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Song B, Yu J, Li X, Li J, Fan J, Liu H, Wei W, Zhang L, Gu K, Liu D, Zhao K, Wu J. Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement. Genome Biol 2024; 25:87. [PMID: 38581061 PMCID: PMC10996114 DOI: 10.1186/s13059-024-03220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown. RESULTS Here, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening. CONCLUSIONS Our study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.
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Affiliation(s)
- Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jinshan Yu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jing Fan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Hainan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Weilin Wei
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Lingchao Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Dongliang Liu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, Jiangsu, China.
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Li Y, Mao X, Li M, Li L, Tong X, Huang L. The predictive value of BTG1 for the response of newly diagnosed acute myeloid leukemia to decitabine. Clin Epigenetics 2024; 16:16. [PMID: 38254153 PMCID: PMC10802042 DOI: 10.1186/s13148-024-01627-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Decitabine has been widely used to treat acute myeloid leukemia (AML); however as AML is a heterogeneous disease, not all patients benefit from decitabine. This study aimed to identify markers for predicting the response to decitabine. METHODS An intersection of in vitro experiments and bioinformatics was performed using a combination of epigenetic and transcriptomic analysis. A tumor-suppressor gene associated with methylation and the response to decitabine was screened. Then the sensitivity and specificity of this marker in predicting the response to decitabine was confirmed in 54 samples from newly diagnosed AML patients treated with decitabine plus IA regimen in a clinical trial (ChiCTR2000037928). RESULTS In vitro experiments showed that decitabine caused hypomethylation and upregulation of BTG1, while downregulation of BTG1 attenuated the inhibitory effect of decitabine. In newly diagnosed AML patients who received decitabine plus IA regimen, the predictive value of BTG1 to predict complete remission (CR) was assigned with a sensitivity of 86.7% and a specificity of 100.0% when BTG1 expression was < 0.292 (determined using real-time quantitative PCR), with area under the curve (AUC) = 0.933, P = 0.021. The predictive value of BTG1 to predict measurable residual disease (MRD) negativity was assigned with a sensitivity of 100.0% and a specificity of 80.0% when BTG1 expression was < 0.292 (AUC = 0.892, P = 0.012). Patients were divided into low and high BTG1 expression groups according to a cutoff of 0.292, and the CR rate of the low-expression group was significantly higher than that of the high-expression group (97.5% vs. 50%, P < 0.001). CONCLUSIONS Low expression of BTG1 was associated with CR and MRD negativity in newly diagnosed AML patients treated with a decitabine-containing regimen, suggesting that BTG1 is a potential marker for predicting the response to decitabine in newly diagnosed AML. CLINICAL TRIAL REGISTRATION ChiCTR2000037928.
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Affiliation(s)
- Yi Li
- Renmin Hospital of Wuhan University, Wuhan, China
| | - Xia Mao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jie-fang Avenue, Wuhan, 430030, Hubei, China
| | - Mengyuan Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jie-fang Avenue, Wuhan, 430030, Hubei, China
| | - Li Li
- Xinqiao Hospital of Army Medical University, Chongqing, China
| | - Xiwen Tong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jie-fang Avenue, Wuhan, 430030, Hubei, China
| | - Lifang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jie-fang Avenue, Wuhan, 430030, Hubei, China.
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Warmbrunn MV, Attaye I, Aron-Wisnewsky J, Rampanelli E, van der Vossen EW, Hao Y, Koopen A, Bergh PO, Stols-Gonçalves D, Mohamed N, Kemper M, Verdoes X, Wortelboer K, Davids M, Belda E, André S, Hazen S, Clement K, Groen B, van Raalte DH, Herrema H, Backhed F, Nieuwdorp M. Oral histidine affects gut microbiota and MAIT cells improving glycemic control in type 2 diabetes patients. Gut Microbes 2024; 16:2370616. [PMID: 38961712 PMCID: PMC11225920 DOI: 10.1080/19490976.2024.2370616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024] Open
Abstract
Amino acids, metabolized by host cells as well as commensal gut bacteria, have signaling effects on host metabolism. Oral supplementation of the essential amino acid histidine has been shown to exert metabolic benefits. To investigate whether dietary histidine aids glycemic control, we performed a case-controlled parallel clinical intervention study in participants with type 2 diabetes (T2D) and healthy controls. Participants received oral histidine for seven weeks. After 2 weeks of histidine supplementation, the microbiome was depleted by antibiotics to determine the microbial contribution to histidine metabolism. We assessed glycemic control, immunophenotyping of peripheral blood mononucelar cells (PBMC), DNA methylation of PBMCs and fecal gut microbiota composition. Histidine improves several markers of glycemic control, including postprandial glucose levels with a concordant increase in the proportion of MAIT cells after two weeks of histidine supplementation. The increase in MAIT cells was associated with changes in gut microbial pathways such as riboflavin biosynthesis and epigenetic changes in the amino acid transporter SLC7A5. Associations between the microbiome and MAIT cells were replicated in the MetaCardis cohort. We propose a conceptual framework for how oral histidine may affect MAIT cells via altered gut microbiota composition and SLC7A5 expression in MAIT cells directly and thereby influencing glycemic control. Future studies should focus on the role of flavin biosynthesis intermediates and SLC7A5 modulation in MAIT cells to modulate glycemic control.
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Affiliation(s)
- Moritz V. Warmbrunn
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Amsterdam Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Research Institute, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Science research institute, Amsterdam, The Netherlands
| | - Ilias Attaye
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Amsterdam Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Research Institute, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Science research institute, Amsterdam, The Netherlands
| | - Judith Aron-Wisnewsky
- Assistante Publique Hôpitaux de Paris, Nutrition Department, Pitié-Salpêtrière Hospital, CRNH Ile de France, Paris, France
- INSERM, Nutrition and Obesities, Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Elena Rampanelli
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Science research institute, Amsterdam, The Netherlands
- Amsterdam Amsterdam institute for Infection and Immunity (AII), Amsterdam, The Netherlands
| | - Eduard W.J. van der Vossen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Youling Hao
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Amsterdam Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Research Institute, Amsterdam, The Netherlands
- Amsterdam Amsterdam institute for Infection and Immunity (AII), Amsterdam, The Netherlands
| | - Annefleur Koopen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Per-Olof Bergh
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Institute of Medicine, University of Gothenburg and Sahlgrenska, Gothenburg, Sweden
| | - Daniela Stols-Gonçalves
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Nadia Mohamed
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Marleen Kemper
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Xanthe Verdoes
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Koen Wortelboer
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Science research institute, Amsterdam, The Netherlands
- Amsterdam Amsterdam institute for Infection and Immunity (AII), Amsterdam, The Netherlands
| | - Mark Davids
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Eugeni Belda
- Assistante Publique Hôpitaux de Paris, Nutrition Department, Pitié-Salpêtrière Hospital, CRNH Ile de France, Paris, France
- INSERM, Nutrition and Obesities, Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Sébastien André
- Assistante Publique Hôpitaux de Paris, Nutrition Department, Pitié-Salpêtrière Hospital, CRNH Ile de France, Paris, France
- INSERM, Nutrition and Obesities, Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Stanley Hazen
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Karine Clement
- Assistante Publique Hôpitaux de Paris, Nutrition Department, Pitié-Salpêtrière Hospital, CRNH Ile de France, Paris, France
- INSERM, Nutrition and Obesities, Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Bert Groen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Daniel H. van Raalte
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Diabetes Center, Department of Internal Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Hilde Herrema
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Fredrik Backhed
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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4
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Wang H, Dang T, Feng J, Wu W, He L, Yang J. Identification of differentially methylated genes for severe acne by genome-wide DNA methylation and gene expression analysis. Epigenetics 2023; 18:2199373. [PMID: 37018476 PMCID: PMC10078136 DOI: 10.1080/15592294.2023.2199373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Severe acne is a chronic inflammatory skin condition that is affected by both genetic and environmental factors. DNA methylation is associated with a variety of inflammatory skin diseases, but its role in severe acne is unclear. In this study, we conducted a two-stage epigenome correlation study using 88 blood samples to identify disease-related differential methylation sites. We found close associations between the DNA methylation at 23 differentially methylated sites (DMSs) and severe acne, including PDGFD, ARHGEF10, etc. Further analysis revealed that differentially methylated genes (PARP8 and MAPKAPK2) were also expressed differently between severe acne and health control groups. These findings lead us to speculation that epigenetic mechanisms may play an important role in the pathogenesis of severe acne.
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Affiliation(s)
- Huai Wang
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Tianyuan Dang
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiaqi Feng
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wenjuan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiankang Yang
- School of Basic Medical Sciences, Dali University, Dali, China
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Wang Z, Heid B, He J, Xie H, Reilly CM, Dai R, Ahmed SA. Egr2 Deletion in Autoimmune-Prone C57BL6/lpr Mice Suppresses the Expression of Methylation-Sensitive Dlk1-Dio3 Cluster MicroRNAs. Immunohorizons 2023; 7:898-907. [PMID: 38153351 PMCID: PMC10759154 DOI: 10.4049/immunohorizons.2300111] [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: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
We previously demonstrated that the upregulation of microRNAs (miRNAs) at the genomic imprinted Dlk1-Dio3 locus in murine lupus is correlated with global DNA hypomethylation. We now report that the Dlk1-Dio3 genomic region in CD4+ T cells of MRL/lpr mice is hypomethylated, linking it to increased Dlk1-Dio3 miRNA expression. We evaluated the gene expression of methylating enzymes, DNA methyltransferases (DNMTs), and demethylating ten-eleven translocation proteins (TETs) to elucidate the molecular basis of DNA hypomethylation in lupus CD4+ T cells. There was a significantly elevated expression of Dnmt1 and Dnmt3b, as well as Tet1 and Tet2, in CD4+ T cells of three different lupus-prone mouse strains compared to controls. These findings suggest that the hypomethylation of murine lupus CD4+ T cells is likely attributed to a TET-mediated active demethylation pathway. Moreover, we found that deletion of early growth response 2 (Egr2), a transcription factor gene in B6/lpr mice markedly reduced maternally expressed miRNA genes but not paternally expressed protein-coding genes at the Dlk1-Dio3 locus in CD4+ T cells. EGR2 has been shown to induce DNA demethylation by recruiting TETs. Surprisingly, we found that deleting Egr2 in B6/lpr mice induced more hypomethylated differentially methylated regions at either the whole-genome level or the Dlk1-Dio3 locus in CD4+ T cells. Although the role of methylation in EGR2-mediated regulation of Dlk1-Dio3 miRNAs is not readily apparent, these are the first data to show that in lupus, Egr2 regulates Dlk1-Dio3 miRNAs, which target major signaling pathways in autoimmunity. These data provide a new perspective on the role of upregulated EGR2 in lupus pathogenesis.
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Affiliation(s)
- Zhuang Wang
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA
| | - Bettina Heid
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA
| | - Jianlin He
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute at Virginia Tech, Blacksburg, VA
| | - Hehuang Xie
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute at Virginia Tech, Blacksburg, VA
| | - Christopher M. Reilly
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine, Blacksburg, VA
| | - Rujuan Dai
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA
| | - S. Ansar Ahmed
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA
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Wozniak J, Loba W, Wysocka A, Dzimira S, Przadka P, Switonski M, Nowacka-Woszuk J. Altered Transcript Levels of MMP13 and VIT Genes in the Muscle and Connective Tissue of Pigs with Umbilical Hernia. Genes (Basel) 2023; 14:1903. [PMID: 37895252 PMCID: PMC10606093 DOI: 10.3390/genes14101903] [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: 09/01/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Umbilical hernia (UH) and inguinal hernia (IH) are among the most common defects in pigs, affecting their welfare and resulting in economic losses. In this study, we aimed to verify the association of previously reported differences in transcript levels of the ACAN, COL6A5, MMP13, and VIT genes with the occurrence of UH and IH. We examined mRNA levels in muscle and connective tissue from 68 animals-34 affected by UH and 34 controls. In a second cohort, we examined inguinal channel samples from 46 pigs (in four groups). We determined DNA methylation levels in muscle tissue for the UH and control animals. The transcript level of MMP13 changed in the UH cases, being upregulated and downregulated in muscle and connective tissue, respectively, and the VIT gene also showed an increased muscular mRNA level. The transcript of the ACAN gene significantly decreased in old pigs with IH. We further observed an increased DNA methylation level for one CpG site within the MMP13 gene in UH individuals. We conclude that these alterations in gene mRNA levels in the UH animals depend on the tissue and can sometimes be a consequence of, not a cause of, the affected phenotype.
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Affiliation(s)
- Jakub Wozniak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| | - Weronika Loba
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| | - Alicja Wysocka
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| | - Stanislaw Dzimira
- Department of Pathology, Wroclaw University of Environmental and Life Sciences, C.K. Norwida 31, 50-375 Wroclaw, Poland;
| | - Przemyslaw Przadka
- Department of Surgery, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 51, 50-366 Wroclaw, Poland;
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
| | - Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland; (J.W.); (W.L.); (A.W.); (M.S.)
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Caiye Z, Song S, Li M, Huang X, Luo Y, Fang S. Genome-wide DNA methylation analysis reveals different methylation patterns in Chinese indigenous sheep with different type of tail. Front Vet Sci 2023; 10:1125262. [PMID: 37215474 PMCID: PMC10196035 DOI: 10.3389/fvets.2023.1125262] [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: 12/16/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Background The study was aimed to analyze the difference of genome-wide DNA differential methylation in Lanzhou Large-tailed sheep, Altay sheep and Tibetan sheep, which the typical breeds with different type tails, as to screen the differentially methylated genes (DMGs) that affect the type of tails. Methods In this study, three Lanzhou Large-tailed sheep, three Altay sheep and three Tibetan sheep were detected by whole genome bisulfite sequencing (WGBS). The degree of genome-wide DNA methylation, differentially methylated regions (DMRs) and DMGs were analyzed. The candidate genes affecting the tail type of sheep were identified by GO and KEGG pathway enrichment analysis of DMGs. Results we identified 68,603 different methylated regions (DMCs) and 75 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in biological process, cellular component and molecular function, Some of the genes in these pathways are involved in fat metabolism: NFATC4, LPIN2, MGAT2 and MAT2B. Conclusion Our results may help to further understand the epigenetic regulation mechanisms of deposition of fat in the tail of sheep and provide new basic data for the study of local sheep.
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Affiliation(s)
- Zhu Caiye
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shuzhen Song
- Institute of Animal and Pasture Science and Green Agriculture, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Minna Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xaioyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yan Luo
- Gansu Institute of Animal Science and Veterinary Medicine, Pingliang, China
| | - Suli Fang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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8
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Vad-Nielsen J, Staunstrup NH, Kjeldsen ML, Dybdal N, Flandin G, De Stradis C, Daugaard TF, Vilsbøll-Larsen T, Maansson CT, Doktor TK, Sorensen BS, Nielsen AL. Genome-wide epigenetic and mRNA-expression profiling followed by CRISPR/Cas9-mediated gene-disruptions corroborate the MIR141/MIR200C-ZEB1/ZEB2-FGFR1 axis in acquired EMT-associated EGFR TKI-resistance in NSCLC cells. Transl Lung Cancer Res 2023; 12:42-65. [PMID: 36762066 PMCID: PMC9903082 DOI: 10.21037/tlcr-22-507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/12/2022] [Indexed: 01/16/2023]
Abstract
Background Epithelial-mesenchymal-transition (EMT) is an epigenetic-based mechanism contributing to the acquired treatment resistance against receptor tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) cells harboring epidermal growth factor receptor (EGFR)-mutations. Delineating the exact epigenetic and gene-expression alterations in EMT-associated EGFR TKI-resistance (EMT-E-TKI-R) is vital for improved diagnosis and treatment of NSCLC patients. Methods We characterized genome-wide changes in mRNA-expression, DNA-methylation and the histone-modification H3K36me3 in EGFR-mutated NSCLC HCC827 cells in result of acquired EMT-E-TKI-R. CRISPR/Cas9 was used to functional examine key findings from the omics analyses. Results Acquired EMT-E-TKI-R was analyzed with three omics approaches. RNA-sequencing identified 2,233 and 1,972 up- and down-regulated genes, respectively, and among these were established EMT-markers. DNA-methylation EPIC array analyses identified 14,163 and 7,999 hyper- and hypo-methylated, respectively, differential methylated positions of which several were present in EMT-markers. Finally, H3K36me3 chromatin immunoprecipitation (ChIP)-sequencing detected 2,873 and 3,836 genes with enrichment and depletion, respectively, and among these were established EMT-markers. Correlation analyses showed that EMT-E-TKI-R mRNA-expression changes correlated better with H3K36me3 changes than with DNA-methylation changes. Moreover, the omics data supported the involvement of the MIR141/MIR200C-ZEB1/ZEB2-FGFR1 signaling axis for acquired EMT-E-TKI-R. CRISPR/Cas9-mediated analyses corroborated the importance of ZEB1 in acquired EMT-E-TKI-R, MIR200C and MIR141 to be in an EMT-E-TKI-R-associated auto-regulatory loop with ZEB1, and FGFR1 to mediate cell survival in EMT-E-TKI-R. Conclusions The current study describes the synchronous genome-wide changes in mRNA-expression, DNA-methylation, and H3K36me3 in NSCLC EMT-E-TKI-R. The omics approaches revealed potential novel diagnostic markers and treatment targets. Besides, the study consolidates the functional impact of the MIR141/MIR200C-ZEB1/ZEB2-FGFR1-signaling axis in NSCLC EMT-E-TKI-R.
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Affiliation(s)
| | | | | | - Nina Dybdal
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | | | | | | | - Christoffer Trier Maansson
- Department of Biomedicine, Aarhus University, Aarhus, Denmark;,Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark;,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark;,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Chen X, Duan X, Chong Q, Li C, Xiao H, Chen S. Genome-Wide DNA Methylation Differences between Bos indicus and Bos taurus. Animals (Basel) 2023; 13:203. [PMID: 36670743 PMCID: PMC9854497 DOI: 10.3390/ani13020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Disease risk is a persistent problem in domestic cattle farming, while economic traits are the main concern. This study aimed to reveal the epigenetic basis for differences between zebu (Bos indicus) and taurine cattle (Bos taurus) in disease, disease resistance, and economic traits, and provide a theoretical basis for the genetic improvement of domestic cattle. In this study, whole genome bisulfite sequencing (WGBS) was used to analyze the whole-genome methylation of spleen and liver samples from Yunnan zebu and Holstein cattle. In the genome-wide methylation pattern analysis, it was found that the methylation pattern of all samples was dominated by the CG type, which accounted for >94.9%. The DNA methylation levels of different functional regions and transcriptional elements in the CG background varied widely. However, the methylation levels of different samples in the same functional regions or transcriptional elements did not differ significantly. In addition, we identified a large number of differentially methylation region (DMR) in both the spleen and liver groups, of which 4713 and 4663 were annotated to functional elements, and most of them were annotated to the intronic and exonic regions of genes. GO and KEGG functional analysis of the same differentially methylation region (DMG) in the spleen and liver groups revealed that significantly enriched pathways were involved in neurological, disease, and growth functions. As a result of the results of DMR localization, we screened six genes (DNM3, INPP4B, PLD, PCYT1B, KCNN2, and SLIT3) that were tissue-specific candidates for economic traits, disease, and disease resistance in Yunnan zebu. In this study, DNA methylation was used to construct links between genotypes and phenotypes in domestic cattle, providing useful information for further screening of epigenetic molecular markers in zebu and taurine cattle.
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Affiliation(s)
- Xiaona Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Xinyu Duan
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Qingqing Chong
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Heng Xiao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
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10
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Zhang X, Wang C, He D, Cheng Y, Yu L, Qi D, Li B, Zheng F. Identification of DNA methylation-regulated genes as potential biomarkers for coronary heart disease via machine learning in the Framingham Heart Study. Clin Epigenetics 2022; 14:122. [PMID: 36180886 PMCID: PMC9526342 DOI: 10.1186/s13148-022-01343-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation-regulated genes have been demonstrated as the crucial participants in the occurrence of coronary heart disease (CHD). The machine learning based on DNA methylation-regulated genes has tremendous potential for mining non-invasive predictive biomarkers and exploring underlying new mechanisms of CHD. Results First, the 2085 age-gender-matched individuals in Framingham Heart Study (FHS) were randomly divided into training set and validation set. We then integrated methylome and transcriptome data of peripheral blood leukocytes (PBLs) from the training set to probe into the methylation and expression patterns of CHD-related genes. A total of five hub DNA methylation-regulated genes were identified in CHD through dimensionality reduction, including ATG7, BACH2, CDKN1B, DHCR24 and MPO. Subsequently, methylation and expression features of the hub DNA methylation-regulated genes were used to construct machine learning models for CHD prediction by LightGBM, XGBoost and Random Forest. The optimal model established by LightGBM exhibited favorable predictive capacity, whose AUC, sensitivity, and specificity were 0.834, 0.672, 0.864 in the validation set, respectively. Furthermore, the methylation and expression statuses of the hub genes were verified in monocytes using methylation microarray and transcriptome sequencing. The methylation statuses of ATG7, DHCR24 and MPO and the expression statuses of ATG7, BACH2 and DHCR24 in monocytes of our study population were consistent with those in PBLs from FHS. Conclusions We identified five DNA methylation-regulated genes based on a predictive model for CHD using machine learning, which may clue the new epigenetic mechanism for CHD. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01343-2.
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Affiliation(s)
- Xiaokang Zhang
- Center for Gene Diagnosis and Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China
| | - Chen Wang
- Center for Gene Diagnosis and Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China
| | - Dingdong He
- Center for Gene Diagnosis and Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.,Department of Clinical Laboratory Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yating Cheng
- Center for Gene Diagnosis and Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China
| | - Li Yu
- Center for Gene Diagnosis and Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China
| | - Daoxi Qi
- Center for Gene Diagnosis and Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China
| | - Boyu Li
- Center for Gene Diagnosis and Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China
| | - Fang Zheng
- Center for Gene Diagnosis and Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
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11
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Domingo-Relloso A, Makhani K, Riffo-Campos AL, Tellez-Plaza M, Klein KO, Subedi P, Zhao J, Moon KA, Bozack AK, Haack K, Goessler W, Umans JG, Best LG, Zhang Y, Herreros-Martinez M, Glabonjat RA, Schilling K, Galvez-Fernandez M, Kent JW, Sanchez TR, Taylor KD, Craig Johnson W, Durda P, Tracy RP, Rotter JI, Rich SS, Berg DVD, Kasela S, Lappalainen T, Vasan RS, Joehanes R, Howard BV, Levy D, Lohman K, Liu Y, Daniele Fallin M, Cole SA, Mann KK, Navas-Acien A. Arsenic Exposure, Blood DNA Methylation, and Cardiovascular Disease. Circ Res 2022; 131:e51-e69. [PMID: 35658476 PMCID: PMC10203287 DOI: 10.1161/circresaha.122.320991] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/18/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Epigenetic dysregulation has been proposed as a key mechanism for arsenic-related cardiovascular disease (CVD). We evaluated differentially methylated positions (DMPs) as potential mediators on the association between arsenic and CVD. METHODS Blood DNA methylation was measured in 2321 participants (mean age 56.2, 58.6% women) of the Strong Heart Study, a prospective cohort of American Indians. Urinary arsenic species were measured using high-performance liquid chromatography coupled to inductively coupled plasma mass spectrometry. We identified DMPs that are potential mediators between arsenic and CVD. In a cross-species analysis, we compared those DMPs with differential liver DNA methylation following early-life arsenic exposure in the apoE knockout (apoE-/-) mouse model of atherosclerosis. RESULTS A total of 20 and 13 DMPs were potential mediators for CVD incidence and mortality, respectively, several of them annotated to genes related to diabetes. Eleven of these DMPs were similarly associated with incident CVD in 3 diverse prospective cohorts (Framingham Heart Study, Women's Health Initiative, and Multi-Ethnic Study of Atherosclerosis). In the mouse model, differentially methylated regions in 20 of those genes and DMPs in 10 genes were associated with arsenic. CONCLUSIONS Differential DNA methylation might be part of the biological link between arsenic and CVD. The gene functions suggest that diabetes might represent a relevant mechanism for arsenic-related cardiovascular risk in populations with a high burden of diabetes.
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Affiliation(s)
- Arce Domingo-Relloso
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
- Department of Statistics and Operations Research, University of Valencia, Spain
| | - Kiran Makhani
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Angela L. Riffo-Campos
- Millennium Nucleus on Sociomedicine (SocioMed) and Vicerrectoría Académica, Universidad de La Frontera, Temuco, Chile
- Department of Computer Science, ETSE, University of Valencia, Valencia, Spain
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Kathleen Oros Klein
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Pooja Subedi
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Katherine A. Moon
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anne K. Bozack
- Department of Environmental Health Sciences, School of Public Health, University of California, Berkeley, USA
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Walter Goessler
- Institute of Chemistry - Analytical Chemistry for Health and Environment, University of Graz, Austria
| | | | - Lyle G. Best
- Missouri Breaks Industries and Research Inc., Eagle Butte, SD, USA
| | - Ying Zhang
- Department of Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, OK, USA
| | | | - Ronald A. Glabonjat
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Kathrin Schilling
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Marta Galvez-Fernandez
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Jack W. Kent
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Tiffany R Sanchez
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Peter Durda
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Russell P. Tracy
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - David Van Den Berg
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Ramachandran S Vasan
- National Heart, Lung, and Blood Institute’s and Boston University’s Framingham Heart Study, Framingham, MA; Sections of Preventive Medicine and Epidemiology and Cardiovascular Medicine, Department of Medicine, department of Epidemiology, Boston University Schools of medicine and Public health, Boston, MA, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
- Framingham Heart Study, Framingham, MA
| | | | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
- Framingham Heart Study, Framingham, MA
| | - Kurt Lohman
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Yongmei Liu
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - M Daniele Fallin
- Departments of Mental Health and Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Shelley A. Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Koren K. Mann
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
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12
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Genome-Wide DNA Methylation Patterns of Muscle and Tail-Fat in DairyMeade Sheep and Mongolian Sheep. Animals (Basel) 2022; 12:ani12111399. [PMID: 35681863 PMCID: PMC9179529 DOI: 10.3390/ani12111399] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary DNA methylation is an important epigenetic modification and plays an important role in the regulation of gene expression. The study of DNA methylation will help to explore the effects of epigenetic modifications, other than DNA sequence variation, on biological phenotypes and physiological functions, promoting the revolution of livestock selection and breeding practices. DairyMeade sheep (thin-tailed) and Mongolian sheep (fat-tailed) have large differences in their dairy and meat production performances, as well as their tail phenotype, thus providing us with good materials for genomic DNA methylation studies. The below results provided a genome-wide DNA methylation landscape of muscle and tail-fat tissues between DairyMeade sheep and Mongolian sheep and a series of differentiated methylation regions (DMRs) in which CAMK2D may play a crucial role in fat metabolism and meat quality traits. These results may help us to understand how DNA methylation affects the economic traits of domestic animals like sheep. Abstract This study aimed to explore the genome-wide DNA methylation differences between muscle and tail-fat tissues of DairyMeade sheep (thin-tailed, lean carcass) and Mongolian sheep (fat-tailed, fat-deposited carcass). Whole-genome bisulfite sequencing (WGBS) was conducted and the global DNA methylation dynamics were mapped. Generally, CGs had a higher DNA methylation level than CHHs and CHGs, and tail-fat tissues had higher CG methylation levels than muscle tissues. For DNA repeat elements, SINE had the highest methylation level, while Simple had the lowest. When dividing the gene promoter region into small bins (200 bp per bin), the bins near the transcription start site (±200 bp) had the highest CG count per bin but the lowest DNA methylation levels. A series of DMRs were identified in muscle and tail-fat tissues between the two breeds. Among them, the introns of gene CAMK2D (calcium/calmodulin-dependent protein kinase II δ) demonstrated significant DNA methylation level differences between the two breeds in both muscle and tail-fat tissues, and it may play a crucial role in fat metabolism and meat quality traits. This study may provide basic datasets and references for further epigenetic modification studies during sheep genetic improvement.
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13
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Braz CU, Taylor T, Namous H, Townsend J, Crenshaw T, Khatib H. Paternal diet induces transgenerational epigenetic inheritance of DNA methylation signatures and phenotypes in sheep model. PNAS NEXUS 2022; 1:pgac040. [PMID: 36713326 PMCID: PMC9802161 DOI: 10.1093/pnasnexus/pgac040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/05/2022] [Accepted: 04/02/2022] [Indexed: 06/18/2023]
Abstract
Transgenerational epigenetic inheritance (TEI) requires transmission of environmentally induced epigenetic changes and associated phenotypes to subsequent generations without continued exposure to the environmental factor that originated the change. TEI is well-established in plants and Caenorhabditis elegans; however, occurrence in mammals is debated and poorly understood. Here, we examined whether paternal diet from weaning to puberty-induced changes in sperm DNA methylation that were transmitted to subsequent generations. Over 100 methylated cytosines, environmentally altered in the F0 generation, were inherited by the F1 and F2 generations. Furthermore, the F0 paternal diet was associated with growth and male fertility phenotypes in subsequent generations. Differentially methylated cytosines were correlated with gene expression. Our results demonstrate that some sperm methylation sites may escape DNA methylation erasure and are transmitted to subsequent generations despite the 2 waves of epigenetic programming: in primordial germ cells and in embryos after fertilization. These results advance our understanding of the complex relationships between nature and nurture.
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Affiliation(s)
- Camila U Braz
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hadjer Namous
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jessica Townsend
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Thomas Crenshaw
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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14
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Jackson WM, Santos HP, Hartwell HJ, Gower WA, Chhabra D, Hagood JS, Laughon MM, Payton A, Smeester L, Roell K, O’Shea TM, Fry RC. Differential placental CpG methylation is associated with chronic lung disease of prematurity. Pediatr Res 2022; 91:1428-1435. [PMID: 34857876 PMCID: PMC9160210 DOI: 10.1038/s41390-021-01868-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 10/26/2021] [Accepted: 11/13/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Chronic lung disease (CLD) is the most common pulmonary morbidity in extremely preterm infants. It is unclear to what extent prenatal exposures influence the risk of CLD. Epigenetic variation in placenta DNA methylation may be associated with differential risk of CLD, and these associations may be dependent upon sex. METHODS Data were obtained from a multi-center cohort of infants born extremely preterm (<28 weeks' gestation) and an epigenome-wide approach was used to identify associations between placental DNA methylation and CLD (n = 423). Associations were evaluated using robust linear regression adjusting for covariates, with a false discovery rate of 0.05. Analyses stratified by sex were used to assess differences in methylation-CLD associations. RESULTS CLD was associated with differential methylation at 49 CpG sites representing 46 genes in the placenta. CLD was associated with differential methylation of probes within genes related to pathways involved in fetal lung development, such as p53 signaling and myo-inositol biosynthesis. Associations between CpG methylation and CLD differed by sex. CONCLUSIONS Differential placental methylation within genes with key roles in fetal lung development may reflect complex cell signaling between the placenta and fetus which mediate CLD risk. These pathways appear to be distinct based on fetal sex. IMPACT In extremely preterm infants, differential methylation of CpG sites within placental genes involved in pathways related to cell signaling, oxidative stress, and trophoblast invasion is associated with chronic lung disease of prematurity. DNA methylation patterns associated with chronic lung disease were distinctly based on fetal sex, suggesting a potential mechanism underlying dimorphic phenotypes. Mechanisms related to fetal hypoxia and placental myo-inositol signaling may play a role in fetal lung programming and the developmental origins of chronic lung disease. Continued research of the relationship between the placental epigenome and chronic lung disease could inform efforts to ameliorate or prevent this condition.
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Affiliation(s)
- Wesley M. Jackson
- Department of Pediatrics, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Hudson P. Santos
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC.,Biobehavioral Laboratory, School of Nursing, The University of North Carolina, Chapel Hill, NC
| | - Hadley J. Hartwell
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC
| | - William Adam Gower
- Department of Pediatrics, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Divya Chhabra
- Department of Pediatrics, University of California, San Diego, CA
| | - James S. Hagood
- Department of Pediatrics, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Matthew M. Laughon
- Department of Pediatrics, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Alexis Payton
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC.,Institute for Environmental Health Solutions, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC
| | - Lisa Smeester
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC.,Institute for Environmental Health Solutions, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC
| | - Kyle Roell
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC.,Institute for Environmental Health Solutions, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC
| | - T. Michael O’Shea
- Department of Pediatrics, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC.,Institute for Environmental Health Solutions, Gilling School of Global Public Health, The University of North Carolina, Chapel Hill, NC
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15
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Muyle A, Seymour D, Darzentas N, Primetis E, Gaut BS, Bousios A. Gene capture by transposable elements leads to epigenetic conflict in maize. MOLECULAR PLANT 2021; 14:237-252. [PMID: 33171302 DOI: 10.1016/j.molp.2020.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Transposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic crosstalk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which may also advantage the TEs. In this study, we examined this model by focusing on Helitrons, Pack-MULEs, and Sirevirus LTR retrotransposons in the maize genome. We documented 1263 TEs containing exon fragments from 1629 donor genes. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture. However, these patterns differed between syntelog versus translocated donor genes. Syntelogs appeared to maintain function, as measured by gene expression, consistent with moderation of silencing for functionally important genes. Epigenetic marks did not spread beyond their captured regions and 24nt crosstalk siRNAs were linked with CHH methylation. Translocated genes, in contrast, bore the signature of silencing. They were highly methylated and less expressed, but also overrepresented among donor genes and located away from chromosomal arms, which suggests a link between capture and gene movement. Splitting genes into potential functional categories based on evolutionary constraint supported the synteny-based findings. TE families captured genes in different ways, but the evidence for their advantage was generally less obvious; nevertheless, TEs with captured fragments were older, mapped fewer siRNAs, and were slightly less methylated than TEs without captured fragments. Collectively, our results argue that TE capture triggers an intragenomic conflict that may not affect the function of important genes but may lead to the pseudogenization of less-constrained genes.
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Affiliation(s)
- Aline Muyle
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA
| | - Danelle Seymour
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA; Department of Botany and Plant Sciences, UC Riverside, Riverside, CA 92521, USA
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Elias Primetis
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA.
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16
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Dynamic DNA methylation changes in early versus late adulthood suggest nondeterministic effects of childhood adversity: a meta-analysis. J Dev Orig Health Dis 2020; 12:768-779. [PMID: 33308369 DOI: 10.1017/s2040174420001075] [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: 11/07/2022]
Abstract
Adverse childhood experiences (ACEs) are associated with a high risk of developing chronic diseases and decreased life expectancy, but no ACE epigenetic biomarkers have been identified until now. The latter may result from the interaction of multiple factors such as age, sex, degree of adversity, and lack of transcriptional effects of DNA methylation changes. We hypothesize that DNA methylation changes are related to childhood adversity levels and current age, and these markers evolve as aging proceeds. Two Gene Expression Omnibus datasets, regarding ACE, were selected (GSE72680 and GSE70603), considering raw- and meta-data availability, including validated ACE index (Childhood Trauma Questionnaire (CTQ) score). For DNA methylation, analyzed probes were restricted to those laying within promoters and first exons, and samples were grouped by CTQ scores terciles, to compare highly (ACE) with non-abused (control) cases. Comparison of control and ACE methylome profile did not retrieve differentially methylated CpG sites (DMCs) after correcting by false discovery rate < 0.05, and this was also observed when samples were separated by sex. In contrast, grouping by decade age ranges (i.e., the 20s, 30s, 40s, and 50s) showed a progressive increase in the number of DMCs and the intensity of changes, mainly related with hypomethylation. Comparison with transcriptome data for ACE subjects in the 40s, and 50s showed a similar age-dependent effect. This study provides evidence that epigenetic markers of ACE are age-dependent, but not defined in the long term. These differences among early, middle, and late adulthood epigenomic profiles suggest a window for interventions aimed to prevent the detrimental effects of ACE.
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17
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Ghose S, Ghosh S, Tanwar VS, Tolani P, Kutum R, Sharma A, Bhardwaj N, Shamsudheen K, Verma A, Jayarajan R, Dash D, Sivasubbu S, Scaria V, Seth S, Sengupta S. Investigating Coronary Artery Disease methylome through targeted bisulfite sequencing. Gene 2019; 721:144107. [DOI: 10.1016/j.gene.2019.144107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 01/02/2023]
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18
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Lim WJ, Kim KH, Kim JY, Kim HJ, Kim M, Park JL, Yoon S, Oh JH, Cho JW, Kim YS, Kim N. Investigation of Gene Expression and DNA Methylation From Seven Different Brain Regions of a Crab-Eating Monkey as Determined by RNA-Seq and Whole-Genome Bisulfite Sequencing. Front Genet 2019; 10:694. [PMID: 31428131 PMCID: PMC6690020 DOI: 10.3389/fgene.2019.00694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/02/2019] [Indexed: 01/04/2023] Open
Abstract
The crab-eating monkey is widely used in biomedical research for pharmacological experiments. Epigenetic regulation in the brain regions of primates involves complex patterns of DNA methylation. Previous studies of methylated CpG-binding domains using microarray technology or peak identification of sequence reads mostly focused on developmental stages or disease, rather than normal brains. To identify correlations between gene expression and DNA methylation levels that may be related to transcriptional regulation, we generated RNA-seq and whole-genome bisulfite sequencing data from seven different brain regions from a single crab-eating monkey. We identified 92 genes whose expression levels were significantly correlated, positively or negatively, with DNA methylation levels. Among them, 11 genes exhibited brain region-specific characteristics, and their expression patterns were strongly correlated with DNA methylation level. Nine genes (SLC2A5, MCM5, DRAM1, TTC12, DHX40, COR01A, LRAT, FLVCR2, and PTER) had effects on brain and eye function and development, and two (LHX6 and MEST) were previously identified as genes in which DNA methylation levels change significantly in the promoter region and are therefore considered brain epigenetic markers. Furthermore, we characterized DNA methylation of repetitive elements at the whole genome through repeat annotation at single-base resolution. Our results reveal the diverse roles of DNA methylation at single-base resolution throughout the genome and reflect the epigenetic variations in adult brain tissues.
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Affiliation(s)
- Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Hee-Jin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Mirang Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Jong-Lyul Park
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Seokjoo Yoon
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Jung-Hwa Oh
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Jae-Woo Cho
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Yong Sung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
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