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Cheng Y, Zhou Y, Wang M. Targeted gene regulation through epigenome editing in plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102552. [PMID: 38776571 DOI: 10.1016/j.pbi.2024.102552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
The precise targeted gene regulation in plants is essential for improving plant traits and gaining a comprehensive understanding of gene functions. The regulation of gene expression in eukaryotes can be achieved through transcriptional and epigenetic mechanisms. Over the last decade, advancements in gene-targeting technologies, along with an expanded understanding of epigenetic gene regulation mechanisms, have significantly contributed to the development of programmable gene regulation tools. In this review, we will discuss the recent progress in targeted plant gene regulation through epigenome editing, emphasizing the role of effector proteins in modulating target gene expression via diverse mechanisms, including DNA methylation, histone modifications, and chromatin remodeling. Additionally, we will also briefly review targeted gene regulation by transcriptional regulation and mRNA modifications in plants.
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Affiliation(s)
- Yuejing Cheng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ming Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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López ME, Denoyes B, Bucher E. Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca). BMC PLANT BIOLOGY 2024; 24:405. [PMID: 38750420 PMCID: PMC11096098 DOI: 10.1186/s12870-024-05093-6] [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: 03/22/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted to assess the heritability of heat stress-induced epigenetic and transcriptomic changes following woodland strawberry (Fragaria vesca) reproduction. Strawberry is an ideal model to study epigenetic inheritance because it presents two modes of reproduction: sexual (self-pollinated plants) and asexual (clonally propagated plants named daughter plants). Taking advantage of this model, we investigated whether heat stress-induced DNA methylation changes can be transmitted via asexual reproduction. RESULTS Our genome-wide study provides evidence for stress memory acquisition and maintenance in F. vesca. We found that specific DNA methylation marks or epimutations are stably transmitted over at least three asexual generations. Some of the epimutations were associated with transcriptional changes after heat stress. CONCLUSION Our findings show that the strawberry methylome and transcriptome respond with a high level of flexibility to heat stress. Notably, independent plants acquired the same epimutations and those were inherited by their asexual progenies. Overall, the asexual progenies can retain some information in the genome of past stresses encountered by their progenitors. This molecular memory, also documented at the transcriptional level, might be involved in functional plasticity and stress adaptation. Finally, these findings may contribute to novel breeding approaches for climate-ready plants.
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Affiliation(s)
- María-Estefanía López
- Crop Genome Dynamics Group, Agroscope, Nyon, 1260, Switzerland
- Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, 1205, Switzerland
| | - Béatrice Denoyes
- INRAE, Biologie du Fruit et Pathologie, Univ. Bordeaux, Villenave d'Ornon, F-33140, France
| | - Etienne Bucher
- Crop Genome Dynamics Group, Agroscope, Nyon, 1260, Switzerland.
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Doddavarapu B, Lata C, Shah JM. Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130580. [PMID: 38325761 DOI: 10.1016/j.bbagen.2024.130580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/25/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.
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Affiliation(s)
- Bhavya Doddavarapu
- Department of Plant Science, Central University of Kerala, Kerala, India
| | - Charu Lata
- Inclusive Health & Traditional Knowledge Studies Division, CSIR- National Institute of Science Communication and Policy Research, New Delhi, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Kerala, India.
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Zhang Y, Zhong J, Munawar A, Cai Y, He W, Zhang Y, Guo H, Gao Y, Zhu Z, Zhou W. Knocking down a DNA demethylase gene affects potato plant defense against a specialist insect herbivore. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:483-499. [PMID: 37781866 DOI: 10.1093/jxb/erad387] [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: 07/19/2023] [Accepted: 09/29/2023] [Indexed: 10/03/2023]
Abstract
DNA demethylase (DML) is involved in plant development and responses to biotic and abiotic stresses; however, its role in plant-herbivore interaction remains elusive. Here, we found that herbivory by the potato tuber moth, Phthorimaea operculella, rapidly induced the genome-wide DNA methylation and accumulation of DML gene transcripts in potato plants. Herbivory induction of DML transcripts was suppressed in jasmonate-deficient plants, whereas exogenous application of methyl jasmonate (MeJA) improved DML transcripts, indicating that the induction of DML transcripts by herbivory is associated with jasmonate signaling. Moreover, P. operculella larvae grew heavier on DML gene (StDML2) knockdown plants than on wild-type plants, and the decreased biosynthesis of jasmonates in the former may be responsible for this difference, since the larvae feeding on these two genotypes supplemented with MeJA showed similar growth. In addition, P. operculella adult moths preferred to oviposit on StDML2 knockdown plants than on wild-type plants, which was associated with the reduced emission of β-caryophyllene in the former. In addition, supplementing β-caryophyllene to these two genotypes further disrupted moths' oviposit choice preference for them. Interestingly, in StDML2 knockdown plants, hypermethylation was found at the promoter regions for the key genes StAOS and StAOC in the jasmonate biosynthetic pathway, as well as for the key gene StTPS12 in β-caryophyllene production. Our findings suggest that knocking down StDML2 can affect herbivore defense via jasmonate signaling and defense compound production in potato plants.
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Affiliation(s)
- Yadong Zhang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Jian Zhong
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Asim Munawar
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yajie Cai
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenjing He
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yixin Zhang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Han Guo
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yulin Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zengrong Zhu
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Wenwu Zhou
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
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5
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Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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Gao S, Sun Y, Chen X, Zhu C, Liu X, Wang W, Gan L, Lu Y, Schaarschmidt F, Herde M, Witte CP, Chen M. Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA. Nucleic Acids Res 2023; 51:7451-7464. [PMID: 37334828 PMCID: PMC10415118 DOI: 10.1093/nar/gkad529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
5-Methylated cytosine is a frequent modification in eukaryotic RNA and DNA influencing mRNA stability and gene expression. Here we show that free 5-methylcytidine (5mC) and 5-methyl-2'-deoxycytidine are generated from nucleic acid turnover in Arabidopsis thaliana, and elucidate how these cytidines are degraded, which is unclear in eukaryotes. First CYTIDINE DEAMINASE produces 5-methyluridine (5mU) and thymidine which are subsequently hydrolyzed by NUCLEOSIDE HYDROLASE 1 (NSH1) to thymine and ribose or deoxyribose. Interestingly, far more thymine is generated from RNA than from DNA turnover, and most 5mU is directly released from RNA without a 5mC intermediate, since 5-methylated uridine (m5U) is an abundant RNA modification (m5U/U ∼1%) in Arabidopsis. We show that m5U is introduced mainly by tRNA-SPECIFIC METHYLTRANSFERASE 2A and 2B. Genetic disruption of 5mU degradation in the NSH1 mutant causes m5U to occur in mRNA and results in reduced seedling growth, which is aggravated by external 5mU supplementation, also leading to more m5U in all RNA species. Given the similarities between pyrimidine catabolism in plants, mammals and other eukaryotes, we hypothesize that the removal of 5mU is an important function of pyrimidine degradation in many organisms, which in plants serves to protect RNA from stochastic m5U modification.
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Affiliation(s)
- Shangyu Gao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Sun
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoguang Chen
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Changhua Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoye Liu
- Department of Criminal Science and Technology, Nanjing Forest Police College, Nanjing 210023, China
| | - Wenlei Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lijun Gan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanwu Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Frank Schaarschmidt
- Department of Biostatistics, Institute of Cell Biology and Biophysics, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Mingjia Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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7
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Li Y, Xia M, Zhao X, Hou H. Water temperature and chlorophyll a density drive the genetic and epigenetic variation of Vallisneria natans across a subtropical freshwater lake. Ecol Evol 2023; 13:e10434. [PMID: 37589037 PMCID: PMC10425707 DOI: 10.1002/ece3.10434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/08/2023] [Accepted: 08/04/2023] [Indexed: 08/18/2023] Open
Abstract
Plant genetic diversity differs in habitat's oscillations, especially species distributed under heterogeneous environmental conditions. Freshwater ecosystems are vulnerable to biotic and abiotic impacts, which affect the genetic and epigenetic variations in aquatic plants. The extent of environmental heterogeneous attributes can be examined based on genetic and epigenetic variations. Such variations under environmental gradient can provide evidence for understanding the correlations between rapid environmental changes and species evolution. In this study, we performed amplified fragment polymorphism length and methylated-sensitive amplified polymorphism analysis to depict the genetic and epigenetic variations of Vallisneria natans in a subtropical lake. Results showed that this species maintained a relatively high genetic diversity (mean H E = 0.320, I = 0.474, PPL = 85.93%) and epigenetic variation (mean eH E = 0.282, eI = 0.428, ePPL = 83.91%). Water body temperature and chlorophyll a density were positively correlated to the genetic and epigenetic variations. The clonal generates of V. natans depicted a relative high methylation level and shew ancestral scenario between the genet and the second clonal generation. These findings revealed that species diversity is unevenly distributed under environmental heterogeneity, even at a fine geographic scale. Environmental characteristics in relation to temperature and chlorophyll a should be considered in the analysis of the genetic and epigenetic variations. Additionally, epigenetic variations between genets and ramets should be considered with caution when applied to analysis of other aquatic species.
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Affiliation(s)
- Yixian Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
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8
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Zhang H, Zhang X, Xiao J. Epigenetic Regulation of Nitrogen Signaling and Adaptation in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2725. [PMID: 37514337 PMCID: PMC10386408 DOI: 10.3390/plants12142725] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Nitrogen (N) is a crucial nutrient that plays a significant role in enhancing crop yield. Its availability, including both supply and deficiency, serves as a crucial signal for plant development. However, excessive N use in agriculture leads to environmental and economic issues. Enhancing nitrogen use efficiency (NUE) is, therefore, essential to minimize negative impacts. Prior studies have investigated the genetic factors involved in N responses and the process of low-nitrogen (LN) adaptation. In this review, we discuss recent advances in understanding how epigenetic modifications, including DNA methylation, histone modification, and small RNA, participate in the regulation of N response and LN adaptation. We highlight the importance of decoding the epigenome at various levels to accelerate the functional study of how plants respond to N availability. Understanding the epigenetic control of N signaling and adaptation can lead to new strategies to improve NUE and enhance crop productivity sustainably.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang 050024, China
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing 100101, China
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Jeh HE, Sanchez R, Beltrán J, Yang X, Kundariya H, Wamboldt Y, Dopp I, Hafner A, Mackenzie SA. Sensory plastid-associated PsbP DOMAIN-CONTAINING PROTEIN 3 triggers plant growth- and defense-related epigenetic responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:414-433. [PMID: 37036138 PMCID: PMC10525003 DOI: 10.1111/tpj.16233] [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: 11/02/2022] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/14/2023]
Abstract
Sensory plastids are important in plant responses to environmental changes. Previous studies show that MutS HOMOLOG 1 (MSH1) perturbation in sensory plastids induces heritable epigenetic phenotype adjustment. Previously, the PsbP homolog DOMAIN-CONTAINING PROTEIN 3 (PPD3), a protein of unknown function, was postulated to be an interactor with MSH1. This study investigates the relationship of PPD3 with MSH1 and with plant environmental sensing. The ppd3 mutant displays a whole-plant phenotype variably altered in growth rate, flowering time, reactive oxygen species (ROS) modulation and response to salt, with effects on meristem growth. Present in both chloroplasts and sensory plastids, PPD3 colocalized with MSH1 in root tips but not in leaf tissues. The suppression or overexpression of PPD3 affected the plant growth rate and stress tolerance, and led to a heritable, heterogenous 'memory' state with both dwarfed and vigorous growth phenotypes. Gene expression and DNA methylome data sets from PPD3-OX and derived memory states showed enrichment in growth versus defense networks and meristem effects. Our results support a model of sensory plastid influence on nuclear epigenetic behavior and ppd3 as a second trigger, functioning within meristem plastids to recalibrate growth plasticity.
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Affiliation(s)
- Ha Eun Jeh
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802
| | - Robersy Sanchez
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802
| | - Jesús Beltrán
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802
- Current Address: Department of Botany and Plant Sciences, University of California, Riverside, Riverside CA 92521
| | - Xiaodong Yang
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802
- Current Address: School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Hardik Kundariya
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802
| | - Yashitola Wamboldt
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588
- Current Address: MatMaCorp, Lincoln, NE
| | - Isaac Dopp
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802
| | - Alenka Hafner
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802
| | - Sally A. Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802
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Epigenetic Changes Occurring in Plant Inbreeding. Int J Mol Sci 2023; 24:ijms24065407. [PMID: 36982483 PMCID: PMC10048984 DOI: 10.3390/ijms24065407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.
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11
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Hafner A, Mackenzie S. Re-analysis of publicly available methylomes using signal detection yields new information. Sci Rep 2023; 13:3307. [PMID: 36849495 PMCID: PMC9971211 DOI: 10.1038/s41598-023-30422-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023] Open
Abstract
Cytosine methylation is an epigenetic mark that participates in regulation of gene expression and chromatin stability in plants. Advancements in whole genome sequencing technologies have enabled investigation of methylome dynamics under different conditions. However, the computational methods for analyzing bisulfite sequence data have not been unified. Contention remains in the correlation of differentially methylated positions with the investigated treatment and exclusion of noise, inherent to these stochastic datasets. The prevalent approaches apply Fisher's exact test, logistic, or beta regression, followed by an arbitrary cut-off for differences in methylation levels. A different strategy, the MethylIT pipeline, utilizes signal detection to determine cut-off based on a fitted generalized gamma probability distribution of methylation divergence. Re-analysis of publicly available BS-seq data from two epigenetic studies in Arabidopsis and applying MethylIT revealed additional, previously unreported results. Methylome repatterning in response to phosphate starvation was confirmed to be tissue-specific and included phosphate assimilation genes in addition to sulfate metabolism genes not implicated in the original study. During seed germination plants undergo major methylome reprogramming and use of MethylIT allowed us to identify stage-specific gene networks. We surmise from these comparative studies that robust methylome experiments must account for data stochasticity to achieve meaningful functional analyses.
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Affiliation(s)
- Alenka Hafner
- grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA 16802 USA ,grid.29857.310000 0001 2097 4281Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA USA
| | - Sally Mackenzie
- Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA. .,Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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12
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Zhang H, Gong Z, Zhu JK. Active DNA demethylation in plants: 20 years of discovery and beyond. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2217-2239. [PMID: 36478523 DOI: 10.1111/jipb.13423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Maintaining proper DNA methylation levels in the genome requires active demethylation of DNA. However, removing the methyl group from a modified cytosine is chemically difficult and therefore, the underlying mechanism of demethylation had remained unclear for many years. The discovery of the first eukaryotic DNA demethylase, Arabidopsis thaliana REPRESSOR OF SILENCING 1 (ROS1), led to elucidation of the 5-methylcytosine base excision repair mechanism of active DNA demethylation. In the 20 years since ROS1 was discovered, our understanding of this active DNA demethylation pathway, as well as its regulation and biological functions in plants, has greatly expanded. These exciting developments have laid the groundwork for further dissecting the regulatory mechanisms of active DNA demethylation, with potential applications in epigenome editing to facilitate crop breeding and gene therapy.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Molecular Plant Genetics, Shanghai Centre for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Jian-Kang Zhu
- School of Life Sciences, Institute of Advanced Biotechnology, Southern University of Science and Technology, Shenzhen, 518055, China
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Sammarco I, Pieters J, Salony S, Toman I, Zolotarov G, Lafon Placette C. Epigenetic targeting of transposon relics: beating the dead horses of the genome? Epigenetics 2022; 17:1331-1344. [PMID: 36255200 PMCID: PMC9586680 DOI: 10.1080/15592294.2021.2022066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Transposable elements (TEs) have been seen as selfish genetic elements that can propagate in a host genome. Their propagation success is however hindered by a combination of mechanisms such as mutations, selection, and their epigenetic silencing by the host genome. As a result, most copies of TEs in a given genome are dead relics: their sequence is too degenerated to allow any transposition. Nevertheless, these TE relics often, but not always, remain epigenetically silenced, and if not to prevent transposition anymore, one can wonder the reason for this phenomenon. The mere self-perpetuating loop inherent to epigenetic silencing could alone explain that even when inactive, TE copies remain silenced. Beyond this process, nevertheless, antagonistic selective forces are likely to act on TE relic silencing. Especially, without the benefit of preventing transposition, TE relic silencing may prove deleterious to the host fitness, suggesting that the maintenance of TE relic silencing is the result of a fine, and perhaps case-by-case, evolutionary trade-off between beneficial and deleterious effects. Ultimately, the release of TE relics silencing may provide a 'safe' ground for adaptive epimutations to arise. In this review, we provide an overview of these questions in both plants and animals.
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Affiliation(s)
- Iris Sammarco
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic,Institute of Botany, Czech Academy of Sciences, Pruhonice, Czech Republic
| | - Janto Pieters
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Prague, Czech Republic,Department of Plant Experimental Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Susnata Salony
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Izabela Toman
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Grygoriy Zolotarov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Clément Lafon Placette
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic,CONTACT Clément Lafon Placette Department of Botany, Faculty of Science, Charles University, PragueCZ-128 01, Czech Republic
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14
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Tang M, Xue W, Li X, Wang L, Wang M, Wang W, Yin X, Chen B, Qu X, Li J, Wu Y, Gao X, Wei X, Bu F, Zhang L, Sui Z, Ding B, Wang Y, Zhang Q, Li Y, Zhang Y. Mitotically heritable epigenetic modifications of CmMYB6 control anthocyanin biosynthesis in chrysanthemum. THE NEW PHYTOLOGIST 2022; 236:1075-1088. [PMID: 35842781 DOI: 10.1111/nph.18389] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Flower color, which is determined by various chemical pigments, is a vital trait for ornamental plants, in which anthocyanin is a major component. However, the epigenetic regulation of anthocyanin biosynthesis remains poorly understood. During chrysanthemum cultivation, we found a heterochromatic chrysanthemum accession (YP) whose progeny generated by asexual reproduction contained both yellow-flowered (YP-Y) and pink-flowered (YP-P) plants. In this study, we aimed to elucidate the epigenetic mechanisms of different flower colors in the YP plant progeny. Metabolome and transcriptome analyses revealed that the difference in flower color between YP-Y and YP-P was caused by expression variation of the anthocyanin biosynthesis gene CmMYB6. Bisulfite sequencing revealed that methylation at the CmMYB6 promoter, especially in the CHH context, was higher in YP-Y than YP-P. After demethylation of the CmMYB6 promoter using the dCas9-TET1cd system, the flower color returned from yellow to pink. Furthermore, the methylation status of the CmMYB6 promoter was higher in YP-Y over three consecutive generations, indicating that this methylation status was heritable mitotically. Finally, investigation of other chrysanthemum cultivars showed that the methylation of CmMYB6 decreased gradually with the increase in anthocyanin content. These results lay an epigenetic foundation for the improvement of flower color in horticultural plants.
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Affiliation(s)
- Mingwei Tang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Wanjie Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xueqi Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Lishan Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Min Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Wanpeng Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xue Yin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Bowei Chen
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xueting Qu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jingyao Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yi Wu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xinyu Gao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xiaofeng Wei
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Fanqi Bu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Lingyu Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhuoran Sui
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Bing Ding
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yu Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Qingzhu Zhang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yuhua Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yang Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
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15
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Wang M, He L, Chen B, Wang Y, Wang L, Zhou W, Zhang T, Cao L, Zhang P, Xie L, Zhang Q. Transgenerationally Transmitted DNA Demethylation of a Spontaneous Epialleles Using CRISPR/dCas9-TET1cd Targeted Epigenetic Editing in Arabidopsis. Int J Mol Sci 2022; 23:ijms231810492. [PMID: 36142407 PMCID: PMC9504898 DOI: 10.3390/ijms231810492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR/dCas9 is an important DNA modification tool in which a disarmed Cas9 protein with no nuclease activity is fused with a specific DNA modifying enzyme. A previous study reported that overexpression of the TET1 catalytic domain (TET1cd) reduces genome-wide methylation in Arabidopsis. A spontaneous naturally occurring methylation region (NMR19-4) was identified in the promoter region of the PPH (Pheophytin Pheophorbide Hydrolase) gene, which encodes an enzyme that can degrade chlorophyll and accelerate leaf senescence. The methylation status of NMR19-4 is associated with PPH expression and leaf senescence in Arabidopsis natural accessions. In this study, we show that the CRISPR/dCas9-TET1cd system can be used to target the methylation of hypermethylated NMR19-4 region to reduce the level of methylation, thereby increasing the expression of PPH and accelerating leaf senescence. Furthermore, hybridization between transgenic demethylated plants and hypermethylated ecotypes showed that the demethylation status of edited NMR19-4, along with the enhanced PPH expression and accelerated leaf senescence, showed Mendelian inheritance in F1 and F2 progeny, indicating that spontaneous epialleles are stably transmitted trans-generationally after demethylation editing. Our results provide a rational approach for future editing of spontaneously mutated epialleles and provide insights into the epigenetic mechanisms that control plant leaf senescence.
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Affiliation(s)
- Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lishan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Wei Zhou
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Peng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Linan Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Correspondence:
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16
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Dhakate P, Sehgal D, Vaishnavi S, Chandra A, Singh A, Raina SN, Rajpal VR. Comprehending the evolution of gene editing platforms for crop trait improvement. Front Genet 2022; 13:876987. [PMID: 36082000 PMCID: PMC9445674 DOI: 10.3389/fgene.2022.876987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system was initially discovered as an underlying mechanism for conferring adaptive immunity to bacteria and archaea against viruses. Over the past decade, this has been repurposed as a genome-editing tool. Numerous gene editing-based crop improvement technologies involving CRISPR/Cas platforms individually or in combination with next-generation sequencing methods have been developed that have revolutionized plant genome-editing methodologies. Initially, CRISPR/Cas nucleases replaced the earlier used sequence-specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), to address the problem of associated off-targets. The adaptation of this platform led to the development of concepts such as epigenome editing, base editing, and prime editing. Epigenome editing employed epi-effectors to manipulate chromatin structure, while base editing uses base editors to engineer precise changes for trait improvement. Newer technologies such as prime editing have now been developed as a “search-and-replace” tool to engineer all possible single-base changes. Owing to the availability of these, the field of genome editing has evolved rapidly to develop crop plants with improved traits. In this review, we present the evolution of the CRISPR/Cas system into new-age methods of genome engineering across various plant species and the impact they have had on tweaking plant genomes and associated outcomes on crop improvement initiatives.
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Affiliation(s)
- Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), México-Veracruz, Mexico
| | | | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
- *Correspondence: Vijay Rani Rajpal, ; Soom Nath Raina,
| | - Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
- *Correspondence: Vijay Rani Rajpal, ; Soom Nath Raina,
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17
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Wang Y, Liu H, Wang Z, Guo Y, Hu T, Zhou X. P25 and P37 proteins encoded by firespike leafroll-associated virus are viral suppressors of RNA silencing. Front Microbiol 2022; 13:964156. [PMID: 36051767 PMCID: PMC9424829 DOI: 10.3389/fmicb.2022.964156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Firespike leafroll-associated virus (FLRaV) is a major pathogen associated with firespike (Odontonema tubaeforme) leafroll disease. Phylogenetic analysis showed that FLRaV possesses typical traits of subgroup II members of ampeloviruses, but encodes two additional proteins, P25 and P37. Here, we determined the microfilament localization of P25 protein. Posttranscriptional gene silencing (PTGS) assay showed that both FLRaV P25 and P37 were able to suppress the local and systemic PTGS and FLRaV P25 was capable of suppressing the green fluorescent protein (GFP) gene silencing triggered by both sense RNA-induced PTGS (S-PTGS) and inverted repeat RNA-induced PTGS (IR-PTGS). In contrast, FLRaV P37 was only able to inhibit the GFP silencing triggered by the S-PTGS but not the IR-PTGS. In the transcriptional gene silencing (TGS) assay, only FLRaV P25 was found to be able to reverse established TGS-mediated silencing of GFP in 16-TGS plants. We also found that FLRaV P25 could aggravate the disease symptom and viral titer of potato virus X in N. benthamiana. These results suggest that FLRaV P25 and P37 may have crucial roles in overcoming host RNA silencing, which provides key insights into our understanding of the molecular mechanisms underlying FLRaV infection.
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Affiliation(s)
- Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Hui Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, China
| | - Yushuang Guo
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Tao Hu,
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Xueping Zhou,
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18
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Zhang RX, Li BB, Yang ZG, Huang JQ, Sun WH, Bhanbhro N, Liu WT, Chen KM. Dissecting Plant Gene Functions Using CRISPR Toolsets for Crop Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7343-7359. [PMID: 35695482 DOI: 10.1021/acs.jafc.2c01754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The CRISPR-based gene editing technology has become more and more powerful in genome manipulation for agricultural breeding, with numerous improved toolsets springing up. In recent years, many CRISPR toolsets for gene editing, such as base editors (BEs), CRISPR interference (CRISPRi), CRISPR activation (CRISPRa), and plant epigenetic editors (PEEs), have been developed to clarify gene function and full-level gene regulation. Here, we comprehensively summarize the application and capacity of the different CRISPR toolsets in the study of plant gene expression regulation, highlighting their potential application in gene regulatory networks' analysis. The general problems in CRISPR application and the optimal solutions in the existing schemes for high-throughput gene function analysis are also discussed. The CRISPR toolsets targeting gene manipulation discussed here provide new solutions for further genetic improvement and molecular breeding of crops.
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Affiliation(s)
- Rui-Xiang Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bin-Bin Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zheng-Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jia-Qi Huang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Wei-Hang Sun
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nadeem Bhanbhro
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm. PLoS Biol 2022; 20:e3001602. [PMID: 35389984 PMCID: PMC9017945 DOI: 10.1371/journal.pbio.3001602] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/19/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
Gene expression in endosperm-a seed tissue that mediates transfer of maternal resources to offspring-is under complex epigenetic control. We show here that plant-specific RNA polymerase IV (Pol IV) mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs (sRNAs), DNA methylation, and mRNAs in Arabidopsis thaliana endosperm from heterozygotes produced by reciprocally crossing wild-type (WT) plants to Pol IV mutants. We find that maternally and paternally acting Pol IV induce distinct effects on endosperm. Loss of maternal or paternal Pol IV impacts sRNAs and DNA methylation at different genomic sites. Strikingly, maternally and paternally acting Pol IV have antagonistic impacts on gene expression at some loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of-origin effects have only rarely been described and are consistent with a gene regulatory system evolving under parental conflict.
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20
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Gardiner J, Ghoshal B, Wang M, Jacobsen SE. CRISPR-Cas-mediated transcriptional control and epi-mutagenesis. PLANT PHYSIOLOGY 2022; 188:1811-1824. [PMID: 35134247 PMCID: PMC8968285 DOI: 10.1093/plphys/kiac033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/13/2022] [Indexed: 05/24/2023]
Abstract
Tools for sequence-specific DNA binding have opened the door to new approaches in investigating fundamental questions in biology and crop development. While there are several platforms to choose from, many of the recent advances in sequence-specific targeting tools are focused on developing Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR Associated (CRISPR-Cas)-based systems. Using a catalytically inactive Cas protein (dCas), this system can act as a vector for different modular catalytic domains (effector domains) to control a gene's expression or alter epigenetic marks such as DNA methylation. Recent trends in developing CRISPR-dCas systems include creating versions that can target multiple copies of effector domains to a single site, targeting epigenetic changes that, in some cases, can be inherited to the next generation in the absence of the targeting construct, and combining effector domains and targeting strategies to create synergies that increase the functionality or efficiency of the system. This review summarizes and compares DNA targeting technologies, the effector domains used to target transcriptional control and epi-mutagenesis, and the different CRISPR-dCas systems used in plants.
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Affiliation(s)
| | | | - Ming Wang
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, USA
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21
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Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y. Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science 2021; 374:1579-1586. [DOI: 10.1126/science.abj9184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Xian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cheng-Li Fang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou-Geng Xu
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Wei Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Gao
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chuan-Miao Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lin-Lin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan-Xi Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Hui Mu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yu Feng
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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22
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Ezhova TA. Paradoxes of Plant Epigenetics. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Plants have a unique ability to adapt ontogenesis to changing environmental conditions and the influence of stress factors. This ability is based on the existence of two specific features of epigenetic regulation in plants, which seem to be mutually exclusive at first glance. On the one hand, plants are capable of partial epigenetic reprogramming of the genome, which can lead to adaptation of physiology and metabolism to changed environmental conditions as well as to changes in ontogenesis programs. On the other hand, plants can show amazing stability of epigenetic modifications and the ability to transmit them to vegetative and sexual generations. The combination of these inextricably linked epigenetic features not only ensures survival in the conditions of a sessile lifestyle but also underlies a surprisingly wide morphological diversity of plants, which can lead to the appearance of morphs within one population and the existence of interpopulation morphological differences. The review discusses the molecular genetic mechanisms that cause a paradoxical combination of the stability and lability properties of epigenetic modifications and underlie the polyvariance of ontogenesis. We also consider the existing approaches for studying the role of epigenetic regulation in the manifestation of polyvariance of ontogenesis and discuss their limitations and prospects.
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Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife 2021; 10:72676. [PMID: 34850679 PMCID: PMC8828055 DOI: 10.7554/elife.72676] [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] [Received: 08/01/2021] [Accepted: 11/30/2021] [Indexed: 11/27/2022] Open
Abstract
Flowering plants utilize small RNA (sRNA) molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here, we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with sRNA biogenesis, and without H1 sRNA production quantitatively expands to non-CG-methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the sRNA-generating branch of RdDM from non-CG-methylated heterochromatin. Cells adapt to different roles by turning different groups of genes on and off. One way cells control which genes are on or off is by creating regions of active and inactive DNA, which are created and maintained by different groups of proteins. Genes in active DNA regions can be turned on, while genes in inactive regions are switched off or silenced. Silenced DNA regions also turn off ‘transposable elements’: pieces of DNA that can copy themselves and move to other regions of the genome if they become active. Transposons can be dangerous if they are activated, because they can disrupt genes or regulatory sequences when they move. There are different types of active and inactive DNA, but it is not always clear why these differences exist, or how they are maintained over time. In plants, such as the commonly-studied weed Arabidopsis thaliana, there are two types of inactive DNA, called E and H, that can silence transposons. In both types, DNA has small chemicals called methyl groups attached to it, which help inactivate the DNA. Type E DNA is methylated by a process called RNA-directed DNA methylation (RdDM), but RdDM is rarely seen in type H DNA. Choi, Lyons and Zilberman showed that RdDM is attracted to E and H regions by previously existing methylated DNA. However, in the H regions, a protein called histone H1 blocks RdDM from attaching methyl groups. This helps focus RdDM onto E regions where it is most needed, because E regions contain the types of transposons RdDM is best suited to silence. When Choi, Lyons and Zilberman examined genetically modified A. thaliana plants that do not produce histone H1, they found that RdDM happened in both E and H regions. There are many more H regions than E regions, so stretching RdDM across both made it less effective at silencing DNA. This work shows how different DNA silencing processes are focused onto specific genetic regions, helping explain why there are different types of active and inactive DNA within cells. RdDM has been studied as a way to affect crop growth and yield by altering DNA methylation. These results may help such studies by explaining how RdDM is naturally targeted.
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Affiliation(s)
- Jaemyung Choi
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - David B Lyons
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Daniel Zilberman
- Department of Cell and Developmental Biology, John Innes Centre, Klosterneuburg, Austria
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Karlson CKS, Mohd-Noor SN, Nolte N, Tan BC. CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences. PLANTS 2021; 10:plants10102055. [PMID: 34685863 PMCID: PMC8540305 DOI: 10.3390/plants10102055] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022]
Abstract
RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional effector and a single guide RNA (sgRNA). This type of dCas9 is incapable to cleave DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The CRISPR/dCas9 system has been explored as a tool for transcriptional modulation and genome imaging. Despite its potential applications and benefits, the challenges and limitations faced by the CRISPR/dCas9 system include the off-target effects, protospacer adjacent motif (PAM) sequence requirements, efficient delivery methods and the CRISPR/dCas9-interfered crops being labeled as genetically modified organisms in several countries. This review highlights the progression of CRISPR/dCas9 technology as well as its applications and potential challenges in crop improvement.
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Affiliation(s)
- Chou Khai Soong Karlson
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Siti Nurfadhlina Mohd-Noor
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia;
| | - Nadja Nolte
- Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Boon Chin Tan
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Correspondence: ; Tel.: +60-3-7967-7982
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Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability. Proc Natl Acad Sci U S A 2021; 118:2107320118. [PMID: 34453006 DOI: 10.1073/pnas.2107320118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeler DDM1 causes hundreds of genomic regions to switch from CMT2 dependency to RdDM dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). Furthermore, we found that dysfunction in both DDM1 and RdDM causes strong reactivation of TEs and a burst of TE transposition in the first generation of mutant plants, indicating that the DDM1 and RdDM pathways together are critical to maintaining TE repression and protecting genomic stability. Our findings reveal the existence of a pathway conversion-based backup mechanism to guarantee the maintenance of DNA methylation and genome integrity.
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles. Int J Mol Sci 2021; 22:ijms22168618. [PMID: 34445323 PMCID: PMC8395315 DOI: 10.3390/ijms22168618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/03/2021] [Accepted: 08/08/2021] [Indexed: 11/17/2022] Open
Abstract
In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.
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Fernie AR, Sonnewald U. Plant biotechnology for sustainable agriculture and food safety. JOURNAL OF PLANT PHYSIOLOGY 2021; 261:153416. [PMID: 33872931 DOI: 10.1016/j.jplph.2021.153416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Uwe Sonnewald
- Division of Biochemistry, Department of Biology, University of Erlangen-Nuremberg, Erlangen, Germany.
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Ono A, Kinoshita T. Epigenetics and plant reproduction: Multiple steps for responsibly handling succession. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102032. [PMID: 33744743 DOI: 10.1016/j.pbi.2021.102032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/31/2021] [Accepted: 02/10/2021] [Indexed: 05/02/2023]
Abstract
Although flowering plants and mammals have distinct life cycles and developmental programs, epigenetic information in both plant and mammalian cells is faithfully inherited across mitotic cell division. In mammals, epigenetic reprograming is a prominent process that is re-established in the zygote and germ line during early development. By contrast, plants do not produce germ cells until later in development. This difference, along with the many examples of the transmission of stable epialleles in plants, suggests that epigenetic reprograming in plants and mammals occurs via distinct mechanisms. In this review, we highlight recent advances in genome-wide epigenetic analyses in plants. These analyses provide insight into dynamic epigenetic regulation in plants and reveal unique processes that maintain genome integrity during plant sexual reproduction.
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Affiliation(s)
- Akemi Ono
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa, 244-0813, Japan.
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa, 244-0813, Japan.
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Wang Z, Butel N, Santos-González J, Simon L, Wärdig C, Köhler C. Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis. Genome Biol 2021; 22:141. [PMID: 33957942 PMCID: PMC8101200 DOI: 10.1186/s13059-021-02359-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/22/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Hybridization of plants that differ in number of chromosome sets (ploidy) frequently causes endosperm failure and seed arrest, a phenomenon referred to as triploid block. In Arabidopsis, loss of function of NRPD1, encoding the largest subunit of the plant-specific RNA polymerase IV (Pol IV), can suppress the triploid block. Pol IV generates short RNAs required to guide de novo methylation in the RNA-directed DNA methylation (RdDM) pathway. Recent work suggests that suppression of the triploid block by mutants in RdDM components differs, depending on whether the diploid pollen is derived from tetraploid plants or from the omission in second division 1 (osd1) mutant. This study aims to understand this difference. RESULTS In this study, we find that the ability of mutants in the RdDM pathway to suppress the triploid block depends on their degree of inbreeding. While first homozygous generation mutants in RdDM components NRPD1, RDR2, NRPE1, and DRM2 have weak or no ability to rescue the triploid block, they are able to suppress the triploid block with successive generations of inbreeding. Inbreeding of nrpd1 was connected with a transgenerational loss of non-CG DNA methylation on sites jointly regulated by CHROMOMETHYLASES 2 and 3. CONCLUSIONS Our data reveal that loss of RdDM function differs in its effect in early and late generations, which has important implications when interpreting the effect of RdDM mutants.
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Affiliation(s)
- Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Present address: College of Horticulture, Nanjing Agricultural University and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, 210095 China
| | - Nicolas Butel
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Lauriane Simon
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Cecilia Wärdig
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Kumar V, Thakur JK, Prasad M. Histone acetylation dynamics regulating plant development and stress responses. Cell Mol Life Sci 2021; 78:4467-4486. [PMID: 33638653 PMCID: PMC11072255 DOI: 10.1007/s00018-021-03794-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022]
Abstract
Crop productivity is directly dependent on the growth and development of plants and their adaptation during different environmental stresses. Histone acetylation is an epigenetic modification that regulates numerous genes essential for various biological processes, including development and stress responses. Here, we have mainly discussed the impact of histone acetylation dynamics on vegetative growth, flower development, fruit ripening, biotic and abiotic stress responses. Besides, we have also emphasized the information gaps which are obligatory to be examined for understanding the complete role of histone acetylation dynamics in plants. A comprehensive knowledge about the histone acetylation dynamics will ultimately help to improve stress resistance and reduce yield losses in different crops due to climate changes.
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Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Baduel P, Colot V. The epiallelic potential of transposable elements and its evolutionary significance in plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200123. [PMID: 33866816 PMCID: PMC8059525 DOI: 10.1098/rstb.2020.0123] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA provides the fundamental framework for heritability, yet heritable trait variation need not be completely ‘hard-wired’ into the DNA sequence. In plants, the epigenetic machinery that controls transposable element (TE) activity, and which includes DNA methylation, underpins most known cases of inherited trait variants that are independent of DNA sequence changes. Here, we review our current knowledge of the extent, mechanisms and potential adaptive contribution of epiallelic variation at TE-containing alleles in this group of species. For the purpose of this review, we focus mainly on DNA methylation, as it provides an easily quantifiable readout of such variation. The picture that emerges is complex. On the one hand, pronounced differences in DNA methylation at TE sequences can either occur spontaneously or be induced experimentally en masse across the genome through genetic means. Many of these epivariants are stably inherited over multiple sexual generations, thus leading to transgenerational epigenetic inheritance. Functional consequences can be significant, yet they are typically of limited magnitude and although the same epivariants can be found in nature, the factors involved in their generation in this setting remain to be determined. On the other hand, moderate DNA methylation variation at TE-containing alleles can be reproducibly induced by the environment, again usually with mild effects, and most of this variation tends to be lost across generations. Based on these considerations, we argue that TE-containing alleles, rather than their inherited epiallelic variants, are the main targets of natural selection. Thus, we propose that the adaptive contribution of TE-associated epivariation, whether stable or not, lies predominantly in its capacity to modulate TE mobilization in response to the environment, hence providing hard-wired opportunities for the flexible exploration of the phenotypic space. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005 Paris, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005 Paris, France
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Song ZT, Zhang LL, Han JJ, Zhou M, Liu JX. Histone H3K4 methyltransferases SDG25 and ATX1 maintain heat-stress gene expression during recovery in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1326-1338. [PMID: 33278042 DOI: 10.1111/tpj.15114] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Plants have short-term stress memory that enables them to maintain the expression state of a substantial subset of heat-inducible genes during stress recovery after heat stress. Little is known about the molecular mechanisms controlling stress-responsive gene expression at the recovery stage in plants, however. In this article, we demonstrate that histone H3K4 methyltransferases SDG25 and ATX1 are required for heat-stress tolerance in Arabidopsis. SDG25 and ATX1 are not only important for stress-responsive gene expression during heat stress, but also for maintaining stress-responsive gene expression during stress recovery. A combination of whole-genome bisulfite sequencing, RNA-sequencing and ChIP-qPCR demonstrated that mutations of SDG25 and ATX1 decrease histone H3K4me3 levels, increase DNA cytosine methylation and inhibit the expression of a subset of heat stress-responsive genes during stress recovery in Arabidopsis. ChIP-qPCR results confirm that ATX1 binds to chromatins associated with these target genes. Our results reveal that histone H3K4me3 affects DNA methylation at regions in the loci associated with heat stress-responsive gene expression during stress recovery, providing insights into heat-stress transcriptional memory in plants.
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Affiliation(s)
- Ze-Ting Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Lin-Lin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jia-Jia Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
| | - Ming Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
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Li A, Hu B, Chu C. Epigenetic regulation of nitrogen and phosphorus responses in plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153363. [PMID: 33508741 DOI: 10.1016/j.jplph.2021.153363] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/31/2020] [Accepted: 01/01/2021] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) and phosphorus (P) are two of the most important nutrients for plant growth and crop yields. In the last decade, plenty of studies have revealed the genetic factors and their regulatory networks which are involved in N and/or P uptake and utilization in different model plant species, especially in Arabidopsis and rice. However, increasing evidences have shown that epigenetic regulation also plays a vital role in modulating plant responses to nutrient availability. In this review, we make a brief summary of epigenetic regulation including histone modifications, DNA methylation, and other chromatin structure alterations in tuning N and P responses. We also give an outlook for future research directions to comprehensively dissect the involvement of epigenetic regulation in modulating nutrient response in plants.
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Affiliation(s)
- Aifu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Hu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China. PLANTS 2021; 10:plants10020291. [PMID: 33546517 PMCID: PMC7913720 DOI: 10.3390/plants10020291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022]
Abstract
Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.
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Scossa F, Alseekh S, Fernie AR. Integrating multi-omics data for crop improvement. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153352. [PMID: 33360148 DOI: 10.1016/j.jplph.2020.153352] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/26/2023]
Abstract
Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178, Rome, Italy.
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
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Halter T, Wang J, Amesefe D, Lastrucci E, Charvin M, Singla Rastogi M, Navarro L. The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions. eLife 2021; 10:e62994. [PMID: 33470193 PMCID: PMC7880685 DOI: 10.7554/elife.62994] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/19/2021] [Indexed: 12/18/2022] Open
Abstract
Active DNA demethylation has emerged as an important regulatory process of plant and mammalian immunity. However, very little is known about the mechanisms by which active demethylation controls transcriptional immune reprogramming and disease resistance. Here, we first show that the Arabidopsis active demethylase ROS1 promotes basal resistance towards Pseudomonas syringae by antagonizing RNA-directed DNA methylation (RdDM). Furthermore, we demonstrate that ROS1 facilitates the flagellin-triggered induction of the disease resistance gene RMG1 by limiting RdDM at the 3' boundary of a transposable element (TE)-derived repeat embedded in its promoter. We further identify flagellin-responsive ROS1 putative primary targets and show that at a subset of promoters, ROS1 erases methylation at discrete regions exhibiting WRKY transcription factors (TFs) binding. In particular, we demonstrate that ROS1 removes methylation at the orphan immune receptor RLP43 promoter, to ensure DNA binding of WRKY TFs. Finally, we show that ROS1-directed demethylation of RMG1 and RLP43 promoters is causal for both flagellin responsiveness of these genes and for basal resistance. Overall, these findings significantly advance our understanding of how active demethylases shape transcriptional immune reprogramming to enable antibacterial resistance.
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Affiliation(s)
- Thierry Halter
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de recherche Paris, Sciences & Lettres (PSL)ParisFrance
| | - Jingyu Wang
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de recherche Paris, Sciences & Lettres (PSL)ParisFrance
| | - Delase Amesefe
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de recherche Paris, Sciences & Lettres (PSL)ParisFrance
| | - Emmanuelle Lastrucci
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de recherche Paris, Sciences & Lettres (PSL)ParisFrance
| | - Magali Charvin
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de recherche Paris, Sciences & Lettres (PSL)ParisFrance
| | - Meenu Singla Rastogi
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de recherche Paris, Sciences & Lettres (PSL)ParisFrance
| | - Lionel Navarro
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de recherche Paris, Sciences & Lettres (PSL)ParisFrance
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Zhan X, Lu Y, Zhu JK, Botella JR. Genome editing for plant research and crop improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:3-33. [PMID: 33369120 DOI: 10.1111/jipb.13063] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/22/2020] [Indexed: 05/27/2023]
Abstract
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state-of-the-art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel (insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.
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Affiliation(s)
- Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Xianyang, 712100, China
| | - Yuming Lu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
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Kong X, Hong Y, Hsu YF, Huang H, Liu X, Song Z, Zhu JK. SIZ1-Mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis. MOLECULAR PLANT 2020; 13:1816-1824. [PMID: 32927102 DOI: 10.1016/j.molp.2020.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/21/2020] [Accepted: 09/08/2020] [Indexed: 05/20/2023]
Abstract
The 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1)-mediated active DNA demethylation is critical for shaping the genomic DNA methylation landscape in Arabidopsis. Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown. Using a methylation-sensitive PCR (CHOP-PCR)-based forward genetic screen for Arabidopsis DNA hyper-methylation mutants, we identified the SUMO E3 ligase SIZ1 as a critical regulator of active DNA demethylation. Dysfunction of SIZ1 leads to hyper-methylation at approximately 1000 genomic regions. SIZ1 physically interacts with ROS1 and mediates the SUMOylation of ROS1. The SUMOylation of ROS1 is reduced in siz1 mutant plants. Compared with that in wild-type plants, the protein level of ROS1 is significantly decreased, whereas there is an increased level of ROS1 transcripts in siz1 mutant plants. Our results suggest that SIZ1-mediated SUMOylation of ROS1 promotes its stability and positively regulates active DNA demethylation.
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Affiliation(s)
- Xiangfeng Kong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yechun Hong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yi-Feng Hsu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Xue Liu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Zhe Song
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
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Kim JS, Kidokoro S, Shinozaki K, Yamaguchi-Shinozaki K. DNA demethylase ROS1 prevents inheritable DREB1A/CBF3 repression by transgene-induced promoter methylation in the Arabidopsis ice1-1 mutant. PLANT MOLECULAR BIOLOGY 2020; 104:575-582. [PMID: 33000386 DOI: 10.1007/s11103-020-01061-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
In the ros1-defective mutant, DREB1A repression by the transgene-induced promoter methylation of ice1-1 became inheritable across generations even in the absence of the causative transgene NICE1. Transgene silencing (TGS) is a widely observed event during plant bioengineering, which is presented as a gradual decrease in ectopic gene expression across generations and occasionally coupled with endogenous gene silencing based on DNA sequence similarity. TGS is known to be established by guided DNA methylation machinery. However, the machinery underlying gene recovery from TGS has not been fully elucidated. We previously reported that in ice1-1 outcross descendants, the expressional repression and recovery of DREB1A/CBF3 were instantly achieved by a newly discovered NICE1 transgene, instead of the formerly proposed ice1-1 mutation in the ICE1 gene. The plants harboring NICE1 produced small RNAs targeting and causing the DREB1A promoter to be hypermethylated and silenced. To analyze the role of the plant-specific active DNA demethylase REPRESSOR OF SILENCING 1 (ROS1) in instant DREB1A recovery, we propagated the NICE1-segregating population upon ros1 dysfunction and evaluated the gene expression and DNA methylation levels of DREB1A through generations. Our results showed that the epigenetic DREB1A repression was substantially sustained in subsequent generations even without NICE1 and stably inherited across generations. Consistent with the gene expression results, only incomplete DNA methylation removal was detected in the same generations. These results indicate that a novel inheritable epiallele emerged by the ros1 dysfunction. Overall, our study reveals the important role of ROS1 in the inheritability of TGS-associated gene repression.
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Affiliation(s)
- June-Sik Kim
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074, Japan
| | - Satoshi Kidokoro
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan.
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Quantitative Epigenetics: A New Avenue for Crop Improvement. EPIGENOMES 2020; 4:epigenomes4040025. [PMID: 34968304 PMCID: PMC8594725 DOI: 10.3390/epigenomes4040025] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/24/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022] Open
Abstract
Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Furthermore, the development of epigenetic recombinant inbred lines (epi-RILs) in model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Likewise, epigenome-wide association study (EWAS) and epi-genotyping by sequencing (epi-GBS) have revolutionized the field of epigenetics research in plants. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can potentially facilitate epigenetic based molecular breeding of important crop plants.
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Geng Y, Chang N, Zhao Y, Qin X, Lu S, Crabbe MJC, Guan Y, Zhang T. Increased epigenetic diversity and transient epigenetic memory in response to salinity stress in Thlaspi arvense. Ecol Evol 2020; 10:11622-11630. [PMID: 33144988 PMCID: PMC7593180 DOI: 10.1002/ece3.6795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 01/20/2023] Open
Abstract
Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (field pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation-sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation changes across individuals in response to salinity stress and whether such an effect of maternal stress could be transferred to offspring for one or two generations in nonstressed environments. Our results based on 306 epiloci indicated no consistent change of DNA methylation status in specific epiloci across individuals within the same conditions. In contrast, we found that the epigenetic diversity at population level increased significantly in response to the stimulation of salinity stress; and this "stimulation effect" could be transferred partially in the form of stress memory to at least two generations of offspring in nonstressed environments. In addition, we observed a parallel change in functionally important traits, that is, phenotypic variation was significantly higher in plants grown under salinity stress compared with those of control groups. Taken together, our results provide novel clues for the increased spontaneous epimutation rate in response to stress in plants, of potential adaptive significance.
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Affiliation(s)
- Yupeng Geng
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Na Chang
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Yuewan Zhao
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Xiaoying Qin
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Shugang Lu
- School of Life SciencesYunnan UniversityKunmingChina
| | - M. James C. Crabbe
- Wolfson CollegeOxford UniversityUK
- Institute of Biomedical and Environmental Science & TechnologyUniversity of BedfordshireLutonUK
- School of Life ScienceShanxi UniversityTaiyuanChina
| | - Yabin Guan
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
- School of Life SciencesYunnan UniversityKunmingChina
| | - Ticao Zhang
- College of Chinese Material MedicaYunnan University of Chinese MedicineKunmingChina
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Affiliation(s)
- Jean Molinier
- Institut de biologie moléculaire des plantes du CNRS, Strasbourg, France.
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Liu J, He Z. Small DNA Methylation, Big Player in Plant Abiotic Stress Responses and Memory. FRONTIERS IN PLANT SCIENCE 2020; 11:595603. [PMID: 33362826 PMCID: PMC7758401 DOI: 10.3389/fpls.2020.595603] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/18/2020] [Indexed: 05/12/2023]
Abstract
DNA methylation is a conserved epigenetic mark that plays important roles in maintaining genome stability and regulating gene expression. As sessile organisms, plants have evolved sophisticated regulatory systems to endure or respond to diverse adverse abiotic environmental challenges, i.e., abiotic stresses, such as extreme temperatures (cold and heat), drought and salinity. Plant stress responses are often accompanied by changes in chromatin modifications at diverse responsive loci, such as 5-methylcytosine (5mC) and N 6-methyladenine (6mA) DNA methylation. Some abiotic stress responses are memorized for several hours or days through mitotic cell divisions and quickly reset to baseline levels after normal conditions are restored, which is referred to as somatic memory. In some cases, stress-induced chromatin marks are meiotically heritable and can impart the memory of stress exposure from parent plants to at least the next stress-free offspring generation through the mechanisms of transgenerational epigenetic inheritance, which may offer the descendants the potential to be adaptive for better fitness. In this review, we briefly summarize recent achievements regarding the establishment, maintenance and reset of DNA methylation, and highlight the diverse roles of DNA methylation in plant responses to abiotic stresses. Further, we discuss the potential role of DNA methylation in abiotic stress-induced somatic memory and transgenerational inheritance. Future research directions are proposed to develop stress-tolerant engineered crops to reduce the negative effects of abiotic stresses.
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Affiliation(s)
- Junzhong Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
- *Correspondence: Junzhong Liu,
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Zuhua He,
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