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Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
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2
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Lee S, Park YS, Rhee JH, Chu H, Frost JM, Choi Y. Insights into plant regeneration: cellular pathways and DNA methylation dynamics. PLANT CELL REPORTS 2024; 43:120. [PMID: 38634973 PMCID: PMC11026228 DOI: 10.1007/s00299-024-03216-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Plants, known for their immobility, employ various mechanisms against stress and damage. A prominent feature is the formation of callus tissue-a cellular growth phenomenon that remains insufficiently explored, despite its distinctive cellular plasticity compared to vertebrates. Callus formation involves dedifferentiated cells, with a subset attaining pluripotency. Calluses exhibit an extraordinary capacity to reinitiate cellular division and undergo structural transformations, generating de novo shoots and roots, thereby developing into regenerated plants-a testament to the heightened developmental plasticity inherent in plants. In this way, plant regeneration through clonal propagation is a widely employed technique for vegetative reproduction. Thus, exploration of the biological components involved in regaining pluripotency contributes to the foundation upon which methods of somatic plant propagation can be advanced. This review provides an overview of the cellular pathway involved in callus and subsequent de novo shoot formation from already differentiated plant tissue, highlighting key genes critical to this process. In addition, it explores the intricate realm of epigenetic regulatory processes, emphasizing the nuanced dynamics of DNA methylation that contribute to plant regeneration. Finally, we briefly discuss somaclonal variation, examining its relation to DNA methylation, and investigating the heritability of epigenomic changes in crops.
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Affiliation(s)
- Seunga Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
| | - Young Seo Park
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Ji Hoon Rhee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
| | - Hyojeong Chu
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
- The Research Institute of Basic Sciences, Seoul National University, Seoul, Korea
| | - Jennifer M Frost
- Genomics and Child Health, The Blizard Institute, Queen Mary University of London, London, UK
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul, Korea.
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea.
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3
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Li J, Zhang Q, Wang Z, Liu Q. The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions. PLANT PHYSIOLOGY 2024; 194:2022-2038. [PMID: 38290051 PMCID: PMC10980418 DOI: 10.1093/plphys/kiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.
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Affiliation(s)
- Jiawen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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Ramakrishnan M, Zhou M, Ceasar SA, Ali DJ, Maharajan T, Vinod KK, Sharma A, Ahmad Z, Wei Q. Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos. PLANT CELL REPORTS 2023; 42:1845-1873. [PMID: 37792027 DOI: 10.1007/s00299-023-03071-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023]
Abstract
KEY MESSAGE This review discusses the epigenetic changes during somatic embryo (SE) development, highlights the genes and miRNAs involved in the transition of somatic cells into SEs as a result of epigenetic changes, and draws insights on biotechnological opportunities to study SE development. Somatic embryogenesis from somatic cells occurs in a series of steps. The transition of somatic cells into somatic embryos (SEs) is the most critical step under genetic and epigenetic regulations. Major regulatory genes such as SERK, WUS, BBM, FUS3/FUSA3, AGL15, and PKL, control SE steps and development by turning on and off other regulatory genes. Gene transcription profiles of somatic cells during SE development is the result of epigenetic changes, such as DNA and histone protein modifications, that control and decide the fate of SE formation. Depending on the type of somatic cells and the treatment with plant growth regulators, epigenetic changes take place dynamically. Either hypermethylation or hypomethylation of SE-related genes promotes the transition of somatic cells. For example, the reduced levels of DNA methylation of SERK and WUS promotes SE initiation. Histone modifications also promote SE induction by regulating SE-related genes in somatic cells. In addition, miRNAs contribute to the various stages of SE by regulating the expression of auxin signaling pathway genes (TIR1, AFB2, ARF6, and ARF8), transcription factors (CUC1 and CUC2), and growth-regulating factors (GRFs) involved in SE formation. These epigenetic and miRNA functions are unique and have the potential to regenerate bipolar structures from somatic cells when a pluripotent state is induced. However, an integrated overview of the key regulators involved in SE development and downstream processes is lacking. Therefore, this review discusses epigenetic modifications involved in SE development, SE-related genes and miRNAs associated with epigenetics, and common cis-regulatory elements in the promoters of SE-related genes. Finally, we highlight future biotechnological opportunities to alter epigenetic pathways using the genome editing tool and to study the transition mechanism of somatic cells.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Stanislaus Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences (Autonomous), Kalamassery, Kochi, 683104, Kerala, India
| | - Doulathunnisa Jaffar Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Theivanayagam Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences (Autonomous), Kalamassery, Kochi, 683104, Kerala, India
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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El-Shehawi AM, Elseehy MA, Elseehy MM. CpG Methylation of the Proximal Promoter Region Regulates the Expression of NAC6D Gene in Response to High Temperature in Wheat (Triticum aestivum). CYTOL GENET+ 2022. [DOI: 10.3103/s009545272205005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zheng B, Liu J, Gao A, Chen X, Gao L, Liao L, Luo B, Ogutu CO, Han Y. Epigenetic reprogramming of H3K27me3 and DNA methylation during leaf-to-callus transition in peach. HORTICULTURE RESEARCH 2022; 9:uhac132. [PMID: 35937864 PMCID: PMC9350832 DOI: 10.1093/hr/uhac132] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/29/2022] [Indexed: 05/30/2023]
Abstract
Plant tissues are capable of developing unorganized cell masses termed calluses in response to the appropriate combination of auxin and cytokinin. Revealing the potential epigenetic mechanisms involved in callus development can improve our understanding of the regeneration process of plant cells, which will be beneficial for overcoming regeneration recalcitrance in peach. In this study, we report on single-base resolution mapping of DNA methylation and reprogramming of the pattern of trimethylation of histone H3 at lysine 27 (H3K27me3) at the genome-wide level during the leaf-to-callus transition in peach. Overall, mCG and mCHH were predominant at the genome-wide level and mCG was predominant in genic regions. H3K27me3 deposition was mainly detected in the gene body and at the TSS site, and GAGA repetitive sequences were prone to recruit H3K27me3 modification. H3K27me3 methylation was negatively correlated with gene expression. In vitro culture of leaf explants was accompanied by DNA hypomethylation and H3K27me3 demethylation, which could activate auxin- and cytokinin-related regulators to induce callus development. The DNA methylation inhibitor 5-azacytidine could significantly increase callus development, while the H3K27me3 demethylase inhibitor GSK-J4 dramatically reduced callus development. These results demonstrate the roles of DNA methylation and H3K27me3 modification in mediating chromatin status during callus development. Our study provides new insights into the epigenetic mechanisms through which differentiated cells acquire proliferative competence to induce callus development in plants.
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Affiliation(s)
- Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingjing Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Anqi Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xiaomei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Lingling Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Binwen Luo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yuepeng Han
- Corresponding author. E-mail:
Equal contribution
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7
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Imran M, Luo X, Hu S, Cao Y, Long Z. Epigenetic and somaclonal divergence in Dendrocalamus farinosus for physiological augmentation and lignin degradation. Biotechnol Appl Biochem 2021; 69:1545-1556. [PMID: 34374452 DOI: 10.1002/bab.2226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/13/2021] [Indexed: 11/08/2022]
Abstract
Epigenetic and molecular variation is a key approach for the improvement of plants. From in vitro tissue culture of Dendrocalamus farinosus; 30 plants were regenerated and after 2 years, the physiological, biochemical, and genomic studies were conducted. The results highlighted that for all phenotypic characteristics, the 30 regenerated plants were superior in comparison with the control (CK). From genetical analysis, a total of 97 bands were witnessed ranging between 212 bp and 2.2 kb. The results for OPU14 showed one additional specific band (723 bp) and one band (700 bp) were missing. The 10 plants were having genetic variability and can be termed as somaclones while the other plants have epigenetic variations. The cellulose and lignin analysis highlighted that somaclone No. 30 has the least cellulose content of 35%; while the somaclones No. 102 and No. 213 have the least 3.21% and 3.48% of lignin contents. Therefore, somaclones No. 30, No. 102, and No. 213 were selected for the histochemical localization. The lignin investigation revealed that somaclone No. 30 is greater while somaclones No. 102 and No. 213 were reduced in vascular bundles in comparison with the CK along with the high expression level of 4CL, C3H, C4H, COMT, and CCoAOMT1 genes.
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Affiliation(s)
- Muhammad Imran
- Plant Cell Engineering Laboratory, Department of Biotechnology, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan Province, China
| | - Xuegang Luo
- Plant Cell Engineering Laboratory, Department of Biotechnology, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan Province, China
| | - Shanglian Hu
- Plant Cell Engineering Laboratory, Department of Biotechnology, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan Province, China
| | - Ying Cao
- Plant Cell Engineering Laboratory, Department of Biotechnology, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan Province, China
| | - Zhijian Long
- Plant Cell Engineering Laboratory, Department of Biotechnology, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan Province, China
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The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection. Proc Natl Acad Sci U S A 2021; 118:2026806118. [PMID: 34266952 PMCID: PMC8307533 DOI: 10.1073/pnas.2026806118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The angiosperm life cycle has alternating diploid (sporophyte) and haploid (gametophyte) generations. The sporophyte generation begins with fertilization of haploid gametes and the gametophyte generation begins after meiosis. In Arabidopsis, the DEMETER (DME) DNA demethylase is essential for reproduction and is expressed in the central cell and vegetative cell of the female and male gametophyte, respectively. Little is known about DME function in the sporophyte. We show that DME activity is required for sporophyte development—seed germination, root hair growth, and cellular proliferation and differentiation during development—and we identify sporophytic genes whose proper expression requires DME activity. Together, our study provides important clues about the genetic circuits regulated by the DME DNA demethylase that control Arabidopsis sporophyte development. The flowering plant life cycle consists of alternating haploid (gametophyte) and diploid (sporophyte) generations, where the sporophytic generation begins with fertilization of haploid gametes. In Arabidopsis, genome-wide DNA demethylation is required for normal development, catalyzed by the DEMETER (DME) DNA demethylase in the gamete companion cells of male and female gametophytes. In the sporophyte, postembryonic growth and development are largely dependent on the activity of numerous stem cell niches, or meristems. Analyzing Arabidopsis plants homozygous for a loss-of-function dme-2 allele, we show that DME influences many aspects of sporophytic growth and development. dme-2 mutants exhibited delayed seed germination, variable root hair growth, aberrant cellular proliferation and differentiation followed by enhanced de novo shoot formation, dysregulation of root quiescence and stomatal precursor cells, and inflorescence meristem (IM) resurrection. We also show that sporophytic DME activity exerts a profound effect on the transcriptome of developing Arabidopsis plants, including discrete groups of regulatory genes that are misregulated in dme-2 mutant tissues, allowing us to potentially link phenotypes to changes in specific gene expression pathways. These results show that DME plays a key role in sporophytic development and suggest that DME-mediated active DNA demethylation may be involved in the maintenance of stem cell activities during the sporophytic life cycle in Arabidopsis.
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9
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Tissue culture-induced DNA methylation in crop plants: a review. Mol Biol Rep 2021; 48:823-841. [PMID: 33394224 DOI: 10.1007/s11033-020-06062-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022]
Abstract
Plant tissue culture techniques have been extensively employed in commercial micropropagation to provide year-round production. Tissue culture regenerants are not always genotypically and phenotypically similar. Due to the changes in the tissue culture microenvironment, plant cells are exposed to additional stress which induces genetic and epigenetic instabilities in the regenerants. These changes lead to tissue culture-induced variations (TCIV) which are also known as somaclonal variations to categorically specify the inducing environment. TCIV includes molecular and phenotypic changes persuaded in the in vitro culture due to continuous sub-culturing and tissue culture-derived stress. Epigenetic variations such as altered DNA methylation pattern are induced due to the above-mentioned factors. Reportedly, alteration in DNA methylation pattern is much more frequent in the plant genome during the tissue culture process. DNA methylation plays an important role in gene expression and regulation of plant development. Variants originated in tissue culture process due to heritable methylation changes, can contribute to intra-species phenotypic variation. Several molecular techniques are available to detect DNA methylation at different stages of in vitro culture. Here, we review the aspects of TCIV with respect to DNA methylation and its effect on crop improvement programs. It is anticipated that a precise and comprehensive knowledge of molecular basis of in vitro-derived DNA methylation will help to design strategies to overcome the bottlenecks of micropropagation system and maintain the clonal fidelity of the regenerants.
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Castander-Olarieta A, Pereira C, Sales E, Meijón M, Arrillaga I, Cañal MJ, Goicoa T, Ugarte MD, Moncaleán P, Montalbán IA. Induction of Radiata Pine Somatic Embryogenesis at High Temperatures Provokes a Long-Term Decrease in DNA Methylation/Hydroxymethylation and Differential Expression of Stress-Related Genes. PLANTS 2020; 9:plants9121762. [PMID: 33322106 PMCID: PMC7762990 DOI: 10.3390/plants9121762] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Based on the hypothesis that embryo development is a crucial stage for the formation of stable epigenetic marks that could modulate the behaviour of the resulting plants, in this study, radiata pine somatic embryogenesis was induced at high temperatures (23 °C, eight weeks, control; 40 °C, 4 h; 60 °C, 5 min) and the global methylation and hydroxymethylation levels of emerging embryonal masses and somatic plants were analysed using LC-ESI-MS/ MS-MRM. In this context, the expression pattern of six genes previously described as stress-mediators was studied throughout the embryogenic process until plant level to assess whether the observed epigenetic changes could have provoked a sustained alteration of the transcriptome. Results indicated that the highest temperatures led to hypomethylation of both embryonal masses and somatic plants. Moreover, we detected for the first time in a pine species the presence of 5-hydroxymethylcytosine, and revealed its tissue specificity and potential involvement in heat-stress responses. Additionally, a heat shock protein-coding gene showed a down-regulation tendency along the process, with a special emphasis given to embryonal masses at first subculture and ex vitro somatic plants. Likewise, the transcripts of several proteins related with translation, oxidative stress response, and drought resilience were differentially expressed.
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Affiliation(s)
| | - Cátia Pereira
- Department of Forestry Science, NEIKER, 01192 Arkaute, Spain; (A.C.-O.); (C.P.)
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Ester Sales
- Departament of Ciencias Agrarias y del Medio Natural, Instituto Universitario de Ciencias Ambientales, Universidad de Zaragoza, Escuela Politécnica Superior, 22071 Huesca, Spain;
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, 33006 Oviedo, Spain; (M.M.); (M.J.C.)
| | - Isabel Arrillaga
- Departamento de Biología Vegetal, Facultad de Farmacia, Instituto BiotecMed, Universidad de Valencia, 46100 Burjassot, Spain;
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, 33006 Oviedo, Spain; (M.M.); (M.J.C.)
| | - Tomás Goicoa
- Department of Statistics, Computer Science and Mathematics, Universidad Pública de Navarra, 31006 Pamplona, Spain; (T.G.); (M.D.U.)
- INAMAT2 (Institute for Advanced Materials and Mathematics), Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - María Dolores Ugarte
- Department of Statistics, Computer Science and Mathematics, Universidad Pública de Navarra, 31006 Pamplona, Spain; (T.G.); (M.D.U.)
- INAMAT2 (Institute for Advanced Materials and Mathematics), Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - Paloma Moncaleán
- Department of Forestry Science, NEIKER, 01192 Arkaute, Spain; (A.C.-O.); (C.P.)
- Correspondence: (P.M.); (I.A.M.)
| | - Itziar A. Montalbán
- Department of Forestry Science, NEIKER, 01192 Arkaute, Spain; (A.C.-O.); (C.P.)
- Correspondence: (P.M.); (I.A.M.)
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Mona Mohamed Elseehy. Differential Transgeneration Methylation of Exogenous Promoters in T1 Transgenic Wheat (Triticum aestivum). CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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12
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Grzybkowska D, Nowak K, Gaj MD. Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis. Int J Mol Sci 2020; 21:E6849. [PMID: 32961931 PMCID: PMC7555384 DOI: 10.3390/ijms21186849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
The auxin-induced embryogenic reprogramming of plant somatic cells is associated with extensive modulation of the gene expression in which epigenetic modifications, including DNA methylation, seem to play a crucial role. However, the function of DNA methylation, including the role of auxin in epigenetic regulation of the SE-controlling genes, remains poorly understood. Hence, in the present study, we analysed the expression and methylation of the TF genes that play a critical regulatory role during SE induction (LEC1, LEC2, BBM, WUS and AGL15) in auxin-treated explants of Arabidopsis. The results showed that auxin treatment substantially affected both the expression and methylation patterns of the SE-involved TF genes in a concentration-dependent manner. The auxin treatment differentially modulated the methylation of the promoter (P) and gene body (GB) sequences of the SE-involved genes. Relevantly, the SE-effective auxin treatment (5.0 µM of 2,4-D) was associated with the stable hypermethylation of the P regions of the SE-involved genes and a significantly higher methylation of the P than the GB fragments was a characteristic feature of the embryogenic culture. The presence of auxin-responsive (AuxRE) motifs in the hypermethylated P regions suggests that auxin might substantially contribute to the DNA methylation-mediated control of the SE-involved genes.
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Affiliation(s)
| | | | - Małgorzata D. Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland; (D.G.); (K.N.)
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13
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Du X, Fang T, Liu Y, Wang M, Zang M, Huang L, Zhen S, Zhang J, Shi Z, Wang G, Fu J, Liu Y. Global profiling of N 6 -methyladenosine methylation in maize callus induction. THE PLANT GENOME 2020; 13:e20018. [PMID: 33016611 DOI: 10.1002/tpg2.20018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 05/26/2023]
Abstract
Callus induction is a dedifferentiation process that accompanies a cell fate transition, and epigenetic regulation plays a crucial role in the process. N6 -methyladenosine (m6A) methylation is an important mechanism in post-transcriptional epigenetic regulation and functions in cell reprogramming. However, the function of m6A methylation during callus induction is still unknown. Here, we performed transcriptome-wide m6A-seq on immature maize embryos after culturing for 2, 4, or 8 days with or without the auxin analogue 2,4-D. A total of 26,794 unique m6A peaks were detected from 17,456 maize genes; and 2,338 specific, 2,4-D-induced m6A peaks (D-specific m6A) were detected only in embryos cultured with 2,4-D. Furthermore, a positive correlation between m6A methylation and mRNA abundance was discovered in the genes with D-specific m6A deposition, especially at the beginning of callus induction. Key genes involved in callus induction, i.e. BABY BOOM and LBD transcription factors, underwent m6A methylation, increasing their transcript levels, thus improving callus induction. These results revealed the importance of m6A methylation during the early stage of callus induction and provided new insights into the molecular mechanism of callus induction at an epitranscriptomic level.
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Affiliation(s)
- Xuemei Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Fang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meng Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Maosen Zang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Liying Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Sihan Zhen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zichen Shi
- Beijing No.4 High School International Campus, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Elseehy MM, El-Shehawi AM. Methylation of Exogenous Promoters Regulates Soybean Isoflavone Synthase (GmIFS) Transgene in T0 Transgenic Wheat (Triticum aestivum). CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720030032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Hu L, Li N, Zhang Z, Meng X, Dong Q, Xu C, Gong L, Liu B. CG hypomethylation leads to complex changes in DNA methylation and transpositional burst of diverse transposable elements in callus cultures of rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:188-203. [PMID: 31529551 DOI: 10.1111/tpj.14531] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
CG methylation (m CG) is essential for preserving genome stability in mammals, but this link remains obscure in plants. OsMET1-2, a major rice DNA methyltransferase, plays critical roles in maintaining m CG in rice. Null mutation of OsMET1-2 causes massive CG hypomethylation, rendering the mutant suitable to address the role of m CG in maintaining genome integrity in plants. Here, we analyzed m CG dynamics and genome stability in tissue cultures of OsMET1-2 homozygous (-/-) and heterozygous (+/-) mutants, and isogenic wild-type (WT). We found m CG levels in cultures of -/- were substantially lower than in those of WT and +/-, as expected. Unexpectedly, m CG levels in 1- and 3-year cultures of -/- were 77.6% and 48.7% higher, respectively, than in shoot, from which the cultures were initiated, suggesting substantial regain of m CG in -/- cultures, which contrasts to the general trend of m CG loss in all WT plant tissue cultures hitherto studied. Transpositional burst of diverse transposable elements (TEs) occurred only in -/- cultures, although no elevation of genome-wide mutation rate in the form of single nucleotide polymorphisms was detected. Altogether, our results establish an essential role of m CG in retaining TE immobility and hence genome stability in rice and likely in plants in general.
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Affiliation(s)
- Lanjuan Hu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- College of Plant Sciences, Faculty of Agriculture, Jilin University, Changchun, 130062, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Qianli Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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16
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Zangi M, Bagherieh Najjar MB, Golalipour M, Aghdasi M. met1 DNA Methyltransferase Controls TERT Gene Expression: A New Insight to The Role of Telomerase in Development. CELL JOURNAL 2019; 22:71-74. [PMID: 31606969 PMCID: PMC6791074 DOI: 10.22074/cellj.2020.6290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/25/2018] [Indexed: 12/11/2022]
Abstract
Objective: DNA methylation systems are essential for proper embryo development. Methylation defects lead to
developmental abnormalities. Furthermore, changes in telomerase gene expression can affect stability of chromosomes
and produces abnormal growth. Therefore, defects in both methylation and telomerase gene expression can lead to
developmental abnormalities. We hypothesized that mutation in the methylation systems may induce developmental
abnormalities through changing telomerase gene expression. Materials and Methods: In this experimental study, we used Arabidopsis thaliana (At) as a developmental model.
DNA was extracted from seedlings leaves. The grown plants were screened using polymerase chain reaction (PCR)
reactions. Total RNA was isolated from the mature leaves, stems and flowers of wild type and met1 mutants. For
gene expression analysis, cDNA was synthesized and then quantitative reverse transcription PCR (qRT-PCR) was
performed. Results: Telomerase gene expression level in homozygous met1 mutant plants showed ~14 fold increase compared
to normal plants. Furthermore, TERT expression in met1 heterozygous was~ 2 fold higher than the wild type plants. Conclusion: Our results suggested that TERT is a methyltransferase-regulated gene which may be involved in
developmental abnormities causing by mutation in met1 methyltransferase system.
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Affiliation(s)
- Maryam Zangi
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | | | - Masoud Golalipour
- Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran. Electronic Address:
| | - Mahnaz Aghdasi
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
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17
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Forgione I, Wołoszyńska M, Pacenza M, Chiappetta A, Greco M, Araniti F, Abenavoli MR, Van Lijsebettens M, Bitonti MB, Bruno L. Hypomethylated drm1 drm2 cmt3 mutant phenotype of Arabidopsis thaliana is related to auxin pathway impairment. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:383-396. [PMID: 30824017 DOI: 10.1016/j.plantsci.2018.12.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/27/2018] [Accepted: 12/29/2018] [Indexed: 05/28/2023]
Abstract
DNA methylation carried out by different methyltransferase classes is a relevant epigenetic modification of DNA which plays a relevant role in the development of eukaryotic organisms. Accordingly, in Arabidopsis thaliana loss of DNA methylation due to combined mutations in genes encoding for DNA methyltransferases causes several developmental abnormalities. The present study describes novel growth disorders in the drm1 drm2 cmt3 triple mutant of Arabidopsis thaliana, defective both in maintenance and de novo DNA methylation, and highlights the correlation between DNA methylation and the auxin hormone pathway. By using an auxin responsive reporter gene, we discovered that auxin accumulation and distribution were affected in the mutant compared to the wild type, from embryo to adult plant stage. In addition, we demonstrated that the defective methylation status also affected the expression of genes that regulate auxin hormone pathways from synthesis to transport and signalling and a direct relationship between differentially expressed auxin-related genes and altered auxin accumulation and distribution in embryo, leaf and root was observed. Finally, we provided evidence of the direct and organ-specific modulation of auxin-related genes through the DNA methylation process.
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Affiliation(s)
- Ivano Forgione
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Magdalena Wołoszyńska
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Marianna Pacenza
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Adriana Chiappetta
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Maria Greco
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy; The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Fabrizio Araniti
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Maria Beatrice Bitonti
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Leonardo Bruno
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy.
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18
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Osorio-Montalvo P, Sáenz-Carbonell L, De-la-Peña C. 5-Azacytidine: A Promoter of Epigenetic Changes in the Quest to Improve Plant Somatic Embryogenesis. Int J Mol Sci 2018; 19:E3182. [PMID: 30332727 PMCID: PMC6214027 DOI: 10.3390/ijms19103182] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023] Open
Abstract
Somatic embryogenesis (SE) is a widely studied process due to its biotechnological potential to generate large quantities of plants in short time frames and from different sources of explants. The success of SE depends on many factors, such as the nature of the explant, the microenvironment generated by in vitro culture conditions, and the regulation of gene expression, among others. Epigenetics has recently been identified as an important factor influencing SE outcome. DNA methylation is one of the most studied epigenetic mechanisms due to its essential role in gene expression, and its participation in SE is crucial. DNA methylation levels can be modified through the use of drugs such as 5-Azacytidine (5-AzaC), an inhibitor of DNA methylation, which has been used during SE protocols. The balance between hypomethylation and hypermethylation seems to be the key to SE success. Here, we discuss the most prominent recent research on the role of 5-AzaC in the regulation of DNA methylation, highlighting its importance during the SE process. Also, the molecular implications that this inhibitor might have for the increase or decrease in the embryogenic potential of various explants are reviewed.
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Affiliation(s)
- Pedro Osorio-Montalvo
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
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19
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Karim R, Tan YS, Singh P, Khalid N, Harikrishna JA. Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:741-751. [PMID: 30150851 PMCID: PMC6103949 DOI: 10.1007/s12298-018-0566-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 05/20/2023]
Abstract
The process of somatic embryogenesis and plant regeneration involve changes in gene expression and have been associated with changes in DNA methylation. Here, we report the expression and DNA methylation patterns of SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), BABY BOOM (BBM), LEAFY COTYLEDON 2 (LEC2) and WUSCHEL (WUS) in meristematic block of newly emerged shoots from rhizome, embryogenic and non-embryogenic calli, prolonged cell suspension culture, ex vitro leaf, and in vitro leaf of regenerated plants of Boesenbergia rotunda. Among all seven samples, based on qRT-PCR, the highest level of expression of SERK, BBM and LEC2 was in embryogenic callus, while WUS was most highly expressed in meristematic block tissue followed by embryogenic callus. Relatively lower expression was observed in cell suspension culture and watery callus for SERK, LEC2 and WUS and in in vitro leaf for BBM. For gene specific methylation determined by bisulfite sequencing data, embryogenic callus samples had the lowest levels of DNA methylation at CG, CHG and CHH contexts of SERK, LEC2 and WUS. We observed negative correlation between DNA methylation at the CG and CHG contexts and the expression levels of SERK, BBM, LEC2 and WUS. Based on our results, we suggest that relatively higher expression and lower level of DNA methylation of SERK, BBM, LEC2 and WUS are associated with somatic embryogenesis and plant regeneration in B. rotunda.
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Affiliation(s)
- Rezaul Karim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
- Department of Botany, Faculty of Life and Earth Sciences, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Yew Seong Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Pooja Singh
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Norzulaani Khalid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
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20
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Xu C, Cao H, Xu E, Zhang S, Hu Y. Genome-Wide Identification of Arabidopsis LBD29 Target Genes Reveals the Molecular Events behind Auxin-Induced Cell Reprogramming during Callus Formation. PLANT & CELL PHYSIOLOGY 2018; 59:744-755. [PMID: 29121271 DOI: 10.1093/pcp/pcx168] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 10/27/2017] [Indexed: 05/18/2023]
Abstract
Auxin-induced callus formation represents an important cell reprogramming process during in vitro regeneration of plants, in which the pericycle or pericycle-like cells within plant organs are reprogrammed into the pluripotent cell mass termed callus that is generally required for subsequent regeneration of root or shoot. However, the molecular events behind cell reprogramming during auxin-induced callus formation are largely elusive. We previously identified that auxin-induced LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors act as the master regulators to trigger auxin-induced callus formation. Here, by ChIP-seq (chromatin immunoprecipitation-based sequencing) and RNA sequencing approaches, we identified the potential LBD29 target genes at the genome-wide level and outlined the molecular events of LBD-triggered cell reprogramming during callus formation. We showed that LBD29 preferentially bound to the G-box (CACGTG) and TGGGC[C/T] motifs and potentially targeted >350 genes, among which the genes related to methylation, reactive oxygen species (ROS) metabolism, cell wall hydrolysis and lipid metabolism were rapidly activated, while most of the light-responsive genes were suppressed by LBD29. Further examination of a few representative genes validated that they were targeted by LBD29 and participated in the regulation of cell reprogramming during callus formation. Our data not only outline a framework of the early molecular events behind auxin-induced cell reprogramming of callus formation, but also provide a valuable resource for identification of genes that regulate cell fate switch during in vitro regeneration of plants.
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Affiliation(s)
- Chongyi Xu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Huifen Cao
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enjun Xu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiqi Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- National Center for Plant Gene Research, Beijing 100093, China
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21
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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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22
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Liu H, Zhang H, Dong YX, Hao YJ, Zhang XS. DNA METHYLTRANSFERASE1-mediated shoot regeneration is regulated by cytokinin-induced cell cycle in Arabidopsis. THE NEW PHYTOLOGIST 2018; 217:219-232. [PMID: 28960381 DOI: 10.1111/nph.14814] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/19/2017] [Indexed: 05/22/2023]
Abstract
DNA methylation plays a critical role in diverse biological processes of plants. Arabidopsis DNA METHYLTRANSFERASE1 (MET1) represses shoot regeneration by inhibiting WUSCHEL (WUS) expression, which is essential for shoot initiation. However, the upstream signals regulating MET1 expression during this process are unclear. We analyzed the signals regulating MET1 expression using a number of established strategies, such as genetic analysis, confocal microscopy, quantitative real-time PCR and chromatin immunoprecipitation. MET1 expression patterns underwent dynamic changes with the initiation of WUS during shoot regeneration. The cell cycle regulator E2FA was characterized as an upstream factor directly promoting MET1 expression. Moreover, cytokinin promoted MET1 expression partially by enhancing CYCD3 expression. Our findings reveal that MET1-mediated shoot regeneration is regulated by the cytokinin-induced cell cycle, and provide new insights into the regulation of DNA methylation in 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, 271018, Shandong, China
| | - Hui Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yu Xiu Dong
- 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, 271018, Shandong, 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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23
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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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24
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Hardcastle TJ. Methods for discovering genomic loci exhibiting complex patterns of differential methylation. BMC Bioinformatics 2017; 18:416. [PMID: 28923005 PMCID: PMC5604413 DOI: 10.1186/s12859-017-1836-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/11/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Cytosine methylation is widespread in most eukaryotic genomes and is known to play a substantial role in various regulatory pathways. Unmethylated cytosines may be converted to uracil through the addition of sodium bisulphite, allowing genome-wide quantification of cytosine methylation via high-throughput sequencing. The data thus acquired allows the discovery of methylation 'loci'; contiguous regions of methylation consistently methylated across biological replicates. The mapping of these loci allows for associations with other genomic factors to be identified, and for analyses of differential methylation to take place. RESULTS The segmentSeq R package is extended to identify methylation loci from high-throughput sequencing data from multiple experimental conditions. A statistical model is then developed that accounts for biological replication and variable rates of non-conversion of cytosines in each sample to compute posterior likelihoods of methylation at each locus within an empirical Bayesian framework. The same model is used as a basis for analysis of differential methylation between multiple experimental conditions with the baySeq R package. We demonstrate the capability of this method to analyse complex data sets in an analysis of data derived from multiple Dicer-like mutants in Arabidopsis. This reveals several novel behaviours at distinct sets of loci in response to loss of one or more of the Dicer-like proteins that indicate an antagonistic relationship between the Dicer-like proteins at at least some methylation loci. Finally, we show in simulation studies that this approach can be significantly more powerful in the detection of differential methylation than many existing methods in data derived from both mammalian and plant systems. CONCLUSIONS The methods developed here make it possible to analyse high-throughput sequencing of the methylome of any given organism under a diverse set of experimental conditions. The methods are able to identify methylation loci and evaluate the likelihood that a region is truly methylated under any given experimental condition, allowing for downstream analyses that characterise differences between methylated and non-methylated regions of the genome. Futhermore, diverse patterns of differential methylation may also be characterised from these data.
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Affiliation(s)
- Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
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25
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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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26
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Masuta Y, Nozawa K, Takagi H, Yaegashi H, Tanaka K, Ito T, Saito H, Kobayashi H, Matsunaga W, Masuda S, Kato A, Ito H. Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture. PLANT & CELL PHYSIOLOGY 2017; 58:375-384. [PMID: 28013279 DOI: 10.1093/pcp/pcw202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
A transposition of a heat-activated retrotransposon named ONSEN required compromise of a small RNA-mediated epigenetic regulation that includes RNA-directed DNA methylation (RdDM) machinery after heat treatment. In the current study, we analyzed the transcriptional and transpositional activation of ONSEN to better understand the underlying molecular mechanism involved in the maintenance and/or induction of transposon activation in plant tissue culture. We found the transposition of heat-primed ONSEN during tissue culture independently of RdDM mutation. The heat activation of ONSEN transcripts was not significantly up-regulated in tissue culture compared with that in heat-stressed seedlings, indicating that the transposition of ONSEN was regulated independently of the transcript level. RdDM-related genes were up-regulated by heat stress in both tissue culture and seedlings. The level of DNA methylation of ONSEN did not show any change in tissue culture, and the amount of ONSEN-derived small RNAs was not affected by heat stress. The results indicated that the transposition of ONSEN was regulated by an alternative mechanism in addition to the RdDM-mediated epigenetic regulation in tissue culture. We applied the tissue culture-induced transposition of ONSEN to Japanese radish, an important breeding species of the family Brassicaceae. Several new insertions were detected in a regenerated plant derived from heat-stressed tissues and its self-fertilized progeny, revealing the possibility of molecular breeding without genetic modification.
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Affiliation(s)
- Yukari Masuta
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Kosuke Nozawa
- Faculty of Science, Hokkaido University, Sappor, Japan
| | | | | | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Tasuku Ito
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Hideyuki Saito
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Seiji Masuda
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Atsushi Kato
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University, Sappor, Japan
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27
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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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28
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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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29
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Makhzoum A, Yousefzadi M, Malik S, Gantet P, Tremouillaux-Guiller J. Strigolactone biology: genes, functional genomics, epigenetics and applications. Crit Rev Biotechnol 2015; 37:151-162. [PMID: 26669271 DOI: 10.3109/07388551.2015.1121967] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Strigolactones (SLs) represent an important new plant hormone class marked by their multifunctional role in plant and rhizosphere interactions. These compounds stimulate hyphal branching in arbuscular mycorrhizal fungi (AMF) and seed germination of root parasitic plants. In addition, they are involved in the control of plant architecture by inhibiting bud outgrowth as well as many other morphological and developmental processes together with other plant hormones such as auxins and cytokinins. The biosynthetic pathway of SLs that are derived from carotenoids was partially decrypted based on the identification of mutants from a variety of plant species. Only a few SL biosynthetic and regulated genes and related regulatory transcription factors have been identified. However, functional genomics and epigenetic studies started to give first elements on the modality of the regulation of SLs related genes. Since they control plant architecture and plant-rhizosphere interaction, SLs start to be used for agronomical and biotechnological applications. Furthermore, the genes involved in the SL biosynthetic pathway and genes regulated by SL constitute interesting targets for plant breeding. Therefore, it is necessary to decipher and better understand the genetic determinants of their regulation at different levels.
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Affiliation(s)
- Abdullah Makhzoum
- a Department of Biology , University of Western Ontario , London , Ontario , Canada
| | - Morteza Yousefzadi
- b Department of Marine Biology , Faculty of Marine Sciences and Technology, Hormozgan University , Bandar Abbas , Iran
| | - Sonia Malik
- c Health Sciences Graduate Program, Biological and Health Sciences Centre, Federal University of Maranhão , São Luís, MA , Brazil
| | - Pascal Gantet
- d Faculté des Sciences , Université de Montpellier , UMR DIADE , Montpellier , France , and
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30
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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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31
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Jiang F, Feng Z, Liu H, Zhu J. Involvement of Plant Stem Cells or Stem Cell-Like Cells in Dedifferentiation. FRONTIERS IN PLANT SCIENCE 2015; 6:1028. [PMID: 26635851 PMCID: PMC4649052 DOI: 10.3389/fpls.2015.01028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 11/05/2015] [Indexed: 05/02/2023]
Abstract
Dedifferentiation is the transformation of cells from a given differentiated state to a less differentiated or stem cell-like state. Stem cell-related genes play important roles in dedifferentiation, which exhibits similar histone modification and DNA methylation features to stem cell maintenance. Hence, stem cell-related factors possibly synergistically function to provide a specific niche beneficial to dedifferentiation. During callus formation in Arabidopsis petioles, cells adjacent to procambium cells (stem cell-like cells) are dedifferentiated and survive more easily than other cell types. This finding indicates that stem cells or stem cell-like cells may influence the dedifferentiating niche. In this paper, we provide a brief overview of stem cell maintenance and dedifferentiation regulation. We also summarize current knowledge of genetic and epigenetic mechanisms underlying the balance between differentiation and dedifferentiation. Furthermore, we discuss the correlation of stem cells or stem cell-like cells with dedifferentiation.
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Affiliation(s)
- Fangwei Jiang
- Department of Molecular and Cell Biology, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Zhenhua Feng
- Department of Molecular and Cell Biology, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Hailiang Liu
- Translational Center for Stem Cell Research, Tongji University School of Medicine, Tongji Hospital, Shanghai, China
- *Correspondence: Hailiang Liu, ; Jian Zhu,
| | - Jian Zhu
- Department of Molecular and Cell Biology, School of Life Science and Technology, Tongji University, Shanghai, China
- *Correspondence: Hailiang Liu, ; Jian Zhu,
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32
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Viñuela-Prieto JM, Sánchez-Quevedo MC, Alfonso-Rodríguez CA, Oliveira AC, Scionti G, Martín-Piedra MA, Moreu G, Campos A, Alaminos M, Garzón I. Sequential keratinocytic differentiation and maturation in a three-dimensional model of human artificial oral mucosa. J Periodontal Res 2014; 50:658-65. [PMID: 25470318 DOI: 10.1111/jre.12247] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND OBJECTIVE Oral mucosa shortage may limit or condition some clinical approaches in maxillofacial, periodontal and implant treatment. The availability of a human oral mucosa model generated by tissue engineering could help clinicians to address the lack of oral mucosa. In this work, we carried out a sequential maturation and differentiation study of the epithelial cell layer of an artificial human oral mucosa substitute based on fibrin-agarose biomaterials with fibroblasts and keratinocytes. MATERIAL AND METHODS Histological, immunohistochemical and gene expression analyses were carried out in artificial human oral mucosa models developed and cultured for 1, 2 and 3 wk. RESULTS Artificial oral mucosa models showed expression of tight junction proteins and cytokeratins from the first week of in vitro development. Mature samples of 3 wk of development subjected to air-liquid conditions showed signs of epithelial differentiation and expressed specific RNAs and proteins corresponding to adherent and gap junctions and basement lamina. Moreover, these mature samples overexpressed some desmosomal and tight junction transcripts, with gap junction components being downregulated. CONCLUSION These results suggest that bioengineered human oral mucosa substitutes form a well-developed epithelial layer that was very similar to human native tissues. In consequence, the epithelial layer could be fully functional in these oral mucosa substitutes, thus implying that these tissues may have clinical usefulness.
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Affiliation(s)
- J M Viñuela-Prieto
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain.,PhD Programme in Biomedicine, University of Granada, Granada, Spain
| | - M C Sánchez-Quevedo
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - C A Alfonso-Rodríguez
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - A C Oliveira
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - G Scionti
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - M A Martín-Piedra
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - G Moreu
- Department of Stomatology, Faculty of Dentistry, University of Granada, Granada, Spain
| | - A Campos
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - M Alaminos
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - I Garzón
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs, Granada, Spain
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33
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Identification of histological patterns in clinically affected and unaffected palm regions in dupuytren's disease. PLoS One 2014; 9:e112457. [PMID: 25379672 PMCID: PMC4224499 DOI: 10.1371/journal.pone.0112457] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 10/15/2014] [Indexed: 11/19/2022] Open
Abstract
Dupuytren's disease is a fibro-proliferative disease characterized by a disorder of the extracellular matrix (ECM) and high myofibroblast proliferation. However, studies failed to determine if the whole palm fascia is affected by the disease. The objective of this study was to analyze several components of the extracellular matrix of three types of tissues—Dupuytren's diseased contracture cords (DDC), palmar fascia clinically unaffected by Dupuytren's disease contracture (NPF), and normal forehand fascia (NFF). Histological analysis, quantification of cells recultured from each type of tissue, mRNA microarrays and immunohistochemistry for smooth muscle actin (SMA), fibrillar ECM components and non-fibrillar ECM components were carried out. The results showed that DDC samples had abundant fibrosis with reticular fibers and few elastic fibers, high cell proliferation and myofibroblasts, laminin and glycoproteins, whereas NFF did not show any of these findings. Interestingly, NPF tissues had more cells showing myofibroblasts differentiation and more collagen and reticular fibers, laminin and glycoproteins than NFF, although at lower level than DDC, with similar elastic fibers than DDC. Immunohistochemical expression of decorin was high in DDC, whereas versican was highly expressed NFF, with no differences for aggrecan. Cluster analysis revealed that the global expression profile of NPF was very similar to DDC, and reculturing methods showed that cells corresponding to DDC tissues proliferated more actively than NPF, and NPF more actively than NFF. All these results suggest that NPF tissues may be affected, and that a modification of the therapeutic approach used for the treatment of Dupuytren's disease should be considered.
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Somatic embryogenesis - Stress-induced remodeling of plant cell fate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:385-402. [PMID: 25038583 DOI: 10.1016/j.bbagrm.2014.07.005] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 01/13/2023]
Abstract
Plants as sessile organisms have remarkable developmental plasticity ensuring heir continuous adaptation to the environment. An extreme example is somatic embryogenesis, the initiation of autonomous embryo development in somatic cells in response to exogenous and/or endogenous signals. In this review I briefly overview the various pathways that can lead to embryo development in plants in addition to the fertilization of the egg cell and highlight the importance of the interaction of stress- and hormone-regulated pathways during the induction of somatic embryogenesis. Somatic embryogenesis can be initiated in planta or in vitro, directly or indirectly, and the requirement for dedifferentiation as well as the way to achieve developmental totipotency in the various systems is discussed in light of our present knowledge. The initiation of all forms of the stress/hormone-induced in vitro as well as the genetically provoked in planta somatic embryogenesis requires extensive and coordinated genetic reprogramming that has to take place at the chromatin level, as the embryogenic program is under strong epigenetic repression in vegetative plant cells. Our present knowledge on chromatin-based mechanisms potentially involved in the somatic-to-embryogenic developmental transition is summarized emphasizing the potential role of the chromatin to integrate stress, hormonal, and developmental pathways leading to the activation of the embryogenic program. The role of stress-related chromatin reorganization in the genetic instability of in vitro cultures is also discussed. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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35
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Teyssier C, Maury S, Beaufour M, Grondin C, Delaunay A, Le Metté C, Ader K, Cadene M, Label P, Lelu-Walter MA. In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses. PHYSIOLOGIA PLANTARUM 2014; 150:271-91. [PMID: 23789891 DOI: 10.1111/ppl.12081] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/08/2013] [Accepted: 05/28/2013] [Indexed: 05/22/2023]
Abstract
A global DNA methylation and proteomics approach was used to investigate somatic embryo maturation in hybrid larch. Each developmental step during somatic embryogenesis was associated with a distinct and significantly different global DNA methylation level: from 45.8% mC for undifferentiated somatic embryos (1-week proliferation) to 61.5% mC for immature somatic embryos (1-week maturation), while maturation was associated with a decrease in DNA methylation to 53.4% for mature cotyledonary somatic embryos (8-weeks maturation). The presence of 5-azacytidine (hypo-methylating agent) or hydroxyurea (hyper-methylating agent) in the maturation medium altered the global DNA methylation status of the embryogenic cultures, and significantly reduced both their relative growth rate and embryogenic potential, suggesting an important role for DNA methylation in embryogenesis. Maturation was also assessed by examining changes in the total protein profile. Storage proteins, identified as legumin- and vicilin-like, appeared at the precotyledonary stage. In the proteomic study, total soluble proteins were extracted from embryos after 1 and 8 weeks of maturation, and separated by two-dimensional gel electrophoresis. There were 147 spots which showed significant differences between the stages of maturation; they were found to be involved mainly in primary metabolism and the stabilization of the resulting metabolites. This indicated that the somatic embryo was still metabolically active at 8 weeks of maturation. This is the first report of analyses of global DNA methylation (including the effects of hyper- and hypo-treatments) and proteome during somatic embryogenesis in hybrid larch, and thus provides novel insights into maturation of conifer somatic embryos.
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Affiliation(s)
- Caroline Teyssier
- INRA, UR 0588, Research Unit for Breeding, Genetics and Physiology of Forest Trees, Orléans, F-45075, France
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36
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Solís MT, Chakrabarti N, Corredor E, Cortés-Eslava J, Rodríguez-Serrano M, Biggiogera M, Risueño MC, Testillano PS. Epigenetic changes accompany developmental programmed cell death in tapetum cells. PLANT & CELL PHYSIOLOGY 2014; 55:16-29. [PMID: 24151205 DOI: 10.1093/pcp/pct152] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The tapetum, the nursing tissue inside anthers, undergoes cellular degradation by programmed cell death (PCD) during late stages of microspore-early pollen development. Despite the key function of tapetum, little is known about the molecular mechanisms regulating this cell death process in which profound nuclear and chromatin changes occur. Epigenetic features (DNA methylation and histone modifications) have been revealed as hallmarks that establish the functional status of chromatin domains, but no evidence on the epigenetic regulation of PCD has been reported. DNA methylation is accomplished by DNA methyltransferases, among which DNA methyl transferase 1 (MET1) constitutes one of the CG maintenance methyltransferase in plants, also showing de novo methyltransferase activity. In this work, the changes in epigenetic marks during the PCD of tapetal cells have been investigated by a multidisciplinary approach to reveal the dynamics of DNA methylation and the pattern of expression of MET1 in relation to the main cellular changes of this PCD process which have also been characterized in two species, Brassica napus and Nicotiana tabacum. The results showed that tapetum PCD progresses with the increase in global DNA methylation and MET1 expression, epigenetic changes that accompanied the reorganization of the nuclear architecture and a high chromatin condensation, activity of caspase 3-like proteases and Cyt c release. The reported data indicate a relationship between the PCD process and the DNA methylation dynamics and MET1 expression in tapetal cells, suggesting a possible new role for the epigenetic marks in the nuclear events occurring during this cell death process and providing new insights into the epigenetic control of plant PCD.
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Affiliation(s)
- María-Teresa Solís
- Pollen Biotechnology of Crop Plants group, Biological Research Center, CIB, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Pulianmackal AJ, Kareem AVK, Durgaprasad K, Trivedi ZB, Prasad K. Competence and regulatory interactions during regeneration in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:142. [PMID: 24782880 PMCID: PMC3990048 DOI: 10.3389/fpls.2014.00142] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 03/25/2014] [Indexed: 05/08/2023]
Abstract
The ability to regenerate is widely exploited by multitudes of organisms ranging from unicellular bacteria to multicellular plants for their propagation and repair. But the levels of competence for regeneration vary from species to species. While variety of living cells of a plant display regeneration ability, only a few set of cells maintain their stemness in mammals. This highly pliable nature of plant cells in-terms of regeneration can be attributed to their high developmental plasticity. De novo organ initiation can be relatively easily achieved in plants by proper hormonal regulations. Elevated levels of plant hormone auxin induces the formation of proliferating mass of pluripotent cells called callus, which predominantly express lateral root meristem markers and hence is having an identity similar to lateral root primordia. Organ formation can be induced from the callus by modulating the ratio of hormones. An alternative for de novo organogenesis is by the forced expression of plant specific transcription factors. The mechanisms by which plant cells attain competence for regeneration on hormonal treatment or forced expression remain largely elusive. Recent studies have provided some insight into how the epigenetic modifications in plants affect this competence. In this review we discuss the present understanding of regenerative biology in plants and scrutinize the future prospectives of this topic. While discussing about the regeneration in the sporophyte of angiosperms which is well studied, here we outline the regenerative biology of the gametophytic phase and discuss about various strategies of regeneration that have evolved in the domain of life so that a common consensus on the entire process of regeneration can be made.
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Affiliation(s)
| | | | | | | | - Kalika Prasad
- *Correspondence: Kalika Prasad, School of Biology Indian Institute of Science Education and Research, Thiruvananthapuram, India e-mail:
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Gohlke J, Deeken R. Plant responses to Agrobacterium tumefaciens and crown gall development. FRONTIERS IN PLANT SCIENCE 2014; 5:155. [PMID: 24795740 PMCID: PMC4006022 DOI: 10.3389/fpls.2014.00155] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/02/2014] [Indexed: 05/17/2023]
Abstract
Agrobacterium tumefaciens causes crown gall disease on various plant species by introducing its T-DNA into the genome. Therefore, Agrobacterium has been extensively studied both as a pathogen and an important biotechnological tool. The infection process involves the transfer of T-DNA and virulence proteins into the plant cell. At that time the gene expression patterns of host plants differ depending on the Agrobacterium strain, plant species and cell-type used. Later on, integration of the T-DNA into the plant host genome, expression of the encoded oncogenes, and increase in phytohormone levels induce a fundamental reprogramming of the transformed cells. This results in their proliferation and finally formation of plant tumors. The process of reprogramming is accompanied by altered gene expression, morphology and metabolism. In addition to changes in the transcriptome and metabolome, further genome-wide ("omic") approaches have recently deepened our understanding of the genetic and epigenetic basis of crown gall tumor formation. This review summarizes the current knowledge about plant responses in the course of tumor development. Special emphasis is placed on the connection between epigenetic, transcriptomic, metabolomic, and morphological changes in the developing tumor. These changes not only result in abnormally proliferating host cells with a heterotrophic and transport-dependent metabolism, but also cause differentiation and serve as mechanisms to balance pathogen defense and adapt to abiotic stress conditions, thereby allowing the coexistence of the crown gall and host plant.
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Affiliation(s)
- Jochen Gohlke
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
| | - Rosalia Deeken
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of WuerzburgWuerzburg, Germany
- *Correspondence: Rosalia Deeken, Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of Wuerzburg, Julius-von-Sachs-Platz 2, 97082 Wuerzburg, Germany e-mail:
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Hou PQ, Lee YI, Hsu KT, Lin YT, Wu WZ, Lin JY, Nam TN, Fu SF. Functional characterization of Nicotiana benthamiana chromomethylase 3 in developmental programs by virus-induced gene silencing. PHYSIOLOGIA PLANTARUM 2014; 150:119-32. [PMID: 23683172 DOI: 10.1111/ppl.12071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 05/02/2013] [Accepted: 05/03/2013] [Indexed: 05/11/2023]
Abstract
DNA methylation is essential for normal developmental processes and genome stability. DNA methyltransferases are key enzymes catalyzing DNA methylation. Chromomethylase (CMT) genes are specific to the plant kingdom and encode chromodomain-containing methyltransferases. However, the function of CMT genes in plants remains elusive. In this study, we isolated and characterized a CMT gene from Nicotiana benthamiana, designated NbCMT3. Alignment of the NbCMT3 amino acid sequence with other plant CMT3s showed conservation of bromo-adjacent-homology and methyltransferase catalytic domains. We investigated the expression patterns of NbCMT3 and its function in developmental programs. NbCMT3 was expressed predominately in proliferating tissues such as apical shoots and young leaves. NbCMT3 protein showed a nuclear location, which could be related to its putative cellular functions. Knocking down NbCMT3 expression by virus-induced gene silencing revealed its vital role(s) in leaf morphogenesis. The formation of palisade cells was defective in NbCMT3-silenced plants as compared with controls. NbCMT3 has a role in developmental programs.
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Affiliation(s)
- Pin-Quan Hou
- Department of Biology, National Chunghua University of Education, No.1, Jin-De Road, 500, Changhua, Taiwan
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Jung KH, Gho HJ, Giong HK, Chandran AKN, Nguyen QN, Choi H, Zhang T, Wang W, Kim JH, Choi HK, An G. Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data. RICE (NEW YORK, N.Y.) 2013; 6:19. [PMID: 24280533 PMCID: PMC4883688 DOI: 10.1186/1939-8433-6-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/07/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Accumulation of genome-wide transcriptome data provides new insight on a genomic scale which cannot be gained by analyses of individual data. The majority of rice (O. sativa) species are japonica and indica cultivars. Genome-wide identification of genes differentially expressed between japonica and indica cultivars will be very useful in understanding the domestication and evolution of rice species. RESULTS In this study, we analyzed 983 of the 1866 entries in the Affymetrix array data in the public database: 595 generated from indica and 388 from japonica rice cultivars. To discover differentially expressed genes in each cultivar, we performed significance analysis of microarrays for normalized data, and identified 490 genes preferentially expressed in japonica and 104 genes in indica. Gene Ontology analyses revealed that defense response-related genes are significantly enriched in both cultivars, indicating that japonica and indica might be under strong selection pressure for these traits during domestication. In addition, 36 (34.6%) of 104 genes preferentially expressed in indica and 256 (52.2%) of 490 genes preferentially expressed in japonica were annotated as genes of unknown function. Biotic stress overview in the MapMan toolkit revealed key elements of the signaling pathway for defense response in japonica or indica eQTLs. CONCLUSIONS The percentage of screened genes preferentially expressed in indica was 4-fold higher (34.6%) and that in japonica was 5-fold (52.2%) higher than expected (11.1%), suggesting that genes of unknown function are responsible for the novel traits that distinguish japonica and indica cultivars. The identification of 10 functionally characterized genes expressed preferentially in either japonica or indica highlights the significance of our candidate genes during the domestication of rice species. Functional analysis of the roles of individual components of stress-mediated signaling pathways will shed light on potential molecular mechanisms to improve disease resistance in rice.
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Affiliation(s)
- Ki-Hong Jung
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Hyun-Jung Gho
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Hoi-Khoanh Giong
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Anil Kumar Nalini Chandran
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Quynh-Nga Nguyen
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - HeeBak Choi
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
| | - Tian Zhang
- />CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China
| | - Wen Wang
- />CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China
| | - Jin-Hyun Kim
- />Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
| | - Hong-Kyu Choi
- />Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
| | - Gynheung An
- />Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701 Republic of Korea
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Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH. Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC PLANT BIOLOGY 2013; 13:92. [PMID: 23799904 PMCID: PMC3728041 DOI: 10.1186/1471-2229-13-92] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 06/12/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation. RESULTS We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes. CONCLUSIONS DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.
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Affiliation(s)
- Kelly Vining
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle R Pomraning
- Molecular and Cellular Biology Program, Corvallis, OR 97331, USA
- Department of Biochemistry and Biophysics, Corvallis, OR 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | | | - Cathleen Ma
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Yanming Di
- Statistics Department, Oregon State University, Corvallis, Oregon, USA
| | - Todd C Mockler
- The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Michael Freitag
- Molecular and Cellular Biology Program, Corvallis, OR 97331, USA
- Department of Biochemistry and Biophysics, Corvallis, OR 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
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Hardcastle TJ. High-throughput sequencing of cytosine methylation in plant DNA. PLANT METHODS 2013; 9:16. [PMID: 23758782 PMCID: PMC3691832 DOI: 10.1186/1746-4811-9-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 03/29/2013] [Indexed: 05/26/2023]
Abstract
: Cytosine methylation is a significant and widespread regulatory factor in plant systems. Methods for the high-throughput sequencing of methylation have allowed a greatly improved characterisation of the methylome. Here we discuss currently available methods for generation and analysis of high-throughput sequencing of methylation data. We also discuss the results previously acquired through sequencing plant methylomes, and highlight remaining challenges in this field.
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Affiliation(s)
- Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB23EA, UK.
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K?í?ová K, Depicker A, Kova?ík A. Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture. Epigenetics 2013; 8:666-76. [PMID: 23770973 PMCID: PMC3857346 DOI: 10.4161/epi.24613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 11/19/2022] Open
Abstract
In plants, silencing is usually accompanied by DNA methylation and heterochromatic histone marks. We studied these epigenetic modifications in different epialleles of 35S promoter (P35S)-driven tobacco transgenes. In locus 1, the T-DNA was organized as an inverted repeat, and the residing neomycin phosphotransferase II reporter gene (P35S-nptII) was silenced at the posttranscriptional (PTGS) level. Transcriptionally silenced (TGS) epialleles were generated by trans-acting RNA signals in hybrids or in a callus culture. PTGS to TGS conversion in callus culture was accompanied by loss of the euchromatic H3K4me3 mark in the transcribed region of locus 1, but this change was not transmitted to the regenerated plants from these calli. In contrast, cytosine methylation that spread from the transcribed region into the promoter was maintained in regenerants. Also, the TGS epialleles generated by trans-acting siRNAs did not change their active histone modifications. Thus, both TGS and PTGS epialleles exhibit euchromatic (H3K4me3 and H3K9ac) histone modifications despite heavy DNA methylation in the promoter and transcribed region, respectively. However, in the TGS locus (271), abundant heterochromatic H3K9me2 marks and DNA methylation were present on P35S. Heterochromatic histone modifications are not automatically installed on transcriptionally silenced loci in tobacco, suggesting that repressive histone marks and cytosine methylation may be uncoupled. However, transient loss of euchromatic modifications may guide de novo DNA methylation leading to formation of stable repressed epialleles with recovered eukaryotic marks. Compilation of available data on epigenetic modification of inactivated P35S in different systems is provided.
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Affiliation(s)
- Kate?ina K?í?ová
- Institute of Biophysics, Academy of Sciences; Královopolská, Brno, Czech Republic
| | - Ann Depicker
- Department of Plant Systems Biology; VIB; Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Gent, Belgium
| | - Ale? Kova?ík
- Institute of Biophysics, Academy of Sciences; Královopolská, Brno, Czech Republic
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Jin X, Pang Y, Jia F, Xiao G, Li Q, Zhu Y. A potential role for CHH DNA methylation in cotton fiber growth patterns. PLoS One 2013; 8:e60547. [PMID: 23593241 PMCID: PMC3625195 DOI: 10.1371/journal.pone.0060547] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/27/2013] [Indexed: 11/18/2022] Open
Abstract
DNA methylation controls many aspects of plant growth and development. Here, we report a novel annual growth potential change that may correlate with changes in levels of the major DNA demethylases and methyltransferases in cotton ovules harvested at different times of the year. The abundances of DNA demethylases, at both the mRNA and protein levels, increased significantly from February to August and decreased during the remainder of the 12-month period, with the opposite pattern observed for DNA methyltransferases. Over the course of one year, substantial changes in methylcytosine content was observed at certain CHH sites (H = A, C, or T) in the promoter regions of the ETHYLENE RESPONSIVE FACTOR 6 (ERF6), SUPPRESSION OF RVS 161 DELTA 4 (SUR4) and 3-KETOACYL-COA SYNTHASE 13 (KCS13), which regulate cotton fiber growth. Three independent techniques were used to confirm the annual fluctuations in DNA methylation. Furthermore, in homozygous RNAi lines specifically targeting REPRESSOR OF SILENCING 1 (ROS1, a conserved DNA demethylase domain), promotion of DNA methylation significantly reduced fiber growth during August.
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Affiliation(s)
- Xiang Jin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yu Pang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Fangxing Jia
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Guanghui Xiao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Qin Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yuxian Zhu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- National Center for Plant Gene Research (Beijing), Beijing, China
- * E-mail:
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Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang GL, Meyers BC, Jacobsen SE. Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife 2013; 2:e00354. [PMID: 23539454 PMCID: PMC3601819 DOI: 10.7554/elife.00354] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 02/11/2013] [Indexed: 12/30/2022] Open
Abstract
Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several regenerated rice lines. We found that all tested regenerated plants had significant losses of methylation compared to non-regenerated plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability. DOI:http://dx.doi.org/10.7554/eLife.00354.001.
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Affiliation(s)
- Hume Stroud
- Department of Molecular, Cell and Developmental Biology , University of California, Los Angeles , Los Angeles , United States
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Appels R, Barrero R, Bellgard M. Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals. Funct Integr Genomics 2013; 13:1-9. [PMID: 23494190 PMCID: PMC3605488 DOI: 10.1007/s10142-013-0319-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/02/2013] [Accepted: 03/03/2013] [Indexed: 11/27/2022]
Abstract
Advances in our understanding of genome structure provide consistent evidence for the existence of a core genome representing species classically defined by phenotype, as well as conditionally dispensable components of the genome that shows extensive variation between individuals of a given species. Generally, conservation of phenotypic features between species reflects conserved features of the genome; however, this is evidently not necessarily always the case as demonstrated by the analysis of the tunicate chordate Oikopleura dioica. In both plants and animals, the methylation activity of DNA and histones continues to present new variables for modifying (eventually) the phenotype of an organism and provides for structural variation that builds on the point mutations, rearrangements, indels, and amplification of retrotransposable elements traditionally considered. The translation of the advances in the structure/function analysis of the genome to industry is facilitated through the capture of research outputs in "toolboxes" that remain accessible in the public domain.
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Affiliation(s)
- R. Appels
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| | - R. Barrero
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| | - M. Bellgard
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
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Latrasse D, Jégu T, Meng PH, Mazubert C, Hudik E, Delarue M, Charon C, Crespi M, Hirt H, Raynaud C, Bergounioux C, Benhamed M. Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator. Nucleic Acids Res 2013; 41:2907-17. [PMID: 23341037 PMCID: PMC3597657 DOI: 10.1093/nar/gks1458] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 12/07/2012] [Accepted: 12/14/2012] [Indexed: 12/16/2022] Open
Abstract
Because regulation of its activity is instrumental either to support cell proliferation and growth or to promote cell death, the universal myo-inositol phosphate synthase (MIPS), responsible for myo-inositol biosynthesis, is a critical enzyme of primary metabolism. Surprisingly, we found this enzyme to be imported in the nucleus and to interact with the histone methyltransferases ATXR5 and ATXR6, raising the question of whether MIPS1 has a function in transcriptional regulation. Here, we demonstrate that MIPS1 binds directly to its promoter to stimulate its own expression by locally inhibiting the spreading of ATXR5/6-dependent heterochromatin marks coming from a transposable element. Furthermore, on activation of pathogen response, MIPS1 expression is reduced epigenetically, providing evidence for a complex regulatory mechanism acting at the transcriptional level. Thus, in plants, MIPS1 appears to have evolved as a protein that connects cellular metabolism, pathogen response and chromatin remodeling.
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Affiliation(s)
- David Latrasse
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Pin-Hong Meng
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Christelle Mazubert
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Elodie Hudik
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Marianne Delarue
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Céline Charon
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Martin Crespi
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Heribert Hirt
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
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Benoit M, Layat E, Tourmente S, Probst AV. Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci. Gene 2013; 526:39-45. [PMID: 23410919 DOI: 10.1016/j.gene.2013.01.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/16/2013] [Accepted: 01/23/2013] [Indexed: 01/01/2023]
Abstract
The Arabidopsis chromosomes contain conspicuous heterochromatin domains comprising the repetitive 45S and 5S ribosomal DNA loci as well as centromeric and pericentromeric repeats that organize into chromocenters during interphase. During developmental phase transitions such as seed maturation, germination, seedling growth and flowering that require large-scale reprogramming of gene expression patterns, the organization of repetitive sequences into chromocenters dynamically changes. Here we illustrate recent studies that shed light on the heterochromatin dynamics in cotyledons, the first aerial tissues preformed in the embryo, and in true leaves. We will summarize available data for the 5S rDNA repeat loci, in particular their chromatin organization and expression dynamics during the first days of post-germination development, and discuss how the plant accommodates 5S rRNA transcription during large-scale chromatin reorganization events.
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Affiliation(s)
- Matthias Benoit
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 24 Avenue des Landais, BP 80026, 63171 Aubière Cedex, France.
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49
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De-la-Peña C, Nic-Can G, Ojeda G, Herrera-Herrera JL, López-Torres A, Wrobel K, Robert-Díaz ML. KNOX1 is expressed and epigenetically regulated during in vitro conditions in Agave spp. BMC PLANT BIOLOGY 2012; 12:203. [PMID: 23126409 PMCID: PMC3541254 DOI: 10.1186/1471-2229-12-203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/23/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND The micropropagation is a powerful tool to scale up plants of economical and agronomical importance, enhancing crop productivity. However, a small but growing body of evidence suggests that epigenetic mechanisms, such as DNA methylation and histone modifications, can be affected under the in vitro conditions characteristic of micropropagation. Here, we tested whether the adaptation to different in vitro systems (Magenta boxes and Bioreactors) modified epigenetically different clones of Agave fourcroydes and A. angustifolia. Furthermore, we assessed whether these epigenetic changes affect the regulatory expression of KNOTTED1-like HOMEOBOX (KNOX) transcription factors. RESULTS To gain a better understanding of epigenetic changes during in vitro and ex vitro conditions in Agave fourcroydes and A. angustifolia, we analyzed global DNA methylation, as well as different histone modification marks, in two different systems: semisolid in Magenta boxes (M) and temporary immersion in modular Bioreactors (B). No significant difference was found in DNA methylation in A. fourcroydes grown in either M or B. However, when A. fourcroydes was compared with A. angustifolia, there was a two-fold difference in DNA methylation between the species, independent of the in vitro system used. Furthermore, we detected an absence or a low amount of the repressive mark H3K9me2 in ex vitro conditions in plants that were cultured earlier either in M or B. Moreover, the expression of AtqKNOX1 and AtqKNOX2, on A. fourcroydes and A. angustifolia clones, is affected during in vitro conditions. Therefore, we used Chromatin ImmunoPrecipitation (ChIP) to know whether these genes were epigenetically regulated. In the case of AtqKNOX1, the H3K4me3 and H3K9me2 were affected during in vitro conditions in comparison with AtqKNOX2. CONCLUSIONS Agave clones plants with higher DNA methylation during in vitro conditions were better adapted to ex vitro conditions. In addition, A. fourcroydes and A. angustifolia clones displayed differential expression of the KNOX1 gene during in vitro conditions, which is epigenetically regulated by the H3K4me3 and H3K9me2 marks. The finding of an epigenetic regulation in key developmental genes will make it important in future studies to identify factors that help to find climate-resistant micropropagated plants.
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Affiliation(s)
- Clelia De-la-Peña
- Unidad Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida, Yucatán, CP 97200, México
| | - Geovanny Nic-Can
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Periférico Norte. Km 33.5, Tablaje catastral 13615 Col. Chuburná de Hidalgo Inn, Merida, Yucatán, C. P. 97203, Mexico
| | - Gabriel Ojeda
- Unidad Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida, Yucatán, CP 97200, México
| | - José L Herrera-Herrera
- Unidad Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida, Yucatán, CP 97200, México
| | | | - Kazimierz Wrobel
- Facultad de Química, Universidad de Guanajuato, Guanajuato, 36000, México
| | - Manuel L Robert-Díaz
- Unidad Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida, Yucatán, CP 97200, México
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50
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Maury S, Trap-Gentil MV, Hébrard C, Weyens G, Delaunay A, Barnes S, Lefebvre M, Joseph C. Genic DNA methylation changes during in vitro organogenesis: organ specificity and conservation between parental lines of epialleles. PHYSIOLOGIA PLANTARUM 2012; 146:321-335. [PMID: 22486767 DOI: 10.1111/j.1399-3054.2012.01634.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
During differentiation, in vitro organogenesis calls for the adjustment of the gene expression program toward a new fate. The role of epigenetic mechanisms including DNA methylation is suggested but little is known about the loci affected by DNA methylation changes, particularly in agronomic plants for witch in vitro technologies are useful such as sugar beet. Here, three pairs of organogenic and non-organogenic in vitro cell lines originating from different sugar beet (Beta vulgaris altissima) cultivars were used to assess the dynamics of DNA methylation at the global or genic levels during shoot or root regeneration. The restriction landmark genome scanning for methylation approach was applied to provide a direct quantitative epigenetic assessment of several CG methylated genes without prior knowledge of gene sequence that is particularly adapted for studies on crop plants without a fully sequenced genome. The cloned sequences had putative roles in cell proliferation, differentiation or unknown functions and displayed organ-specific DNA polymorphism for methylation and changes in expression during in vitro organogenesis. Among them, a potential ubiquitin extension protein 6 (UBI6) was shown, in different cultivars, to exhibit repeatable variations of DNA methylation and gene expression during shoot regeneration. In addition, abnormal development and callogenesis were observed in a T-DNA insertion mutant (ubi6) for a homologous sequence in Arabidopsis. Our data showed that DNA methylation is changed in an organ-specific way for genes exhibiting variations of expression and playing potential role during organogenesis. These epialleles could be conserved between parental lines opening perspectives for molecular markers.
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Affiliation(s)
- Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, USC1328 ARCHE INRA, rue de Chartres, BP 6759, Faculté des Sciences, Université d'Orléans, 45067 Orléans cedex 2, France.
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