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Yang C, He J, Mao J, Ren Y, Liu G, Wei C, Zhang G, Tian K, Huang X. Genome-Wide DNA Methylation Analysis and Functional Validation of Litter Size Traits in Jining Grey Goats. Genes (Basel) 2024; 15:353. [PMID: 38540412 PMCID: PMC10970512 DOI: 10.3390/genes15030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 06/14/2024] Open
Abstract
DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (SERPINB2: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, CFAP43: chr26_27046601_27046800, LRP1B. chr2_79720201_79720400, EPHA6: chr1_40088601_40088800, TTC29: chr17_59385801_59386000, PDE11A: chr2_117418601_117418800 and PGF: chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size.
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Affiliation(s)
- Cunming Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Junmin He
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Jingyi Mao
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Yifan Ren
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Guifen Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Chen Wei
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Guoping Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
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Rodríguez-Díaz R, Blanes-Zamora R, Vaca-Sánchez R, Gómez-Rodríguez J, Hardisson A, González-Weller D, Gutiérrez ÁJ, Paz S, Rubio C, González-Dávila E. Influence of Seminal Metals on Assisted Reproduction Outcome. Biol Trace Elem Res 2023; 201:1120-1134. [PMID: 35543968 PMCID: PMC9898355 DOI: 10.1007/s12011-022-03256-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Increased levels of metal ions in human seminal fluid have a significant correlation with male fertility. Few publications explain the effect of metals in semen and their influence on assisted reproductive treatments. Semen parameters and the levels of twenty-two metals were measured in the seminal fluid of 102 men attended in a Reproductive Unit. Metals were determined by optical emission spectrophotometry. A statistical relationship was found between spermiogram and iron, which was lower than expected in pathological spermiograms (p = 0.032); zinc (p = 0.066), calcium (p = 0.047), and magnesium (p = 0.048) mean levels were higher in normozoospermics. More days of sexual abstinence correlates with higher seminal zinc (p = 0.001) and magnesium levels (p = 0.002). Lower vanadium values were found to be associated with higher fertilization rates (p = 0.039). Higher values of lead (p = 0.052) and vanadium (p = 0.032) were obtained in patients who did not reach 100% embryo cleavage rate. Aluminium (p = 0.042) and sodium (p = 0.002) were found in lower amounts associated with better blastocyst rates. The implantation rate shows an inverse association with women's age and iron and calcium content, compared to magnesium and sodium which presented a significant direct association with this percentage. A significant direct relationship was found between the positive evolution of pregnancy and the values of zinc (p = 0.004), calcium (p = 0.013), potassium (p = 0.002), and magnesium (p = 0.009). The study confirms that zinc, iron, calcium, sodium, aluminium, magnesium, vanadium, and lead have positive-negative effects on reproduction and support the analysis of metals in semen as a new line of study on male fertility with implications for reproductive outcomes.
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Affiliation(s)
- Rubí Rodríguez-Díaz
- Human Reproduction Unit, Canary Islands University Hospital, San Cristobal de La Laguna, Spain.
- Obstetrics and Gynecology, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain.
| | - Raquel Blanes-Zamora
- Human Reproduction Unit, Canary Islands University Hospital, San Cristobal de La Laguna, Spain
- Obstetrics and Gynecology, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain
| | - Rebeca Vaca-Sánchez
- Human Reproduction Unit, Canary Islands University Hospital, San Cristobal de La Laguna, Spain
- Obstetrics and Gynecology, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain
| | - Jorge Gómez-Rodríguez
- Human Reproduction Unit, Canary Islands University Hospital, San Cristobal de La Laguna, Spain
- Obstetrics and Gynecology, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain
| | - Arturo Hardisson
- Toxicology, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain
| | | | - Ángel J Gutiérrez
- Toxicology, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain
| | - Soraya Paz
- Toxicology, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain
| | - Carmen Rubio
- Toxicology, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain
| | - E González-Dávila
- Mathematics, Statistics and Operations Research, University of La Laguna, San Cristobal de La Laguna, Tenerife, Spain
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Ripon Rouf ASM, Amin MA, Islam MK, Haque F, Ahmed KR, Rahman MA, Islam MZ, Kim B. Statistical Bioinformatics to Uncover the Underlying Biological Mechanisms That Linked Smoking with Type 2 Diabetes Patients Using Transcritpomic and GWAS Analysis. Molecules 2022; 27:molecules27144390. [PMID: 35889263 PMCID: PMC9323276 DOI: 10.3390/molecules27144390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022] Open
Abstract
Type 2 diabetes (T2D) is a chronic metabolic disease defined by insulin insensitivity corresponding to impaired insulin sensitivity, decreased insulin production, and eventually failure of beta cells in the pancreas. There is a 30–40 percent higher risk of developing T2D in active smokers. Moreover, T2D patients with active smoking may gradually develop many complications. However, there is still no significant research conducted to solve the issue. Hence, we have proposed a highthroughput network-based quantitative pipeline employing statistical methods. Transcriptomic and GWAS data were analysed and obtained from type 2 diabetes patients and active smokers. Differentially Expressed Genes (DEGs) resulted by comparing T2D patients’ and smokers’ tissue samples to those of healthy controls of gene expression transcriptomic datasets. We have found 55 dysregulated genes shared in people with type 2 diabetes and those who smoked, 27 of which were upregulated and 28 of which were downregulated. These identified DEGs were functionally annotated to reveal the involvement of cell-associated molecular pathways and GO terms. Moreover, protein–protein interaction analysis was conducted to discover hub proteins in the pathways. We have also identified transcriptional and post-transcriptional regulators associated with T2D and smoking. Moreover, we have analysed GWAS data and found 57 common biomarker genes between T2D and smokers. Then, Transcriptomic and GWAS analyses are compared for more robust outcomes and identified 1 significant common gene, 19 shared significant pathways and 12 shared significant GOs. Finally, we have discovered protein–drug interactions for our identified biomarkers.
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Affiliation(s)
| | - Md. Al Amin
- Department of Computer Science & Engineering, Prime University, Dhaka 1216, Bangladesh;
| | - Md. Khairul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia 7003, Bangladesh;
| | - Farzana Haque
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh;
| | - Kazi Rejvee Ahmed
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
| | - Md. Ataur Rahman
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
- Correspondence: (M.A.R.); (M.Z.I.); (B.K.)
| | - Md. Zahidul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia 7003, Bangladesh;
- Correspondence: (M.A.R.); (M.Z.I.); (B.K.)
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
- Correspondence: (M.A.R.); (M.Z.I.); (B.K.)
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Laqqan MM, Yassin MM. Cigarette heavy smoking alters DNA methylation patterns and gene transcription levels in humans spermatozoa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:26835-26849. [PMID: 34855177 DOI: 10.1007/s11356-021-17786-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/27/2023]
Abstract
Tobacco smoking is considered the most common reason of death and infertility around the world. This study was designed to assess the impact of tobacco heavy smoking on sperm DNA methylation patterns and to determine whether the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes is different in heavy smokers compared to non-smokers. As a screening study, the 450 K array was used to assess the alteration in DNA methylation patterns between heavy smokers (n = 15) and non-smokers (n = 15). Then, four CpGs that have the highest difference in methylation level (cg16338278, cg08408433, cg05799088, and cg07227024) were selected for validation using deep bisulfite sequencing in an independent cohort of heavy smokers (n = 200) and non-smokers (n = 100). A significant variation was found between heavy smokers and non-smokers in the methylation level at all CpGs within the PRICKLE2 and ALS2CR12 gene amplicon (P < 0.001). Similarly, a significant variation was found in the methylation level at nine out of thirteen CpGs within the ALDH3B2 gene amplicon (P < 0.01). Additionally, eighteen CpGs out of the twenty-six within the PTGIR gene amplicon have a significant difference in the methylation level between heavy smokers and non-smokers (P < 0.01). The study showed a significant difference in sperm global DNA methylation, chromatin non-condensation, and DNA fragmentation (P < 0.001) between heavy smokers and non-smokers. A significant decline was shown in the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes (P < 0.001) in heavy smokers. In conclusion, heavy smoking influences DNA methylation at several CpGs, sperm global DNA methylation, and transcription level of the PRICKLE2, ALS2CR12, ALDH3B2, and PTGIR genes, which affects negatively the semen parameters of heavy smokers.
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Affiliation(s)
- Mohammed M Laqqan
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Islamic University, Gaza, Palestinian Territories, Palestine.
| | - Maged M Yassin
- Department of Human Physiology, Faculty of Medicine, Islamic University, Gaza, Palestinian Territories, Palestine
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