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Singroha G, Kumar S, Gupta OP, Singh GP, Sharma P. Uncovering the Epigenetic Marks Involved in Mediating Salt Stress Tolerance in Plants. Front Genet 2022; 13:811732. [PMID: 35495170 PMCID: PMC9053670 DOI: 10.3389/fgene.2022.811732] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 12/29/2022] Open
Abstract
The toxic effects of salinity on agricultural productivity necessitate development of salt stress tolerance in food crops in order to meet the escalating demands. Plants use sophisticated epigenetic systems to fine-tune their responses to environmental cues. Epigenetics is the study of heritable, covalent modifications of DNA and histone proteins that regulate gene expression without altering the underlying nucleotide sequence and consequently modify the phenotype. Epigenetic processes such as covalent changes in DNA, histone modification, histone variants, and certain non-coding RNAs (ncRNA) influence chromatin architecture to regulate its accessibility to the transcriptional machinery. Under salt stress conditions, there is a high frequency of hypermethylation at promoter located CpG sites. Salt stress results in the accumulation of active histones marks like H3K9K14Ac and H3K4me3 and the downfall of repressive histone marks such as H3K9me2 and H3K27me3 on salt-tolerance genes. Similarly, the H2A.Z variant of H2A histone is reported to be down regulated under salt stress conditions. A thorough understanding of the plasticity provided by epigenetic regulation enables a modern approach to genetic modification of salt-resistant cultivars. In this review, we summarize recent developments in understanding the epigenetic mechanisms, particularly those that may play a governing role in the designing of climate smart crops in response to salt stress.
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Ackah M, Guo L, Li S, Jin X, Asakiya C, Aboagye ET, Yuan F, Wu M, Essoh LG, Adjibolosoo D, Attaribo T, Zhang Q, Qiu C, Lin Q, Zhao W. DNA Methylation Changes and Its Associated Genes in Mulberry ( Morus alba L.) Yu-711 Response to Drought Stress Using MethylRAD Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020190. [PMID: 35050078 PMCID: PMC8780187 DOI: 10.3390/plants11020190] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 05/31/2023]
Abstract
Drought stress remains one of the most detrimental environmental cues affecting plant growth and survival. In this work, the DNA methylome changes in mulberry leaves under drought stress (EG) and control (CK) and their impact on gene regulation were investigated by MethylRAD sequencing. The results show 138,464 (37.37%) and 56,241 (28.81%) methylation at the CG and CWG sites (W = A or T), respectively, in the mulberry genome between drought stress and control. The distribution of the methylome was prevalent in the intergenic, exonic, intronic and downstream regions of the mulberry plant genome. In addition, we discovered 170 DMGs (129 in CG sites and 41 in CWG sites) and 581 DMS (413 in CG sites and 168 in CWG sites). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicates that phenylpropanoid biosynthesis, spliceosome, amino acid biosynthesis, carbon metabolism, RNA transport, plant hormone, signal transduction pathways, and quorum sensing play a crucial role in mulberry response to drought stress. Furthermore, the qRT-PCR analysis indicates that the selected 23 genes enriched in the KEGG pathways are differentially expressed, and 86.96% of the genes share downregulated methylation and 13.04% share upregulation methylation status, indicating the complex link between DNA methylation and gene regulation. This study serves as fundamentals in discovering the epigenomic status and the pathways that will significantly enhance mulberry breeding for adaptation to a wide range of environments.
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Affiliation(s)
- Michael Ackah
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
| | - Liangliang Guo
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
| | - Shaocong Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
| | - Xin Jin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
| | - Charles Asakiya
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China;
| | - Evans Tawiah Aboagye
- Key Laboratory of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
| | - Feng Yuan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
| | - Mengmeng Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
| | - Lionnelle Gyllye Essoh
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
| | - Daniel Adjibolosoo
- Key Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Thomas Attaribo
- School of Agriculture, C. K. Tedam University of Technology and Applied Sciences, Navrongo UK-0215-5321, Ghana;
| | - Qiaonan Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
| | - Changyu Qiu
- Sericultural Research Institute, Guangxi Zhuang Autonomous Region, Nanning 530007, China; (C.Q.); (Q.L.)
| | - Qiang Lin
- Sericultural Research Institute, Guangxi Zhuang Autonomous Region, Nanning 530007, China; (C.Q.); (Q.L.)
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.G.); (S.L.); (X.J.); (F.Y.); (M.W.); (L.G.E.); (Q.Z.)
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Skorupa M, Szczepanek J, Mazur J, Domagalski K, Tretyn A, Tyburski J. Salt stress and salt shock differently affect DNA methylation in salt-responsive genes in sugar beet and its wild, halophytic ancestor. PLoS One 2021; 16:e0251675. [PMID: 34043649 PMCID: PMC8158878 DOI: 10.1371/journal.pone.0251675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/29/2021] [Indexed: 01/19/2023] Open
Abstract
Here we determined the impact of salt shock and salt stress on the level of DNA methylation in selected CpG islands localized in promoters or first exons of sixteen salt-responsive genes in beets. Two subspecies differing in salt tolerance were subjected for analysis, a moderately salt-tolerant sugar beet Beta vulgaris ssp. vulgaris cv. Huzar and a halophytic beet, Beta vulgaris ssp. maritima. The CpG island methylation status was determined. All target sequences were hyper- or hypomethylated under salt shock and/or salt stress in one or both beet subspecies. It was revealed that the genomic regions analyzed were highly methylated in both, the salt treated plants and untreated controls. Methylation of the target sequences changed in a salt-dependent manner, being affected by either one or both treatments. Under both shock and stress, the hypomethylation was a predominant response in sugar beet. In Beta vulgaris ssp. maritima, the hypermethylation occurred with higher frequency than hypomethylation, especially under salt stress and in the promoter-located CpG sites. Conversely, the hypomethylation of the promoter-located CpG sites predominated in sugar beet plants subjected to salt stress. This findings suggest that DNA methylation may be involved in salt-tolerance and transcriptomic response to salinity in beets.
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Affiliation(s)
- Monika Skorupa
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
- * E-mail:
| | - Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Justyna Mazur
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Domagalski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Department of Immunology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Andrzej Tretyn
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Jarosław Tyburski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
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Seawater Culture Increases Omega-3 Long-Chain Polyunsaturated Fatty Acids (N-3 LC-PUFA) Levels in Japanese Sea Bass ( Lateolabrax japonicus), Probably by Upregulating Elovl5. Animals (Basel) 2020; 10:ani10091681. [PMID: 32957627 PMCID: PMC7552620 DOI: 10.3390/ani10091681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
The fatty acid compositions of the fish muscle and liver are substantially affected by rearing environment. However, the mechanisms underlying this effect have not been thoroughly described. In this study, we investigated the effects of different culture patterns, i.e., marine cage culture and freshwater pond culture, on long-chain polyunsaturated fatty acids (LC-PUFA) biosynthesis in an aquaculturally important fish, the Japanese sea bass (Lateolabrax japonicus). Fish were obtained from two commercial farms in the Guangdong province, one of which raises Japanese sea bass in freshwater, while the other cultures sea bass in marine cages. Fish were fed the same commercial diet. We found that omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) levels in the livers and muscles of the marine cage cultured fish were significantly higher than those in the livers and muscles of the freshwater pond cultured fish. Quantitative real-time PCRs indicated that fatty acid desaturase 2 (FADS2) transcript abundance was significantly lower in the livers of the marine cage reared fish as compared to the freshwater pond reared fish, but that fatty acid elongase 5 (Elovl5) transcript abundance was significantly higher. Consistent with this, two of the 28 CpG loci in the FADS2 promoter region were heavily methylated in the marine cage cultured fish, but were only slightly methylated in freshwater pond cultured fish (n = 5 per group). Although the Elovl5 promoter was less methylated in the marine cage reared fish as compared to the freshwater pond reared fish, this difference was not significant. Thus, our results might indicate that Elovl5, not FADS2, plays an important role in the enhancing LC-PUFA synthesis in marine cage cultures.
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Li R, Hu F, Li B, Zhang Y, Chen M, Fan T, Wang T. Whole genome bisulfite sequencing methylome analysis of mulberry (Morus alba) reveals epigenome modifications in response to drought stress. Sci Rep 2020; 10:8013. [PMID: 32415195 PMCID: PMC7228953 DOI: 10.1038/s41598-020-64975-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/24/2020] [Indexed: 01/09/2023] Open
Abstract
DNA methylation plays a significant role in many biological processes. Although some studies of DNA methylation have been performed in woody plant, none is known about the methylation patterns of mulberry (Morus alba). In this study, we performed whole genome bisulfite sequencing under drought stress to generate a methylated cytosines map and assessed the effects of the changes on gene expression combined with transcriptomics. We found that the percentage of methylated cytosines varied depending on the local sequence context (CG, CHG and CHH) and external treatment (control, CK; drought stress, DS). The methylation levels under DS were 8.64% higher than that of CK, and differences that were mainly due to the contribution of mCG (6.24%). Additionally, there were 3,243 different methylation and expression associated genes. In addition, methylated genes were enriched within GO subcategories including catalytic activity, cellular process, metabolic process, response to stimulus and regulation of biological process. This is the first study to comprehensively present methylation patterns in mulberry and reveal widespread DNA methylation changes in response to drought stress, which has the potential to enhance our understanding of links between DNA methylation and the modulation of gene expression in plants subjected to abiotic stresses.
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Affiliation(s)
- Ruixue Li
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230061, China
| | - Fei Hu
- Plant Protection and Agroproducts Safety Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230031, China
| | - Bing Li
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230061, China
| | - Yuping Zhang
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230061, China
| | - Ming Chen
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230061, China
| | - Tao Fan
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230061, China
| | - Taichu Wang
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230061, China.
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Yuan L, Xie S, Nie L, Zheng Y, Wang J, Huang J, Zhao M, Zhu S, Hou J, Chen G, Wang C. Comparative Proteomics Reveals Cold Acclimation Machinery Through Enhanced Carbohydrate and Amino Acid Metabolism in Wucai ( Brassica Campestris L.). PLANTS (BASEL, SWITZERLAND) 2019; 8:E474. [PMID: 31698739 PMCID: PMC6918420 DOI: 10.3390/plants8110474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 05/30/2023]
Abstract
Limited information is available on the cold acclimation of non-heading Chinese cabbage (NHCC) under low temperatures. In this study, the isobaric tags for relative and absolute quantification (iTRAQ) were used to illustrate the molecular machinery of cold acclimation. Compared to the control (Cont), altogether, 89 differentially expressed proteins (DEPs) were identified in wucai leaves responding to low temperatures (LT). Among these proteins, 35 proteins were up-regulated ((and 54 were down-regulated). These differentially expressed proteins were categorized as having roles in carbohydrate metabolism, photosynthesis and energy metabolism, oxidative defense, amino acid metabolism, metabolic progress, cold regulation, methylation progress, and signal transduction. The fructose, glucose, and sucrose were dramatically increased in response to cold acclimation. It was firstly reported that aspartate, serine, glutamate, proline, and threonine were significantly accumulated under low temperatures. Results of quantitative real-time PCR analysis of nine DEPs displayed that the transcriptional expression patterns of six genes were consistent with their protein expression abundance. Our results demonstrated that wucai acclimated to low temperatures through regulating the expression of several crucial proteins. Additionally, carbohydrate and amino acid conversion played indispensable and vital roles in improving cold assimilation in wucai.
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Affiliation(s)
- Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Shilei Xie
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Libing Nie
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Yushan Zheng
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Jie Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Ju Huang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
| | - Mengru Zhao
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
| | - Shidong Zhu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (L.Y.); (S.X.); (L.N.); (Y.Z.); (J.W.); (J.H.); (M.Z.); (S.Z.); (J.H.); (G.C.)
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
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Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare). EPIGENOMES 2018. [DOI: 10.3390/epigenomes2020012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Wang T, Huang D, Chen B, Mao N, Qiao Y, Ji M. Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp. Genes Genomics 2018; 40:321-331. [DOI: 10.1007/s13258-018-0647-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/04/2018] [Indexed: 12/26/2022]
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Zhang X, Li Q, Kong L, Yu H. DNA methylation changes detected by methylation-sensitive amplified polymorphism in the Pacific oyster (Crassostrea gigas) in response to salinity stress. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0583-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Lu X, Wang X, Chen X, Shu N, Wang J, Wang D, Wang S, Fan W, Guo L, Guo X, Ye W. Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress. BMC Genomics 2017; 18:297. [PMID: 28407801 PMCID: PMC5390369 DOI: 10.1186/s12864-017-3681-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/05/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation, with a cryptic role in genome stability, gene transcription and expression, is involved in the drought response process in plants, but the complex regulatory mechanism is still largely unknown. RESULTS Here, we performed whole-genome bisulfite sequencing (WGBS) and identified long non-coding RNAs on cotton leaves under drought stress and re-watering treatments. We obtained 31,223 and 30,997 differentially methylated regions (representing 2.48% of the genome) after drought stress and re-watering treatments, respectively. Our data also showed that three sequence contexts, including mCpG, mCHG, mCHH, all presented a hyper-methylation pattern under drought stress and were nearly restored to normal levels after the re-watering treatment. Among all the methylation variations, asymmetric CHH methylation was the most consistent with external environments, suggesting that methylation/demethylation in a CHH context may constitute a novel epigenetic modification in response to drought stress. Combined with the targets of long non-coding RNAs, we found that long non-coding RNAs may mediate variations in methylation patterns by splicing into microRNAs. Furthermore, the many hormone-related genes with methylation variations suggested that plant hormones might be a potential mechanism in the drought response. CONCLUSIONS Future crop-improvement strategies may benefit by taking into account not only the DNA genetic variations in cotton varieties but also the epigenetic modifications of the genome.
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Affiliation(s)
- Xuke Lu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China.,College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xiaoge Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Na Shu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Delong Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Shuai Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Weili Fan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Lixue Guo
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Xiaoning Guo
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Key Laboratory for Cotton Genetic Improvement, Anyang, 455000, Henan, China.
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