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Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
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Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
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Wang W, Zhang X, Garcia S, Leitch AR, Kovařík A. Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity (Edinb) 2023; 131:179-188. [PMID: 37402824 PMCID: PMC10462631 DOI: 10.1038/s41437-023-00634-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
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Affiliation(s)
- Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | - Andrew R Leitch
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61200, Czech Republic.
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Zhang Y, Viejo M, Yakovlev I, Tengs T, Krokene P, Hytönen T, Grini PE, Fossdal CG. Major transcriptomic differences are induced by warmer temperature conditions experienced during asexual and sexual reproduction in Fragaria vesca ecotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1213311. [PMID: 37521931 PMCID: PMC10379642 DOI: 10.3389/fpls.2023.1213311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023]
Abstract
A major challenge for plants in a rapidly changing climate is to adapt to rising temperatures. Some plants adapt to temperature conditions by generating an epigenetic memory that can be transmitted both meiotically and mitotically. Such epigenetic memories may increase phenotypic variation to global warming and provide time for adaptation to occur through classical genetic selection. The goal of this study was to understand how warmer temperature conditions experienced during sexual and asexual reproduction affect the transcriptomes of different strawberry (Fragaria vesca) ecotypes. We let four European F. vesca ecotypes reproduce at two contrasting temperatures (18 and 28°C), either asexually through stolon formation for several generations, or sexually by seeds (achenes). We then analyzed the transcriptome of unfolding leaves, with emphasis on differential expression of genes belonging to the epigenetic machinery. For asexually reproduced plants we found a general transcriptomic response to temperature conditions but for sexually reproduced plants we found less significant responses. We predicted several splicing isoforms for important genes (e.g. a SOC1, LHY, and SVP homolog), and found significantly more differentially presented splicing event variants following asexual vs. sexual reproduction. This difference could be due to the stochastic character of recombination during meiosis or to differential creation or erasure of epigenetic marks during embryogenesis and seed development. Strikingly, very few differentially expressed genes were shared between ecotypes, perhaps because ecotypes differ greatly both genetically and epigenetically. Genes related to the epigenetic machinery were predominantly upregulated at 28°C during asexual reproduction but downregulated after sexual reproduction, indicating that temperature-induced change affects the epigenetic machinery differently during the two types of reproduction.
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Affiliation(s)
- Yupeng Zhang
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
- EVOGENE, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marcos Viejo
- Department of Functional Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Igor Yakovlev
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Torstein Tengs
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Paal Krokene
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Paul E. Grini
- EVOGENE, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carl Gunnar Fossdal
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
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Vatov E, Zentgraf U, Ludewig U. Moderate DNA methylation changes associated with nitrogen remobilization and leaf senescence in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4733-4752. [PMID: 35552412 PMCID: PMC9366325 DOI: 10.1093/jxb/erac167] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The lifespan of plants is restricted by environmental and genetic components. Following the transition to reproductive growth, leaf senescence ends cellular life in monocarpic plants to remobilize nutrients to storage organs. In Arabidopsis, we initially observed altered leaf to seed ratios, faster senescence progression, altered leaf nitrogen recovery after transient nitrogen removal, and ultimately enhanced nitrogen remobilization from the leaves in two methylation mutants (ros1 and the triple dmr1/2 cmt3 knockout). Analysis of the DNA methylome in wild type Col-0 leaves identified an initial moderate decline of cytosine methylation with progressing leaf senescence, predominantly in the CG context. Late senescence was associated with moderate de novo methylation of cytosines, primarily in the CHH context. Relatively few differentially methylated regions, including one in the ROS1 promoter linked to down-regulation of ROS1, were present, but these were unrelated to known senescence-associated genes. Differential methylation patterns were identified in transcription factor binding sites, such as the W-boxes that are targeted by WRKYs. Methylation in artificial binding sites impaired transcription factor binding in vitro. However, it remains unclear how moderate methylome changes during leaf senescence are linked with up-regulated genes during senescence.
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Affiliation(s)
- Emil Vatov
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, D-70593, Germany
- Center for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, D-72076, Germany
| | - Ulrike Zentgraf
- Center for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, D-72076, Germany
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Liu Y, Liu Q, Xu X, Xiao Y, Liao M, Deng Q, Zhang H, Lin L. Effects of intercropping with Solanum photeinocarpum and its post-grafting generations on cadmium accumulation in loquat ( Eriobotrya japonica). INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 24:753-762. [PMID: 34514885 DOI: 10.1080/15226514.2021.1972927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) contamination of orchard soils is a global problem that has been increasing. To decrease the Cd accumulation in fruits, intercropping the orchard crops with hyperaccumulator plants has been used for soil remediation. A pot and a field experiment were conducted to study the effects of intercropping the potential Cd-hyperaccumulator Solanum photeinocarpum and its post-grafting generations with loquat (Eriobotrya japonica) on the growth and Cd uptake of these two plant species. In the pot experiment, intercropping improved the biomass, Cd content, Cd extraction, and root-to-shoot Cd translocation in both species. Intercropping increased the DNA methylation levels, antioxidant enzyme activity, and soluble protein content of loquat seedlings. These results indicate that intercropping could improve the phytoremediation of S. photeinocarpum and its post-grafting generations and increase the Cd uptake in loquat seedlings. In the field experiment, intercropping increased the Cd contents in the old branches, while it decreased that in the young branches and fruits of loquat. These findings indicate that intercropping could increase the Cd uptake in old tissues but reduce the Cd uptake in young tissues and fruits of loquat. So, intercropping loquat with S. photeinocarpum and its post-grafting generations could be used in Cd-contaminated orchards.
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Affiliation(s)
- Yuan Liu
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Qin Liu
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Xiangting Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yunying Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ming'an Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Qunxian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Huifen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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Lephatsi MM, Meyer V, Piater LA, Dubery IA, Tugizimana F. Plant Responses to Abiotic Stresses and Rhizobacterial Biostimulants: Metabolomics and Epigenetics Perspectives. Metabolites 2021; 11:457. [PMID: 34357351 PMCID: PMC8305699 DOI: 10.3390/metabo11070457] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 01/14/2023] Open
Abstract
In response to abiotic stresses, plants mount comprehensive stress-specific responses which mediate signal transduction cascades, transcription of relevant responsive genes and the accumulation of numerous different stress-specific transcripts and metabolites, as well as coordinated stress-specific biochemical and physiological readjustments. These natural mechanisms employed by plants are however not always sufficient to ensure plant survival under abiotic stress conditions. Biostimulants such as plant growth-promoting rhizobacteria (PGPR) formulation are emerging as novel strategies for improving crop quality, yield and resilience against adverse environmental conditions. However, to successfully formulate these microbial-based biostimulants and design efficient application programs, the understanding of molecular and physiological mechanisms that govern biostimulant-plant interactions is imperatively required. Systems biology approaches, such as metabolomics, can unravel insights on the complex network of plant-PGPR interactions allowing for the identification of molecular targets responsible for improved growth and crop quality. Thus, this review highlights the current models on plant defence responses to abiotic stresses, from perception to the activation of cellular and molecular events. It further highlights the current knowledge on the application of microbial biostimulants and the use of epigenetics and metabolomics approaches to elucidate mechanisms of action of microbial biostimulants.
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Affiliation(s)
- Motseoa M. Lephatsi
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Vanessa Meyer
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, WITS, Johannesburg 2050, South Africa;
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa
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Papanikolaou S, Vourda A, Syggelos S, Gyftopoulos K. Cell Plasticity and Prostate Cancer: The Role of Epithelial-Mesenchymal Transition in Tumor Progression, Invasion, Metastasis and Cancer Therapy Resistance. Cancers (Basel) 2021; 13:cancers13112795. [PMID: 34199763 PMCID: PMC8199975 DOI: 10.3390/cancers13112795] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Simple Summary Although epithelial-to-mesenchymal transition (EMT) is a well-known cellular process involved during normal embryogenesis and wound healing, it also has a dark side; it is a complex process that provides tumor cells with a more aggressive phenotype, facilitating tumor metastasis and even resistance to therapy. This review focuses on the key pathways of EMT in the pathogenesis of prostate cancer and the development of metastases and evasion of currently available treatments. Abstract Prostate cancer, the second most common malignancy in men, is characterized by high heterogeneity that poses several therapeutic challenges. Epithelial–mesenchymal transition (EMT) is a dynamic, reversible cellular process which is essential in normal embryonic morphogenesis and wound healing. However, the cellular changes that are induced by EMT suggest that it may also play a central role in tumor progression, invasion, metastasis, and resistance to current therapeutic options. These changes include enhanced motility and loss of cell–cell adhesion that form a more aggressive cellular phenotype. Moreover, the reverse process (MET) is a necessary element of the metastatic tumor process. It is highly probable that this cell plasticity reflects a hybrid state between epithelial and mesenchymal status. In this review, we describe the underlying key mechanisms of the EMT-induced phenotype modulation that contribute to prostate tumor aggressiveness and cancer therapy resistance, in an effort to provide a framework of this complex cellular process.
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Lin L, Sun J, Cui T, Zhou X, Liao M, Huan Y, Yang L, Wu C, Xia X, Wang Y, Li Z, Zhu J, Wang Z. Selenium accumulation characteristics of Cyphomandra betacea ( Solanum betaceum) seedlings. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1375-1383. [PMID: 32647455 PMCID: PMC7326803 DOI: 10.1007/s12298-020-00838-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/23/2020] [Accepted: 06/12/2020] [Indexed: 05/13/2023]
Abstract
A pot experiment was conducted to study the selenium (Se) accumulation characteristics and the tolerance of Cyphomandra betacea (Solanum betaceum) seedlings under different soil Se concentrations. The 5 mg/kg soil Se concentration increased the C. betacea seedling biomass and photosynthetic pigment contents (chlorophyll a, chlorophyll b, total chlorophyll, and carotenoid), whereas the other soil Se concentrations (10, 25, and 50 mg/kg) inhibited seedling growth. Increases in the soil Se concentrations tended to decrease the superoxide dismutase activity and soluble protein content, but had the opposite effect on the peroxidase and catalase activities. The 5, 10, and 25 mg/kg soil Se concentrations decreased the DNA methylation levels of C. betacea seedlings because of an increase in demethylation patterns (versus 0 mg/kg), whereas the 50 mg/kg soil Se concentration increased the DNA methylation levels because of an increase in hypermethylation patterns (versus 0 mg/kg). Increases in the soil Se concentrations were accompanied by an increasing trend in the Se content of C. betacea seedlings. Moreover, the amount of Se extracted by the shoots was highest for the 25 mg/kg soil Se concentration. Therefore, C. betacea may be able to accumulate relatively large amounts of Se and its growth may be promoted in 5 mg/kg soil Se.
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Affiliation(s)
- Linjin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Jing Sun
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Tonghao Cui
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Xiong Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Ming’an Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Yunmin Huan
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Liu Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Caifang Wu
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Xianmin Xia
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Yuxi Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Zhiyu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Jinpeng Zhu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan China
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Liao Y, Xu K. Epigenetic regulation of prostate cancer: the theories and the clinical implications. Asian J Androl 2020; 21:279-290. [PMID: 30084432 PMCID: PMC6498736 DOI: 10.4103/aja.aja_53_18] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Epigenetics is the main mechanism that controls transcription of specific genes with no changes in the underlying DNA sequences. Epigenetic alterations lead to abnormal gene expression patterns that contribute to carcinogenesis and persist throughout disease progression. Because of the reversible nature, epigenetic modifications emerge as promising anticancer drug targets. Several compounds have been developed to reverse the aberrant activities of enzymes involved in epigenetic regulation, and some of them show encouraging results in both preclinical and clinical studies. In this article, we comprehensively review the up-to-date roles of epigenetics in the development and progression of prostate cancer. We especially focus on three epigenetic mechanisms: DNA methylation, histone modifications, and noncoding RNAs. We elaborate on current models/theories that explain the necessity of these epigenetic programs in driving the malignant phenotypes of prostate cancer cells. In particular, we elucidate how certain epigenetic regulators crosstalk with critical biological pathways, such as androgen receptor (AR) signaling, and how the cooperation dynamically controls cancer-oriented transcriptional profiles. Restoration of a "normal" epigenetic landscape holds promise as a cure for prostate cancer, so we concluded by highlighting particular epigenetic modifications as diagnostic and prognostic biomarkers or new therapeutic targets for treatment of the disease.
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Affiliation(s)
- Yiji Liao
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Kexin Xu
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA.,Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
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Lin L, Wu C, Wang J, Liao M, Yang D, Deng H, Lv X, Xia H, Liang D, Deng Q. Effects of reciprocal hybridization on cadmium accumulation in F1 hybrids of two Solanum photeinocarpum ecotypes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:7120-7129. [PMID: 31883078 DOI: 10.1007/s11356-019-07446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
In this study, farmland and mining ecotypes of Solanum photeinocarpum (a potential cadmium (Cd) hyperaccumulator plant) were reciprocally hybridized each other, and the Cd accumulation characteristics of the F1 hybrids were studied. In pot experiments, higher biomasses and Cd extraction abilities were found for two S. photeinocarpum F1 hybrids than for the parents, but the Cd contents in various organs were lower in the hybrids than the parents. However, the differences between the Cd contents in the two hybrids were not significant. The antioxidant enzyme (superoxide dismutase and peroxidase) activities were higher for the S. photeinocarpum F1 hybrids than the parents. Less DNA methylation was found in the hybrids than the parents because more demethylation occurred in the hybrids than the parents. The biomass, Cd content, and Cd extraction ability effects in field experiments were similar to the effects in the pot experiments. It was concluded that reciprocally hybridizing different S. photeinocarpum ecotypes improved the ability of S. photeinocarpum to be used to phytoremediate contaminated land.
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Affiliation(s)
- Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Caifang Wu
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming'an Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Daiyu Yang
- Ya'an Poverty Alleviation and Immigration Bureau, Ya'an, 625000, China
| | - Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiulan Lv
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Xia
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dong Liang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qunxian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
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Kuźnicki D, Meller B, Arasimowicz-Jelonek M, Braszewska-Zalewska A, Drozda A, Floryszak-Wieczorek J. BABA-Induced DNA Methylome Adjustment to Intergenerational Defense Priming in Potato to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2019; 10:650. [PMID: 31214209 PMCID: PMC6554679 DOI: 10.3389/fpls.2019.00650] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 04/30/2019] [Indexed: 05/21/2023]
Abstract
We provide evidence that alterations in DNA methylation patterns contribute to the regulation of stress-responsive gene expression for an intergenerational resistance of β-aminobutyric acid (BABA)-primed potato to Phytophthora infestans. Plants exposed to BABA rapidly modified their methylation capacity toward genome-wide DNA hypermethylation. De novo induced DNA methylation (5-mC) correlated with the up-regulation of Chromomethylase 3 (CMT3), Domains rearranged methyltransferase 2 (DRM2), and Repressor of silencing 1 (ROS1) genes in potato. BABA transiently activated DNA hypermethylation in the promoter region of the R3a resistance gene triggering its downregulation in the absence of the oomycete pathogen. However, in the successive stages of priming, an excessive DNA methylation state changed into demethylation with the active involvement of potato DNA glycosylases. Interestingly, the 5-mC-mediated changes were transmitted into the next generation in the form of intergenerational stress memory. Descendants of the primed potato, which derived from tubers or seeds carrying the less methylated R3a promoter, showed a higher transcription of R3a that associated with an augmented intergenerational resistance to virulent P. infestans when compared to the inoculated progeny of unprimed plants. Furthermore, our study revealed that enhanced transcription of some SA-dependent genes (NPR1, StWRKY1, and PR1) was not directly linked with DNA methylation changes in the promoter region of these genes, but was a consequence of methylation-dependent alterations in the transcriptional network.
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Affiliation(s)
- Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Agnieszka Braszewska-Zalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, The University of Silesia in Katowice, Katowice, Poland
| | - Andżelika Drozda
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Jolanta Floryszak-Wieczorek
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
- *Correspondence: Jolanta Floryszak-Wieczorek,
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Hu L, Xiao P, Jiang Y, Dong M, Chen Z, Li H, Hu Z, Lei A, Wang J. Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium. Front Microbiol 2018; 9:1479. [PMID: 30022974 PMCID: PMC6039552 DOI: 10.3389/fmicb.2018.01479] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/13/2018] [Indexed: 11/19/2022] Open
Abstract
Epigenetic modifications such as DNA methylation are well known as connected with many important biological processes. Rapid accumulating evidence shows environmental stress can generate particular defense epigenetic changes across generations in eukaryotes. This transgenerational epigenetic inheritance in animals and plants has gained interest over the last years. Cyanobacteria play very crucial role in the earth, and as the primary producer they can adapt to nearly all diverse environments. However, few knowledge about the genome wide epigenetic information such as methylome information in cyanobacteria, especially under any environment stress, was reported so far. In this study we profiled the genome-wide cytosine methylation from a model cyanobacterium Synechocystis sp. PCC 6803, and explored the possibility of transgenerational epigenetic process in this ancient single-celled prokaryote by comparing the DNA methylomes among normal nitrogen medium cultivation, nitrogen starvation for 72 h and nitrogen recovery for about 12 generations. Our results shows that DNA methylation patterns in nitrogen starvation and nitrogen recovery are much more similar with each other, significantly different from that of the normal nitrogen. This study reveals the difference in global DNA methylation pattern of cyanobacteria between normal and nutrient stress conditions and reports the evidence of transgenerational epigenetic process in cyanobacteria. The results of this study may contribute to a better understanding of epigenetic regulation in prokaryotic adaptation to and survive in the ever changing environment.
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Affiliation(s)
- Lang Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
| | - Peng Xiao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yongguang Jiang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Mingjie Dong
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zixi Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hui Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Anping Lei
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
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13
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Yao D, Huo X, Zenda T, Liu S, Liu Y, Dai L, Duan H. Effects of ethephon on DNA methylation and gene expressions associated with shortened internodes in maize. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1386591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Daxuan Yao
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Agricultural University of Hebei, Baoding, China
| | - Xiuai Huo
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Agricultural University of Hebei, Baoding, China
| | - Tinashe Zenda
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Agricultural University of Hebei, Baoding, China
| | - Songtao Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Agricultural University of Hebei, Baoding, China
| | - Yunting Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Agricultural University of Hebei, Baoding, China
| | - Liang Dai
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Agricultural University of Hebei, Baoding, China
| | - Huijun Duan
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Agricultural University of Hebei, Baoding, China
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14
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Viggiano L, de Pinto MC. Dynamic DNA Methylation Patterns in Stress Response. PLANT EPIGENETICS 2017. [DOI: 10.1007/978-3-319-55520-1_15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Nonogaki H. Seed Biology Updates - Highlights and New Discoveries in Seed Dormancy and Germination Research. FRONTIERS IN PLANT SCIENCE 2017; 8:524. [PMID: 28443117 PMCID: PMC5387071 DOI: 10.3389/fpls.2017.00524] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/24/2017] [Indexed: 05/05/2023]
Abstract
An understanding of the biology of seeds has been greatly advanced in recent years. The progresses, particularly in the field of seed dormancy and germination research, have been made at a remarkable speed. Some of the possible epigenetic mechanisms, including an involvement of non-coding RNA, which were predicted for DELAY OF GERMINATION1 just a few years ago, have now been demonstrated with strong molecular and genetic evidence. Imprinting, or parent-of-origin-specific gene silencing/expression, which was characterized particularly for developing seeds, was also found in imbibed seeds and suggested for dormancy mechanisms. Hormone biology in seeds, which is the most advanced and almost a traditional area of seed research, also presents a new dimension. Upstream regulators of hormone metabolism and hormone transporters, such as abscisic acid and gibberellin influx/efflux carriers, have been identified. Characterization of the novel posttranslational modification pathways, including the N-end rule and S-nitrosylation pathways, which play a critical role in turnover of the major hormone signal transduction proteins, also expanded our knowledge about the complexity of hormone signaling in seeds. These progresses made at the molecular level are significant steps toward a better understanding of how seeds translate soil and other environmental signals into their internal hormone biology and make an important decision to stay dormant or commence with germination.
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Elhamamsy AR. DNA methylation dynamics in plants and mammals: overview of regulation and dysregulation. Cell Biochem Funct 2016; 34:289-98. [PMID: 27003927 DOI: 10.1002/cbf.3183] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 12/22/2022]
Abstract
DNA methylation is a major epigenetic marking mechanism regulating various biological functions in mammals and plant. The crucial role of DNA methylation has been observed in cellular differentiation, embryogenesis, genomic imprinting and X-chromosome inactivation. Furthermore, DNA methylation takes part in disease susceptibility, responses to environmental stimuli and the biodiversity of natural populations. In plant, different types of environmental stress have demonstrated the ability to alter the archetype of DNA methylation through the genome, change gene expression and confer a mechanism of adaptation. DNA methylation dynamics are regulated by three processes de novo DNA methylation, methylation maintenance and DNA demethylation. These processes have their similarities and differences between mammals and plants. Furthermore, the dysregulation of DNA methylation dynamics represents one of the primary molecular mechanisms of developing diseases in mammals. This review discusses the regulation and dysregulation of DNA methylation in plants and mammals. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Amr Rafat Elhamamsy
- Clinical Pharmacy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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17
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Lin L, Yang D, Wang X, Liao M, Wang Z, Lv X, Tang F, Liang D, Xia H, Lai Y, Tang Y. Effects of grafting on the cadmium accumulation characteristics of the potential Cd-hyperaccumulator Solanum photeinocarpum. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:82. [PMID: 26739012 DOI: 10.1007/s10661-015-5084-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
The effects of grafting on the cadmium (Cd) accumulation characteristics of the potential Cd-hyperaccumulator Solanum photeinocarpum were studied under Cd stress in our experiment. Four treatments were used in the experiment: ungrafted (UG), self-rooted grafting by the same S. photeinocarpum seedling (SG), self-rooted grafting by two different development stages of S. photeinocarpum seedlings (DG), and grafting on the rootstock of wild potato (PG). SG and DG decreased the root, scion stem, leaf, whole shoot, and whole plant biomasses compared with UG, but increased the rootstock stem biomass, while only PG increased the root and whole plant biomasses. SG and DG increased the Cd contents in the different organs of S. photeinocarpum compared with UG, while PG decreased the Cd content compared with UG. The Cd extraction by the whole plant of S. photeinocarpum was ranked as DG > SG > UG > PG. Additionally, the antioxidant enzyme activities in SG and DG were enhanced compared with UG, while that of PG was reduced compared with UG. The grafting increased the DNA methylation levels and changed the methylation patterns of S. photeinocarpum compared with UG. Therefore, SG and DG can increase the Cd accumulation in S. photeinocarpum, which can be used for the phytoremediation of Cd-contaminated soil.
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Affiliation(s)
- Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Daiyu Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xun Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ming'an Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiulan Lv
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Fuyi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dong Liang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Hui Xia
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yunsong Lai
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yi Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
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18
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Fukuyo M, Nakano T, Zhang Y, Furuta Y, Ishikawa K, Watanabe-Matsui M, Yano H, Hamakawa T, Ide H, Kobayashi I. Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities. Nucleic Acids Res 2015; 43:2841-52. [PMID: 25697504 PMCID: PMC4357717 DOI: 10.1093/nar/gkv116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The restriction-modification systems use epigenetic modification to distinguish between self and nonself DNA. A modification enzyme transfers a methyl group to a base in a specific DNA sequence while its cognate restriction enzyme introduces breaks in DNA lacking this methyl group. So far, all the restriction enzymes hydrolyze phosphodiester bonds linking the monomer units of DNA. We recently reported that a restriction enzyme (R.PabI) of the PabI superfamily with half-pipe fold has DNA glycosylase activity that excises an adenine base in the recognition sequence (5′-GTAC). We now found a second activity in this enzyme: at the resulting apurinic/apyrimidinic (AP) (abasic) site (5′-GT#C, # = AP), its AP lyase activity generates an atypical strand break. Although the lyase activity is weak and lacks sequence specificity, its covalent DNA–R.PabI reaction intermediates can be trapped by NaBH4 reduction. The base excision is not coupled with the strand breakage and yet causes restriction because the restriction enzyme action can impair transformation ability of unmethylated DNA even in the absence of strand breaks in vitro. The base excision of R.PabI is inhibited by methylation of the target adenine base. These findings expand our understanding of genetic and epigenetic processes linking those in prokaryotes and eukaryotes.
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Affiliation(s)
- Masaki Fukuyo
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Yingbiao Zhang
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Ken Ishikawa
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-8654, Japan
| | - Miki Watanabe-Matsui
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hirokazu Yano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Takeshi Hamakawa
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-8654, Japan
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19
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Aging-associated excess formaldehyde leads to spatial memory deficits. Sci Rep 2013; 3:1807. [PMID: 23657727 PMCID: PMC3648839 DOI: 10.1038/srep01807] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/23/2013] [Indexed: 01/24/2023] Open
Abstract
Recent studies show that formaldehyde participates in DNA demethylation/methylation cycle. Emerging evidence identifies that neuronal activity induces global DNA demethylation and re-methylation; and DNA methylation is a critical step for memory formation. These data suggest that endogenous formaldehyde may intrinsically link learning-responsive DNA methylation status and memory formation. Here, we report that during spatial memory formation process, spatial training induces an initial global DNA demethylation and subsequent re-methylation associated with hippocampal formaldehyde elevation then decline to baseline level in Sprague Dawley rats. Scavenging this elevated formaldehyde by formaldehyde-degrading enzyme (FDH), or enhancing DNA demethylation by a DNA demethylating agent, both led to spatial memory deficits by blocking DNA re-methylation in rats. Furthermore, we found that the normal adult rats intrahippocampally injected with excess formaldehyde can imitate the aged-related spatial memory deficits and global DNA methylation decline. These findings indicate that aging-associated excess formaldheyde contributes to cognitive decline during aging.
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20
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Franchini DM, Schmitz KM, Petersen-Mahrt SK. 5-Methylcytosine DNA demethylation: more than losing a methyl group. Annu Rev Genet 2012; 46:419-41. [PMID: 22974304 DOI: 10.1146/annurev-genet-110711-155451] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Demethylation of 5-methylcytosine in DNA is integral to the maintenance of an intact epigenome. The balance between the presence or absence of 5-methylcytosine determines many physiological aspects of cell metabolism, with a turnover that can be measured in minutes to years. Biochemically, addition of the methyl group is shared among all living kingdoms and has been well characterized, whereas the removal or reversion of this mark seems diverse and much less understood. Here, we present a summary of how DNA demethylation can be initiated directly, utilizing the ten-eleven translocation (TET) family of proteins, activation-induced deaminase (AID), or other DNA modifying enzymes, or indirectly, via transcription, RNA metabolism, or DNA repair; how intermediates in those pathways are substrates of the DNA repair machinery; and how demethylation pathways are linked and possibly balanced, avoiding mutations.
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Affiliation(s)
- Don-Marc Franchini
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Istituto FIRC di Oncologia Molecolare, 20139 Milano, Italy.
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21
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Li J, Berger F. Endosperm: food for humankind and fodder for scientific discoveries. THE NEW PHYTOLOGIST 2012; 195:290-305. [PMID: 22642307 DOI: 10.1111/j.1469-8137.2012.04182.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The endosperm is an essential constituent of seeds in flowering plants. It originates from a fertilization event parallel to the fertilization that gives rise to the embryo. The endosperm nurtures embryo development and, in some species including cereals, stores the seed reserves and represents a major source of food for humankind. Endosperm biology is characterized by specific features, including idiosyncratic cellular controls of cell division and epigenetic controls associated with parental genomic imprinting. This review attempts a comprehensive summary of our current knowledge of endosperm development and highlights recent advances in this field.
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Affiliation(s)
- Jing Li
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Frédéric Berger
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
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22
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Ikeda Y. Plant imprinted genes identified by genome-wide approaches and their regulatory mechanisms. PLANT & CELL PHYSIOLOGY 2012; 53:809-816. [PMID: 22492232 DOI: 10.1093/pcp/pcs049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon found in mammals and flowering plants that leads to differential allelic gene expression depending on their parent of origin. In plants, genomic imprinting primarily occurs in the endosperm, and it is associated with seed development. The imprinted expression is driven by the epigenetic memory programmed in each lineage of female and male germlines. Several imprinted genes have been identified based on genetic studies in maize and Arabidopsis. Recent advances in genome-wide analyses made it possible to identify multiple imprinted genes including many nuclear proteins, such as transcription factors and chromatin-related proteins in different plant species. Some of these genes are conserved in Arabidopsis, rice and maize, but many are species specific. Genome-wide analyses also clarified the regulation mechanism of imprinted genes orchestrated by DNA methylation and histone methylation marks. Additionally, genetic analyses using Arabidopsis revealed new regulatory factors of DNA demethylation and imprinting and shed light on the more precise mechanisms.
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Affiliation(s)
- Yoko Ikeda
- Plant Reproductive Genetics, GCOE Research Group, Graduate School of Biological Science, Nara Institute of Science and Technology, Japan.
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23
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Saze H. Transgenerational inheritance of induced changes in the epigenetic state of chromatin in plants. Genes Genet Syst 2012; 87:145-52. [DOI: 10.1266/ggs.87.145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University
- PRESTO, Japan Science and Technology Agency (JST)
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24
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Santos AP, Serra T, Figueiredo DD, Barros P, Lourenço T, Chander S, Oliveira MM, Saibo NJM. Transcription regulation of abiotic stress responses in rice: a combined action of transcription factors and epigenetic mechanisms. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:839-57. [PMID: 22136664 DOI: 10.1089/omi.2011.0095] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plant growth and crop production are highly reduced by adverse environmental conditions and rice is particularly sensitive to abiotic stresses. Plants have developed a number of different mechanisms to respond and try to adapt to abiotic stress. Plant response to stress such as drought, cold, and high salinity, implies rapid and coordinated changes at transcriptional level of entire gene networks. During the last decade many transcription factors, belonging to different families, have been shown to act as positive or negative regulators of stress responsive genes, thus playing an extremely important role in stress signaling. More recently, epigenetic mechanisms have been also involved in the regulation of the stress responsive genes. In this review, we have performed a comprehensive analysis of the rice transcription factors reported so far as being involved in abiotic stress responses. The impact of abiotic stresses on epigenomes is also addressed. Finally, we update the connections made so far between DNA-binding transcription factors (TFs), and epigenetic mechanisms (DNA methylation and histones methylation or acetylation) emphasizing an integrative view of transcription regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológica, Oeiras. Portugal
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25
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Mannuss A, Trapp O, Puchta H. Gene regulation in response to DNA damage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:154-65. [PMID: 21867786 DOI: 10.1016/j.bbagrm.2011.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/25/2011] [Accepted: 08/04/2011] [Indexed: 11/17/2022]
Abstract
To deal with different kinds of DNA damages, there are a number of repair pathways that must be carefully orchestrated to guarantee genomic stability. Many proteins that play a role in DNA repair are involved in multiple pathways and need to be tightly regulated to conduct the functions required for efficient repair of different DNA damage types, such as double strand breaks or DNA crosslinks caused by radiation or genotoxins. While most of the factors involved in DNA repair are conserved throughout the different kingdoms, recent results have shown that the regulation of their expression is variable between different organisms. In the following paper, we give an overview of what is currently known about regulating factors and gene expression in response to DNA damage and put this knowledge in context with the different DNA repair pathways in plants. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
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Affiliation(s)
- Anja Mannuss
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
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26
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Jeffries MA, Sawalha AH. Epigenetics in systemic lupus erythematosus: leading the way for specific therapeutic agents. ACTA ACUST UNITED AC 2011; 6:423-439. [PMID: 22184503 DOI: 10.2217/ijr.11.32] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder of an unclearly determined etiology. Past studies, both epidemiological and biological, have implicated epigenetic influences in disease etiology and pathogenesis. Epigenetics describes changes in gene expression not linked to alterations in the underlying genomic sequence, and is most often typified by three modifications: methylation of DNA, addition of various side chains to histone groups and transcriptional regulation via short ncRNA sequences. The purpose of this article is to review the most important advances that link epigenetic changes to lupus. The contribution of DNA methylation changes to lupus pathogenesis is discussed. These include the role of apoptotic DNA, ultraviolet radiation, endogenous retroviruses, dietary contributions and aging. Hypomethylation of specific genes overexpressed in lupus T cells such as ITGAL (CD11a), CD40LG (CD40L), TNFSF7 (CD70), KIR2DL4 and PRF1 (perforin), and CD5 in lupus B cells seem to play an important role. Moreover, histone modifications such as increased global H4 acetylation in monocytes are highly associated with SLE. NcRNAs, especially miR-21, miR-148a and miR-126, control other elements of epigenetic regulation; particularly, transcription of the maintenance DNA methylation enzyme DNMT1. Epigenetic contributions to SLE etiology have been well established, but much is still unknown. Epigenome-wide studies coupled with functional analysis of the epigenomic changes discovered will uncover novel pathways important in disease pathogenesis. Epigenetic therapies for SLE may be feasible in the future, particularly if they are designed to target specific regions within the genome.
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Affiliation(s)
- Matlock A Jeffries
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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27
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Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2011; 11:204-20. [PMID: 20142834 DOI: 10.1038/nrg2719] [Citation(s) in RCA: 2480] [Impact Index Per Article: 190.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation. Recent findings in plants and animals have greatly increased our understanding of the pathways used to accurately target, maintain and modify patterns of DNA methylation and have revealed unanticipated mechanistic similarities between these organisms. Key roles have emerged for small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these processes. Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation.
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Affiliation(s)
- Julie A Law
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, 90095-1606, USA
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Abstract
DNA methylation is a prominent epigenetic mark and extensively found within plant genomes. It has two major roles- first, defending the genome against invasive DNA and second, regulation of gene expression. Since the first report of 5-methylcytosine found in wheat germ, many improvements in detection of methylated cytosine residues have been made and genome-wide methylation maps for Arabidopsis thaliana are now available. The development of fast, reproducible, and single-base pair resolving detection methods for DNA methylation at defined loci advanced our understanding of the establishment and maintenance of DNA methylation patterns. Bisulphite conversion of unmethylated cytosine residues followed by detection methods such as sequencing of distinct loci has become accepted as the gold standard for detecting 5-methylcytosines. Treatment of single-stranded DNA with bisulphite under acidic conditions leads to the conversion of cytosine residues to uracil whereas 5-methylcytosine is less sensitive and remains unchanged. Here, a detailed protocol for bisulphite conversion, primer design, and optimization of PCR conditions is given. Specific requirements for plant DNA are discussed.
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Abstract
Flowering plants have evolved to be a predominant life form on earth. A common principle of flowering plants and probably one of the main reasons for their evolutionary success is the rapid development of an embryo next to a supporting tissue called the endosperm. The embryo and the endosperm are protected by surrounding maternal tissues, the integuments, and the trinity of integuments, embryo and endosperm comprise the plant seed. For proper seed development, these three structures have to develop in a highly controlled and co-ordinated manner, representing a paradigm for cell-cell communication during development. Communication pathways between the endosperm and the seed coat are now beginning to be unravelled. Moreover, recently isolated mutants affecting plant reproduction have allowed a genetic dissection of seed development, and revealed that the embryo plays a previously unrecognized yet important role in co-ordinating seed development.
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Martienssen RA. Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. THE NEW PHYTOLOGIST 2010; 186:46-53. [PMID: 20409176 PMCID: PMC3756494 DOI: 10.1111/j.1469-8137.2010.03193.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In many plants, including Arabidopsis, hybrids between species and subspecies encounter postfertilization barriers in which hybrid seed fail to develop, or else give rise to infertile progeny. In Arabidopsis, some of these barriers are sensitive to ploidy and to the epigenetic status of donor and recipient genomes. Recently, a role has been proposed for heterochromatin in reprogramming events that occur in reproductive cells, as well as in the embryo and endosperm after fertilization. 21 nt small interfering RNA (siRNA) from activated transposable elements accumulate in pollen, and are translocated from companion vegetative cells into the sperm, while in the maturing seed 24 nt siRNA are primarily maternal in origin. Thus maternal and paternal genomes likely contribute differing small RNA to the zygote and to the endosperm. As heterochromatic sequences also differ radically between, and within, species, small RNA sequences will diverge in hybrids. If transposable elements in the seed are not targeted by small RNA from the pollen, or vice versa, this could lead to hybrid seed failure, in a mechanism reminiscent of hybrid dysgenesis in Drosophila. Heterochromatin also plays a role in apomixis and nucleolar dominance, and may utilize a similar mechanism.
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31
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Imprinting and epigenetic changes in the early embryo. Mamm Genome 2009; 20:532-43. [PMID: 19760320 DOI: 10.1007/s00335-009-9225-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 06/18/2009] [Indexed: 10/20/2022]
Abstract
Imprinted genes are epigenetically regulated so that only one allele is expressed in a parent-of-origin-dependent manner. Although they represent a small subset of the mammalian genome, imprinted genes are essential for normal development. The regulatory mechanisms underlying imprinting are complex and have been the subject of extensive investigation. DNA methylation is the best-established epigenetic mark that is critical for the allele-specific expression of imprinted genes. This mark must be correctly established in the germline, maintained throughout life, and erased and reestablished in the germline the next generation. These events coincide with the genome-wide epigenetic reprogramming that occurs during gametogenesis and early embryogenesis; therefore, the establishment and maintenance of DNA methylation must be tightly regulated. Studies on enzymes that participate in both de novo methylation and its maintenance (i.e., the DNMT family) have provided information on how methylation influences imprinting. However, many aspects of the regulation of DNA methylation are unknown, including how methylation complexes are targeted and the molecular mechanisms underlying DNA demethylation. In this review we focus on the epigenetic changes that occur in the germline and early embryo, with an emphasis on imprinting. We summarize recent findings on factors influencing DNA methylation establishment, maintenance, and erasure that have further elucidated the mechanisms of imprinting, while highlighting topics that require further investigation.
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Ishikawa R, Kinoshita T. Epigenetic programming: the challenge to species hybridization. MOLECULAR PLANT 2009; 2:589-599. [PMID: 19825641 DOI: 10.1093/mp/ssp028] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In many organisms, the genomes of individual species are isolated by a range of reproductive barriers that act before or after fertilization. Successful mating between species results in the presence of different genomes within a cell (hybridization), which can lead to incompatibility in cellular events due to adverse genetic interactions. In addition to such genetic interactions, recent studies have shown that the epigenetic control of the genome, silencing of transposons, control of non-additive gene expression and genomic imprinting might also contribute to reproductive barriers in plant and animal species. These genetic and epigenetic mechanisms play a significant role in the prevention of gene flow between species. In this review, we focus on aspects of epigenetic control related to hybrid incompatibility during species hybridization, and also consider key mechanism(s) in the interaction between different genomes.
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Affiliation(s)
- Ryo Ishikawa
- Plant Reproductive Genetics, GCOE Research Group, Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Tetsu Kinoshita
- Plant Reproductive Genetics, GCOE Research Group, Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
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