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Zhang W, Zhang L, Feng Y, Lin D, Yang Z, Zhang Z, Ma Y. Genome-wide profiling of DNA methylome and transcriptome reveals epigenetic regulation of Urechis unicinctus response to sulfide stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172238. [PMID: 38582121 DOI: 10.1016/j.scitotenv.2024.172238] [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: 01/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Sulfide is a well-known environmental pollutant that can have detrimental effects on most organisms. However, few metazoans living in sulfide-rich environments have developed mechanisms to tolerate and adapt to sulfide stress. Epigenetic mechanisms, including DNA methylation, have been shown to play a vital role in environmental stress adaptation. Nevertheless, the precise function of DNA methylation in biological sulfide adaptation remains unclear. Urechis unicinctus, a benthic organism inhabiting sulfide-rich intertidal environments, is an ideal model organism for studying adaptation to sulfide environments. In this study, we conducted a comprehensive analysis of the DNA methylome and transcriptome of U. unicinctus after exposure to 50 μM sulfide. The results revealed dynamic changes in the DNA methylation (5-methylcytosine) landscape in response to sulfide stress, with U. unicinctus exhibiting elevated DNA methylation levels following stress exposure. Integrating differentially expressed genes (DEGs) and differentially methylated regions (DMRs), we identified a crucial role of gene body methylation in predicting gene expression. Furthermore, using a DNA methyltransferase inhibitor, we validated the involvement of DNA methylation in the sulfide stress response and the gene regulatory network influenced by DNA methylation. The results indicated that by modulating DNA methylation levels during sulfide stress, the expression of glutathione S-transferase, glutamyl aminopeptidase, and cytochrome c oxidase could be up-regulated, thereby facilitating the metabolism and detoxification of exogenous sulfides. Moreover, DNA methylation was found to regulate and enhance the oxidative phosphorylation pathway, including NADH dehydrogenase, isocitrate dehydrogenase, and ATP synthase. Additionally, DNA methylation influenced the regulation of Cytochrome P450 and macrophage migration inhibitory factor, both of which are closely associated with oxidative stress and stress resistance. Our findings not only emphasize the role of DNA methylation in sulfide adaptation but also provide novel insights into the potential mechanisms through which marine organisms adapt to environmental changes.
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Affiliation(s)
- Wenqing Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Long Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Yuxin Feng
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Dawei Lin
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhifeng Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China; Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Liu P, Qu X, Zhang X, Ma R. Flexible Sensing Enabled Nondestructive Detection on Viability/Quality of Live Edible Oyster. Foods 2024; 13:167. [PMID: 38201196 PMCID: PMC10778624 DOI: 10.3390/foods13010167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Environmental and physiological fluctuations in the live oyster cold chain can result in reduced survival and quality. In this study, a flexible wireless sensor network (F-WSN) monitoring system combined with knowledge engineering was designed and developed to monitor environmental information and physiological fluctuations in the live oyster cold chain. Based on the Hazard Analysis and Critical Control Point (HACCP) plan to identify the critical control points (CCPs) in the live oyster cold chain, the F-WSN was utilized to conduct tracking and collection experiments in real scenarios from Yantai, Shandong Province, to Beijing. The knowledge model for shelf-life and quality prediction based on environmental information and physiological fluctuations was established, and the prediction accuracies of TVB-N, TVC, and pH were 96%, 85%, and 97%, respectively, and the prediction accuracy of viability was 96%. Relevant managers, workers, and experts were invited to participate in the efficiency and applicability assessment of the established system. The results indicated that combining F-WSN monitoring with knowledge-based HACCP modeling is an effective approach to improving the transparency of cold chain management, reducing quality and safety risks in the oyster industry, and promoting the sharing and reuse of HACCP knowledge in the oyster cold chain.
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Affiliation(s)
| | | | | | - Ruiqin Ma
- College of Engineering, China Agricultural University, Beijing 100083, China; (P.L.); (X.Q.); (X.Z.)
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Rahman MS, Billah MM, Rangel V, Cantu E. Elevated temperature triggers increase in global DNA methylation, 5-methylcytosine expression levels, apoptosis and NOx levels in the gonads of Atlantic sea urchin. Comp Biochem Physiol B Biochem Mol Biol 2024; 269:110899. [PMID: 37673203 DOI: 10.1016/j.cbpb.2023.110899] [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: 06/21/2023] [Revised: 08/24/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
Global warming is one of the greatest threats to living organisms. Among them, marine invertebrates are severely impacted on reproductive fitness by rising seawater surface temperatures due to climate change (e.g., massive heat waves). In this study, we used highly sensitive radioimmunoassay, immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), in situ TUNEL assay, luminescence assay, and colorimetric assay techniques to investigate the impacts of high temperatures on global DNA methylation, cellular apoptosis, and nitrative stress in gonads of Atlantic sea urchin (Arbacia punctulata, a commercially important species). Young adult sea urchins were exposed to 24, 28, and 32 °C for one week in a controlled laboratory setting. High temperatures (28 and 32 °C) markedly increased global DNA methylation (around 1.1-1.5-fold in testes and ~ 1.7-fold in ovaries) and 5-methylcytosine (5-mC) levels in gonads (around 2.7- to ~5.1-fold in ovaries and ~ 3.5- to ~6.2-fold in testes) compared with controls (24 °C). The number of apoptotic nuclei in gonads was much higher in high-temperature groups. The caspase activity also increased significantly (P < 0.05) in gonads in high-temperature groups. Nitrate/nitrites (NOx, a biomarker of reactive nitrogen species) levels were increased around 2.6- to ~5.2-fold in testes and ~ 1.9- to ~3.8-fold in ovaries in high-temperature groups. Collectively, these outcomes indicate that high temperatures drastically induce global DNA methylation, 5-mC expression levels, cellular apoptosis, and NOx levels in the gonads of Atlantic sea urchin.
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Affiliation(s)
- Md Saydur Rahman
- School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA.
| | - Mohammad Maruf Billah
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Victor Rangel
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Esmirna Cantu
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
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Li A, Zhao M, Zhang Z, Wang C, Zhang K, Zhang X, De Wit PR, Wang W, Gao J, Guo X, Zhang G, Li L. Genome architecture and selective signals compensatorily shape plastic response to a new environment. Innovation (N Y) 2023; 4:100464. [PMID: 37485076 PMCID: PMC10362523 DOI: 10.1016/j.xinn.2023.100464] [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: 12/29/2022] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Transcriptional plasticity interacts with natural selection in complex ways and is crucial for the survival of species under rapid climate change. How 3D genome architecture affects transcriptional plasticity and its interaction with genetic adaptation are unclear. We transplanted estuarine oysters to a new environment and found that genes located in active chromatin regions exhibited greater transcriptional plasticity, and changes in these regions were negatively correlated with selective signals. This indicates a trade-off between 3D active regions and selective signals in shaping plastic responses to a new environment. Specifically, a mutation, lincRNA, and changes in the accessibility of a distal enhancer potentially affect its interaction with the ManⅡa gene, which regulates the muscle function and survival of oysters. Our findings reveal that 3D genome architecture compensates for the role of genetic adaptation in environmental response to new environments and provide insights into synergetic genetic and epigenetic interactions critical for fitness-related trait and survival in a model marine species.
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Affiliation(s)
- Ao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Mingjie Zhao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaogang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kexin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Zhang
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Pierre Raoul De Wit
- Department of Marine Sciences, University of Gothenburg, Stromstad 45296, Sweden
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, Qingdao 266000, China
| | - Juntao Gao
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, Qingdao 266000, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, Qingdao 266000, China
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Wang X, Cong R, Li A, Wang W, Zhang G, Li L. Experimental DNA Demethylation Reduces Expression Plasticity and Thermal Tolerance in Pacific Oysters. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10208-5. [PMID: 37079122 DOI: 10.1007/s10126-023-10208-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Increasing seawater temperatures pose a great threat to marine organisms, especially those settled in fluctuating intertidal areas. DNA methylation, which can be induced by environmental variation, can influence gene expression and mediate phenotypic plasticity. However, the regulatory mechanisms of DNA methylation in gene expression-mediated adaptation to environmental stress have rarely been elucidated. In this study, DNA demethylation experiments were conducted on a typical intertidal species, the Pacific oyster (Crassostrea gigas), to determine the direct role of DNA methylation in regulating gene expression and adaptability under thermal stress. The global methylation level and the expression level of DNA methyltransferases (DNMT1, DNMT3a) showed an accordant variation trend under high temperatures, supporting that the genomic methylation status was catalyzed by DNMTs. DNA methylation inhibitor 5-Azacytidine (5-Aza) effectively inhibited DNA methylation level and decreased methylation plasticity at the 6th hour in thermal conditions. In total, 88 genes were identified as candidate DNA methylation-regulated thermal response genes; they exhibited reduced expression plasticity in response to heat stress, possibly caused by the decreased methylation plasticity. Post-heat shock, the thermal tolerance indicated by the survival curve was reduced when oysters were pretreated with 5-Aza, meaning that DNA demethylation negatively affected thermal adaptation in oysters. This study provides direct evidence for the crucial role of DNA methylation in mediating stress adaptation in marine invertebrates and contributes to the theoretical foundations underlying marine resource conservation and aquaculture.
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Affiliation(s)
- Xinxing Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Rihao Cong
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Ao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science,, Institute of Oceanology, Chinese Academy of Sciences, 266071, Shandong, Qingdao, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China.
- Shandong Technology Innovation Center of Oyster Seed Industry, 266000, Qingdao, China.
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