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Townsend J, Braz CU, Taylor T, Khatib H. Effects of paternal methionine supplementation on sperm DNA methylation and embryo transcriptome in sheep. ENVIRONMENTAL EPIGENETICS 2022; 9:dvac029. [PMID: 36727109 PMCID: PMC9885981 DOI: 10.1093/eep/dvac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Environmental effects on gene expression and offspring development can be mediated by epigenetic modifications. It is well established that maternal diet influences DNA methylation patterns and phenotypes in the offspring; however, the epigenetic effects of paternal diet on developing offspring warrants further investigation. Here, we examined how a prepubertal methionine-enriched paternal diet affected sperm DNA methylation and its subsequent effects on embryo gene expression. Three treatment and three control rams were bred to seven ewes, and blastocysts were flushed for RNA extraction. Semen was collected from all rams and submitted for reduced representation bisulfite sequencing analysis. In total, 166 differentially methylated cytosines were identified in the sperm from treatment versus control rams. Nine genes were found to be differentially expressed in embryos produced from treatment versus control rams, and seven differentially methylated cytosines in the sperm were found to be highly correlated with gene expression in the embryos. Our results demonstrate that sperm methylation differences induced by diet may influence fetal programming.
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Affiliation(s)
- Jessica Townsend
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Camila U Braz
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
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Wang N, Yang Q, Wang J, Shi R, Li M, Gao J, Xu W, Yang Y, Chen Y, Chen S. Integration of Transcriptome and Methylome Highlights the Roles of Cell Cycle and Hippo Signaling Pathway in Flatfish Sexual Size Dimorphism. Front Cell Dev Biol 2021; 9:743722. [PMID: 34926443 PMCID: PMC8675331 DOI: 10.3389/fcell.2021.743722] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/29/2021] [Indexed: 01/14/2023] Open
Abstract
Sexual size dimorphism (SSD) is the difference in segments or body size between sexes prevalent in various species. Understanding the genetic architecture of SSD has remained a significant challenge owing to the complexity of growth mechanisms and the sexual influences among species. The Chinese tongue sole (Cynoglossus semilaevis), which exhibits a female-biased SSD and sex reversal from female to pseudomale, is an ideal model for exploring SSD mechanism at the molecular level. The present study aimed to integrate transcriptome and methylome analysis to unravel the genetic and epigenetic changes in female, male, and pseudomale C. semilaevis. The somatotropic and reproductive tissues (brain, liver, gonad, and muscle) transcriptomes were characterized by RNA-seq technology. Transcriptomic analysis unravelled numerous differentially expressed genes (DEGs) involved in cell growth and death-related pathways. The gonad and muscle methylomes were further employed for screening differentially methylated genes (DMGs). Relatively higher DNA methylation levels were observed in the male and pseudomale individuals. In detail, hypermethylation of the chromosome W was pronounced in the pseudomale group than in the female group. Furthermore, weighted gene co-expression network analysis showed that turquoise and brown modules positively and negatively correlated with the female-biased SSD, respectively. A combined analysis of the module genes and DMGs revealed the female-biased mRNA transcripts and hypomethylated levels in the upstream and downstream regions across the cell cycle-related genes. Moreover, the male and pseudomale-biased gene expression in the hippo signaling pathway were positively correlated with their hypermethylation levels in the gene body. These findings implied that the activation of the cell cycle and the inhibition of the hippo signaling pathway were implicated in C. semilaevis female-biased SSD. In addition, the dynamic expression pattern of the epigenetic regulatory factors, including dnmt1, dnmt3a, dnmt3b, and uhrf1, among the different sexes correspond with their distinct DNA methylation levels. Herein, we provide valuable clues for understanding female-biased SSD in C. semilaevis.
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Affiliation(s)
- Na Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Qian Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jialin Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Rui Shi
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Ming Li
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jin Gao
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenteng Xu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Yingming Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Yadong Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
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Si Y, He F, Wen H, Li S, He H. Effects of low salinity on epigenetic changes of growth hormone and growth hormone receptor in half smooth tongue sole (Cynoglossus semilaevis). REPRODUCTION AND BREEDING 2021. [DOI: 10.1016/j.repbre.2021.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Abstract
Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.
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Affiliation(s)
- Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Center for Coastal Oceans Research, Institute for Water and Environment, Florida International University, North Miami, Florida 33181, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
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Namous H, Peñagaricano F, Del Corvo M, Capra E, Thomas DL, Stella A, Williams JL, Marsan PA, Khatib H. Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy. BMC Genomics 2018; 19:123. [PMID: 29409445 PMCID: PMC5801776 DOI: 10.1186/s12864-018-4509-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of their offspring. In previous studies in sheep, we demonstrated that different maternal diets altered the transcriptome of fetal tissues. However, the mechanisms underlying transcriptomic changes are poorly understood. DNA methylation is an epigenetic mark regulating transcription and is largely influenced by dietary components of the one-carbon cycle that generate the methyl group donor, SAM. Therefore, in the present study, we tested whether different maternal diets during pregnancy would alter the DNA methylation and gene expression patterns in fetal tissues. RESULTS Pregnant ewes were randomly divided into two groups which received either hay or corn diet from mid-gestation (day 67 ± 5) until day 131 ± 1 when fetuses were collected by necropsy. A total of 1516 fetal longissimus dorsi (LD) tissues were used for DNA methylation analysis and gene expression profiling. Whole genome DNA methylation using methyl-binding domain enrichment analysis revealed 60 differentially methylated regions (DMRs) between hay and corn fetuses with 39 DMRs more highly methylated in the hay fetuses vs. 21 DMRs more highly methylated in the corn fetuses. Three DMRs (LPAR3, PLIN5-PLIN4, and the differential methylation of a novel lincRNA) were validated using bisulfite sequencing. These DMRs were associated with differential gene expression. Additionally, significant DNA methylation differences were found at the single CpG level. Integrative methylome and transcriptome analysis revealed an association between gene expression and inter-/intragenic methylated regions. Furthermore, intragenic DMRs were found to be associated with expression of neighboring genes. CONCLUSIONS The findings of this study imply that maternal diet from mid- to late-gestation can shape the epigenome and the transcriptome of fetal tissues, and putatively affect phenotypes of the lambs.
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Affiliation(s)
- Hadjer Namous
- Department of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI 53706 USA
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida Genetics Institute, University of Florida, Florida, USA
| | - Marcello Del Corvo
- Institute of Zootechnics and PRONUTRIGEN Research Center, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - David L. Thomas
- Department of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI 53706 USA
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Australia
| | - Paolo Ajmone Marsan
- Institute of Zootechnics and PRONUTRIGEN Research Center, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI 53706 USA
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Si Y, He F, Wen H, Li J, Zhao J, Ren Y, Zhao M, Ji L, Huang Z, Zhang M, Chen S. Genetic polymorphisms and DNA methylation in exon 1 CpG-rich regions of PACAP gene and its effect on mRNA expression and growth traits in half smooth tongue sole (Cynoglossus semilaevis). FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:407-421. [PMID: 26494141 DOI: 10.1007/s10695-015-0147-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 10/16/2015] [Indexed: 06/05/2023]
Abstract
The pituitary adenylate cyclase activating polypeptide (PACAP) is a new type of hypophysiotropic hormone and plays an important role in regulating the synthesis and secretion of growth hormone and gonadotropin. The research on the relationship between PACAP and different growth traits would contribute to explain its function during the process of growth. Moreover, epigenetic modifications, especially DNA methylation at the CpG sites of the SNPs, play important roles in regulating gene expression. The results suggest that a SNP mutation (c.C151G) in the PACAP gene of male half smooth tongue sole (Cynoglossus semilaevis) is significantly associated with growth traits and serum physiological and biochemical parameters such as inorganic phosphorus (P < 0.05). The SNP is located in a CpG-rich region of exon 1. Intriguingly, the transition (C→G) added a new methylation site of PACAP gene. This SNP was also significantly related to the expression and methylation level of PACAP (P < 0.05). Individuals with GG genotype had faster growth rates than those of CG and CC genotypes. Moreover, GG genotype had significantly higher PACAP expression level and lower methylation level than CG and CC genotypes. In the serum indexes, only inorganic phosphorus content within GG genotypes was significantly higher than CC genotypes. This implied that the mutation and methylation status of PACAP gene could influence growth traits and this locus could be considered as a candidate genetic or epigenetic marker for Cynoglossus semilaevis molecular breeding.
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Affiliation(s)
- Yufeng Si
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Feng He
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.
- Fisheries College, Ocean University of China, Qingdao, China.
| | - Haishen Wen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Jifang Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Junli Zhao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Yuanyuan Ren
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Meilin Zhao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Liqin Ji
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Zhengju Huang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Mo Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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