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Nasrullah, Hussain A, Ahmed S, Rasool M, Shah AJ. DNA methylation across the tree of life, from micro to macro-organism. Bioengineered 2022; 13:1666-1685. [PMID: 34986742 PMCID: PMC8805842 DOI: 10.1080/21655979.2021.2014387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is a process in which methyl (CH3) groups are added to the DNA molecule. The DNA segment does not change in the sequence, but DNA methylation could alter the action of DNA. Different enzymes like DNA methyltransferases (DNMTs) take part in methylation of cytosine/adenine nucleosides in DNA. In prokaryotes, DNA methylation is performed to prevent the attack of phage and also plays a role in the chromosome replication and repair. In fungi, DNA methylation is studied to see the transcriptional changes, as in insects, the DNA methylation is not that well-known, it plays a different role like other organisms. In mammals, the DNA methylation is related to different types of cancers and plays the most important role in the placental development and abnormal DNA methylation connected with diseases like cancer, autoimmune diseases, and rheumatoid arthritis.
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Affiliation(s)
- Nasrullah
- Center for Advanced Studies in Vaccinology & Biotechnology (Casvab), University of Baluchistan, Quetta- Pakistan. E-mails:
| | - Abrar Hussain
- Department of Biotechnology, Faculty of Life Sciences, Buitems, Quetta-Pakistan. E-mails:
| | - Sagheer Ahmed
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan. E-mails:
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. E-mails:
| | - Abdul Jabbar Shah
- Department of Pharmaceutical Sciences, Comsats University, Abbottabad. E-mails:
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Abstract
With the increasing incidence of male infertility, routine detection of semen is insufficient to accurately assess male fertility. Infertile men, who have lower odds of conceiving naturally, exhibit high levels of sperm DNA fragmentation (SDF). The mechanisms driving SDF include abnormal spermatogenesis, oxidative stress damage, and abnormal sperm apoptosis. As these factors can induce SDF and subsequent radical changes leading to male infertility, detection of the extent of SDF has become an efficient routine method for semen analysis. Although it is still debated, SDF detection has become a research hotspot in the field of reproductive medicine as a more accurate indicator for assessing sperm quality and male fertility. SDF may be involved in male infertility, reproductive assisted outcomes, and growth and development of offspring. The effective detection methods of SDF are sperm chromatin structure analysis (SCSA), terminal transferase-mediated dUTP end labeling (TUNEL) assay, single-cell gel electrophoresis (SCGE) assay, and sperm chromatin dispersion (SCD) test, and all of these methods are valuable for assisted reproductive techniques. Currently, the preferred method for detecting sperm DNA integrity is SCSA. However, the regulation network of SDF is very complex because the sperm DNA differs from the somatic cell DNA with its unique structure. A multitude of molecular factors, including coding genes, non-coding genes, or methylated DNA, participate in the complex physiological regulation activities associated with SDF. Studying SDF occurrence and the underlying mechanisms may effectively improve its clinical treatments. This review aimed to outline the research status of SDF mechanism and detection technology-related issues, as well as the effect of increased SDF rate, aiming to provide a basis for clinical male infertility diagnosis and treatment.
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Affiliation(s)
- Ying Qiu
- The Reproductive Medical Center, Nanning Second People's Hospital, Nanning, Guangxi, China (mainland)
| | - Hua Yang
- The Reproductive Medical Center, Nanning Second People's Hospital, Nanning, Guangxi, China (mainland)
| | - Chunyuan Li
- The Reproductive Medical Center, Nanning Second People's Hospital, Nanning, Guangxi, China (mainland)
| | - Changlong Xu
- The Reproductive Medical Center, Nanning Second People's Hospital, Nanning, Guangxi, China (mainland)
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Klf14 is an imprinted transcription factor that regulates placental growth. Placenta 2019; 88:61-67. [PMID: 31675530 DOI: 10.1016/j.placenta.2019.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Imprinted genes are preferentially expressed from one parentally inherited allele, and many are crucial to the regulation of placental function and fetal growth. Murine Krüppel-like factor 14 (Klf14) is a maternally expressed imprinted transcription factor that is a component of the Mest imprinted gene cluster on mouse chromosome 6. We sought to determine if loss of Klf14 expression alters the course of normal mouse extraembryonic development. We also used high-throughput RNA sequencing (RNAseq) to identify a set of differentially expressed genes (DEGs) in placentas with loss of Klf14. METHODS We generated a Klf14 knockout (Klf14null) mouse using recombineering and transgenic approaches. To identify DEGs in the mouse placenta we compared mRNA transcriptomes derived from 17.5dpc Klf14matKO and wild-type littermate placentas by RNAseq. Candidate DEGs were confirmed with quantitative reverse transcription PCR (qPCR) on an independent cohort of male and female gestational age matched Klf14matKO placentas. RESULTS We found that 17.5dpc placentas inheriting a maternal null allele (Klf14matKO) had a modest overgrowth phenotype and a near complete ablation of Klf14 expression. However, there was no effect on fetal growth. We identified 20 DEGs differentially expressed in Klf14matKO placentas by RNAseq, and subsequently validated five that are highly upregulated (Begain, Col26a1, Fbln5, Gdf10, and Nell1) by qPCR. The most enriched functional gene-networks included those classified as regulating cellular development and metabolism. CONCLUSION These results suggest that loss of the maternal Klf14 locus in the mouse placenta acts results in changes in gene expression patterns that modulate placental growth.
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Whidden L, Martel J, Rahimi S, Chaillet JR, Chan D, Trasler JM. Compromised oocyte quality and assisted reproduction contribute to sex-specific effects on offspring outcomes and epigenetic patterning. Hum Mol Genet 2018; 25:4649-4660. [PMID: 28173052 DOI: 10.1093/hmg/ddw293] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/04/2016] [Accepted: 08/25/2016] [Indexed: 11/13/2022] Open
Abstract
Clinical studies have revealed an increased incidence of growth and genomic imprinting disorders in children conceived using assisted reproductive technologies (ARTs), and aberrant DNA methylation has been implicated. We propose that compromised oocyte quality associated with female infertility may make embryos more susceptible to the induction of epigenetic defects by ART. DNA methylation patterns in the preimplantation embryo are dependent on the oocyte-specific DNA methyltransferase 1o (DNMT1o), levels of which are decreased in mature oocytes of aging females. Here, we assessed the effects of maternal deficiency in DNMT1o (Dnmt1Δ1o/+) in combination with superovulation and embryo transfer on offspring DNA methylation and development. We demonstrated a significant increase in the rates of morphological abnormalities in offspring collected from Dnmt1Δ1o/+ females only when combined with ART. Together, maternal oocyte DNMT1o deficiency and ART resulted in an accentuation of placental imprinting defects and the induction of genome-wide DNA methylation alterations, which were exacerbated in the placenta compared to the embryo. Significant sex-specific trends were also apparent, with a preponderance of DNA hypomethylation in females. Among genic regions affected, a significant enrichment for neurodevelopmental pathways was observed. Taken together, our results demonstrate that oocyte DNMT1o-deficiency exacerbates genome-wide DNA methylation abnormalities induced by ART in a sex-specific manner and plays a role in mediating poor embryonic outcome.
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Affiliation(s)
- Laura Whidden
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Josée Martel
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Sophia Rahimi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - J Richard Chaillet
- Department of OB/GYN and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donovan Chan
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jacquetta M Trasler
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada,Department of Human Genetics, McGill University, Montreal, QC, Canada,Department of Pediatrics, McGill University, Montreal, QC, Canada
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Makaroun SP, Himes KP. Differential Methylation of Syncytin-1 and 2 Distinguishes Fetal Growth Restriction from Physiologic Small for Gestational Age. AJP Rep 2018; 8:e18-e24. [PMID: 29472990 PMCID: PMC5821508 DOI: 10.1055/s-0038-1627473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/09/2017] [Indexed: 12/26/2022] Open
Abstract
Objective The retroviral genes encoding Syncytin-1 ( SYN1 ) and Syncytin-2 ( SYN2 ) are epigenetically regulated, uniquely expressed in the placenta and critical to placental function. We sought to determine if placental expression and methylation patterns of SYN1 and SYN2 from pregnancies complicated by fetal growth restriction (FGR) differed from physiologic small for gestational age (SGA) and appropriate for gestational age (AGA) controls. Study Design Placental biopsies were obtained from AGA, SGA and FGR neonates delivered at >36 weeks gestation. SGA and FGR were defined as birth weight <10% with FGR additionally requiring abnormal fetal testing. We quantified DNA methylation of SYN1 and SYN2 by EpiTyper and gene expression by RT-qPCR. Results We identified 10 AGA, 9 SGA and 7 FGR placentas. There was decreased methylation in SYN1 and SYN2 in FGR relative to AGA and SGA. When the sum of SYN1 and SYN2 methylation was used for prediction of FGR from SGA, the area under the receiver operator characteristic curve was 0.9048 (0.7602, 1). Conclusion SYN1 and SYN2 methylation marks differ in FGR and SGA. We plan future studies to examine these markers in cell free DNA to determine if these methylation changes could be used as a biomarker for FGR.
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Affiliation(s)
- Sami P Makaroun
- Division of Maternal Fetal Medicine, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Katherine P Himes
- Division of Maternal Fetal Medicine, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
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He N, Lim SJ, Moreira de Mello JC, Navarro I, Bialecka M, Salvatori DCF, van der Westerlaken LAJ, Pereira LV, Chuva de Sousa Lopes SM. At Term, XmO and XpO Mouse Placentas Show Differences in Glucose Metabolism in the Trophectoderm-Derived Outer Zone. Front Cell Dev Biol 2017; 5:63. [PMID: 28680878 PMCID: PMC5478694 DOI: 10.3389/fcell.2017.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/06/2017] [Indexed: 12/21/2022] Open
Abstract
Genetic mouse model (39,XO) for human Turner Syndrome (45,XO) harboring either a single maternally inherited (Xm) or paternally inherited (Xp) chromosome show a pronounced difference in survival rate at term. However, a detailed comparison of XmO and XpO placentas to explain this difference is lacking. We aimed to investigate the morphological and molecular differences between XmO and XpO term mouse placentas. We observed that XpO placentas at term contained a significantly larger area of glycogen cells (GCs) in their outer zone, compared to XmO, XX, and XY placentas. In addition, the outer zone of XpO placentas showed higher expression levels of lactate dehydrogenase (Ldha) than XmO, XX, and XY placentas, suggestive of increased anaerobic glycolysis. In the labyrinth, we detected significantly lower expression level of trophectoderm (TE)-marker keratin 19 (Krt19) in XpO placentas than in XX placentas. The expression of other TE-markers was comparable as well as the area of TE-derived cells between XO and wild-type labyrinths. XpO placentas exhibited specific defects in the amount of GCs and glucose metabolism in the outer zone, suggestive of increased anaerobic glycolysis, as a consequence of having inherited a single Xp chromosome. In conclusion, the XpO genotype results in a more severe placental phenotype at term, with distinct abnormalities regarding glucose metabolism in the outer zone.
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Affiliation(s)
- Nannan He
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands
| | - Shujing J Lim
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands
| | | | - Injerreau Navarro
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands
| | - Monika Bialecka
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands
| | - Daniela C F Salvatori
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands.,Central Laboratory Animal Facility, Leiden University Medical CenterLeiden, Netherlands
| | | | - Lygia V Pereira
- Department of Genetics and Evolutionary Biology, University of São PauloSão Paulo, Brazil
| | - Susana M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical CenterLeiden, Netherlands.,Department for Reproductive Medicine, Ghent University HospitalGhent, Belgium
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Abstract
Epidemiological evidence links an individual's susceptibility to chronic disease in adult life to events during their intrauterine phase of development. Biologically this should not be unexpected, for organ systems are at their most plastic when progenitor cells are proliferating and differentiating. Influences operating at this time can permanently affect their structure and functional capacity, and the activity of enzyme systems and endocrine axes. It is now appreciated that such effects lay the foundations for a diverse array of diseases that become manifest many years later, often in response to secondary environmental stressors. Fetal development is underpinned by the placenta, the organ that forms the interface between the fetus and its mother. All nutrients and oxygen reaching the fetus must pass through this organ. The placenta also has major endocrine functions, orchestrating maternal adaptations to pregnancy and mobilizing resources for fetal use. In addition, it acts as a selective barrier, creating a protective milieu by minimizing exposure of the fetus to maternal hormones, such as glucocorticoids, xenobiotics, pathogens, and parasites. The placenta shows a remarkable capacity to adapt to adverse environmental cues and lessen their impact on the fetus. However, if placental function is impaired, or its capacity to adapt is exceeded, then fetal development may be compromised. Here, we explore the complex relationships between the placental phenotype and developmental programming of chronic disease in the offspring. Ensuring optimal placentation offers a new approach to the prevention of disorders such as cardiovascular disease, diabetes, and obesity, which are reaching epidemic proportions.
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Affiliation(s)
- Graham J Burton
- Centre for Trophoblast Research and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom; and Department of Medicine, Knight Cardiovascular Institute, and Moore Institute for Nutrition and Wellness, Oregon Health and Science University, Portland, Oregon
| | - Abigail L Fowden
- Centre for Trophoblast Research and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom; and Department of Medicine, Knight Cardiovascular Institute, and Moore Institute for Nutrition and Wellness, Oregon Health and Science University, Portland, Oregon
| | - Kent L Thornburg
- Centre for Trophoblast Research and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom; and Department of Medicine, Knight Cardiovascular Institute, and Moore Institute for Nutrition and Wellness, Oregon Health and Science University, Portland, Oregon
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Ross PJ, Canovas S. Mechanisms of epigenetic remodelling during preimplantation development. Reprod Fertil Dev 2017; 28:25-40. [PMID: 27062872 DOI: 10.1071/rd15365] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epigenetics involves mechanisms independent of modifications in the DNA sequence that result in changes in gene expression and are maintained through cell divisions. Because all cells in the organism contain the same genetic blueprint, epigenetics allows for cells to assume different phenotypes and maintain them upon cell replication. As such, during the life cycle, there are moments in which the epigenetic information needs to be reset for the initiation of a new organism. In mammals, the resetting of epigenetic marks occurs at two different moments, which both happen to be during gestation, and include primordial germ cells (PGCs) and early preimplantation embryos. Because epigenetic information is reversible and sensitive to environmental changes, it is probably no coincidence that both these extensive periods of epigenetic remodelling happen in the female reproductive tract, under a finely controlled maternal environment. It is becoming evident that perturbations during the extensive epigenetic remodelling in PGCs and embryos can lead to permanent and inheritable changes to the epigenome that can result in long-term changes to the offspring derived from them, as indicated by the Developmental Origins of Health and Disease (DOHaD) hypothesis and recent demonstration of inter- and trans-generational epigenetic alterations. In this context, an understanding of the mechanisms of epigenetic remodelling during early embryo development is important to assess the potential for gametic epigenetic mutations to contribute to the offspring and for new epimutations to be established during embryo manipulations that could affect a large number of cells in the offspring. It is of particular interest to understand whether and how epigenetic information can be passed on from the gametes to the embryo or offspring, and whether abnormalities in this process could lead to transgenerationally inheritable phenotypes. The aim of this review is to highlight recent progress made in understanding the nature and mechanisms of epigenetic remodelling that ensue after fertilisation.
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Affiliation(s)
- Pablo Juan Ross
- Department of Animal Science, University of California, Davis, CA 95616 USA
| | - Sebastian Canovas
- LARCEL (Laboratorio Andaluz de Reprogramación Celular), BIONAND, Centro Andaluz de Nanomedicina y Biotecnología Campanillas, Malaga 29590, Spain
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Epigenetic legacy of parental experiences: Dynamic and interactive pathways to inheritance. Dev Psychopathol 2016; 28:1219-1228. [PMID: 27687718 DOI: 10.1017/s0954579416000808] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The quality of the environment experienced by an individual across his or her lifespan can result in a unique developmental trajectory with consequences for adult phenotype and reproductive success. However, it is also evident that these experiences can impact the development of offspring with continued effect on subsequent generations. Epigenetic mechanisms have been proposed as a mediator of both these within- and across-generation effects, and there is increasing evidence to support the role of environmentally induced changes in DNA methylation, posttranslational histone modifications, and noncoding RNAs in predicting these outcomes. Advances in our understanding of these molecular modifications contribute to increasingly nuanced perspectives on plasticity and transmission of phenotypes across generations. A challenge that emerges from this research is in how we integrate these "new" perspectives with traditional views of development, reproduction, and inheritance. This paper will highlight evidence suggestive of an epigenetic impact of the environment on mothers, fathers, and their offspring, and illustrate the importance of considering the dynamic nature of reproduction and development and inclusive views of inheritance within the evolving field of behavioral and environmental epigenetics.
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Koppes E, Himes KP, Chaillet JR. Partial Loss of Genomic Imprinting Reveals Important Roles for Kcnq1 and Peg10 Imprinted Domains in Placental Development. PLoS One 2015; 10:e0135202. [PMID: 26241757 PMCID: PMC4524636 DOI: 10.1371/journal.pone.0135202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/19/2015] [Indexed: 01/24/2023] Open
Abstract
Mutations in imprinted genes or their imprint control regions (ICRs) produce changes in imprinted gene expression and distinct abnormalities in placental structure, indicating the importance of genomic imprinting to placental development. We have recently shown that a very broad spectrum of placental abnormalities associated with altered imprinted gene expression occurs in the absence of the oocyte-derived DNMT1o cytosine methyltransferase, which normally maintains parent-specific imprinted methylation during preimplantation. The absence of DNMT1o partially reduces inherited imprinted methylation while retaining the genetic integrity of imprinted genes and their ICRs. Using this novel system, we undertook a broad and inclusive approach to identifying key ICRs involved in placental development by correlating loss of imprinted DNA methylation with abnormal placental phenotypes in a mid-gestation window (E12.5-E15.5). To these ends we measured DNA CpG methylation at 15 imprinted gametic differentially methylated domains (gDMDs) that overlap known ICRs using EpiTYPER-mass array technology, and linked these epigenetic measurements to histomorphological defects. Methylation of some imprinted gDMDs, most notably Dlk1, was nearly normal in mid-gestation DNMT1o-deficient placentas, consistent with the notion that cells having lost methylation on these DMDs do not contribute significantly to placental development. Most imprinted gDMDs however showed a wide range of methylation loss among DNMT1o-deficient placentas. Two striking associations were observed. First, loss of DNA methylation at the Peg10 imprinted gDMD associated with decreased embryonic viability and decreased labyrinthine volume. Second, loss of methylation at the Kcnq1 imprinted gDMD was strongly associated with trophoblast giant cell (TGC) expansion. We conclude that the Peg10 and Kcnq1 ICRs are key regulators of mid-gestation placental function.
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Affiliation(s)
- Erik Koppes
- Magee-Womens Research Institute, Program in Integrative Molecular Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Katherine P. Himes
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - J. Richard Chaillet
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas. PLoS Genet 2015; 11:e1005442. [PMID: 26241857 PMCID: PMC4524645 DOI: 10.1371/journal.pgen.1005442] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/14/2015] [Indexed: 12/11/2022] Open
Abstract
Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylated domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.
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Himes KP, Young A, Koppes E, Stolz D, Barak Y, Sadovsky Y, Chaillet JR. Loss of inherited genomic imprints in mice leads to severe disruption in placental lipid metabolism. Placenta 2015; 36:389-96. [PMID: 25662615 PMCID: PMC4359963 DOI: 10.1016/j.placenta.2015.01.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/29/2014] [Accepted: 01/22/2015] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Monoallelic expression of imprinted genes is necessary for placental development and normal fetal growth. Differentially methylated domains (DMDs) largely determine the parental-specific monoallelic expression of imprinted genes. Maternally derived DNA (cytosine-5-) -methyltransferase 1o (DNMT1o) maintains DMDs during the eight-cell stage of development. DNMT1o-deficient mouse placentas have a generalized disruption of genomic imprints. Previous studies have demonstrated that DNMT1o deficiency alters placental morphology and broadens the embryonic weight distribution in late gestation. Lipids are critical for fetal growth. Thus, we assessed the impact of disrupted imprinting on placental lipids. METHODS Lipids were quantified from DNMT1o-deficient mouse placentas and embryos at E17.5 using a modified Folch method. Expression of select genes critical for lipid metabolism was quantified with RT-qPCR. Mitochondrial morphology was assessed by TEM and mitochondrial aconitase and cytoplasmic citrate concentrations quantified. DMD methylation was determined by EpiTYPER. RESULTS We found that DNMT1o deficiency is associated with increased placental triacylglycerol levels. Neither fetal triacylglycerol concentrations nor expression of select genes that mediate placental lipid transport were different from wild type. Placental triacylglycerol accumulation was associated with impaired beta-oxidation and abnormal citrate metabolism with decreased mitochondrial aconitase activity and increased cytoplasmic citrate concentrations. Loss of methylation at the MEST DMD was strongly associated with placental triacylglycerol accumulation. DISCUSSION A generalized disruption of genomic imprints leads to triacylglycerol accumulation and abnormal mitochondrial function. This could stem directly from a loss of methylation at a given DMD, such as MEST, or represent a consequence of abnormal placental development.
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Affiliation(s)
- K P Himes
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Avenue, Pittsburgh, PA 15213, USA.
| | - A Young
- Magee-Womens Research Institute, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 204 Craft Avenue, Pittsburgh, PA 15213, USA.
| | - E Koppes
- Magee-Womens Research Institute, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 204 Craft Avenue, Pittsburgh, PA 15213, USA.
| | - D Stolz
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
| | - Y Barak
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Avenue, Pittsburgh, PA 15213, USA; Magee-Womens Research Institute, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 204 Craft Avenue, Pittsburgh, PA 15213, USA.
| | - Y Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Avenue, Pittsburgh, PA 15213, USA; Magee-Womens Research Institute, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 204 Craft Avenue, Pittsburgh, PA 15213, USA.
| | - J R Chaillet
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 204 Craft Avenue, Pittsburgh, PA 15213, USA.
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McGraw S, Zhang JX, Farag M, Chan D, Caron M, Konermann C, Oakes CC, Mohan KN, Plass C, Pastinen T, Bourque G, Chaillet JR, Trasler JM. Transient DNMT1 suppression reveals hidden heritable marks in the genome. Nucleic Acids Res 2015; 43:1485-97. [PMID: 25578964 PMCID: PMC4330356 DOI: 10.1093/nar/gku1386] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genome-wide demethylation and remethylation of DNA during early embryogenesis is essential for development. Imprinted germline differentially methylated domains (gDMDs) established by sex-specific methylation in either male or female germ cells, must escape these dynamic changes and sustain precise inheritance of both methylated and unmethylated parental alleles. To identify other, gDMD-like sequences with the same epigenetic inheritance properties, we used a modified embryonic stem (ES) cell line that emulates the early embryonic demethylation and remethylation waves. Transient DNMT1 suppression revealed gDMD-like sequences requiring continuous DNMT1 activity to sustain a highly methylated state. Remethylation of these sequences was also compromised in vivo in a mouse model of transient DNMT1 loss in the preimplantation embryo. These novel regions, possessing heritable epigenetic features similar to imprinted-gDMDs are required for normal physiological and developmental processes and when disrupted are associated with disorders such as cancer and autism spectrum disorders. This study presents new perspectives on DNA methylation heritability during early embryo development that extend beyond conventional imprinted-gDMDs.
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Affiliation(s)
- Serge McGraw
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
| | - Jacques X Zhang
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
| | - Mena Farag
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
| | - Donovan Chan
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - Carolin Konermann
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg 69120, Germany
| | - Christopher C Oakes
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg 69120, Germany
| | - K Naga Mohan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad 500 078, India
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg 69120, Germany
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - J Richard Chaillet
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213-3005, USA
| | - Jacquetta M Trasler
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
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14
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Tissue factor expression and methylation regulation in differentiation of embryonic stem cells into trophoblast. ASIAN PAC J TROP MED 2014; 7:557-61. [DOI: 10.1016/s1995-7645(14)60093-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/15/2014] [Accepted: 06/15/2014] [Indexed: 11/22/2022] Open
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15
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Venhoranta H, Li S, Salamon S, Flisikowska T, Andersson M, Switonski M, Kind A, Schnieke A, Flisikowski K. Non-CpG hypermethylation in placenta of mutation-induced intrauterine growth restricted bovine foetuses. Biochem Biophys Res Commun 2014; 444:391-4. [PMID: 24480436 DOI: 10.1016/j.bbrc.2014.01.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/17/2014] [Indexed: 11/20/2022]
Abstract
The existence of non-CpG methylation in mammalian DNA has mainly been observed in embryonic stem cells, but its functional significance is uncertain. We found an age-dependent non-CpG hypermethylation in DMR at the 3' end of the MIMT1 in the placenta of intrauterine growth restricted foetuses in cattle. Data suggest that this DMR play a role in epigenetic regulation of the PEG3 domain.
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Affiliation(s)
- Heli Venhoranta
- Department of Production Animal Medicine, University of Helsinki, Saarentaus, Finland
| | - Shun Li
- Chair of Livestock Biotechnology, Technische Universität München, Freising, Germany
| | - Sylwia Salamon
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Tatiana Flisikowska
- Chair of Livestock Biotechnology, Technische Universität München, Freising, Germany
| | - Magnus Andersson
- Department of Production Animal Medicine, University of Helsinki, Saarentaus, Finland
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Alexander Kind
- Chair of Livestock Biotechnology, Technische Universität München, Freising, Germany
| | - Angelika Schnieke
- Chair of Livestock Biotechnology, Technische Universität München, Freising, Germany
| | - Krzysztof Flisikowski
- Chair of Livestock Biotechnology, Technische Universität München, Freising, Germany.
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16
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McGraw S, Oakes CC, Martel J, Cirio MC, de Zeeuw P, Mak W, Plass C, Bartolomei MS, Chaillet JR, Trasler JM. Loss of DNMT1o disrupts imprinted X chromosome inactivation and accentuates placental defects in females. PLoS Genet 2013; 9:e1003873. [PMID: 24278026 PMCID: PMC3836718 DOI: 10.1371/journal.pgen.1003873] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 08/28/2013] [Indexed: 01/04/2023] Open
Abstract
The maintenance of key germline derived DNA methylation patterns during preimplantation development depends on stores of DNA cytosine methyltransferase-1o (DNMT1o) provided by the oocyte. Dnmt1omat−/− mouse embryos born to Dnmt1Δ1o/Δ1o female mice lack DNMT1o protein and have disrupted genomic imprinting and associated phenotypic abnormalities. Here, we describe additional female-specific morphological abnormalities and DNA hypomethylation defects outside imprinted loci, restricted to extraembryonic tissue. Compared to male offspring, the placentae of female offspring of Dnmt1Δ1o/Δ1o mothers displayed a higher incidence of genic and intergenic hypomethylation and more frequent and extreme placental dysmorphology. The majority of the affected loci were concentrated on the X chromosome and associated with aberrant biallelic expression, indicating that imprinted X-inactivation was perturbed. Hypomethylation of a key regulatory region of Xite within the X-inactivation center was present in female blastocysts shortly after the absence of methylation maintenance by DNMT1o at the 8-cell stage. The female preponderance of placental DNA hypomethylation associated with maternal DNMT1o deficiency provides evidence of additional roles beyond the maintenance of genomic imprints for DNA methylation events in the preimplantation embryo, including a role in imprinted X chromosome inactivation. During oocyte growth and maturation, vital proteins and enzymes are produced to ensure that, when fertilized, a healthy embryo will arise. When this natural process is interrupted, one or more of these essential elements can fail to be produced thus compromising the health of the future embryo. We are using a mouse model, lacking an enzyme (DNMT1o) produced in the oocyte and only required post-fertilization in the early embryo for the maintenance of inherited DNA methylation marks. Here, we reveal that oocytes lacking DNMT1o, when fertilized, generated conceptuses with a wide variety of placental abnormalities. These placental abnormalities were more frequent and severe in females, and showed specific genomic regions constantly deprived of their normal methylation marks. The affected genomic regions were concentrated on the X chromosome. Interestingly, we also found that a region important for the regulation of the X chromosome inactivation process was hypomethylated in female blastocysts and was associated with sex-specific abnormalities in the placenta, relaxation of imprinted X chromosome inactivation, and disruption of DNA methylation later in development. Our findings provide a novel unanticipated role for DNA methylation events taking place within the first few days of life specifically in female preimplantation embryos.
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Affiliation(s)
- Serge McGraw
- Departments of Pharmacology & Therapeutics, Pediatrics and Human Genetics, Research Institute at The Montreal Children's Hospital of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Christopher C. Oakes
- Department of Epigenomics and Cancer Risk Factors, The German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany
| | - Josée Martel
- Departments of Pharmacology & Therapeutics, Pediatrics and Human Genetics, Research Institute at The Montreal Children's Hospital of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - M. Cecilia Cirio
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Pauline de Zeeuw
- Departments of Pharmacology & Therapeutics, Pediatrics and Human Genetics, Research Institute at The Montreal Children's Hospital of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Winifred Mak
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Christoph Plass
- Department of Epigenomics and Cancer Risk Factors, The German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - J. Richard Chaillet
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacquetta M. Trasler
- Departments of Pharmacology & Therapeutics, Pediatrics and Human Genetics, Research Institute at The Montreal Children's Hospital of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
- * E-mail:
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