exhibit cellular specialization but still lack an epigenetic restriction on cell fate alteration.
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Affiliation(s)
- Kenneth D Birnbaum
- Center for Genomics and Systems Biology New York University 12 Waverly Place, New York NY 10003 USA
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR 8197 Institut National de la Santé et de la Recherche Médicale (INSERM) U1024 Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05 France; Laboratoire de Reproduction et Développement des Plantes, Centre National de la Recherche Scientifique (CNRS) UMR 5667, Institut National de la Recherche Agronomique (INRA) UMR 879, Ecole Normale Supérieure de LyonUniversité Lyon 1 (UCBL) 46 Allée d'Italie, 69364 Lyon Cedex 07 France
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118
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Mozgová I, Muñoz-Viana R, Hennig L. PRC2 Represses Hormone-Induced Somatic Embryogenesis in Vegetative Tissue of Arabidopsis thaliana. PLoS Genet 2017; 13:e1006562. [PMID: 28095419 PMCID: PMC5283764 DOI: 10.1371/journal.pgen.1006562] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 01/31/2017] [Accepted: 01/02/2017] [Indexed: 01/18/2023] Open
Abstract
Many plant cells can be reprogrammed into a pluripotent state that allows ectopic organ development. Inducing totipotent states to stimulate somatic embryo (SE) development is, however, challenging due to insufficient understanding of molecular barriers that prevent somatic cell dedifferentiation. Here we show that Polycomb repressive complex 2 (PRC2)-activity imposes a barrier to hormone-mediated transcriptional reprogramming towards somatic embryogenesis in vegetative tissue of Arabidopsis thaliana. We identify factors that enable SE development in PRC2-depleted shoot and root tissue and demonstrate that the establishment of embryogenic potential is marked by ectopic co-activation of crucial developmental regulators that specify shoot, root and embryo identity. Using inducible activation of PRC2 in PRC2-depleted cells, we demonstrate that transient reduction of PRC2 activity is sufficient for SE formation. We suggest that modulation of PRC2 activity in plant vegetative tissue combined with targeted activation of developmental pathways will open possibilities for novel approaches to cell reprogramming. Somatic embryogenesis provides the strongest support for plant cell totipotency but reprogramming of non-reproductive tissue is problematic or even impossible in many plant species. Here we show that the activity of Polycomb Repressive Complex 2 (PRC2) constitutes a major barrier to hormone-mediated establishment of embryogenic competence in plant vegetative tissue. We identify a conservative set of transcription factors whose expression coincides with the establishment of embryogenic competence in vegetative tissue, among which are key developmental regulators of root, shoot and embryo development. We show that lowering the PRC2-imposed barrier combined with activating hormone treatments establishes embryogenic competence in different tissue types, which opens possibilities for novel strategies to plant cell identity reprogramming.
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Affiliation(s)
- Iva Mozgová
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Institute of Microbiology, Centre Algatech, Opatovický mlýn, Třeboň, Czech Republic
- * E-mail: (IM); (LH)
| | - Rafael Muñoz-Viana
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- * E-mail: (IM); (LH)
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119
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Yu J, Liu W, Liu J, Qin P, Xu L. Auxin Control of Root Organogenesis from Callus in Tissue Culture. FRONTIERS IN PLANT SCIENCE 2017; 8:1385. [PMID: 28848586 PMCID: PMC5550681 DOI: 10.3389/fpls.2017.01385] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 07/25/2017] [Indexed: 05/11/2023]
Affiliation(s)
- Jie Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Jie Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- University of Chinese Academy of SciencesBeijing, China
| | - Peng Qin
- Department of Instrument Science and Engineering, Shanghai Jiao Tong UniversityShanghai, China
- *Correspondence: Peng Qin
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- University of Chinese Academy of SciencesBeijing, China
- Lin Xu
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120
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Lebedeva MA, Tvorogova VE, Tikhodeyev ON. Epigenetic mechanisms and their role in plant development. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795417090083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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121
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Liu H, Ma X, Han HN, Hao YJ, Zhang XS. AtPRMT5 Regulates Shoot Regeneration through Mediating Histone H4R3 Dimethylation on KRPs and Pre-mRNA Splicing of RKP in Arabidopsis. MOLECULAR PLANT 2016; 9:1634-1646. [PMID: 27780782 DOI: 10.1016/j.molp.2016.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/25/2023]
Abstract
Protein arginine methylation plays important roles in diverse biological processes, but its role in regulating shoot regeneration remains elusive. In this study, we characterized the function of the protein arginine methyltransferase AtPRMT5 during de novo shoot regeneration in Arabidopsis. AtPRMT5 encodes a type II protein arginine methyltransferase that methylates proteins, including histones and RNA splicing factors. The frequency of shoot regeneration and the number of shoots per callus were decreased in the atprmt5 mutant compared with those in the wild type. Chromatin immunoprecipitation analysis revealed that AtPRMT5 targets KIP-RELATED PROTEINs (KRPs), which encode the cyclin-dependent kinase inhibitors that repress the cell cycle. During shoot regeneration, the KRP transcript level increased in the atprmt5 mutant, which resulted from reduced histone H4R3 methylation in the KRP promoter. Overexpression of KRP significantly reduced the frequency of shoot regeneration and shoot number per callus. Furthermore, abnormal pre-mRNA splicing in the gene RELATED TO KPC1 (RKP), which encodes an ubiquitin E3 ligase, was detected in the atprmt5 mutant. RKP functions in regulating KRP protein degradation, and mutation in RKP inhibited shoot regeneration. Thus, AtPRMT5 regulated shoot regeneration through histone modification-mediated KRP transcription and RKP pre-mRNA splicing. Our findings provide new insights into the function of protein arginine methylation in de novo shoot regeneration.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xu Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Hua Nan Han
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yu Jin Hao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China.
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122
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Hu X, Xu L. Transcription Factors WOX11/12 Directly Activate WOX5/7 to Promote Root Primordia Initiation and Organogenesis. PLANT PHYSIOLOGY 2016; 172:2363-2373. [PMID: 27784768 PMCID: PMC5129711 DOI: 10.1104/pp.16.01067] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/25/2016] [Indexed: 05/18/2023]
Abstract
De novo organogenesis, which gives rise to adventitious roots and shoots, is a type of plant regeneration for survival after wounding. In Arabidopsis (Arabidopsis thaliana), two main cell fate transition steps are required to establish the root primordium during de novo root organogenesis from leaf explants. The first step from regeneration-competent cells to root founder cells involves activation of WUSCHEL-RELATED HOMEOBOX11 (WOX11) and WOX12 (WOX11/12) expression by auxin. However, the molecular mechanism controlling the second step of fate transition from root founder cells to root primordium is poorly understood. In this study, we show that the expression levels of WOX11/12 decrease while those of WOX5 and 7 (WOX5/7) increase during the transition from root founder cells to the root primordium. WOX11/12 function genetically upstream of WOX5/7, and the WOX11/12 proteins directly bind to the promoters of WOX5/7 to activate their transcription. Mutations in WOX5/7 result in defective primordium formation. Overall, our data indicate that the expression switch from WOX11/12 to WOX5/7 is critical for initiation of the root primordium during de novo root organogenesis.
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Affiliation(s)
- Xiaomei Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (X.H., L.X.); and
- University of Chinese Academy of Sciences, Beijing, 100049, China (X.H.)
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (X.H., L.X.); and
- University of Chinese Academy of Sciences, Beijing, 100049, China (X.H.)
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123
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Liu X, Wei X, Sheng Z, Jiao G, Tang S, Luo J, Hu P. Polycomb Protein OsFIE2 Affects Plant Height and Grain Yield in Rice. PLoS One 2016; 11:e0164748. [PMID: 27764161 PMCID: PMC5072591 DOI: 10.1371/journal.pone.0164748] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 09/29/2016] [Indexed: 01/15/2023] Open
Abstract
Polycomb group (PcG) proteins have been shown to affect growth and development in plants. To further elucidate their role in these processes in rice, we isolated and characterized a rice mutant which exhibits dwarfism, reduced seed setting rate, defective floral organ, and small grains. Map-based cloning revealed that abnormal phenotypes were attributed to a mutation of the Fertilization Independent Endosperm 2 (OsFIE2) protein, which belongs to the PcG protein family. So we named the mutant as osfie2-1. Histological analysis revealed that the number of longitudinal cells in the internodes decreased in osfie2-1, and that lateral cell layer of the internodes was markedly thinner than wild-type. In addition, compared to wild-type, the number of large and small vascular bundles decreased in osfie2-1, as well as cell number and cell size in spikelet hulls. OsFIE2 is expressed in most tissues and the coded protein localizes in both nucleus and cytoplasm. Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that OsFIE2 interacts with OsiEZ1 which encodes an enhancer of zeste protein previously identified as a histone methylation enzyme. RNA sequencing-based transcriptome profiling and qRT-PCR analysis revealed that some homeotic genes and genes involved in endosperm starch synthesis, cell division/expansion and hormone synthesis and signaling are differentially expressed between osfie2-1 and wild-type. In addition, the contents of IAA, GA3, ABA, JA and SA in osfie2-1 are significantly different from those in wild-type. Taken together, these results indicate that OsFIE2 plays an important role in the regulation of plant height and grain yield in rice.
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Affiliation(s)
- Xianbo Liu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ju Luo
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 310006, China
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124
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Chen L, Sun B, Xu L, Liu W. Wound signaling: The missing link in plant regeneration. PLANT SIGNALING & BEHAVIOR 2016; 11:e1238548. [PMID: 27662421 PMCID: PMC5257141 DOI: 10.1080/15592324.2016.1238548] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 05/21/2023]
Abstract
Wounding is the first event that occurs in plant regeneration. However, wound signaling in plant regeneration is barely understood. Using a simple system of de novo root organogenesis from Arabidopsis thaliana leaf explants, we analyzed the genes downstream of wound signaling. Leaf explants may produce at least two kinds of wound signals to trigger short-term and long-term wound signaling. Short-term wound signaling is primarily involved in controlling auxin behavior and the fate transition of regeneration-competent cells, while long-term wound signaling mainly modulates the cellular environment at the wound site and maintains the auxin level in regeneration-competent cells. YUCCA (YUC) genes, which are involved in auxin biogenesis, are targets of short-term wound signaling in mesophyll cells and of long-term wound signaling in regeneration-competent cells. The expression patterns of YUCs provide important information about the molecular basis of wound signaling in plant regeneration.
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Affiliation(s)
- Lyuqin Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Beibei Sun
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- CONTACT Lin Xu ; Wu Liu
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- CONTACT Lin Xu ; Wu Liu
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125
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de Lucas M, Pu L, Turco G, Gaudinier A, Morao AK, Harashima H, Kim D, Ron M, Sugimoto K, Roudier F, Brady SM. Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation. THE PLANT CELL 2016; 28:2616-2631. [PMID: 27650334 PMCID: PMC5134969 DOI: 10.1105/tpc.15.00744] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 08/29/2016] [Accepted: 09/14/2016] [Indexed: 05/21/2023]
Abstract
Spatiotemporal regulation of transcription is fine-tuned at multiple levels, including chromatin compaction. Polycomb Repressive Complex 2 (PRC2) catalyzes the trimethylation of Histone 3 at lysine 27 (H3K27me3), which is the hallmark of a repressive chromatin state. Multiple PRC2 complexes have been reported in Arabidopsis thaliana to control the expression of genes involved in developmental transitions and maintenance of organ identity. Here, we show that PRC2 member genes display complex spatiotemporal gene expression patterns and function in root meristem and vascular cell proliferation and specification. Furthermore, PRC2 gene expression patterns correspond with vascular and nonvascular tissue-specific H3K27me3-marked genes. This tissue-specific repression via H3K27me3 regulates the balance between cell proliferation and differentiation. Using enhanced yeast one-hybrid analysis, upstream regulators of the PRC2 member genes are identified, and genetic analysis demonstrates that transcriptional regulation of some PRC2 genes plays an important role in determining PRC2 spatiotemporal activity within a developing organ.
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Affiliation(s)
- Miguel de Lucas
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Li Pu
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Gina Turco
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France
| | - Hirofumi Harashima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Dahae Kim
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mily Ron
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Francois Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
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126
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Kral N, Hanna Ougolnikova A, Sena G. Externally imposed electric field enhances plant root tip regeneration. ACTA ACUST UNITED AC 2016; 3:156-67. [PMID: 27606066 PMCID: PMC5011479 DOI: 10.1002/reg2.59] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/24/2016] [Accepted: 06/29/2016] [Indexed: 11/12/2022]
Abstract
In plants, shoot and root regeneration can be induced in the distinctive conditions of tissue culture (in vitro) but is also observed in intact individuals (in planta) recovering from tissue damage. Roots, for example, can regenerate their fully excised meristems in planta, even in mutants with impaired apical stem cell niches. Unfortunately, to date a comprehensive understanding of regeneration in plants is still missing. Here, we provide evidence that an imposed electric field can perturb apical root regeneration in Arabidopsis. Crucially, we explored both spatial and temporal competences of the stump to respond to electrical stimulation, by varying respectively the position of the cut and the time interval between excision and stimulation. Our data indicate that a brief pulse of an electric field parallel to the root is sufficient to increase by up to two‐fold the probability of its regeneration, and to perturb the local distribution of the hormone auxin, as well as cell division regulation. Remarkably, the orientation of the root towards the anode or the cathode is shown to play a role.
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Affiliation(s)
- Nicolas Kral
- Department of Life Sciences Imperial College London London UK
| | | | - Giovanni Sena
- Department of Life Sciences Imperial College London London UK
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127
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Kareem A, Radhakrishnan D, Sondhi Y, Aiyaz M, Roy MV, Sugimoto K, Prasad K. De novo assembly of plant body plan: a step ahead of Deadpool. REGENERATION (OXFORD, ENGLAND) 2016; 3:182-197. [PMID: 27800169 PMCID: PMC5084358 DOI: 10.1002/reg2.68] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/12/2016] [Accepted: 08/24/2016] [Indexed: 12/20/2022]
Abstract
While in the movie Deadpool it is possible for a human to recreate an arm from scratch, in reality plants can even surpass that. Not only can they regenerate lost parts, but also the whole plant body can be reborn from a few existing cells. Despite the decades old realization that plant cells possess the ability to regenerate a complete shoot and root system, it is only now that the underlying mechanisms are being unraveled. De novo plant regeneration involves the initiation of regenerative mass, acquisition of the pluripotent state, reconstitution of stem cells and assembly of regulatory interactions. Recent studies have furthered our understanding on the making of a complete plant system in the absence of embryonic positional cues. We review the recent studies probing the molecular mechanisms of de novo plant regeneration in response to external inductive cues and our current knowledge of direct reprogramming of root to shoot and vice versa. We further discuss how de novo regeneration can be exploited to meet the demands of green culture industries and to serve as a general model to address the fundamental questions of regeneration across the plant kingdom.
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Affiliation(s)
- Abdul Kareem
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Dhanya Radhakrishnan
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Yash Sondhi
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Mohammed Aiyaz
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Merin V. Roy
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Kaoru Sugimoto
- Department of Applied Biological ScienceFaculty of Science and TechnologyTokyo University of Science2641 YamazakiNodaChiba278‐8510Japan
| | - Kalika Prasad
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
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128
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Chen L, Tong J, Xiao L, Ruan Y, Liu J, Zeng M, Huang H, Wang JW, Xu L. YUCCA-mediated auxin biogenesis is required for cell fate transition occurring during de novo root organogenesis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4273-84. [PMID: 27255928 PMCID: PMC5301932 DOI: 10.1093/jxb/erw213] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Many plant organs have the ability to regenerate a new plant after detachment or wounding via de novo organogenesis. During de novo root organogenesis from Arabidopsis thaliana leaf explants, endogenic auxin is essential for the fate transition of regeneration-competent cells to become root founder cells via activation of WUSCHEL-RELATED HOMEOBOX 11 (WOX11). However, the molecular events from leaf explant detachment to auxin-mediated cell fate transition are poorly understood. In this study, we used an assay to determine the concentration of indole-3-acetic acid (IAA) to provide direct evidence that auxin is produced after leaf explant detachment, a process that involves YUCCA (YUC)-mediated auxin biogenesis. Inhibition of YUC prevents expression of WOX11 and fate transition of competent cells, resulting in the blocking of rooting. Further analysis showed that YUC1 and YUC4 act quickly (within 4 hours) in response to wounding after detachment in both light and dark conditions and promote auxin biogenesis in both mesophyll and competent cells, whereas YUC5, YUC8, and YUC9 primarily respond in dark conditions. In addition, YUC2 and YUC6 contribute to rooting by providing a basal auxin level in the leaf. Overall, our study indicates that YUC genes exhibit a division of labour during de novo root organogenesis from leaf explants in response to multiple signals.
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Affiliation(s)
- Lyuqin Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jianhua Tong
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Langtao Xiao
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Ying Ruan
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jingchun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Minhuan Zeng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Hai Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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129
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Lee K, Park OS, Seo PJ. RNA-Seq Analysis of the Arabidopsis Transcriptome in Pluripotent Calli. Mol Cells 2016; 39:484-94. [PMID: 27215197 PMCID: PMC4916400 DOI: 10.14348/molcells.2016.0049] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 11/27/2022] Open
Abstract
Plant cells have a remarkable ability to induce pluripotent cell masses and regenerate whole plant organs under the appropriate culture conditions. Although the in vitro regeneration system is widely applied to manipulate agronomic traits, an understanding of the molecular mechanisms underlying callus formation is starting to emerge. Here, we performed genome-wide transcriptome profiling of wild-type leaves and leaf explant-derived calli for comparison and identified 10,405 differentially expressed genes (> two-fold change). In addition to the well-defined signaling pathways involved in callus formation, we uncovered additional biological processes that may contribute to robust cellular dedifferentiation. Particular emphasis is placed on molecular components involved in leaf development, circadian clock, stress and hormone signaling, carbohydrate metabolism, and chromatin organization. Genetic and pharmacological analyses further supported that homeostasis of clock activity and stress signaling is crucial for proper callus induction. In addition, gibberellic acid (GA) and brassinosteroid (BR) signaling also participates in intricate cellular reprogramming. Collectively, our findings indicate that multiple signaling pathways are intertwined to allow reversible transition of cellular differentiation and dedifferentiation.
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Affiliation(s)
- Kyounghee Lee
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756,
Korea
| | - Ok-Sun Park
- Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756,
Korea
| | - Pil Joon Seo
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756,
Korea
- Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756,
Korea
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130
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Stem cell lineage in body layer specialization and vascular patterning of rice root and leaf. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-015-0849-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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131
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Liu J, Deng S, Wang H, Ye J, Wu HW, Sun HX, Chua NH. CURLY LEAF Regulates Gene Sets Coordinating Seed Size and Lipid Biosynthesis. PLANT PHYSIOLOGY 2016; 171:424-36. [PMID: 26945048 PMCID: PMC4854673 DOI: 10.1104/pp.15.01335] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 03/03/2016] [Indexed: 05/05/2023]
Abstract
CURLY LEAF (CLF), a histone methyltransferase of Polycomb Repressive Complex 2 (PRC2) for trimethylation of histone H3 Lys 27 (H3K27me3), has been thought as a negative regulator controlling mainly postgermination growth in Arabidopsis (Arabidopsis thaliana). Approximately 14% to 29% of genic regions are decorated by H3K27me3 in the Arabidopsis genome; however, transcriptional repression activities of PRC2 on a majority of these regions remain unclear. Here, by analysis of transcriptome profiles, we found that approximately 11.6% genes in the Arabidopsis genome were repressed by CLF in various organs. Unexpectedly, approximately 54% of these genes were preferentially repressed in siliques. Further analyses of 118 transcriptome datasets uncovered a group of genes that was preferentially expressed and repressed by CLF in embryos at the mature-green stage. This observation suggests that CLF mediates a large-scale H3K27me3 programming/reprogramming event during embryonic development. Plants of clf-28 produced bigger and heavier seeds with higher oil content, larger oil bodies, and altered long-chain fatty acid composition compared with wild type. Around 46% of CLF-repressed genes were associated with H3K27me3 marks; moreover, we verified histone modification and transcriptional repression by CLF on regulatory genes. Our results suggest that CLF silences specific gene expression modules. Genes operating within a module have various molecular functions, but they cooperate to regulate a similar physiological function during embryo development.
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Affiliation(s)
- Jun Liu
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Shulin Deng
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Huan Wang
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Jian Ye
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Hui-Wen Wu
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Hai-Xi Sun
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
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132
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Ikeuchi M, Ogawa Y, Iwase A, Sugimoto K. Plant regeneration: cellular origins and molecular mechanisms. Development 2016; 143:1442-51. [DOI: 10.1242/dev.134668] [Citation(s) in RCA: 276] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Compared with animals, plants generally possess a high degree of developmental plasticity and display various types of tissue or organ regeneration. This regenerative capacity can be enhanced by exogenously supplied plant hormones in vitro, wherein the balance between auxin and cytokinin determines the developmental fate of regenerating organs. Accumulating evidence suggests that some forms of plant regeneration involve reprogramming of differentiated somatic cells, whereas others are induced through the activation of relatively undifferentiated cells in somatic tissues. We summarize the current understanding of how plants control various types of regeneration and discuss how developmental and environmental constraints influence these regulatory mechanisms.
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Affiliation(s)
- Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yoichi Ogawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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133
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Zeng J, Ding Q, Fukuda H, He XQ. Fertilization Independent Endosperm genes repress NbGH3.6 and regulate the auxin level during shoot development in Nicotiana benthamiana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2207-17. [PMID: 26873977 PMCID: PMC4809283 DOI: 10.1093/jxb/erw024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The Fertilization Independent Endosperm (FIE) gene is required to restrict endosperm development without fertilization, and it represses flowering during embryo and seedling development in Arabidopsis thaliana However, the regulatory mechanism of the FIE gene in postembryonic shoot development is not well understood. Silencing of Nicotiana benthamiana homologues of the FIE gene, NbFIE1 and NbFIE2, resulted in the enhanced outgrowth of axillary buds and the impairment of secondary xylem differentiation. RNA sequencing analysis found that one of the auxin-responsive GRETCHEN HAGEN 3(GH3) family genes, NbGH3.6, was upregulated and maintained a high expression during the time course of silencing NbFIE genes. Chromatin immunoprecipiation (ChIP)-PCR results showed a lack of H3K27me3 marks on NbGH3.6 chromatin in NbFIE-silenced plants compared with negative control plants, indicating that NbGH3.6 was a direct target of NbFIE genes during postembryonic shoot development. Moreover, the free IAA content was reduced significantly in NbFIE-silenced plants, which might cause the enhanced outgrowth of axillary buds as well as impaired secondary xylem differentiation. These results clearly indicated that NbGH3.6 was a primary target of NbFIE genes during postembryonic shoot development, and NbFIE genes regulated axillary bud growth and secondary xylem formation through tuning endogenous auxin homeostasis, possibly by regulating the expression of the NbGH3.6 gene.
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Affiliation(s)
- Jun Zeng
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Qi Ding
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Xin-Qiang He
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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134
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Chen X, Cheng J, Chen L, Zhang G, Huang H, Zhang Y, Xu L. Auxin-Independent NAC Pathway Acts in Response to Explant-Specific Wounding and Promotes Root Tip Emergence during de Novo Root Organogenesis in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:2136-45. [PMID: 26850273 PMCID: PMC4825153 DOI: 10.1104/pp.15.01733] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/02/2016] [Indexed: 05/21/2023]
Abstract
Plants have powerful regenerative abilities that allow them to recover from damage and survive in nature. De novo organogenesis is one type of plant regeneration in which adventitious roots and shoots are produced from wounded and detached organs. By studying de novo root organogenesis using leaf explants of Arabidopsis (Arabidopsis thaliana), we previously suggested that wounding is the first event that provides signals to trigger the whole regenerative process. However, our knowledge of the role of wounding in regeneration remains limited. In this study, we show that wounding not only triggers the auxin-mediated fate transition of regeneration-competent cells, but also induces the NAC pathway for root tip emergence. The NAC1 transcription factor gene was specifically expressed in response to wounding in the leaf explant, but not in the wounded leaf residue of the source plant. Inhibition of the NAC1 pathway severely affected the emergence of adventitious root tips. However, the NAC1 pathway functioned independently of auxin-mediated cell fate transition and regulates expression of CEP genes, which encode proteins that might have a role in degradation of extensin proteins in the cell wall. Overall, our results suggest that wounding has multiple roles in de novo root organogenesis and that NAC1 acts as one downstream branch in regulating the cellular environment for organ emergence.
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Affiliation(s)
- Xiaodong Chen
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingfei Cheng
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lyuqin Chen
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guifang Zhang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hai Huang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yijing Zhang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lin Xu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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135
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Lee K, Park OS, Jung SJ, Seo PJ. Histone deacetylation-mediated cellular dedifferentiation in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2016; 191:95-100. [PMID: 26724747 DOI: 10.1016/j.jplph.2015.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/24/2015] [Accepted: 12/11/2015] [Indexed: 05/20/2023]
Abstract
Chromatin structure determines the accessibility of transcriptional regulators to target DNA and contributes to regulation of gene expression. Posttranslational modifications of core histone proteins underlie the reversible changes in chromatin structure. Epigenetic regulation is closely associated with cellular differentiation. Consistently, we found that histone deacetylation is required for callus formation from leaf explants in Arabidopsis . Treatment with trichostatin A (TSA) led to defective callus formation on callus-inducing medium (CIM). Gene expression profiling revealed that a subset of HDAC genes, including HISTONE DEACETYLASE 9 (HDA9), HD-TUINS PROTEIN 1 (HDT1), HDT2, HDT4, and SIRTUIN 1 (SRT1), was significantly up-regulated in calli. In support of this, genetic mutations of HDA9 or HDT1 showed reduced capability of callus formation, probably owing to their roles in regulating auxin and embryonic and meristematic developmental signaling. Taken together, our findings suggest that histone deacetylation is intimately associated with the leaf-to-callus transition, and multiple signaling pathways are controlled by means of histone modification during cellular dedifferentiation.
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Affiliation(s)
- Kyounghee Lee
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Ok-Sun Park
- Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Su-Jin Jung
- Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Pil Joon Seo
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, Republic of Korea; Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea.
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136
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Wang H, Liu C, Cheng J, Liu J, Zhang L, He C, Shen WH, Jin H, Xu L, Zhang Y. Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements. PLoS Genet 2016; 12:e1005771. [PMID: 26760036 PMCID: PMC4711971 DOI: 10.1371/journal.pgen.1005771] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 12/04/2015] [Indexed: 11/19/2022] Open
Abstract
Polycomb repressive complexes (PRCs) play crucial roles in transcriptional repression and developmental regulation in both plants and animals. In plants, depletion of different members of PRCs causes both overlapping and unique phenotypic defects. However, the underlying molecular mechanism determining the target specificity and functional diversity is not sufficiently characterized. Here, we quantitatively compared changes of tri-methylation at H3K27 in Arabidopsis mutants deprived of various key PRC components. We show that CURLY LEAF (CLF), a major catalytic subunit of PRC2, coordinates with different members of PRC1 in suppression of distinct plant developmental programs. We found that expression of flower development genes is repressed in seedlings preferentially via non-redundant role of CLF, which specifically associated with LIKE HETEROCHROMATIN PROTEIN1 (LHP1). In contrast, expression of embryo development genes is repressed by PRC1-catalytic core subunits AtBMI1 and AtRING1 in common with PRC2-catalytic enzymes CLF or SWINGER (SWN). This context-dependent role of CLF corresponds well with the change in H3K27me3 profiles, and is remarkably associated with differential co-occupancy of binding motifs of transcription factors (TFs), including MADS box and ABA-related factors. We propose that different combinations of PRC members distinctively regulate different developmental programs, and their target specificity is modulated by specific TFs. Polycomb group proteins (PcGs) are essential for development in both animals and plants. Studies in plants are advantageous for elucidation of specific effects of PcGs during development, since most PcG mutants are viable in plants but not in animals. Previous efforts in genetic study of plant PcGs revealed that different PcGs have both common and unique effects on plant development, but the mechanisms underlying the specific regulation of different developmental programs by PcGs are still far from clear. In this study, we quantitatively compared the change in H3K27me3 and gene expression profiles between mutants of key PcG members on a genome-wide scale in Arabidopsis seedlings, and successfully unraveled different developmental programs that are specifically regulated by different combinations of PcGs. This context specific effect of PcGs is closely associated with different sets of transcription factor binding motifs. Together, we revealed on a genome-wide scale that different combinations of PcGs, as well as their association with the binding sites of different TFs, serve to explain the specific regulation of different developmental programs by PcGs.
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Affiliation(s)
- Hua Wang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chunmei Liu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jingfei Cheng
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian Liu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Chongsheng He
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Hong Jin
- Department of Chemistry, Fudan University, Shanghai, China
- Institute of Biomedical Science, Fudan University, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
| | - Lin Xu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
| | - Yijing Zhang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
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137
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Ikeuchi M, Iwase A, Sugimoto K. Control of plant cell differentiation by histone modification and DNA methylation. CURRENT OPINION IN PLANT BIOLOGY 2015; 28:60-7. [PMID: 26454697 DOI: 10.1016/j.pbi.2015.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/03/2015] [Accepted: 09/05/2015] [Indexed: 05/10/2023]
Abstract
How cells differentiate and acquire diverse arrays of determined states in multicellular organisms is a fundamental and yet unanswered question in biology. Molecular genetic studies over the last few decades have identified many transcriptional regulators that activate or repress gene expression to promote cell differentiation in plant development. What has recently emerged as an additional important regulatory layer is the control at the epigenetic level by which locus-specific DNA methylation and histone modification alter the chromatin state and limit the expression of key developmental regulators to specific windows of time and space. Accumulating evidence suggests that histone acetylation is commonly linked with active transcription and this mechanism is adopted to control sequential progression of cell differentiation. Histone H3 trimethylation at lysine 27 and DNA methylation are both associated with gene repression, and these mechanisms are often utilised to promote and/or maintain the differentiated status of plant cells.
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Affiliation(s)
- Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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138
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King GJ. Crop epigenetics and the molecular hardware of genotype × environment interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:968. [PMID: 26594221 PMCID: PMC4635209 DOI: 10.3389/fpls.2015.00968] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/22/2015] [Indexed: 05/04/2023]
Abstract
Crop plants encounter thermal environments which fluctuate on a diurnal and seasonal basis. Future climate resilient cultivars will need to respond to thermal profiles reflecting more variable conditions, and harness plasticity that involves regulation of epigenetic processes and complex genomic regulatory networks. Compartmentalization within plant cells insulates the genomic central processing unit within the interphase nucleus. This review addresses the properties of the chromatin hardware in which the genome is embedded, focusing on the biophysical and thermodynamic properties of DNA, histones and nucleosomes. It explores the consequences of thermal and ionic variation on the biophysical behavior of epigenetic marks such as DNA cytosine methylation (5mC), and histone variants such as H2A.Z, and how these contribute to maintenance of chromatin integrity in the nucleus, while enabling specific subsets of genes to be regulated. Information is drawn from theoretical molecular in vitro studies as well as model and crop plants and incorporates recent insights into the role epigenetic processes play in mediating between environmental signals and genomic regulation. A preliminary speculative framework is outlined, based on the evidence of what appears to be a cohesive set of interactions at molecular, biophysical and electrostatic level between the various components contributing to chromatin conformation and dynamics. It proposes that within plant nuclei, general and localized ionic homeostasis plays an important role in maintaining chromatin conformation, whilst maintaining complex genomic regulation that involves specific patterns of epigenetic marks. More generally, reversible changes in DNA methylation appear to be consistent with the ability of nuclear chromatin to manage variation in external ionic and temperature environment. Whilst tentative, this framework provides scope to develop experimental approaches to understand in greater detail the internal environment of plant nuclei. It is hoped that this will generate a deeper understanding of the molecular mechanisms underlying genotype × environment interactions that may be beneficial for long-term improvement of crop performance in less predictable climates.
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Affiliation(s)
- Graham J. King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
- National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Crops for the Future, Biotechnology and Breeding Systems, Semenyih, Malaysia
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139
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de la Paz Sanchez M, Aceves-García P, Petrone E, Steckenborn S, Vega-León R, Álvarez-Buylla ER, Garay-Arroyo A, García-Ponce B. The impact of Polycomb group (PcG) and Trithorax group (TrxG) epigenetic factors in plant plasticity. THE NEW PHYTOLOGIST 2015; 208:684-694. [PMID: 26037337 DOI: 10.1111/nph.13486] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/25/2015] [Indexed: 06/04/2023]
Abstract
Current advances indicate that epigenetic mechanisms play important roles in the regulatory networks involved in plant developmental responses to environmental conditions. Hence, understanding the role of such components becomes crucial to understanding the mechanisms underlying the plasticity and variability of plant traits, and thus the ecology and evolution of plant development. We now know that important components of phenotypic variation may result from heritable and reversible epigenetic mechanisms without genetic alterations. The epigenetic factors Polycomb group (PcG) and Trithorax group (TrxG) are involved in developmental processes that respond to environmental signals, playing important roles in plant plasticity. In this review, we discuss current knowledge of TrxG and PcG functions in different developmental processes in response to internal and environmental cues and we also integrate the emerging evidence concerning their function in plant plasticity. Many such plastic responses rely on meristematic cell behavior, including stem cell niche maintenance, cellular reprogramming, flowering and dormancy as well as stress memory. This information will help to determine how to integrate the role of epigenetic regulation into models of gene regulatory networks, which have mostly included transcriptional interactions underlying various aspects of plant development and its plastic response to environmental conditions.
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Affiliation(s)
- Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Pamela Aceves-García
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Emilio Petrone
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Stefan Steckenborn
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Rosario Vega-León
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
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140
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Shemer O, Landau U, Candela H, Zemach A, Eshed Williams L. Competency for shoot regeneration from Arabidopsis root explants is regulated by DNA methylation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:251-61. [PMID: 26259192 DOI: 10.1016/j.plantsci.2015.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/08/2015] [Accepted: 06/14/2015] [Indexed: 05/11/2023]
Abstract
Plants exhibit high capacity to regenerate in three alternative pathways: tissue repair, somatic embryogenesis and de novo organogenesis. For most plants, de novo organ initiation can be easily achieved in tissue culture by exposing explants to auxin and/or cytokinin, yet the competence to regenerate varies among species and within tissues from the same plant. In Arabidopsis, root explants incubated directly on cytokinin-rich shoot inducing medium (SIM-direct), are incapable of regenerating shoots, and a pre-incubation step on auxin-rich callus inducing medium (CIM) is required to acquire competency to regenerate on the SIM. However the mechanism underlying competency acquisition still remains elusive. Here we show that the chromomethylase 3 (cmt3) mutant which exhibits significant reduction in CHG methylation, shows high capacity to regenerate on SIM-direct and that regeneration occurs via direct organogenesis. In WT, WUSCHEL (WUS) promoter, an essential gene for shoot formation, is highly methylated, and its expression on SIM requires pre-incubation on CIM. However, in cmt3, WUS expression induced by SIM-direct. We propose that pre-incubation on CIM is required for the re-activation of cell division. Following the transfer of roots to SIM, the intensive cell division activity continues, and in the presence of cytokinin leads to a dilution in DNA methylation that allows certain genes required for shoot regeneration to respond to SIM, thereby advancing shoot formation.
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Affiliation(s)
- Or Shemer
- The Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Udi Landau
- The Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Assaf Zemach
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Leor Eshed Williams
- The Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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141
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Mozgova I, Köhler C, Hennig L. Keeping the gate closed: functions of the polycomb repressive complex PRC2 in development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:121-32. [PMID: 25762111 DOI: 10.1111/tpj.12828] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 05/08/2023]
Abstract
Plant ontogeny relies on the correct timing and sequence of transitions between individual developmental phases. These are specified by gene expression patterns that are established by the balanced action of activators and repressors. Polycomb repressive complexes (PRCs) represent an evolutionarily conserved system of epigenetic gene repression that governs the establishment and maintenance of cell, tissue and organ identity, contributing to the correct execution of the developmental programs. PRC2 is a four-subunit histone methyltransferase complex that catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), which contributes to the change of chromatin structure and long-lasting gene repression. Here, we review the composition and molecular function of the different known PRC2 complexes in plants, and focus on the role of PRC2 in mediating the establishment of different developmental phases and transitions between them.
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Affiliation(s)
- Iva Mozgova
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
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142
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Adrian J, Chang J, Ballenger CE, Bargmann BOR, Alassimone J, Davies KA, Lau OS, Matos JL, Hachez C, Lanctot A, Vatén A, Birnbaum KD, Bergmann DC. Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population. Dev Cell 2015; 33:107-18. [PMID: 25850675 DOI: 10.1016/j.devcel.2015.01.025] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/30/2014] [Accepted: 01/21/2015] [Indexed: 12/17/2022]
Abstract
Developmental transitions can be described in terms of morphology and the roles of individual genes, but also in terms of global transcriptional and epigenetic changes. Temporal dissections of transcriptome changes, however, are rare for intact, developing tissues. We used RNA sequencing and microarray platforms to quantify gene expression from labeled cells isolated by fluorescence-activated cell sorting to generate cell-type-specific transcriptomes during development of an adult stem-cell lineage in the Arabidopsis leaf. We show that regulatory modules in this early lineage link cell types that had previously been considered to be under separate control and provide evidence for recruitment of individual members of gene families for different developmental decisions. Because stomata are physiologically important and because stomatal lineage cells exhibit exemplary division, cell fate, and cell signaling behaviors, this dataset serves as a valuable resource for further investigations of fundamental developmental processes.
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Affiliation(s)
- Jessika Adrian
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jessica Chang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Bastiaan O R Bargmann
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | | | - Kelli A Davies
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - On Sun Lau
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Juliana L Matos
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Charles Hachez
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Amy Lanctot
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Anne Vatén
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kenneth D Birnbaum
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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143
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Valledor L, Pascual J, Meijón M, Escandón M, Cañal MJ. Conserved Epigenetic Mechanisms Could Play a Key Role in Regulation of Photosynthesis and Development-Related Genes during Needle Development of Pinus radiata. PLoS One 2015; 10:e0126405. [PMID: 25965766 PMCID: PMC4429063 DOI: 10.1371/journal.pone.0126405] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/01/2015] [Indexed: 11/28/2022] Open
Abstract
Needle maturation is a complex process that involves cell growth, differentiation and tissue remodelling towards the acquisition of full physiological competence. Leaf induction mechanisms are well known; however, those underlying the acquisition of physiological competence are still poorly understood, especially in conifers. We studied the specific epigenetic regulation of genes defining organ function (PrRBCS and PrRBCA) and competence and stress response (PrCSDP2 and PrSHMT4) during three stages of needle development and one de-differentiated control. Gene-specific changes in DNA methylation and histone were analysed by bisulfite sequencing and chromatin immunoprecipitation (ChIP). The expression of PrRBCA and PrRBCS increased during needle maturation and was associated with the progressive loss of H3K9me3, H3K27me3 and the increase in AcH4. The maturation-related silencing of PrSHMT4 was correlated with increased H3K9me3 levels, and the repression of PrCSDP2, to the interplay between AcH4, H3K27me3, H3K9me3 and specific DNA methylation. The employ of HAT and HDAC inhibitors led to a further determination of the role of histone acetylation in the regulation of our target genes. The integration of these results with high-throughput analyses in Arabidopsis thaliana and Populus trichocarpa suggests that the specific epigenetic mechanisms that regulate photosynthetic genes are conserved between the analysed species.
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Affiliation(s)
- Luis Valledor
- Plant Physiology, Faculty of Biology, University of Oviedo, Cat. Rodrígo Uría s/n, E-33071, Oviedo, Spain
- Department of Biology and CESAM, University of Aveiro, Campus Universitario de Santiago, P-3810-193, Aveiro, Portugal
- * E-mail: (LV); (MJC)
| | - Jesús Pascual
- Plant Physiology, Faculty of Biology, University of Oviedo, Cat. Rodrígo Uría s/n, E-33071, Oviedo, Spain
| | - Mónica Meijón
- Regional Institute for Research and Agro-Food Development (SERIDA), Finca Experimental La Mata s/n, E-33825, Grado, Spain
| | - Mónica Escandón
- Plant Physiology, Faculty of Biology, University of Oviedo, Cat. Rodrígo Uría s/n, E-33071, Oviedo, Spain
| | - María Jesús Cañal
- Plant Physiology, Faculty of Biology, University of Oviedo, Cat. Rodrígo Uría s/n, E-33071, Oviedo, Spain
- * E-mail: (LV); (MJC)
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144
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Vinogradova AP, Lebedeva MA, Lutova LA. Meristematic characteristics of tumors initiated by Agrobacterium tumefaciens in pea plants. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415010123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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145
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Xiao J, Wagner D. Polycomb repression in the regulation of growth and development in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:15-24. [PMID: 25449722 DOI: 10.1016/j.pbi.2014.10.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/01/2014] [Accepted: 10/06/2014] [Indexed: 05/18/2023]
Abstract
Chromatin state is critical for cell identity and development in multicellular eukaryotes. Among the regulators of chromatin state, Polycomb group (PcG) proteins stand out because of their role in both establishment and maintenance of cell identity. PcG proteins act in two major complexes in metazoans and plants. These complexes function to epigenetically-in a mitotically heritable manner-prevent expression of important developmental regulators at the wrong stage of development or in the wrong tissue. In Arabidopsis, PcG function is required throughout the life cycle from seed germination to embryo formation. Recent studies have expanded our knowledge regarding the biological roles and the regulation of the activity of PcG complexes. In this review, we discuss novel functions of Polycomb repression in plant development as well as advances in understanding PcG complex recruitment, activity regulation and removal in Arabidopsis and other plant species.
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Affiliation(s)
- Jun Xiao
- 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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146
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Lebedeva Osipova MA, Tvorogova VE, Vinogradova AP, Gancheva MS, Azarakhsh M, Ilina EL, Demchenko KN, Dodueva IE, Lutova LA. Initiation of spontaneous tumors in radish (Raphanus sativus): Cellular, molecular and physiological events. JOURNAL OF PLANT PHYSIOLOGY 2015; 173:97-104. [PMID: 25462083 DOI: 10.1016/j.jplph.2014.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 07/24/2014] [Accepted: 07/28/2014] [Indexed: 05/04/2023]
Abstract
In plant meristems, the balance of cell proliferation and differentiation is maintained by phytohormones, specifically auxin and cytokinin, as well as transcription factors. Changing of the cytokinin/auxin balance in plants may lead to developmental abnormalities, and in particular, to the formation of tumors. The examples of spontaneous tumor formation in plants include tumors formed on the roots of radish (Raphanus sativus) inbred lines. Previously, it was found that the cytokinin/auxin ratio is altered in radish tumors. In this study, a detailed histological analysis of spontaneous radish tumors was performed, revealing a possible mechanism of tumor formation, namely abnormal cambial activity. The analysis of cell proliferation patterns revealed meristematic foci in radish tumors. By using a fusion of an auxin-responsive promoter (DR5) and a reporter gene, the involvement of auxin in developmental processes in tumors was shown. In addition, the expression of the root meristem-specific WUSCHEL-related homeobox 5 (WOX5) gene was observed in cells adjacent to meristematic foci. Taken together, the results of the present study show that tumor tissues share some characteristics with root apical meristems, including the presence of auxin-response maxima in meristematic foci with adjacent cells expressing WOX5.
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Affiliation(s)
- Maria A Lebedeva Osipova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia.
| | - Varvara E Tvorogova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia.
| | - Alena P Vinogradova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia.
| | - Maria S Gancheva
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia.
| | - Mahboobeh Azarakhsh
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia.
| | - Elena L Ilina
- Komarov Botanical Institute, Russian Academy of Sciences, Laboratory of Anatomy and Morphology, Prof. Popov Street 2, 197376 Saint-Petersburg, Russia.
| | - Kirill N Demchenko
- Komarov Botanical Institute, Russian Academy of Sciences, Laboratory of Anatomy and Morphology, Prof. Popov Street 2, 197376 Saint-Petersburg, Russia.
| | - Irina E Dodueva
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia.
| | - Lyudmila A Lutova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb. 7/9, 199034 Saint-Petersburg, Russia.
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147
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Abstract
Correct expression of specific sets of genes in time and space ensures the establishment and maintenance of cell identity, which is required for proper development of multicellular organisms. Polycomb and Trithorax group proteins form multisubunit complexes that antagonistically act in epigenetic gene repression and activation, respectively. The traditional view of Polycomb repressive complexes (PRCs) as executors of long-lasting and stable gene repression is being extended by evidence of flexible repression in response to developmental and environmental cues, increasing the complexity of mechanisms that ensure selective and properly timed PRC targeting and release of Polycomb repression. Here, we review advances in understanding of the composition, mechanisms of targeting, and function of plant PRCs and discuss the parallels and differences between plant and animal models.
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Affiliation(s)
- Iva Mozgova
- Department of Plant Biology, Uppsala BioCenter, and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; ,
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148
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Choi Y, Mango SE. Hunting for Darwin's gemmules and Lamarck's fluid: Transgenerational signaling and histone methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1440-53. [DOI: 10.1016/j.bbagrm.2014.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 01/22/2023]
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149
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Grossniklaus U, Paro R. Transcriptional silencing by polycomb-group proteins. Cold Spring Harb Perspect Biol 2014; 6:a019331. [PMID: 25367972 DOI: 10.1101/cshperspect.a019331] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Polycomb-group (PcG) genes encode chromatin proteins involved in stable and heritable transcriptional silencing. PcG proteins participate in distinct multimeric complexes that deposit, or bind to, specific histone modifications (e.g., H3K27me3 and H2AK119ub1) to prevent gene activation and maintain repressed chromatin domains. PcG proteins are evolutionary conserved and play a role in processes ranging from vernalization and seed development in plants, over X-chromosome inactivation in mammals, to the maintenance of stem cell identity. PcG silencing is medically relevant as it is often observed in human disorders, including cancer, and tissue regeneration, which involve the reprogramming of PcG-controlled target genes.
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Affiliation(s)
- Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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150
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Berke L, Snel B. The histone modification H3K27me3 is retained after gene duplication and correlates with conserved noncoding sequences in Arabidopsis. Genome Biol Evol 2014; 6:572-9. [PMID: 24567304 PMCID: PMC3971591 DOI: 10.1093/gbe/evu040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The histone modification H3K27me3 is involved in repression of transcription and plays a crucial role in developmental transitions in both animals and plants. It is deposited by PRC2 (Polycomb repressive complex 2), a conserved protein complex. In Arabidopsis thaliana, H3K27me3 is found at 15% of all genes. These tend to encode transcription factors and other regulators important for development. However, it is not known how PRC2 is recruited to target loci nor how this set of target genes arose during Arabidopsis evolution. To resolve the latter, we integrated A. thaliana gene families with five independent genome-wide H3K27me3 data sets. Gene families were either significantly enriched or depleted of H3K27me3, showing a strong impact of shared ancestry to H3K27me3 distribution. To quantify this, we performed ancestral state reconstruction of H3K27me3 on phylogenetic trees of gene families. The set of H3K27me3-marked genes changed less than expected by chance, suggesting that H3K27me3 was retained after gene duplication. This retention suggests that the PRC2-recruiting signal could be encoded in the DNA and also conserved among certain duplicated genes. Indeed, H3K27me3-marked genes were overrepresented among paralogs sharing conserved noncoding sequences (CNSs) that are enriched with transcription factor binding sites. The association of upstream CNSs with H3K27me3-marked genes represents the first genome-wide connection between H3K27me3 and potential regulatory elements in plants. Thus, we propose that CNSs likely function as part of the PRC2 recruitment in plants.
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Affiliation(s)
- Lidija Berke
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, The Netherlands
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