1
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Sakkers TR, Mokry M, Civelek M, Erdmann J, Pasterkamp G, Diez Benavente E, den Ruijter HM. Sex differences in the genetic and molecular mechanisms of coronary artery disease. Atherosclerosis 2023; 384:117279. [PMID: 37805337 DOI: 10.1016/j.atherosclerosis.2023.117279] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/09/2023] [Accepted: 09/01/2023] [Indexed: 10/09/2023]
Abstract
Sex differences in coronary artery disease (CAD) presentation, risk factors and prognosis have been widely studied. Similarly, studies on atherosclerosis have shown prominent sex differences in plaque biology. Our understanding of the underlying genetic and molecular mechanisms that drive these differences remains fragmented and largely understudied. Through reviewing genetic and epigenetic studies, we identified more than 40 sex-differential candidate genes (13 within known CAD loci) that may explain, at least in part, sex differences in vascular remodeling, lipid metabolism and endothelial dysfunction. Studies with transcriptomic and single-cell RNA sequencing data from atherosclerotic plaques highlight potential sex differences in smooth muscle cell and endothelial cell biology. Especially, phenotypic switching of smooth muscle cells seems to play a crucial role in female atherosclerosis. This matches the known sex differences in atherosclerotic phenotypes, with men being more prone to lipid-rich plaques, while women are more likely to develop fibrous plaques with endothelial dysfunction. To unravel the complex mechanisms that drive sex differences in CAD, increased statistical power and adjustments to study designs and analysis strategies are required. This entails increasing inclusion rates of women, performing well-defined sex-stratified analyses and the integration of multi-omics data.
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Affiliation(s)
- Tim R Sakkers
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508, GA, Utrecht, the Netherlands
| | - Michal Mokry
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508, GA, Utrecht, the Netherlands; Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508, GA, Utrecht, the Netherlands
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, 1335 Lee St, Charlottesville, VA, 22908, USA; Department of Biomedical Engineering, University of Virginia, 351 McCormick Road, Charlottesville, VA, 22904, USA
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Gerard Pasterkamp
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508, GA, Utrecht, the Netherlands
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508, GA, Utrecht, the Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3508, GA, Utrecht, the Netherlands.
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2
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Wang Q, Bi Y, Wang Z, Zhu H, Liu M, Wu X, Pan C. Goat SNX29: mRNA expression, InDel and CNV detection, and their associations with litter size. Front Vet Sci 2022; 9:981315. [PMID: 36032302 PMCID: PMC9399746 DOI: 10.3389/fvets.2022.981315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
The sorting nexin 29 (SNX29) gene, a member of the SNX family, is associated with material transport and lipid metabolism. Previous studies have shown that lipid metabolism affects reproductive function in animals. Thus, we hypothesized there is a correlation between the SNX29 gene and reproductive trait. To date, studies on the relationship between the SNX29 gene and reproductive traits are limited. Therefore, the purpose of this study was to examine the polymorphism in the SNX29 gene and its correlation with litter size. Herein, the mRNA expression levels of SNX29 were assayed in various goat tissue. Surprisingly, we found that SNX29 was highly expressed in the corpus luteum, large and small follicles. This result led us to suggest that the SNX29 gene has a critical role in reproduction. We further detected potential polymorphisms in Shaanbei white cashmere (SBWC) goats, including insertion/deletion (InDel, n = 2,057) and copy number variation (CNV, n = 1,402), which were related to fertility. The 17 bp deletion (n = 1004) and the 20 bp deletion (n = 1,053) within the SNX29 gene were discovered to be significantly associated with litter size (P < 0.05), and individuals the ID genotype of P1-Del-17 bp and the DD genotype of P2-Del-20bp had larger litter size. Additionally, the four CNV loci had significant correlations with litter size (P < 0.01) in our detected population. In CNV5, individuals with the median genotype were superior compared to those with loss or gain genotype in term of litter size, and in other three CNVs showed better reproductive trait in the gain genotype. Briefly, these findings suggest that SNX29 could be used as a candidate gene for litter size in goat breeding through marker-assisted selection (MAS).
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Affiliation(s)
- Qian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Yi Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Zhiying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- Life Science Research Center, Yulin University, Yulin, China
| | - Mei Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xianfeng Wu
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, China
- *Correspondence: Chuanying Pan
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
- Xianfeng Wu
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3
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Tachibana K, Kawazoe S, Onoda A, Umezawa M, Takeda K. Effects of Prenatal Exposure to Titanium Dioxide Nanoparticles on DNA Methylation and Gene Expression Profile in the Mouse Brain. FRONTIERS IN TOXICOLOGY 2022; 3:705910. [PMID: 35295148 PMCID: PMC8915839 DOI: 10.3389/ftox.2021.705910] [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: 05/06/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Objectives: Titanium dioxide nanoparticles (TiO2-NP) are important materials used in commercial practice. Reportedly, TiO2-NP exposure during pregnancy can affect the development of the central nervous system in mouse offspring; however, the underlying mechanism remains unknown. In the present study, we investigated the impact of prenatal TiO2-NP exposure on global DNA methylation and mRNA expression patterns in the brains of neonatal mice. Materials and Methods: Pregnant C57BL/6J mice were intratracheally administered a TiO2-NP suspension (100 μg/mouse) on gestational day 10.5, and brains were collected from male and female offspring at day 1 postpartum. After extraction of methylated DNA by immunoprecipitation, the DNA methylation profile was analyzed using a mouse CpG island microarray. Total RNA was obtained, and mRNA expression profiles were comprehensively assessed using microarray analysis. Results: Among genes in the CpG island microarray, DNA methylation was increased in 614 and 2,924 genes and decreased in 6,220 and 6,477 genes in male and female offspring, respectively. Combined with mRNA microarray analysis, 88 and 89 genes were upregulated (≥1.5-fold) accompanied by demethylation of CpG islands, whereas 13 and 33 genes were downregulated (≤0.67-fold) accompanied by methylation of CpG islands in male and female offspring mice, respectively. Gene Set Enrichment Analysis (GSEA) revealed that these genes were enriched in gene ontology terms related to the regulation of transcription factors, cell proliferation, and organism development. Additionally, MeSH terms related to stem cells and morphogenesis were enriched. Conclusion: Prenatal TiO2-NP exposure induced genome-wide alterations in DNA methylation and mRNA expression in the brains of male and female offspring. Based on GSEA findings, it can be speculated that prenatal TiO2-NP exposure causes adverse effects on brain functions by altering the DNA methylation state of the fetal brain, especially neural stem cells, resulting in the subsequent abnormal regulation of transcription factors that modulate development and differentiation.
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Affiliation(s)
- Ken Tachibana
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Shotaro Kawazoe
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Atsuto Onoda
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Masakazu Umezawa
- The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan.,Department of Materials Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Katsushika, Japan
| | - Ken Takeda
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
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4
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Boua PR, Brandenburg JT, Choudhury A, Sorgho H, Nonterah EA, Agongo G, Asiki G, Micklesfield L, Choma S, Gómez-Olivé FX, Hazelhurst S, Tinto H, Crowther NJ, Mathew CG, Ramsay M. Genetic associations with carotid intima-media thickness link to atherosclerosis with sex-specific effects in sub-Saharan Africans. Nat Commun 2022; 13:855. [PMID: 35165267 PMCID: PMC8844072 DOI: 10.1038/s41467-022-28276-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
Atherosclerosis precedes the onset of clinical manifestations of cardiovascular diseases (CVDs). We used carotid intima-media thickness (cIMT) to investigate genetic susceptibility to atherosclerosis in 7894 unrelated adults (3963 women, 3931 men; 40 to 60 years) resident in four sub-Saharan African countries. cIMT was measured by ultrasound and genotyping was performed on the H3Africa SNP Array. Two new African-specific genome-wide significant loci for mean-max cIMT, SIRPA (p = 4.7E-08), and FBXL17 (p = 2.5E-08), were identified. Sex-stratified analysis revealed associations with one male-specific locus, SNX29 (p = 6.3E-09), and two female-specific loci, LARP6 (p = 2.4E-09) and PROK1 (p = 1.0E-08). We replicate previous cIMT associations with different lead SNPs in linkage disequilibrium with SNPs primarily identified in European populations. Our study find significant enrichment for genes involved in oestrogen response from female-specific signals. The genes identified show biological relevance to atherosclerosis and/or CVDs, sex-differences and transferability of signals from non-African studies.
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Affiliation(s)
- Palwende Romuald Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Centre national de la Recherche scientifique et technologique (CNRST), Nanoro, Burkina Faso.
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Centre national de la Recherche scientifique et technologique (CNRST), Nanoro, Burkina Faso
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Julius Global Health, Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht University, Utrecht, The Netherlands
| | - Godfred Agongo
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Gershim Asiki
- African Population and Health Research Center, Nairobi, Kenya
| | - Lisa Micklesfield
- MRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Solomon Choma
- Department of Pathology and Medical Sciences, University of Limpopo, Polokwane, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Halidou Tinto
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Centre national de la Recherche scientifique et technologique (CNRST), Nanoro, Burkina Faso
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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5
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AlOgayil N, Bauermeister K, Galvez JH, Venkatesh VS, Zhuang QKW, Chang ML, Davey RA, Zajac JD, Ida K, Kamiya A, Taketo T, Bourque G, Naumova AK. Distinct roles of androgen receptor, estrogen receptor alpha, and BCL6 in the establishment of sex-biased DNA methylation in mouse liver. Sci Rep 2021; 11:13766. [PMID: 34215813 PMCID: PMC8253761 DOI: 10.1038/s41598-021-93216-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Sexual dimorphism in gene regulation, including DNA methylation, is the main driver of sexual dimorphism in phenotypes. However, the questions of how and when sex shapes DNA methylation remain unresolved. Recently, using mice with different combinations of genetic and phenotypic sex, we identified sex-associated differentially methylated regions (sDMRs) that depended on the sex phenotype. Focusing on a panel of validated sex-phenotype dependent male- and female-biased sDMRs, we tested the developmental dynamics of sex bias in liver methylation and the impacts of mutations in the androgen receptor, estrogen receptor alpha, or the transcriptional repressor Bcl6 gene. True hermaphrodites that carry both unilateral ovaries and contralateral testes were also tested. Our data show that sex bias in methylation either coincides with or follows sex bias in the expression of sDMR-proximal genes, suggesting that sex bias in gene expression may be required for demethylation at certain sDMRs. Global ablation of AR, ESR1, or a liver-specific loss of BCL6, all alter sDMR methylation, whereas presence of both an ovary and a testis delays the establishment of male-type methylation levels in hermaphrodites. Moreover, the Bcl6-LKO shows dissociation between expression and methylation, suggesting a distinct role of BCL6 in demethylation of intragenic sDMRs.
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Affiliation(s)
- Najla AlOgayil
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | | | | | - Varun S Venkatesh
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia
| | | | - Matthew L Chang
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Rachel A Davey
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia
| | - Jeffrey D Zajac
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia
| | - Kinuyo Ida
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Akihide Kamiya
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Teruko Taketo
- The Research Institute of the McGill University Health Centre, Montreal, QC, H4A 1J3, Canada.,Department of Surgery, McGill University, Montreal, QC, Canada.,Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montréal, QC, Canada. .,The Research Institute of the McGill University Health Centre, Montreal, QC, H4A 1J3, Canada. .,Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada.
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6
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Gao C, Wen Y, Jiang F, Gu X, Zhu X. Circular RNA circ_0008274 upregulates granulin to promote the progression of hepatocellular carcinoma via sponging microRNA -140-3p. Bioengineered 2021; 12:1890-1901. [PMID: 34002672 PMCID: PMC8806606 DOI: 10.1080/21655979.2021.1926195] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Circular RNA (circRNA) features prominently in the progression of hepatocellular carcinoma (HCC), of which the biological function and potential mechanism of circ_0008274 in HCC are obscure. The present study aims to explore circ_ 0008274's biological functions and underlying mechanisms in HCC. The expressions of circ_0008274, miR-140-3p and Granulin (GRN) mRNA in HCC tissues and cells were investigated by quantitative real-time polymerase chain reaction. Besides, GRN protein expression was measured by Western blot. Furthermore, chi-square test was used to probe the interrelation between circ_0008274 expression and clinicopathological parameters. In addition, cell counting kit-8 (CCK-8) and EdU assays were applied to detect cell proliferation. Moreover, transwell assay was used to detect cell migration and invasion. What's more, bioinformatics prediction, dual-luciferase reporter gene assay and RNA Immunoprecipitation experiments were used to corroborate the targeting interrelations among circ_0008274, miR-140-3p and GRN. Herein we reported that circ_0008274 was highly expressed in HCC, and its high expression enhanced the proliferation, migration, and invasion of HCC cells, while depleting circ_0008274 inhibited the malignant biological behaviors of HCC cells. Mechanistically, circ_0008274 upregulates GRN expressions via adsorbing miR-140-3p to expedite the progression of HCC.
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Affiliation(s)
- Chanchan Gao
- Department of Oncology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
| | - Yazhou Wen
- Department of Oncology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
| | - Feng Jiang
- Department of Oncology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
| | - Xuyu Gu
- Department of Oncology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
| | - Xinhua Zhu
- Department of General Surgery, Nanjing Drum Tower Hospital, Nanjing, China
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7
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STAT5 Regulation of Sex-Dependent Hepatic CpG Methylation at Distal Regulatory Elements Mapping to Sex-Biased Genes. Mol Cell Biol 2021; 41:MCB.00166-20. [PMID: 33199496 DOI: 10.1128/mcb.00166-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Growth hormone-activated STAT5b is an essential regulator of sex-differential gene expression in mouse liver; however, its impact on hepatic gene expression and epigenetic responses is poorly understood. Here, we found a substantial, albeit incomplete loss of liver sex bias in hepatocyte-specific STAT5a/STAT5b (collectively, STAT5)-deficient mouse liver. In male liver, many male-biased genes were downregulated in direct association with the loss of STAT5 binding; many female-biased genes, which show low STAT5 binding, were derepressed, indicating an indirect mechanism for repression by STAT5. Extensive changes in CpG methylation were seen in STAT5-deficient liver, where sex differences were abolished at 88% of ∼1,500 sex-differentially methylated regions, largely due to increased DNA methylation upon STAT5 loss. STAT5-dependent CpG hypomethylation was rarely found at proximal promoters of STAT5-dependent genes. Rather, STAT5 primarily regulated the methylation of distal enhancers, where STAT5 deficiency induced widespread hypermethylation at genomic regions enriched for accessible chromatin, enhancer histone marks (histone H3 lysine 4 monomethylation [H3K4me1] and histone H3 lysine 27 acetylation [H3K27ac]), STAT5 binding, and DNA motifs for STAT5 and other transcription factors implicated in liver sex differences. Thus, the sex-dependent binding of STAT5 to liver chromatin is closely linked to the sex-dependent demethylation of distal regulatory elements linked to STAT5-dependent genes important for liver sex bias.
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8
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Zhuang QKW, Galvez JH, Xiao Q, AlOgayil N, Hyacinthe J, Taketo T, Bourque G, Naumova AK. Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver. Cells 2020; 9:E1436. [PMID: 32527045 PMCID: PMC7349295 DOI: 10.3390/cells9061436] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Sex biases in the genome-wide distribution of DNA methylation and gene expression levels are some of the manifestations of sexual dimorphism in mammals. To advance our understanding of the mechanisms that contribute to sex biases in DNA methylation and gene expression, we conducted whole genome bisulfite sequencing (WGBS) as well as RNA-seq on liver samples from mice with different combinations of sex phenotype and sex-chromosome complement. We compared groups of animals with different sex phenotypes, but the same genetic sexes, and vice versa, same sex phenotypes, but different sex-chromosome complements. We also compared sex-biased DNA methylation in mouse and human livers. Our data show that sex phenotype, X-chromosome dosage, and the presence of Y chromosome shape the differences in DNA methylation between males and females. We also demonstrate that sex bias in autosomal methylation is associated with sex bias in gene expression, whereas X-chromosome dosage-dependent methylation differences are not, as expected for a dosage-compensation mechanism. Furthermore, we find partial conservation between the repertoires of mouse and human genes that are associated with sex-biased methylation, an indication that gene function is likely to be an important factor in this phenomenon.
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Affiliation(s)
- Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
| | - Jose Hector Galvez
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Qian Xiao
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA;
| | - Najla AlOgayil
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
| | - Jeffrey Hyacinthe
- Department of Quantitative Life Sciences, McGill University, Montréal, QC H3A 0G4, Canada;
| | - Teruko Taketo
- The Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada;
- Department of Surgery, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Anna K. Naumova
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
- The Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada;
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC H4A 3J1, Canada
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9
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Elsner VR, Cechinel LR, de Meireles LCF, Bertoldi K, Siqueira IR. Epigenetic marks are modulated by gender and time of the day in the hippocampi of adolescent rats: A preliminary study. Neural Regen Res 2018; 13:2160-2163. [PMID: 30323148 PMCID: PMC6199939 DOI: 10.4103/1673-5374.241467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Although the involvement of gender in epigenetic machinery in peripheral tissues during the neonatal period has been suggested, the gender-related epigenetic profile of brain areas during the adolescent period is rarely exploited. Furthermore, the influence of time of day on hippocampal acetylation marks has been demonstrated in young adult and aged rats; however, there are no studies reporting epigenetic changes in the adolescent period. Therefore, this study aimed to investigate the effects of gender on hippocampal DNA methyltransferase 1 content and histone deacetylase (HDAC) activity of adolescent rats at different time points, specifically early morning and afternoon. Both epigenetic markers increased significantly in the hippocampi of female rats compared to the male group, an indicator of reduced transcriptional activity. In addition, HDAC activity during the early morning was higher compared to afternoon groups in both male and female rats, while DNA methyltransferase 1 content was not altered by the time of day. Our findings demonstrate that hippocampal DNA methylation and histone acetylation status can be influenced by gender during the adolescent period, while the time of the day impacts HDAC activity.
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Affiliation(s)
- Viviane Rostirola Elsner
- Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul; Programa de Pós-Graduação em Biociências e Reabilitação, Centro Universitário Metodista-IPA; Curso de Fisioterapia, Centro Universitário Metodista-IPA, Porto Alegre, Rio Grande do Sul, Brasil
| | - Laura Reck Cechinel
- Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Louisiana Carolina Ferreira de Meireles
- Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Karine Bertoldi
- Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Ionara Rodrigues Siqueira
- Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
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Cousminer DL, Widén E, Palmert MR. The genetics of pubertal timing in the general population: recent advances and evidence for sex-specificity. Curr Opin Endocrinol Diabetes Obes 2016; 23:57-65. [PMID: 26574646 PMCID: PMC4734379 DOI: 10.1097/med.0000000000000213] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW This article overviews advances in the genetics of puberty based on studies in the general population, describes evidence for sex-specific genetic effects on pubertal timing, and briefly reviews possible mechanisms mediating sexually dimorphic genetic effects. RECENT FINDINGS Pubertal timing is highly polygenic, and many loci are conserved among ethnicities. A number of identified loci underlie both pubertal timing and related traits such as height and BMI. It is increasingly apparent that understanding the factors modulating the onset of puberty is important because the timing of this developmental stage is associated with a wider range of adult health outcomes than previously appreciated. Although most of the genetic effects underlying the timing of puberty are common between boys and girls, some effects show sex-specificity and many are epigenetically modulated. Several potential mechanisms, including hormone-independent ones, may be responsible for observed sex differences. SUMMARY Studies of pubertal timing in the general population have provided new knowledge about the genetic architecture of this complex trait. Increasing attention paid to sex-specific effects may provide key insights into the sexual dimorphism in pubertal timing and even into the associations between puberty and adult health risks by identifying common underlying biological pathways.
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Affiliation(s)
- Diana L. Cousminer
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elisabeth Widén
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | - Mark R. Palmert
- Division of Endocrinology, the Hospital for Sick Children
- The Departments of Pediatrics and Physiology, University of Toronto, Canada
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