1
|
Abbas A, Hammad AS, Al-Shafai M. The role of genetic and epigenetic GNAS alterations in the development of early-onset obesity. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108487. [PMID: 38103632 DOI: 10.1016/j.mrrev.2023.108487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND GNAS (guanine nucleotide-binding protein, alpha stimulating) is an imprinted gene that encodes Gsα, the α subunit of the heterotrimeric stimulatory G protein. This subunit mediates the signalling of a diverse array of G protein-coupled receptors (GPCRs), including the melanocortin 4 receptor (MC4R) that serves a pivotal role in regulating food intake, energy homoeostasis, and body weight. Genetic or epigenetic alterations in GNAS are known to cause pseudohypoparathyroidism in its different subtypes and have been recently associated with isolated, early-onset, severe obesity. Given the diverse biological functions that Gsα serves, multiple molecular mechanisms involving various GPCRs, such as MC4R, β2- and β3-adrenoceptors, and corticotropin-releasing hormone receptor, have been implicated in the pathophysiology of severe, early-onset obesity that results from genetic or epigenetic GNAS changes. SCOPE OF REVIEW This review examines the structure and function of GNAS and provides an overview of the disorders that are caused by defects in this gene and may feature early-onset obesity. Moreover, it elucidates the potential molecular mechanisms underlying Gsα deficiency-induced early-onset obesity, highlighting some of their implications for the diagnosis, management, and treatment of this complex condition. MAJOR CONCLUSIONS Gsα deficiency is an underappreciated cause of early-onset, severe obesity. Therefore, screening children with unexplained, severe obesity for GNAS defects is recommended, to enhance the molecular diagnosis and management of this condition.
Collapse
Affiliation(s)
- Alaa Abbas
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Ayat S Hammad
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar; Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar; Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Ayache L, Bushell A, Lee J, Salminen I, Crespi B. Mother's warmth from maternal genes: genomic imprinting of brown adipose tissue. Evol Med Public Health 2023; 11:379-385. [PMID: 37928960 PMCID: PMC10621903 DOI: 10.1093/emph/eoad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/04/2023] [Indexed: 11/07/2023] Open
Abstract
Background and objectives Brown adipose tissue (BAT) plays key roles in mammalian physiology, most notably with regard to thermoregulation in infants and juveniles. Previous studies have suggested that intragenomic conflict, in the form of genomic imprinting, mediates BAT thermogenesis, because it represents a public good for groups of siblings, or a mother with her offspring, who huddle together to conserve warmth. By this hypothesis, maternally expressed imprinted genes should promote BAT, while paternally expressed genes should repress it. Methodology We systematically searched the literature using two curated lists of genes imprinted in humans and/or mice, in association with evidence regarding effects of perturbation to imprinted gene expression on BAT development or activity. Results Overall, enhanced BAT was associated with relatively higher expression of maternally expressed imprinted genes, and relatively lower expression of paternally expressed imprinted genes; this pattern was found for 16 of the 19 genes with sufficient information for robust ascertainment (Binomial test, P < 0.005, 2-tailed). Conclusions and implications These results support the kinship theory of imprinting and indicate that future studies of BAT, and its roles in human health and disease, may usefully focus on effects of imprinted genes and associated genomic conflicts.
Collapse
Affiliation(s)
- Lynn Ayache
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Aiden Bushell
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jessica Lee
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Iiro Salminen
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
4
|
Di Michele F, Chillón I, Feil R. Imprinted Long Non-Coding RNAs in Mammalian Development and Disease. Int J Mol Sci 2023; 24:13647. [PMID: 37686455 PMCID: PMC10487962 DOI: 10.3390/ijms241713647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Imprinted genes play diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express one or more long non-coding RNAs (lncRNAs). Several of these lncRNAs are strictly nuclear and their mono-allelic expression controls in cis the expression of protein-coding genes, often developmentally regulated. Some imprinted lncRNAs act in trans as well, controlling target gene expression elsewhere in the genome. The regulation of imprinted gene expression-including that of imprinted lncRNAs-is susceptible to stochastic and environmentally triggered epigenetic changes in the early embryo. These aberrant changes persist during subsequent development and have long-term phenotypic consequences. This review focuses on the expression and the cis- and trans-regulatory roles of imprinted lncRNAs and describes human disease syndromes associated with their perturbed expression.
Collapse
Affiliation(s)
- Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Isabel Chillón
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| |
Collapse
|
5
|
Iwasaki Y, Aksu C, Reyes M, Ay B, He Q, Bastepe M. The long-range interaction between two GNAS imprinting control regions delineates pseudohypoparathyroidism type 1B pathogenesis. J Clin Invest 2023; 133:e167953. [PMID: 36853809 PMCID: PMC10104902 DOI: 10.1172/jci167953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/21/2023] [Indexed: 03/01/2023] Open
Abstract
Genetic defects of GNAS, the imprinted gene encoding the stimulatory G protein α-subunit, are responsible for multiple diseases. Abnormal GNAS imprinting causes pseudohypoparathyroidism type 1B (PHP1B), a prototype of mammalian end-organ hormone resistance. Hypomethylation at the maternally methylated GNAS A/B region is the only shared defect in patients with PHP1B. In autosomal dominant (AD) PHP1B kindreds, A/B hypomethylation is associated with maternal microdeletions at either the GNAS NESP55 differentially methylated region or the STX16 gene located approximately 170 kb upstream. Functional evidence is meager regarding the causality of these microdeletions. Moreover, the mechanisms linking A/B methylation and the putative imprinting control regions (ICRs) NESP-ICR and STX16-ICR remain unknown. Here, we generated a human embryonic stem cell model of AD-PHP1B by introducing ICR deletions using CRISPR/Cas9. With this model, we showed that the NESP-ICR is required for methylation and transcriptional silencing of A/B on the maternal allele. We also found that the SXT16-ICR is a long-range enhancer of NESP55 transcription, which originates from the maternal NESP-ICR. Furthermore, we demonstrated that the STX16-ICR is an embryonic stage-specific enhancer enabled by the direct binding of pluripotency factors. Our findings uncover an essential GNAS imprinting control mechanism and advance the molecular understanding of PHP1B pathogenesis.
Collapse
Affiliation(s)
- Yorihiro Iwasaki
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka, Japan
| | - Cagri Aksu
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Monica Reyes
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Birol Ay
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Qing He
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory for Oral Biomedicine of the Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
6
|
McIlfatrick S, O’Leary S, Okada T, Penn A, Nguyen VHT, McKenny L, Huang SY, Andreas E, Finnie J, Kirkwood R, St. John JC. Does supplementation of oocytes with additional mtDNA influence developmental outcome? iScience 2023; 26:105956. [PMID: 36711242 PMCID: PMC9876745 DOI: 10.1016/j.isci.2023.105956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/07/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Introducing extra mitochondrial DNA (mtDNA) into oocytes at fertilization can rescue poor quality oocytes. However, supplementation alters DNA methylation and gene expression profiles of preimplantation embryos. To determine if these alterations impacted offspring, we introduced mtDNA from failed-to-mature sister (autologous) or third party (heterologous) oocytes into mature oocytes and transferred zygotes into surrogates. Founders exhibited significantly greater daily weight gain (heterologous) and growth rates (heterologous and autologous) to controls. In weaners, cholesterol, bilirubin (heterologous and autologous), anion gap, and lymphocyte count (autologous) were elevated. In mature pigs, potassium (heterologous) and bicarbonate (autologous) were altered. mtDNA and imprinted gene analyses did not reveal aberrant profiles. Neither group exhibited gross anatomical, morphological, or histopathological differences that would lead to clinically significant lesions. Female founders were fertile and their offspring exhibited modified weight and height gain, biochemical, and hematological profiles. mtDNA supplementation induced minor differences that did not affect health and well-being.
Collapse
Affiliation(s)
- Stephen McIlfatrick
- Mitochondrial Genetics Group, School of Biomedicine, Faculty of Health and Medical Sciences, and Robinson Research Institute, The University of Adelaide, Adelaide Health and Medical Sciences Building, Adelaide, SA 5000, Australia
| | - Sean O’Leary
- Mitochondrial Genetics Group, School of Biomedicine, Faculty of Health and Medical Sciences, and Robinson Research Institute, The University of Adelaide, Adelaide Health and Medical Sciences Building, Adelaide, SA 5000, Australia
| | - Takashi Okada
- Mitochondrial Genetics Group, School of Biomedicine, Faculty of Health and Medical Sciences, and Robinson Research Institute, The University of Adelaide, Adelaide Health and Medical Sciences Building, Adelaide, SA 5000, Australia
| | - Alexander Penn
- Mitochondrial Genetics Group, School of Biomedicine, Faculty of Health and Medical Sciences, and Robinson Research Institute, The University of Adelaide, Adelaide Health and Medical Sciences Building, Adelaide, SA 5000, Australia
| | - Vy Hoang Thao Nguyen
- Mitochondrial Genetics Group, School of Biomedicine, Faculty of Health and Medical Sciences, and Robinson Research Institute, The University of Adelaide, Adelaide Health and Medical Sciences Building, Adelaide, SA 5000, Australia
| | - Lisa McKenny
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Roseworthy, SA 5371, Australia
| | - Shang-Yu Huang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital-Linkou Medical Center, Taoyuan, Taiwan,Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Eryk Andreas
- Mitochondrial Genetics Group, School of Biomedicine, Faculty of Health and Medical Sciences, and Robinson Research Institute, The University of Adelaide, Adelaide Health and Medical Sciences Building, Adelaide, SA 5000, Australia
| | - John Finnie
- University Veterinarian & AWO, Office of the Deputy Vice-Chancellor (Research), The University of Adelaide, Adelaide Health and Medical Sciences Building, Adelaide, SA 5000, Australia
| | - Roy Kirkwood
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Roseworthy, SA 5371, Australia
| | - Justin C. St. John
- Mitochondrial Genetics Group, School of Biomedicine, Faculty of Health and Medical Sciences, and Robinson Research Institute, The University of Adelaide, Adelaide Health and Medical Sciences Building, Adelaide, SA 5000, Australia,Corresponding author
| |
Collapse
|
7
|
Mechanisms of DNA methylation and histone modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:51-92. [PMID: 37019597 DOI: 10.1016/bs.pmbts.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The field of genetics has expanded a lot in the past few decades due to the accessibility of human genome sequences, but still, the regulation of transcription cannot be explicated exclusively by the sequence of DNA of an individual. The coordination and crosstalk between chromatin factors which are conserved is indispensable for all living creatures. The regulation of gene expression has been dependent on the methylation of DNA, post-translational modifications of histones, effector proteins, chromatin remodeler enzymes that affect the chromatin structure and function, and other cellular activities such as DNA replication, DNA repair, proliferation and growth. The mutation and deletion of these factors can lead to human diseases. Various studies are being performed to identify and understand the gene regulatory mechanisms in the diseased state. The information from these high throughput screening studies is able to aid the treatment developments based on the epigenetics regulatory mechanisms. This book chapter will discourse on various modifications and their mechanisms that take place on histones and DNA that regulate the transcription of genes.
Collapse
|
8
|
Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022; 149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation is a highly conserved epigenetic modification that plays essential roles in mammalian gene regulation, genome stability and development. Despite being primarily considered a stable and heritable epigenetic silencing mechanism at heterochromatic and repetitive regions, whole genome methylome analysis reveals that DNA methylation can be highly cell-type specific and dynamic within proximal and distal gene regulatory elements during early embryonic development, stem cell differentiation and reprogramming, and tissue maturation. In this Review, we focus on the mechanisms and functions of regulated DNA methylation and demethylation, highlighting how these dynamics, together with crosstalk between DNA methylation and histone modifications at distinct regulatory regions, contribute to mammalian development and tissue maturation. We also discuss how recent technological advances in single-cell and long-read methylome sequencing, along with targeted epigenome-editing, are enabling unprecedented high-resolution and mechanistic dissection of DNA methylome dynamics.
Collapse
Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
9
|
Chao Y, Qin Y, Zou X, Wang X, Hu C, Xia F, Zou C. Promising therapeutic aspects in human genetic imprinting disorders. Clin Epigenetics 2022; 14:146. [PMID: 36371218 PMCID: PMC9655922 DOI: 10.1186/s13148-022-01369-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon of monoallelic gene expression pattern depending on parental origin. In humans, congenital imprinting disruptions resulting from genetic or epigenetic mechanisms can cause a group of diseases known as genetic imprinting disorders (IDs). Genetic IDs involve several distinct syndromes sharing homologies in terms of genetic etiologies and phenotypic features. However, the molecular pathogenesis of genetic IDs is complex and remains largely uncharacterized, resulting in a lack of effective therapeutic approaches for patients. In this review, we begin with an overview of the genomic and epigenomic molecular basis of human genetic IDs. Notably, we address ethical aspects as a priority of employing emerging techniques for therapeutic applications in human IDs. With a particular focus, we delineate the current field of emerging therapeutics for genetic IDs. We briefly summarize novel symptomatic drugs and highlight the key milestones of new techniques and therapeutic programs as they stand today which can offer highly promising disease-modifying interventions for genetic IDs accompanied by various challenges.
Collapse
Affiliation(s)
- Yunqi Chao
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Yifang Qin
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Xinyi Zou
- grid.13402.340000 0004 1759 700XZhejiang University City College, Hangzhou, 310015 Zhejiang China
| | - Xiangzhi Wang
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Chenxi Hu
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Fangling Xia
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Chaochun Zou
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| |
Collapse
|
10
|
Okada T, McIlfatrick S, Hin N, Aryamanesh N, Breen J, St John JC. Mitochondrial supplementation of Sus scrofa metaphase II oocytes alters DNA methylation and gene expression profiles of blastocysts. Epigenetics Chromatin 2022; 15:12. [PMID: 35428319 PMCID: PMC9013150 DOI: 10.1186/s13072-022-00442-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/03/2022] [Indexed: 12/13/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) copy number in oocytes correlates with oocyte quality and fertilisation outcome. The introduction of additional copies of mtDNA through mitochondrial supplementation of mtDNA-deficient Sus scrofa oocytes resulted in: (1) improved rates of fertilisation; (2) increased mtDNA copy number in the 2-cell stage embryo; and (3) improved development of the embryo to the blastocyst stage. Furthermore, a subset of genes showed changes in gene expression. However, it is still unknown if mitochondrial supplementation alters global and local DNA methylation patterns during early development. Results We generated a series of embryos in a model animal, Sus scrofa, by intracytoplasmic sperm injection (ICSI) and mitochondrial supplementation in combination with ICSI (mICSI). The DNA methylation status of ICSI- and mICSI-derived blastocysts was analysed by whole genome bisulfite sequencing. At a global level, the additional copies of mtDNA did not affect nuclear DNA methylation profiles of blastocysts, though over 2000 local genomic regions exhibited differential levels of DNA methylation. In terms of the imprinted genes, DNA methylation patterns were conserved in putative imprint control regions; and the gene expression profile of these genes and genes involved in embryonic genome activation were not affected by mitochondrial supplementation. However, 52 genes showed significant differences in expression as demonstrated by RNAseq analysis. The affected gene networks involved haematological system development and function, tissue morphology and cell cycle. Furthermore, seven mtDNA-encoded t-RNAs were downregulated in mICSI-derived blastocysts suggesting that extra copies of mtDNA affected tRNA processing and/or turnover, hence protein synthesis in blastocysts. We also showed a potential association between differentially methylated regions and changes in expression for 55 genes due to mitochondrial supplementation. Conclusions The addition of just an extra ~ 800 copies of mtDNA into oocytes can have a significant impact on both gene expression and DNA methylation profiles in Sus scrofa blastocysts by altering the epigenetic programming established during oogenesis. Some of these changes may affect specific tissue-types later in life. Consequently, it is important to determine the longitudinal effect of these molecular changes on growth and development before considering human clinical practice. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00442-x.
Collapse
Affiliation(s)
- Takashi Okada
- Mitochondrial Genetics Group, Robinson Research Institute, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Stephen McIlfatrick
- Mitochondrial Genetics Group, Robinson Research Institute, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Nhi Hin
- South Australian Genomics Centre, South Australian Health and Medical Research Institute, SAHMRI, Adelaide, SA, 5000, Australia
| | - Nader Aryamanesh
- South Australian Genomics Centre, South Australian Health and Medical Research Institute, SAHMRI, Adelaide, SA, 5000, Australia.,Embryology Research Unit, Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - James Breen
- South Australian Genomics Centre, South Australian Health and Medical Research Institute, SAHMRI, Adelaide, SA, 5000, Australia
| | - Justin C St John
- Mitochondrial Genetics Group, Robinson Research Institute, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5000, Australia.
| |
Collapse
|
11
|
Abstract
In mammals, parthenogenesis is limited because of problems arising from genomic imprinting. Here, we report live mammalian offspring derived from single unfertilized eggs. This was achieved by the targeted DNA methylation rewriting of seven imprinting control regions. By designing guide RNAs with protospacer adjacent motif (PAM) sequences matching one allele but not the other, dCas9-Dnmt3a or dCpf1-Tet1 enables targeted DNA methylation editing in an allele-specific manner. The success of parthenogenesis in mammals opens many opportunities in agriculture, research, and medicine. In mammals, a new life starts with the fusion of an oocyte and a sperm cell. Parthenogenesis, a way of generating offspring solely from female gametes, is limited because of problems arising from genomic imprinting. Here, we report live mammalian offspring derived from single unfertilized oocytes, which was achieved by targeted DNA methylation rewriting of seven imprinting control regions. Oocyte coinjection of catalytically inactive Cas9 (dCas9)-Dnmt3a or dCpf1-Tet1 messenger RNA (mRNA) with single-guide RNAs (sgRNAs) targeting specific regions induced de novo methylation or demethylation, respectively, of the targeted region. Following parthenogenetic activation, these edited regions showed maintenance of methylation as naturally established regions during early preimplantation development. The transfer of modified parthenogenetic embryos into foster mothers resulted in significantly extended development and finally in the generation of viable full-term offspring. These data demonstrate that parthenogenesis can be achieved by targeted epigenetic rewriting of multiple critical imprinting control regions.
Collapse
|
12
|
Kiuchi Z, Reyes M, Hanna P, Sharma A, DeClue T, Olney RC, Tebben P, Jüppner H. Progression of PTH Resistance in Autosomal Dominant Pseudohypoparathyroidism Type Ib Due to Maternal STX16 Deletions. J Clin Endocrinol Metab 2022; 107:e681-e687. [PMID: 34477200 PMCID: PMC8899049 DOI: 10.1210/clinem/dgab660] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/04/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Maternally inherited STX16 deletions that cause loss of methylation at GNAS exon A/B and thereby reduce Gsα expression are the most frequent cause of autosomal dominant pseudohypoparathyroidism type Ib (AD-PHP1B). Early identification of these disease-causing variants in the children of affected and unaffected female carriers would prompt treatment with calcium and calcitriol once parathyroid hormone (PTH) levels increase, thereby preventing hypocalcemia and associated complications. OBJECTIVE This study aimed to determine when PTH and calcium abnormalities develop after birth if a STX16 deletion is inherited maternally. METHODS Forty-four children of affected (n = 7) or unaffected (n = 7) females with a STX16 deletion were investigated for the presence of these variants. If a deletion was identified, measurement of PTH, calcium, phosphate, and thyrotropin (TSH) was advised. RESULTS The STX16 deletion that causes AD-PHP1B was identified in 25 children. Pretreatment laboratory results were available for 19 of those cases. Elevated PTH levels were detected by 2 years of age, and these were progressively higher if laboratory testing was first performed after establishing the genetic defect later in life. Total serum calcium levels remained within normal limits until about 5 years of age. TSH levels showed no consistent rise over time. CONCLUSION Establishing whether a STX16 deletion is inherited from a female carrier of a disease-causing variant rapidly establishes the diagnosis of AD-PHP1B. Several years before overt hypocalcemia developed, PTH levels increased, thereby establishing the onset of PTH resistance. Our findings provide diagnostic guidance and when treatment with calcium and calcitriol should be considered in order to prevent hypocalcemia and associated sequelae.
Collapse
Affiliation(s)
- Zentaro Kiuchi
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Monica Reyes
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Patrick Hanna
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Anu Sharma
- Division of Diabetes, Endocrinology and Metabolism, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Terry DeClue
- St Joseph’s Children’s Hospital, Tampa, FL 33607, USA
| | - Robert C Olney
- Nemours Children’s Specialty Care, Jacksonville, FL 32207, USA
| | - Peter Tebben
- Departments of Internal Medicine and Pediatrics, Divisions of Endocrinology and Metabolism, Mayo Clinic, Rochester, MN 55905, USA
| | - Harald Jüppner
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Pediatric Nephrology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| |
Collapse
|
13
|
Danzig J, Li D, Jan de Beur S, Levine MA. High-throughput Molecular Analysis of Pseudohypoparathyroidism 1b Patients Reveals Novel Genetic and Epigenetic Defects. J Clin Endocrinol Metab 2021; 106:e4603-e4620. [PMID: 34157100 PMCID: PMC8677598 DOI: 10.1210/clinem/dgab460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Patients with pseudohypoparathyroidism type 1b (PHP1b) show disordered imprinting of the maternal GNAS allele or paternal uniparental disomy (UPD). Genetic deletions in STX16 or in upstream exons of GNAS are present in many familial but not sporadic cases. OBJECTIVE Characterization of epigenetic and genetic defects in patients with PHP1b. DESIGN AND PATIENTS DNA from 84 subjects, including 26 subjects with sporadic PHP1b, 27 affected subjects and 17 unaffected and/or obligate gene carriers from 12 PHP1b families, 11 healthy individuals, and 3 subjects with PHP1a was subjected to quantitative pyrosequencing of GNAS differentially methylated regions (DMRs), microarray analysis, and microsatellite haplotype analysis. SETTING Academic medical center. MAIN OUTCOME MEASUREMENTS Molecular pathology of PHP1b. RESULTS Healthy subjects, unaffected family members and obligate carriers of paternal PHP1b alleles, and subjects with PHP1a showed normal methylation of all DMRs. All PHP1b subjects showed loss of methylation (LOM) at the exon A/B DMR. Affected members of 9 PHP1b kindreds showed LOM only at the exon A/B DMR, which was associated with a 3-kb deletion of STX16 exons 4 through 6 in 7 families and a novel deletion of STX16 and adjacent NEPEPL1 in 1 family. A novel NESP deletion was found in 1 of 2 other families with more extensive methylation defects. One sporadic PHP1b had UPD of 20q, 2 had 3-kb STX16 deletions, and 5 had apparent epigenetic mosaicism. CONCLUSIONS We found diverse patterns of defective methylation and identified novel or previously known mutations in 9 of 12 PHP1b families.
Collapse
Affiliation(s)
- Jennifer Danzig
- Division of Endocrinology and Diabetes, and The Children’s Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dong Li
- Center for Applied Genomics, The Children’s Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Suzanne Jan de Beur
- Division of Endocrinology and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael A Levine
- Division of Endocrinology and Diabetes, and The Children’s Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| |
Collapse
|
14
|
Cui Q, Aksu C, Ay B, Remillard CE, Plagge A, Gardezi M, Dunlap M, Gerstenfeld LC, He Q, Bastepe M. Maternal GNAS Contributes to the Extra-Large G Protein α-Subunit (XLαs) Expression in a Cell Type-Specific Manner. Front Genet 2021; 12:680537. [PMID: 34220953 PMCID: PMC8247768 DOI: 10.3389/fgene.2021.680537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022] Open
Abstract
GNAS encodes the stimulatory G protein alpha-subunit (Gsα) and its large variant XLαs. Studies have suggested that XLαs is expressed exclusively paternally. Thus, XLαs deficiency is considered to be responsible for certain findings in patients with paternal GNAS mutations, such as pseudo-pseudohypoparathyroidism, and the phenotypes associated with maternal uniparental disomy of chromosome 20, which comprises GNAS. However, a study of bone marrow stromal cells (BMSC) suggested that XLαs could be biallelically expressed. Aberrant BMSC differentiation due to constitutively activating GNAS mutations affecting both Gsα and XLαs is the underlying pathology in fibrous dysplasia of bone. To investigate allelic XLαs expression, we employed next-generation sequencing and a polymorphism common to XLαs and Gsα, as well as A/B, another paternally expressed GNAS transcript. In mouse BMSCs, Gsα transcripts were 48.4 ± 0.3% paternal, while A/B was 99.8 ± 0.2% paternal. In contrast, XLαs expression varied among different samples, paternal contribution ranging from 43.0 to 99.9%. Sample-to-sample variation in paternal XLαs expression was also detected in bone (83.7-99.6%) and cerebellum (83.8 to 100%) but not in cultured calvarial osteoblasts (99.1 ± 0.1%). Osteoblastic differentiation of BMSCs shifted the paternal XLαs expression from 83.9 ± 1.5% at baseline to 97.2 ± 1.1%. In two human BMSC samples grown under osteoinductive conditions, XLαs expression was also predominantly monoallelic (91.3 or 99.6%). Thus, the maternal GNAS contributes significantly to XLαs expression in BMSCs but not osteoblasts. Altered XLαs activity may thus occur in certain cell types irrespective of the parental origin of a GNAS defect.
Collapse
Affiliation(s)
- Qiuxia Cui
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Cagri Aksu
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Birol Ay
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Claire E. Remillard
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Antonius Plagge
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Mina Gardezi
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA, United States
| | - Margaret Dunlap
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA, United States
| | - Louis C. Gerstenfeld
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA, United States
| | - Qing He
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- School of Stomatology, Wuhan University, Wuhan, China
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| |
Collapse
|
15
|
Abstract
ZFP57 is a master regulator of genomic imprinting. It has both maternal and zygotic functions that are partially redundant in maintaining DNA methylation at some imprinting control regions (ICRs). In this study, we found that DNA methylation was lost at most known ICRs in Zfp57 mutant embryos. Furthermore, loss of ZFP57 caused loss of parent-of-origin-dependent monoallelic expression of the target imprinted genes. The allelic expression switch occurred in the ZFP57 target imprinted genes upon loss of differential DNA methylation at the ICRs in Zfp57 mutant embryos. Specifically, upon loss of ZFP57, the alleles of the imprinted genes located on the same chromosome with the originally methylated ICR switched their expression to mimic their counterparts on the other chromosome with unmethylated ICR. Consistent with our previous study, ZFP57 could regulate the NOTCH signaling pathway in mouse embryos by impacting allelic expression of a few regulators in the NOTCH pathway. In addition, the imprinted Dlk1 gene that has been implicated in the NOTCH pathway was significantly down-regulated in Zfp57 mutant embryos. Our allelic expression switch models apply to the examined target imprinted genes controlled by either maternally or paternally methylated ICRs. Our results support the view that ZFP57 controls imprinted expression of its target imprinted genes primarily through maintaining differential DNA methylation at the ICRs.
Collapse
|
16
|
Luo D, Qi X, Liu L, Su Y, Fang L, Guan Q. Genetic and Epigenetic Characteristics of Autosomal Dominant Pseudohypoparathyroidism Type 1B: Case Reports and Literature Review. Horm Metab Res 2021; 53:225-235. [PMID: 33513624 DOI: 10.1055/a-1341-9891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Autosomal dominant pseudohypoparathyroidism 1B (AD-PHP1B) is a rare endocrine and imprinted disorder. The objective of this study is to clarify the imprinted regulation of the guanine nucleotide binding-protein α-stimulating activity polypeptide 1 (GNAS) cluster in the occurrence and development of AD-PHP1B based on animal and clinical patient studies. The methylation-specific multiples ligation-dependent probe amplification (MS-MLPA) was conducted to detect the copy number variation in syntaxin-16 (STX16) gene and methylation status of the GNAS differentially methylated regions (DMRs). Long-range PCR was used to confirm deletion at STX16 gene. In the first family, DNA analysis of the proband and proband's mother revealed an isolated loss of methylation (LOM) at exon A/B and a 3.0 kb STX16 deletion. The patient's healthy grandmother had the 3.0 kb STX16 deletion but no epigenetic abnormality. The patient's healthy maternal aunt showed no genetic or epigenetic abnormality. In the second family, the analysis of long-range PCR revealed the 3.0 kb STX16 deletion for the proband but not her children. In this study, 3.0 kb STX16 deletion causes isolated LOM at exon A/B in two families, which is the most common genetic mutation of AD-PHP1B. The deletion involving NESP55 or AS or genomic rearrangements of GNAS can also result in AD-PHP1B, but it's rare. LOM at exon A/B DMR is prerequisite methylation defect of AD-PHP1B. STX16 and NESP55 directly control the imprinting at exon A/B, while AS controls the imprinting at exon A/B by regulating the transcriptional level of NESP55.
Collapse
Affiliation(s)
- Dandan Luo
- Department of Endocrinology and Metabolism, Shandong University, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - Xiangyu Qi
- Department of Endocrinology and Metabolism, Shandong University, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - Luna Liu
- Department of Endocrinology and Metabolism, Shandong University, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - Yu Su
- Department of Endocrinology and Metabolism, Shandong University, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - Li Fang
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - Qingbo Guan
- Department of Endocrinology and Metabolism, Shandong University, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| |
Collapse
|
17
|
Reyes M, Kagami M, Kawashima S, Pallotta J, Schnabel D, Fukami M, Jüppner H. A Novel GNAS Duplication Associated With Loss-of-Methylation Restricted to Exon A/B Causes Pseudohypoparathyroidism Type Ib (PHP1B). J Bone Miner Res 2021; 36:546-552. [PMID: 33180333 PMCID: PMC8048081 DOI: 10.1002/jbmr.4209] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/03/2020] [Accepted: 11/01/2020] [Indexed: 11/09/2022]
Abstract
Pseudohypoparathyroidism type Ib (PHP1B) is characterized by resistance to parathyroid hormone (PTH) leading to hypocalcemia and hyperphosphatemia, and in some cases resistance toward additional hormones. Patients affected by this disorder all share a loss-of-methylation (LOM) at the differentially methylated GNAS exon A/B, which reduces expression of the stimulatory G protein α-subunit (Gsα) from the maternal allele. This leads in the proximal renal tubules, where the paternal GNAS allele does not contribute much to expression of this signaling protein, to little or no Gsα expression thereby causing PTH resistance. We now describe a PHP1B patient with a de novo genomic GNAS duplication of approximately 88 kb, which is associated with LOM restricted to exon A/B alone. Multiplex ligation-dependent probe amplification (MLPA), comparative genomic hybridization (CGH), and whole-genome sequencing (WGS) established that the duplicated DNA fragment extends from GNAS exon AS1 (telomeric breakpoint) to a small region between two imperfect repeats just upstream of LOC105372695 (centromeric breakpoint). Our novel duplication is considerably shorter than previously described duplications/triplications in that portion of chromosome 20q13 and it does not affect methylation at exons AS and XL. Based on these and previous findings, it appears plausible that the identified genomic abnormality disrupts in cis the actions of a transcript that is required for establishing or maintaining exon A/B methylation. Our findings extend the molecular causes of PHP1B and provide additional insights into structural GNAS features that are required for maintaining maternal Gsα expression and for preventing PTH-resistance. © 2020 American Society for Bone and Mineral Research (ASBMR).
Collapse
Affiliation(s)
- Monica Reyes
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Sayaka Kawashima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Johanna Pallotta
- Pediatric Nephrology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dirk Schnabel
- Center for Chronically Sick Children, Pediatric Endocrinology, Charité University Medicine, Berlin, Germany
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Harald Jüppner
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Pediatric Nephrology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| |
Collapse
|
18
|
Use of DNA methylation profiling in translational oncology. Semin Cancer Biol 2020; 83:523-535. [PMID: 33352265 DOI: 10.1016/j.semcancer.2020.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023]
Abstract
DNA methylation is a highly regulated process that has a critical role in human development and homeostatic control of the cell. The number of genes affected by anomalous DNA methylation in cancer-associated pathways is swiftly accelerating and with the advancement of molecular technologies, new layers of complexity are opening up and refining our strategies to combat cancer. DNA methylation profiling is an essential facet to understanding malignant transformation and is becoming an increasingly important tool for cancer diagnosis, prognosis and therapy monitoring. In this review, the role of DNA methylation in normal cellular function is discussed, as well as how epigenetic aberrations override normal cellular cues that lead to tumor initiation and propagation. The review also focuses on the latest advancements in DNA methylation profiling as a biomarker for early cancer detection, predicting patient clinical outcomes and responses to treatment and provides new insights into epigenetic-based therapy in clinical oncology.
Collapse
|
19
|
Abstract
Genomic imprinting is a parent-of-origin dependent phenomenon that restricts transcription to predominantly one parental allele. Since the discovery of the first long noncoding RNA (lncRNA), which notably was an imprinted lncRNA, a body of knowledge has demonstrated pivotal roles for imprinted lncRNAs in regulating parental-specific expression of neighboring imprinted genes. In this Review, we will discuss the multiple functionalities attributed to lncRNAs and how they regulate imprinted gene expression. We also raise unresolved questions about imprinted lncRNA function, which may lead to new avenues of investigation. This Review is dedicated to the memory of Denise Barlow, a giant in the field of genomic imprinting and functional lncRNAs. With her passion for understanding the inner workings of science, her indominable spirit and her consummate curiosity, Denise blazed a path of scientific investigation that made many seminal contributions to genomic imprinting and the wider field of epigenetic regulation, in addition to inspiring future generations of scientists.
Collapse
Affiliation(s)
- William A. MacDonald
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mellissa R. W. Mann
- Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
20
|
Maternal Folic Acid Supplementation Mediates Offspring Health via DNA Methylation. Reprod Sci 2020; 27:963-976. [PMID: 32124397 DOI: 10.1007/s43032-020-00161-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 10/24/2022]
Abstract
The clinical significance of periconceptional folic acid supplementation (FAS) in the prevention of neonatal neural tube defects (NTDs) has been recognized for decades. Epidemiological data and experimental findings have consistently been indicating an association between folate deficiency in the first trimester of pregnancy and poor fetal development as well as offspring health (i.e., NTDs, isolated orofacial clefts, neurodevelopmental disorders). Moreover, compelling evidence has suggested adverse effects of folate overload during perinatal period on offspring health (i.e., immune diseases, autism, lipid disorders). In addition to several single-nucleotide polymorphisms (SNPs) in genes related to folate one-carbon metabolism (FOCM), folate concentrations in maternal serum/plasma/red blood cells must be considered when counseling FAS. Epigenetic information encoded by 5-methylcytosines (5mC) plays a critical role in fetal development and offspring health. S-adenosylmethionine (SAM), a methyl donor for 5mC, could be derived from FOCM. As such, folic acid plays a double-edged sword role in offspring health via mediating DNA methylation. However, the underlying epigenetic mechanism is still largely unclear. In this review, we summarized the link across DNA methylation, maternal FAS, and offspring health to provide more evidence for clinical guidance in terms of precise FAS dosage and time point. Future studies are, therefore, required to set up the reference intervals of folate concentrations at different trimesters of pregnancy for different populations and to clarify the epigenetic mechanism for specific offspring diseases.
Collapse
|
21
|
|
22
|
Ahn J, Wu H, Lee J, Hwang IS, Yu D, Ahn JS, Lee JW, Hwang S, Lee K. Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses. Genes (Basel) 2020; 11:genes11010096. [PMID: 31947640 PMCID: PMC7017182 DOI: 10.3390/genes11010096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 12/27/2022] Open
Abstract
Genomic imprinting in domestic animals contributes to the variance of performance traits. However, research remains to be done on large-scale detection of epigenetic landscape of porcine imprinted loci including the GNAS complex locus. The purpose of this study was to generate porcine parthenogenetic fetuses and comprehensively identify imprinting patterns of the GNAS locus in transcript levels. To this end, both normally fertilized and bimaternal (uniparental) parthenogenetic porcine fetuses were generated, and whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) were performed to construct methylome and transcriptome, respectively. Differentially methylated regions (DMRs) between the fetuses were identified through methylome analysis, and parental-origin-specific expression patterns of transcripts were examined with transcriptome. As a result, three major DMRs were identified: paternally methylated Nesp DMR, maternally methylated Nespas-Gnasxl DMR, and maternally methylated Exon1B–Exon1A DMR. Parental-origin-specific expressions of those five DMR-affected transcripts were found, including a novel imprinted transcript, Exon1B, in pigs. In conclusion, using parthenotes, parental-origin-specific imprinting patterns in the porcine GNAS locus was comprehensively identified, and our approach paves the way for the discovery of novel imprinted genes and loci in a genomic context across species.
Collapse
Affiliation(s)
- Jinsoo Ahn
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
| | - Huiguang Wu
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Joonbum Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, RDA, Jeonbuk 55365, Korea;
| | - Debing Yu
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
- Department of Animal Breeding & Genetics, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin-Seop Ahn
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (J.-S.A.)
| | - Jeong-Woong Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (J.-S.A.)
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, RDA, Jeonbuk 55365, Korea;
- Correspondence: (S.H.); (K.L.)
| | - Kichoon Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
- Correspondence: (S.H.); (K.L.)
| |
Collapse
|
23
|
Hara S, Terao M, Muramatsu A, Takada S. Efficient production and transmission of CRISPR/Cas9-mediated mutant alleles at the IG-DMR via generation of mosaic mice using a modified 2CC method. Sci Rep 2019; 9:20202. [PMID: 31882978 PMCID: PMC6934616 DOI: 10.1038/s41598-019-56676-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/16/2019] [Indexed: 01/01/2023] Open
Abstract
Generation of mutant imprinting control region (ICR) mice using genome editing is an important approach for elucidating ICR functions. IG-DMR is an ICR in the Dlk1-Dio3 imprinted domain that contains functional regions—in both parental alleles—that are essential for embryonic development. One drawback of this approach is that embryonic lethality can occur from aberrant expression of the imprinted genes if IG-DMR gets mutated in either the paternal or maternal allele. To overcome this problem, we generated mosaic mice that contained cells with modified IG-DMR alleles and wild-type cells using the 2CC method that allowed for microinjection of the CRISPR/Cas9 constructs into a blastomere of 2-cell embryos. This method improved the birth rate of the founder pups relative to that obtained using the standard protocol. We also successfully produced mosaic mice in which the tandem repeat array sequence in the IG-DMR had been replaced by homology directed repair. Additionally, paternal transmission of the replaced allele caused aberrant expression of the imprinted genes due to hypomethylation of the IG-DMR, indicating that the replaced allele recapitulated our deletion model. Our results indicate that this method is useful for the generation of mutant mice in which a genomic locus essential for normal development has been genetically edited.
Collapse
Affiliation(s)
- Satoshi Hara
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan. .,Division of Molecular Genetics & Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
| | - Miho Terao
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Akari Muramatsu
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.
| |
Collapse
|
24
|
Nechin J, Tunstall E, Raymond N, Hamagami N, Pathmanabhan C, Forestier S, Davis TL. Hemimethylation of CpG dyads is characteristic of secondary DMRs associated with imprinted loci and correlates with 5-hydroxymethylcytosine at paternally methylated sequences. Epigenetics Chromatin 2019; 12:64. [PMID: 31623686 PMCID: PMC6796366 DOI: 10.1186/s13072-019-0309-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/09/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammals, the regulation of imprinted genes is controlled by differential methylation at imprinting control regions which acquire parent of origin-specific methylation patterns during gametogenesis and retain differences in allelic methylation status throughout fertilization and subsequent somatic cell divisions. In addition, many imprinted genes acquire differential methylation during post-implantation development; these secondary differentially methylated regions appear necessary to maintain the imprinted expression state of individual genes. Despite the requirement for both types of differentially methylated sequence elements to achieve proper expression across imprinting clusters, methylation patterns are more labile at secondary differentially methylated regions. To understand the nature of this variability, we analyzed CpG dyad methylation patterns at both paternally and maternally methylated imprinted loci within multiple imprinting clusters. RESULTS We determined that both paternally and maternally methylated secondary differentially methylated regions associated with imprinted genes display high levels of hemimethylation, 29-49%, in comparison to imprinting control regions which exhibited 8-12% hemimethylation. To explore how hemimethylation could arise, we assessed the differentially methylated regions for the presence of 5-hydroxymethylcytosine which could cause methylation to be lost via either passive and/or active demethylation mechanisms. We found enrichment of 5-hydroxymethylcytosine at paternally methylated secondary differentially methylated regions, but not at the maternally methylated sites we analyzed in this study. CONCLUSIONS We found high levels of hemimethylation to be a generalizable characteristic of secondary differentially methylated regions associated with imprinted genes. We propose that 5-hydroxymethylcytosine enrichment may be responsible for the variability in methylation status at paternally methylated secondary differentially methylated regions associated with imprinted genes. We further suggest that the high incidence of hemimethylation at secondary differentially methylated regions must be counteracted by continuous methylation acquisition at these loci.
Collapse
Affiliation(s)
- Julianna Nechin
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Emma Tunstall
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Naideline Raymond
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Nicole Hamagami
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Chris Pathmanabhan
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Samantha Forestier
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Tamara L Davis
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA.
| |
Collapse
|
25
|
The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol 2019; 20:590-607. [PMID: 31399642 DOI: 10.1038/s41580-019-0159-6] [Citation(s) in RCA: 1054] [Impact Index Per Article: 210.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.
Collapse
|
26
|
Being in a loop: how long non-coding RNAs organise genome architecture. Essays Biochem 2019; 63:177-186. [DOI: 10.1042/ebc20180057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Abstract
Chromatin architecture has a significant impact on gene expression. Evidence in the last two decades support RNA as an important component of chromatin structure [Genes Dev. (2005) 19, 1635–1655; PLoS ONE (2007) 2, e1182; Nat. Genet. (2002) 30, 329–334]. Long non-coding RNAs (lncRNAs) are able to control chromatin structure through nucleosome positioning, interaction with chromatin re-modellers and chromosome looping. These functions are carried out in cis at the site of lncRNAs transcription or in trans at distant loci. While the evidence for a role in lncRNAs in regulating gene expression through chromatin interactions is increasing, there is still very little conclusive evidence for a potential role in looping organisation. Here, we review models for the involvement of lncRNAs in genome architecture and the experimental evidence to support them.
Collapse
|
27
|
Thamban T, Sowpati DT, Pai V, Nithianandam V, Abe T, Shioi G, Mishra RK, Khosla S. The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene. Epigenomics 2019; 11:251-266. [DOI: 10.2217/epi-2018-0060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Aim: To investigate the regulatory potential of the Nnat second intron within the Nnat/Blcap micro-imprinted domain. Materials & methods: Mice with deletion of Nnat second intron at the endogenous Nnat/Blcap micro-imprinted domain were used to examine the effect of Nnat second intron on the transcriptional regulation of the Nnat and Blcap genes. Results & conclusion: Deletion of Nnat second intron affected Nnat expression in cis leading to the loss of Nnat expression from the active paternal allele. Nnat second intron was found to have the characteristics of an imprint control region including allele-specific DNA methylation and histone modifications and it also regulated the epigenetic profile of Nnat promoter by acting as an enhancer. Nnat second intron was also found to be regulating the expression of the Blcap transcripts.
Collapse
Affiliation(s)
- Thushara Thamban
- Laboratory of Mammalian Genetics, Centre for DNA Fingerprinting & Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad, India
- Graduate studies, Manipal University, Manipal, India
| | - Divya Tej Sowpati
- Laboratory of Mammalian Genetics, Centre for DNA Fingerprinting & Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad, India
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research (CSIR), Uppal Road, Hyderabad, India
| | - Vaishnavo Pai
- Laboratory of Mammalian Genetics, Centre for DNA Fingerprinting & Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad, India
| | - Vanitha Nithianandam
- Laboratory of Mammalian Genetics, Centre for DNA Fingerprinting & Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad, India
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Takaya Abe
- Laboratory for Animal Resources & Genetic Engineering, RIKEN Center for Developmental Biology, 2-2-3 Minatojima Minami, Chuou-ku, Kobe 650-0047, Japan
| | - Go Shioi
- Laboratory for Animal Resources & Genetic Engineering, RIKEN Center for Developmental Biology, 2-2-3 Minatojima Minami, Chuou-ku, Kobe 650-0047, Japan
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research (CSIR), Uppal Road, Hyderabad, India
| | - Sanjeev Khosla
- Laboratory of Mammalian Genetics, Centre for DNA Fingerprinting & Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad, India
| |
Collapse
|
28
|
Ji M, Wang X, Wu W, Guan Y, Liu J, Wang J, Liu W, Shen C. ART manipulation after controlled ovarian stimulation may not increase the risk of abnormal expression and DNA methylation at some CpG sites of H19,IGF2 and SNRPN in foetuses: a pilot study. Reprod Biol Endocrinol 2018; 16:63. [PMID: 29976200 PMCID: PMC6034287 DOI: 10.1186/s12958-018-0344-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/08/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND To examine the effects of IVF, ICSI and FET, as well as in vitro culture, on the safety of offspring, this study was conducted from the perspective of genetic imprinting to investigate whether assisted reproductive technology would influence the parental and maternal imprinting genes. METHODS Eighteen foetuses were collected from multifoetal reduction and divided into 6 groups: multifoetal reduction after IVF fresh transferred D3 embryos (n = 3), multifoetal reduction after IVF frozen transferred D3 embryos (n = 3), multifoetal reduction after IVF frozen transferred D5 embryos (n = 3), multifoetal reduction after ICSI fresh transferred D3 embryos (n = 3), multifoetal reduction after ICSI frozen transferred D3 embryos (n = 3), and multifoetal reduction after controlled ovarian hyperstimulation (COH) (n = 3). The imprinted genes H19, IGF2 and SNRPN were selected for analysis. The expression and DNA methylation at some CpG sites of H19, IGF2, and SNRPN were examined using real-time quantitative polymerase chain reaction (PCR) and pyrosequencing. RESULTS There were no significant differences in the mRNA expression levels among the groups. The mean percentage of H19 methylation (eight CpG sites), IGF2 methylation (five CpG sites) and SNRPN methylation (nine CpG sites) did not differ significantly. CONCLUSIONS The results suggest that ARTs after controlled ovarian stimulation (IVF, ICSI, cryopreservation and duration of in vitro culture) may not increase the risk of abnormal expression and DNA methylation at some CpG sites of H19, IGF2 and SNRPN in foetuses. Further study with strict design, expanded sample size and CpG sites is essential.
Collapse
Affiliation(s)
- Menglu Ji
- grid.412719.8Department of Reproductive Medical Center, Third Affiliated Hospital of Zhengzhou University, 7 Kangfuqian Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Xingling Wang
- grid.412719.8Department of Reproductive Medical Center, Third Affiliated Hospital of Zhengzhou University, 7 Kangfuqian Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Wenbin Wu
- grid.412719.8Department of Reproductive Medical Center, Third Affiliated Hospital of Zhengzhou University, 7 Kangfuqian Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Yichun Guan
- grid.412719.8Department of Reproductive Medical Center, Third Affiliated Hospital of Zhengzhou University, 7 Kangfuqian Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Jing Liu
- grid.412719.8Department of Reproductive Medical Center, Third Affiliated Hospital of Zhengzhou University, 7 Kangfuqian Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Jingyan Wang
- grid.412719.8Department of Reproductive Medical Center, Third Affiliated Hospital of Zhengzhou University, 7 Kangfuqian Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Wenxia Liu
- grid.412719.8Department of Reproductive Medical Center, Third Affiliated Hospital of Zhengzhou University, 7 Kangfuqian Road, Zhengzhou, 450052 Henan People’s Republic of China
| | - Chunyan Shen
- grid.412719.8Department of Reproductive Medical Center, Third Affiliated Hospital of Zhengzhou University, 7 Kangfuqian Road, Zhengzhou, 450052 Henan People’s Republic of China
| |
Collapse
|
29
|
Kochmanski JJ, Marchlewicz EH, Cavalcante RG, Perera BPU, Sartor MA, Dolinoy DC. Longitudinal Effects of Developmental Bisphenol A Exposure on Epigenome-Wide DNA Hydroxymethylation at Imprinted Loci in Mouse Blood. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:077006. [PMID: 30044229 PMCID: PMC6108846 DOI: 10.1289/ehp3441] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Epigenetic machinery plays an important role in genomic imprinting, a developmental process that establishes parent-of-origin-specific monoallelic gene expression. Although a number of studies have investigated the role of 5-methylcytosine in imprinting control, the contribution of 5-hydroxymethylcytosine (5-hmC) to this epigenetic phenomenon remains unclear. OBJECTIVES Using matched mouse blood samples (from mice at 2, 4, and 10 months of age), our objective was to examine the effects of perinatal bisphenol A (BPA) exposure (50 μg/kg diet) on longitudinal 5-hmC patterns at imprinted regions. We also aimed to test the hypothesis that 5-hmC would show defined patterns at imprinted genes that persist across the life course. METHODS Genome-wide 5-hmC levels were measured using hydroxymethylated DNA immunoprecipitation sequencing (HMeDIP-seq). Modeling of differential hydroxymethylation by BPA exposure was performed using a pipeline of bioinformatics tools, including the csaw R package. RESULTS Based on BPA exposure, we identified 5,950 differentially hydroxymethylated regions (DHMRs), including 12 DHMRs that were annotated to murine imprinted genes—Gnas, Grb10, Plagl1, Klf14, Pde10a, Snrpn, Airn, Cmah, Ppp1r9a, Kcnq1, Phactr2, and Pde4d. When visualized, these imprinted gene DHMRs showed clear, consistent patterns of differential 5-hmC by developmental BPA exposure that persisted throughout adulthood. CONCLUSIONS These data show long-term establishment of 5-hmC marks at imprinted loci during development. Further, the effect of perinatal BPA exposure on 5-hmC at specific imprinted loci indicates that developmental exposure to environmental toxicants may alter long-term imprinted gene regulation via an epigenetic mechanism. https://doi.org/10.1289/EHP3441.
Collapse
Affiliation(s)
- Joseph J Kochmanski
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Elizabeth H Marchlewicz
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| |
Collapse
|
30
|
Chu X, Zhu Y, Wang O, Nie M, Quan T, Xue Y, Wang W, Jiang Y, Li M, Xia W, Xing X. Clinical and genetic characteristics of Pseudohypoparathyroidism in the Chinese population. Clin Endocrinol (Oxf) 2018; 88:285-294. [PMID: 29136292 DOI: 10.1111/cen.13516] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/03/2017] [Accepted: 11/04/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Pseudohypoparathyroidism (PHP) is caused by mutations and epimutations in the GNAS locus, and characterized by the possibility of resistance to multiple hormones and Albright's hereditary osteodystrophy. PHP can be classified into the forms 1A/C, sporadic 1B and familial 1B. OBJECTIVES To obtain an overall view of the clinical and genetic characteristics of the Chinese PHP patient population. METHODS From 2000 to 2016, 120 patients were recruited and studied using Sanger sequencing, methylation-specific multiple ligation-dependent probe amplification (MS-MLPA) and combined bisulfite restriction analysis (COBRA). Of these patients, 104 had positive molecular alterations indicative of certain forms of PHP and were included in data analysis. Clinical and laboratory features were compared between PHP1A/C and PHP1B patients. RESULTS Ten PHP1A/C, 21 familial PHP1B and 73 sporadic PHP1B patients were identified. Four novel GNAS mutations were discovered in these patients, including c.1038+1G>T, c.530+2T>C, c.880_883delCAAG and c.311_312delAAG, insT. The most common symptoms in this series were recurrent tetany (89.4%) and epilepsy (47.1%). The prevalence of weight excess increased with age for PHP1B (10%-35%) and PHP1A/C (50%-75%). Intracranial calcification had a prevalence of 94.6% and correlated with seizures (r = .227, P = .029). Cataracts occurred in 56.2% PHP patients, and there was a trend towards longer disease duration in patients with cataracts (P = .051). Statistically significant differences (P < .05) were observed when comparing certain clinical characteristics between PHP1B and PHP1A/C patients, including age of onset (10 vs 7 year), short stature (21.3% vs 70%), rounded face (60.6% vs 100%), brachydactyly (25.5% vs 100%), ectopic ossification (1.1% vs 40%) and TSH resistance (44.6% vs 90%), respectively. CONCLUSIONS This study is the largest single-centre series of PHP patients and summarizes the clinical and genetic features of the Chinese PHP population. While there was substantial clinical overlap between PHP1A/C and PHP1B, differences in disease progression were observed.
Collapse
Affiliation(s)
- Xueying Chu
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Yan Zhu
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Ou Wang
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Min Nie
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Tingting Quan
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Yu Xue
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Wenbo Wang
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Yan Jiang
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Mei Li
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Weibo Xia
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Xiaoping Xing
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| |
Collapse
|
31
|
Luu PL, Gerovska D, Schöler HR, Araúzo-Bravo MJ. Rules governing the mechanism of epigenetic reprogramming memory. Epigenomics 2018; 10:149-174. [PMID: 29334780 DOI: 10.2217/epi-2017-0098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AIM Disclosing the mechanisms that regulate reprogramming memory. MATERIALS & METHODS We established computational procedure to find DNA methylation somatic memory sites (SMSs) at single CpGs and integrated them with genomics, epigenomics, transcriptomics and imprinting information. RESULTS & CONCLUSION Reprogramming memory persists at late passages in low methylated regions. Contrarily to hypomethylated, hypermethylated SMSs occur at evolutionary conserved sites overlapping active transcription loci in dynamic chromatin regions. The epigenetic-memory molecular origin is the expression of source-cell transcription factors protecting hypomethylated SMSs in euchromatin from de novo methylation, keeping source-cell lineage-specific loci in induced pluripotent stem (iPS) cells incompletely silenced. Sites in lineage-specific genes of different-from-those-of-the-source-cell lineages remain hypermethylated in heterochromatin regions becoming permanently silenced. SMSs cause differential expression between iPS cells and embryonic stem cells through two mechanisms: 'epigenetic/expression memory rule', the DNA unreprogramming methylation status coupled with chromatin states induces differentially expressed genes. 'Imprinting control', the change of DNA methylation status in imprinting control regions induces differential expression of imprinted genes.
Collapse
Affiliation(s)
- Phuc-Loi Luu
- Computational Biology & Bioinformatics Group, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Daniela Gerovska
- Group of Computational Biology & Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
| | - Hans R Schöler
- Department of Cell & Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.,Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Marcos J Araúzo-Bravo
- Computational Biology & Bioinformatics Group, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.,Group of Computational Biology & Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| |
Collapse
|
32
|
Wang L, Chang S, Wang Z, Wang S, Huo J, Ding G, Li R, Liu C, Shangguan S, Lu X, Zhang T, Qiu Z, Wu J. Altered GNAS imprinting due to folic acid deficiency contributes to poor embryo development and may lead to neural tube defects. Oncotarget 2017; 8:110797-110810. [PMID: 29340017 PMCID: PMC5762285 DOI: 10.18632/oncotarget.22731] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/29/2017] [Indexed: 01/28/2023] Open
Abstract
Disturbed epigenetic modifications have been linked to the pathogenesis of Neural Tube Defects (NTDs) in those with folate deficiency during pregnancy. However, evidence is lacking to delineate the critical region in epigenome regulated by parental folic acid and mechanisms by which folate deficiency affects normal embryogenesis. Our data from clinical samples revealed the presence of aberrant DNA methylation in GNAS imprinting cluster in NTD samples with low folate concentrations. Results from mouse models indicated that the establishment of GNAS imprinting was influenced by both maternal and paternal folate-deficient diets. Such aberrant GNAS imprinting was present prior to the gametogenesis period. Imprinting in Exon1A/GNAS gDMR was abolished in both spermatozoa and oocytes upon treating with a parental folate-deficient diet (3.6% in spermatozoa, 9.8% in oocytes). Interestingly, loss of imprinting in the GNAS gene cluster altered chromatin structure to an overwhelmingly open structure (58.48% in the folate-free medium group vs. 39.51% in the folate-normal medium group; P < 0.05), and led to a disturbed expression of genes in this region. Furthermore, an elevated cyclic AMP levels was observed in folate acid deficiency group. Our results imply that GNAS imprinting plays major roles in folic acid metabolism regulation during embryogenesis. Aberrant GNAS imprinting is an attribute to NTDs, providing a new perspective for explaining the molecular mechanisms by which folate supplementation in human pregnancy provides protection from NTDs.
Collapse
Affiliation(s)
- Li Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Zhen Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Junsheng Huo
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing, P.R. China
| | - Gangqiang Ding
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing, P.R. China
| | - Rui Li
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Chi Liu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Shaofang Shangguan
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Xiaolin Lu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Zhiyong Qiu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Jianxin Wu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, P.R. China
| |
Collapse
|
33
|
Lozano-Ureña A, Montalbán-Loro R, Ferguson-Smith AC, Ferrón SR. Genomic Imprinting and the Regulation of Postnatal Neurogenesis. Brain Plast 2017; 3:89-98. [PMID: 29765862 PMCID: PMC5928554 DOI: 10.3233/bpl-160041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Most genes required for mammalian development are expressed from both maternally and paternally inherited chromosomal homologues. However, there are a small number of genes known as “imprinted genes” that only express a single allele from one parent, which is repressed on the gene from the other parent. Imprinted genes are dependent on epigenetic mechanisms such as DNA methylation and post-translational modifications of the DNA-associated histone proteins to establish and maintain their parental identity. In the brain, multiple transcripts have been identified which show parental origin-specific expression biases. However, the mechanistic relationship with canonical imprinting is unknown. Recent studies on the postnatal neurogenic niches raise many intriguing questions concerning the role of genomic imprinting and gene dosage during postnatal neurogenesis, including how imprinted genes operate in concert with signalling cues to contribute to newborn neurons’ formation during adulthood. Here we have gathered the current knowledge on the imprinting process in the neurogenic niches. We also review the phenotypes associated with genetic mutations at particular imprinted loci in order to consider the impact of imprinted genes in the maintenance and/or differentiation of the neural stem cell pool in vivo and during brain tumour formation.
Collapse
Affiliation(s)
- Anna Lozano-Ureña
- ERI BiotecMed Departamento de Biología Celular, Universidad de Valencia, Spain
| | | | | | - Sacri R Ferrón
- ERI BiotecMed Departamento de Biología Celular, Universidad de Valencia, Spain
| |
Collapse
|
34
|
Patten MM, Cowley M, Oakey RJ, Feil R. Regulatory links between imprinted genes: evolutionary predictions and consequences. Proc Biol Sci 2017; 283:rspb.2015.2760. [PMID: 26842569 PMCID: PMC4760173 DOI: 10.1098/rspb.2015.2760] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.
Collapse
Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, DC 20057, USA
| | - Michael Cowley
- Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Robert Feil
- Centre National de Recherche Scientifique (CNRS), Institute of Molecular Genetics (IGMM), 1919 route de Mende, Montpellier 34293, France University of Montpellier, 163 rue Auguste Broussonnet, Montpellier 34090, France Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
35
|
Long non-coding RNAs: Mechanism of action and functional utility. Noncoding RNA Res 2016; 1:43-50. [PMID: 30159410 PMCID: PMC6096411 DOI: 10.1016/j.ncrna.2016.11.002] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 12/22/2022] Open
Abstract
Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs) are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA), small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs) are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological and pathological processes. LncRNAs are dysfunctional in a variety of human diseases varying from cancerous to non-cancerous diseases. Characterization of these lncRNA genes and their modes of action may allow their use for diagnosis, monitoring of progression and targeted therapies in various diseases. In this review, we summarize the functional perspectives as well as the mechanism of action of lncRNAs.
Collapse
|
36
|
Takatani R, Molinaro A, Grigelioniene G, Tafaj O, Watanabe T, Reyes M, Sharma A, Singhal V, Raymond FL, Linglart A, Jüppner H. Analysis of Multiple Families With Single Individuals Affected by Pseudohypoparathyroidism Type Ib (PHP1B) Reveals Only One Novel Maternally Inherited GNAS Deletion. J Bone Miner Res 2016; 31:796-805. [PMID: 26479409 PMCID: PMC4826817 DOI: 10.1002/jbmr.2731] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/05/2015] [Accepted: 10/12/2015] [Indexed: 01/22/2023]
Abstract
Proximal tubular resistance to parathyroid hormone (PTH) resulting in hypocalcemia and hyperphosphatemia are preeminent abnormalities in pseudohypoparathyroidism type Ib (PHP1B), but resistance toward other hormones as well as variable features of Albright's Hereditary Osteodystrophy (AHO) can occur also. Genomic DNA from PHP1B patients shows epigenetic changes at one or multiple differentially methylated regions (DMRs) within GNAS, the gene encoding Gαs and splice variants thereof. In the autosomal dominant disease variant, these methylation abnormalities are caused by deletions in STX16 or GNAS on the maternal allele. The molecular defect(s) leading to sporadic PHP1B (sporPHP1B) remains in most cases unknown and we therefore analyzed 60 sporPHP1B patients and available family members by microsatellite markers, single nucleotide polymorphisms (SNPs), multiplex ligation-dependent probe amplification (MLPA), and methylation-specific MLPA (MS-MLPA). All investigated cases revealed broad GNAS methylation changes, but no evidence for inheritance of two paternal chromosome 20q alleles. Some patients with partial epigenetic modifications in DNA from peripheral blood cells showed more complete GNAS methylation changes when testing their immortalized lymphoblastoid cells. Analysis of siblings and children of sporPHP1B patients provided no evidence for an abnormal mineral ion regulation and no changes in GNAS methylation. Only one patient revealed, based on MLPA and microsatellite analyses, evidence for an allelic loss, which resulted in the discovery of two adjacent, maternally inherited deletions (37,597 and 1427 bp, respectively) that remove the area between GNAS antisense exons 3 and 5, including exon NESP. Our findings thus emphasize that the region comprising antisense exons 3 and 4 is required for establishing all maternal GNAS methylation imprints. The genetic defect(s) leading in sporPHP1B to epigenetic GNAS changes and thus PTH-resistance remains unknown, but it seems unlikely that this disease variant is caused by heterozygous inherited or de novo mutations involving GNAS.
Collapse
Affiliation(s)
- Rieko Takatani
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Angelo Molinaro
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Giedre Grigelioniene
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Olta Tafaj
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tomoyuki Watanabe
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Monica Reyes
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Amita Sharma
- Pediatric Nephrology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Vibha Singhal
- Pediatric Endocrinology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Lucy Raymond
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Agnès Linglart
- Paediatric Endocrinology and Diabetology, French National Reference Centre for Rare Disorders of Mineral Metabolism, AP-HP Hôpital Bicêtre Paris Sud, le Kremlin-Bicêtre, France
- Faculté de Médecine, Université Paris Sud, le Kremlin-Bicêtre, France
| | - Harald Jüppner
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Nephrology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| |
Collapse
|
37
|
Tibbit CJ, Williamson CM, Mehta S, Ball ST, Chotalia M, Nottingham WT, Eaton SA, Quwailid MM, Teboul L, Kelsey G, Peters J. Antisense Activity across the Nesp Promoter is Required for Nespas-Mediated Silencing in the Imprinted Gnas Cluster. Noncoding RNA 2015; 1:246-265. [PMID: 29861426 PMCID: PMC5932550 DOI: 10.3390/ncrna1030246] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/17/2015] [Accepted: 11/17/2015] [Indexed: 12/03/2022] Open
Abstract
Macro long non-coding RNAs (lncRNAs) play major roles in gene silencing in inprinted gene clusters. Within the imprinted Gnas cluster, the paternally expressed Nespas lncRNA downregulates its sense counterpart Nesp. To explore the mechanism of action of Nespas, we generated two new knock-in alleles to truncate Nespas upstream and downstream of the Nesp promoter. We show that Nespas is essential for methylation of the Nesp differentially methylated region (DMR), but higher levels of Nespas are required for methylation than are needed for downregulation of Nesp. Although Nespas is transcribed for over 27 kb, only Nespas transcript/transcription across a 2.6 kb region that includes the Nesp promoter is necessary for methylation of the Nesp DMR. In both mutants, the levels of Nespas were extraordinarily high, due at least in part to increased stability, an effect not seen with other imprinted lncRNAs. However, even when levels were greatly raised, Nespas remained exclusively cis-acting. We propose Nespas regulates Nesp methylation and expression to ensure appropriate levels of expression of the protein coding transcripts Gnasxl and Gnas on the paternal chromosome. Thus, Nespas mediates paternal gene expression over the entire Gnas cluster via a single gene, Nesp.
Collapse
Affiliation(s)
- Charlotte J Tibbit
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: MRC Functional Genomics Unit, Department of Physiology Anatomy & Genetics, Le Gros Clark Building, University of Oxford, South Parks Road, Oxford OX13QX, UK.
| | - Christine M Williamson
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current Address: MRC Harwell, Harwell Campus, Oxfordshire OX110RD, UK.
| | - Stuti Mehta
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: GI Division, Their 340, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Simon T Ball
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire OX110RD, UK.
| | - Mita Chotalia
- Epigenetics Programme, The Babraham Institute, Cambridge CB223AT, UK.
- Current address: Genome Function Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, London W120NN, UK.
| | - Wade T Nottingham
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: West London Free School, 2 Bridge Avenue, Hammersmith, London W69JP, UK.
| | - Sally A Eaton
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
- Current address: Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.
| | - Mohamed M Quwailid
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
| | - Lydia Teboul
- Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire OX110RD, UK.
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge CB223AT, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB23EG, UK.
| | - Jo Peters
- MRC Harwell, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX110RD, UK.
| |
Collapse
|
38
|
Tammen SA, Park LK, Dolnikowski GG, Ausman LM, Friso S, Choi SW. Hepatic DNA hydroxymethylation is site-specifically altered by chronic alcohol consumption and aging. Eur J Nutr 2015; 56:535-544. [PMID: 26578530 DOI: 10.1007/s00394-015-1098-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 11/04/2015] [Indexed: 01/03/2023]
Abstract
PURPOSE Global DNA hydroxymethylation is markedly decreased in human cancers, including hepatocellular carcinoma, which is associated with chronic alcohol consumption and aging. Because gene-specific changes in hydroxymethylcytosine may affect gene transcription, giving rise to a carcinogenic environment, we determined genome-wide site-specific changes in hepatic hydroxymethylcytosine that are associated with chronic alcohol consumption and aging. METHODS Young (4 months) and old (18 months) male C57Bl/6 mice were fed either an ethanol-containing Lieber-DeCarli liquid diet or an isocaloric control diet for 5 weeks. Genomic and gene-specific hydroxymethylcytosine patterns were determined through hydroxymethyl DNA immunoprecipitation array in hepatic DNA. RESULTS Hydroxymethylcytosine patterns were more perturbed by alcohol consumption in young mice than in old mice (431 differentially hydroxymethylated regions, DhMRs, in young vs 189 DhMRs in old). A CpG island ~2.5 kb upstream of the glucocorticoid receptor gene, Nr3c1, had increased hydroxymethylation as well as increased mRNA expression (p = 0.015) in young mice fed alcohol relative to the control group. Aging alone also altered hydroxymethylcytosine patterns, with 331 DhMRs, but alcohol attenuated this effect. Aging was associated with a decrease in hydroxymethylcytosine ~1 kb upstream of the leptin receptor gene, Lepr, and decreased transcription of this gene (p = 0.029). Nr3c1 and Lepr are both involved in hepatic lipid homeostasis and hepatosteatosis, which may create a carcinogenic environment. CONCLUSIONS These results suggest that the location of hydroxymethylcytosine in the genome is site specific and not random, and that changes in hydroxymethylation may play a role in the liver's response to aging and alcohol.
Collapse
Affiliation(s)
- Stephanie A Tammen
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA.,Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Lara K Park
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA.,Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Gregory G Dolnikowski
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA.,Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Lynne M Ausman
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA.,Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | | | - Sang-Woon Choi
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA. .,Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA. .,Chaum Life Center, CHA University School of Medicine, 442, Dosan-daero, Gangnam-gu, Seoul, 135-948, Korea.
| |
Collapse
|
39
|
Abstract
The GNAS complex locus encodes the alpha-subunit of the stimulatory G protein (Gsα), a ubiquitous signaling protein mediating the actions of many hormones, neurotransmitters, and paracrine/autocrine factors via generation of the second messenger cAMP. GNAS gives rise to other gene products, most of which exhibit exclusively monoallelic expression. In contrast, Gsα is expressed biallelically in most tissues; however, paternal Gsα expression is silenced in a small number of tissues through as-yet-poorly understood mechanisms that involve differential methylation within GNAS. Gsα-coding GNAS mutations that lead to diminished Gsα expression and/or function result in Albright's hereditary osteodystrophy (AHO) with or without hormone resistance, i.e., pseudohypoparathyroidism type-Ia/Ic and pseudo-pseudohypoparathyroidism, respectively. Microdeletions that alter GNAS methylation and, thereby, diminish Gsα expression in tissues in which the paternal Gsα allele is normally silenced also cause hormone resistance, which occurs typically in the absence of AHO, a disorder termed pseudohypoparathyroidism type-Ib. Mutations of GNAS that cause constitutive Gsα signaling are found in patients with McCune-Albright syndrome, fibrous dysplasia of bone, and different endocrine and non-endocrine tumors. Clinical features of these diseases depend significantly on the parental allelic origin of the GNAS mutation, reflecting the tissue-specific paternal Gsα silencing. In this article, we review the pathogenesis and the phenotypes of these human diseases.
Collapse
Affiliation(s)
- Serap Turan
- Pediatric Endocrinology, Marmara University School of Medicine Hospital, Istanbul, Turkey;
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114;
| |
Collapse
|
40
|
Strogantsev R, Krueger F, Yamazawa K, Shi H, Gould P, Goldman-Roberts M, McEwen K, Sun B, Pedersen R, Ferguson-Smith AC. Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression. Genome Biol 2015; 16:112. [PMID: 26025256 PMCID: PMC4491874 DOI: 10.1186/s13059-015-0672-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/11/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Selective maintenance of genomic epigenetic imprints during pre-implantation development is required for parental origin-specific expression of imprinted genes. The Kruppel-like zinc finger protein ZFP57 acts as a factor necessary for maintaining the DNA methylation memory at multiple imprinting control regions in early mouse embryos and embryonic stem (ES) cells. Maternal-zygotic deletion of ZFP57 in mice presents a highly penetrant phenotype with no animals surviving to birth. Additionally, several cases of human transient neonatal diabetes are associated with somatic mutations in the ZFP57 coding sequence. RESULTS Here, we comprehensively map sequence-specific ZFP57 binding sites in an allele-specific manner using hybrid ES cell lines from reciprocal crosses between C57BL/6J and Cast/EiJ mice, assigning allele specificity to approximately two-thirds of all binding sites. While half of these are biallelic and include endogenous retrovirus (ERV) targets, the rest show monoallelic binding based either on parental origin or on genetic background of the allele. Parental-origin allele-specific binding is methylation-dependent and maps only to imprinting control differentially methylated regions (DMRs) established in the germline. We identify a novel imprinted gene, Fkbp6, which has a critical function in mouse male germ cell development. Genetic background-specific sequence differences also influence ZFP57 binding, as genetic variation that disrupts the consensus binding motif and its methylation is often associated with monoallelic expression of neighboring genes. CONCLUSIONS The work described here uncovers further roles for ZFP57-mediated regulation of genomic imprinting and identifies a novel mechanism for genetically determined monoallelic gene expression.
Collapse
Affiliation(s)
- Ruslan Strogantsev
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3EG, UK. .,Present address: Epigenetics ISP, Babraham Institute, Cambridge, CB22 3AT, UK.
| | - Felix Krueger
- Bioinformatics Department, Babraham Institute, Cambridge, CB22 3AT, UK.
| | - Kazuki Yamazawa
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3EG, UK.
| | - Hui Shi
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3EG, UK.
| | - Poppy Gould
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3EG, UK.
| | - Megan Goldman-Roberts
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3EG, UK.
| | - Kirsten McEwen
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3EG, UK.
| | - Bowen Sun
- The Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK.
| | - Roger Pedersen
- The Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK.
| | - Anne C Ferguson-Smith
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3EG, UK. .,Present address: Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
| |
Collapse
|
41
|
Kanduri C. Long noncoding RNAs: Lessons from genomic imprinting. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:102-11. [PMID: 26004516 DOI: 10.1016/j.bbagrm.2015.05.006] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/12/2015] [Accepted: 05/15/2015] [Indexed: 12/17/2022]
Abstract
Genomic imprinting has been a great resource for studying transcriptional and post-transcriptional-based gene regulation by long noncoding RNAs (lncRNAs). In this article, I overview the functional role of intergenic lncRNAs (H19, IPW, and MEG3), antisense lncRNAs (Kcnq1ot1, Airn, Nespas, Ube3a-ATS), and enhancer lncRNAs (IG-DMR eRNAs) to understand the diverse mechanisms being employed by them in cis and/or trans to regulate the parent-of-origin-specific expression of target genes. Recent evidence suggests that some of the lncRNAs regulate imprinting by promoting intra-chromosomal higher-order chromatin compartmentalization, affecting replication timing and subnuclear positioning. Whereas others act via transcriptional occlusion or transcriptional collision-based mechanisms. By establishing genomic imprinting of target genes, the lncRNAs play a critical role in important biological functions, such as placental and embryonic growth, pluripotency maintenance, cell differentiation, and neural-related functions such as synaptic development and plasticity. An emerging consensus from the recent evidence is that the imprinted lncRNAs fine-tune gene expression of the protein-coding genes to maintain their dosage in cell. Hence, lncRNAs from imprinted clusters offer insights into their mode of action, and these mechanisms have been the basis for uncovering the mode of action of lncRNAs in several other biological contexts. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
Collapse
Affiliation(s)
- Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden.
| |
Collapse
|
42
|
Anifandis G, Messini CI, Dafopoulos K, Messinis IE. Genes and Conditions Controlling Mammalian Pre- and Post-implantation Embryo Development. Curr Genomics 2015; 16:32-46. [PMID: 25937812 PMCID: PMC4412963 DOI: 10.2174/1389202916666141224205025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/20/2014] [Accepted: 12/23/2014] [Indexed: 01/06/2023] Open
Abstract
Embryo quality during the in vitro developmental period is of great clinical importance. Experimental genetic studies during this period have demonstrated the association between specific gene expression profiles and the production of healthy blastocysts. Although the quality of the oocyte may play a major role in embryo development, it has been well established that the post - fertilization period also has an important and crucial role in the determination of blastocyst quality. A variety of genes (such as OCT, SOX2, NANOG) and their related signaling pathways as well as transcription molecules (such as TGF-β, BMP) have been implicated in the pre- and post-implantation period. Furthermore, DNA methylation has been lately characterized as an epigenetic mark since it is one of the most important processes involved in the maintenance of genome stability. Physiological embryo development appears to depend upon the correct DNA methylation pattern. Due to the fact that soon after fertilization the zygote undergoes several morphogenetic and developmental events including activation of embryonic genome through the transition of the maternal genome, a diverse gene expression pattern may lead to clinically important conditions, such as apoptosis or the production of a chromosomically abnormal embryo. The present review focused on genes and their role during pre-implantation embryo development, giving emphasis on the various parameters that may alter gene expression or DNA methylation patterns. The pre-implantation embryos derived from in vitro culture systems (in vitro fertilization) and the possible effects on gene expression after the prolonged culture conditions are also discussed.
Collapse
Affiliation(s)
- G Anifandis
- Department of Obstetrics and Gynaecology ; Embryology Lab, University of Thessalia, School of Health Sciences, Faculty of Medicine, Larisa, Greece
| | | | | | | |
Collapse
|
43
|
Mantovani G, Elli FM. Pseudohypoparathyroidism type Ib in 2015. ANNALES D'ENDOCRINOLOGIE 2015; 76:101-4. [PMID: 25910998 DOI: 10.1016/j.ando.2015.03.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/11/2015] [Indexed: 10/23/2022]
Abstract
The term pseudohypoparathryoidism (PHP) refers to a group of rare genetic and epigenetic disorders characterized by resistance to the action of parathyroid hormone (PTH) that activates cAMP signaling in target cells. Together with pseudohypoparathyroidism, Albright hereditary osteodystrophy (AHO) and progressive osseous heteroplasia (POH) represent rare, related and deeply impairing disorders encompassing heterogeneous features, such as brachydactyly, ectopic ossifications, short stature, mental retardation and endocrine deficiencies due to resistance to the action of different hormones. The two main subtypes, PHP-Ia and PHP-Ib, are caused by mutations in GNAS exons 1-13 and methylation defects in the imprinted GNAS cluster respectively, while mutations in the PRKAR1A and PDE4D genes (also involved in mediating cAMP signalling) have been demonstrated in patients with acrodysostosis, a disease of bone formation with characteristics similar to AHO. The molecular overlap among these disorders indicates the need for different classification models and seriously alters our understanding of the mechanisms through which GNAS defects, together with the new recently described defects involving other components of the cAMP signalling cascade, cause AHO-related disorders.
Collapse
Affiliation(s)
- Giovanna Mantovani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Endocrinology and Diabetology Unit, Department of Clinical Sciences and Community Health, University of Milan, Via F. Sforza, 35, 20122 Milan, Italy.
| | - Francesca M Elli
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Endocrinology and Diabetology Unit, Department of Clinical Sciences and Community Health, University of Milan, Via F. Sforza, 35, 20122 Milan, Italy
| |
Collapse
|
44
|
Mehta S, Williamson CM, Ball S, Tibbit C, Beechey C, Fray M, Peters J. Transcription driven somatic DNA methylation within the imprinted Gnas cluster. PLoS One 2015; 10:e0117378. [PMID: 25659103 PMCID: PMC4319783 DOI: 10.1371/journal.pone.0117378] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/25/2014] [Indexed: 12/14/2022] Open
Abstract
Differential marking of genes in female and male gametes by DNA methylation is essential to genomic imprinting. In female gametes transcription traversing differentially methylated regions (DMRs) is a common requirement for de novo methylation at DMRs. At the imprinted Gnas cluster oocyte specific transcription of a protein-coding transcript, Nesp, is needed for methylation of two DMRs intragenic to Nesp, namely the Nespas-Gnasxl DMR and the Exon1A DMR, thereby enabling expression of the Gnas transcript and repression of the Gnasxl transcript. On the paternal allele, Nesp is repressed, the germline DMRs are unmethylated, Gnas is repressed and Gnasxl is expressed. Using mutant mouse models, we show that on the paternal allele, ectopic transcription of Nesp traversing the intragenic Exon1A DMR (which regulates Gnas expression) results in de novo methylation of the Exon1A DMR and de-repression of Gnas just as on the maternal allele. However, unlike the maternal allele, methylation on the mutant paternal allele occurs post-fertilisation, i.e. in somatic cells. This, to our knowledge is the first example of transcript/transcription driven DNA methylation of an intragenic CpG island, in somatic tissues, suggesting that transcription driven de novo methylation is not restricted to the germline in the mouse. Additionally, Gnasxl is repressed on a paternal chromosome on which Nesp is ectopically expressed. Thus, a paternally inherited Gnas cluster showing ectopic expression of Nesp is “maternalised” in terms of Gnasxl and Gnas expression. We show that these mice have a phenotype similar to mutants with two expressed doses of Gnas and none of Gnasxl.
Collapse
Affiliation(s)
- Stuti Mehta
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, United Kingdom
- * E-mail:
| | - Christine M. Williamson
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, United Kingdom
| | - Simon Ball
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, United Kingdom
| | - Charlotte Tibbit
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, United Kingdom
| | - Colin Beechey
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, United Kingdom
| | - Martin Fray
- Mary Lyon Centre, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, United Kingdom
| | - Jo Peters
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, United Kingdom
| |
Collapse
|
45
|
Varmuza S, Miri K. What does genetics tell us about imprinting and the placenta connection? Cell Mol Life Sci 2015; 72:51-72. [PMID: 25194419 PMCID: PMC11114082 DOI: 10.1007/s00018-014-1714-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 01/07/2023]
Abstract
Genomic imprinting is an epigenetic gene silencing phenomenon that is specific to eutherians in the vertebrate lineage. The acquisition of both placentation and genomic imprinting has spurred interest in the possible evolutionary link for many years. In this review we examine the genetic evidence and find that while many imprinted domains are anchored by genes required for proper placenta development in a parent of origin fashion, an equal number of imprinted genes have no apparent function that depends on imprinting. Examination of recent data from studies of molecular and genetic mechanisms points to a maternal control of the selection and maintenance of imprint marks, reinforcing the importance of the oocyte in the healthy development of the placenta and fetus.
Collapse
Affiliation(s)
- Susannah Varmuza
- Department of Cell and Systems Biology, University of Toronto, 611-25 Harbord Street, Toronto, M5S 3G5, Canada,
| | | |
Collapse
|
46
|
de Araújo E, Vasques L, Stabellini R, Krepischi A, Pereira L. Stability of XIST repression in relation to genomic imprinting following global genome demethylation in a human cell line. Braz J Med Biol Res 2014; 47:1029-35. [PMID: 25387668 PMCID: PMC4244667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/27/2014] [Indexed: 12/16/2023] Open
Abstract
DNA methylation is essential in X chromosome inactivation and genomic imprinting, maintaining repression of XIST in the active X chromosome and monoallelic repression of imprinted genes. Disruption of the DNA methyltransferase genes DNMT1 and DNMT3B in the HCT116 cell line (DKO cells) leads to global DNA hypomethylation and biallelic expression of the imprinted gene IGF2 but does not lead to reactivation of XIST expression, suggesting that XIST repression is due to a more stable epigenetic mark than imprinting. To test this hypothesis, we induced acute hypomethylation in HCT116 cells by 5-aza-2'-deoxycytidine (5-aza-CdR) treatment (HCT116-5-aza-CdR) and compared that to DKO cells, evaluating DNA methylation by microarray and monitoring the expression of XIST and imprinted genes IGF2, H19, and PEG10. Whereas imprinted genes showed biallelic expression in HCT116-5-aza-CdR and DKO cells, the XIST locus was hypomethylated and weakly expressed only under acute hypomethylation conditions, indicating the importance of XIST repression in the active X to cell survival. Given that DNMT3A is the only active DNMT in DKO cells, it may be responsible for ensuring the repression of XIST in those cells. Taken together, our data suggest that XIST repression is more tightly controlled than genomic imprinting and, at least in part, is due to DNMT3A.
Collapse
Affiliation(s)
- E.S.S. de Araújo
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São
Paulo, SP, Brasil
| | - L.R. Vasques
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
| | - R. Stabellini
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São
Paulo, SP, Brasil
| | - A.C.V. Krepischi
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São
Paulo, SP, Brasil
| | - L.V. Pereira
- Departamento de Genética e Biologia Evolutiva, Instituto de
Biociências, Universidade de São Paulo, São Paulo, SP,
Brasil
| |
Collapse
|
47
|
Xiang R, Lee AMC, Eindorf T, Javadmanesh A, Ghanipoor-Samami M, Gugger M, Fitzsimmons CJ, Kruk ZA, Pitchford WS, Leviton AJ, Thomsen DA, Beckman I, Anderson GI, Burns BM, Rutley DL, Xian CJ, Hiendleder S. Widespread differential maternal and paternal genome effects on fetal bone phenotype at mid-gestation. J Bone Miner Res 2014; 29:2392-404. [PMID: 24753181 DOI: 10.1002/jbmr.2263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 03/09/2014] [Accepted: 04/03/2014] [Indexed: 11/06/2022]
Abstract
Parent-of-origin-dependent (epi)genetic factors are important determinants of prenatal development that program adult phenotype. However, data on magnitude and specificity of maternal and paternal genome effects on fetal bone are lacking. We used an outbred bovine model to dissect and quantify effects of parental genomes, fetal sex, and nongenetic maternal effects on the fetal skeleton and analyzed phenotypic and molecular relationships between fetal muscle and bone. Analysis of 51 bone morphometric and weight parameters from 72 fetuses recovered at day 153 gestation (54% term) identified six principal components (PC1-6) that explained 80% of the variation in skeletal parameters. Parental genomes accounted for most of the variation in bone wet weight (PC1, 72.1%), limb ossification (PC2, 99.8%), flat bone size (PC4, 99.7%), and axial skeletal growth (PC5, 96.9%). Limb length showed lesser effects of parental genomes (PC3, 40.8%) and a significant nongenetic maternal effect (gestational weight gain, 29%). Fetal sex affected bone wet weight (PC1, p < 0.0001) and limb length (PC3, p < 0.05). Partitioning of variation explained by parental genomes revealed strong maternal genome effects on bone wet weight (74.1%, p < 0.0001) and axial skeletal growth (93.5%, p < 0.001), whereas paternal genome controlled limb ossification (95.1%, p < 0.0001). Histomorphometric data revealed strong maternal genome effects on growth plate height (98.6%, p < 0.0001) and trabecular thickness (85.5%, p < 0.0001) in distal femur. Parental genome effects on fetal bone were mirrored by maternal genome effects on fetal serum 25-hydroxyvitamin D (96.9%, p < 0.001) and paternal genome effects on alkaline phosphatase (90.0%, p < 0.001) and their correlations with maternally controlled bone wet weight and paternally controlled limb ossification, respectively. Bone wet weight and flat bone size correlated positively with muscle weight (r = 0.84 and 0.77, p < 0.0001) and negatively with muscle H19 expression (r = -0.34 and -0.31, p < 0.01). Because imprinted maternally expressed H19 regulates growth factors by miRNA interference, this suggests muscle-bone interaction via epigenetic factors.
Collapse
Affiliation(s)
- Ruidong Xiang
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia; JS Davies Epigenetics and Genetics Group, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Adelaide, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
de Araújo E, Vasques L, Stabellini R, Krepischi A, Pereira L. Stability of XIST repression in relation to genomic imprinting following global genome demethylation in a human cell line. Braz J Med Biol Res 2014. [PMID: 25387668 PMCID: PMC4244667 DOI: 10.1590/1414-431x20144058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA methylation is essential in X chromosome inactivation and genomic imprinting,
maintaining repression of XIST in the active X chromosome and
monoallelic repression of imprinted genes. Disruption of the DNA methyltransferase
genes DNMT1 and DNMT3B in the HCT116 cell line (DKO
cells) leads to global DNA hypomethylation and biallelic expression of the imprinted
gene IGF2 but does not lead to reactivation of XIST
expression, suggesting that XIST repression is due to a more stable
epigenetic mark than imprinting. To test this hypothesis, we induced acute
hypomethylation in HCT116 cells by 5-aza-2′-deoxycytidine (5-aza-CdR) treatment
(HCT116-5-aza-CdR) and compared that to DKO cells, evaluating DNA methylation by
microarray and monitoring the expression of XIST and imprinted genes
IGF2, H19, and PEG10. Whereas
imprinted genes showed biallelic expression in HCT116-5-aza-CdR and DKO cells, the
XIST locus was hypomethylated and weakly expressed only under
acute hypomethylation conditions, indicating the importance of XIST
repression in the active X to cell survival. Given that DNMT3A is the only active
DNMT in DKO cells, it may be responsible for ensuring the repression of
XIST in those cells. Taken together, our data suggest that
XIST repression is more tightly controlled than genomic
imprinting and, at least in part, is due to DNMT3A.
Collapse
Affiliation(s)
- E.S.S. de Araújo
- Universidade de São Paulo, Brasil; A.C. Camargo Cancer Center, Brasil
| | | | - R. Stabellini
- Universidade de São Paulo, Brasil; A.C. Camargo Cancer Center, Brasil
| | - A.C.V. Krepischi
- Universidade de São Paulo, Brasil; A.C. Camargo Cancer Center, Brasil
| | | |
Collapse
|
49
|
Congras A, Yerle-Bouissou M, Pinton A, Vignoles F, Liaubet L, Ferchaud S, Acloque H. Sperm DNA methylation analysis in swine reveals conserved and species-specific methylation patterns and highlights an altered methylation at the GNAS locus in infertile boars. Biol Reprod 2014; 91:137. [PMID: 25320151 DOI: 10.1095/biolreprod.114.119610] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Male infertility is an increasing health issue in today's society for both human and livestock populations. In livestock, male infertility slows the improvement of animal selection programs and agricultural productivity. There is increasing evidence that epigenetic marks play an important role in the production of good-quality sperm. We therefore screened for specific or common epigenetic signatures of livestock infertility. To do so, we compared DNA methylation level in sperm DNA from fertile and infertile boars. We evaluated first the global level of sperm DNA methylation and found no difference between the two groups of boars. We then selected 42 loci of interest, most of them known to be imprinted in human or mice, and assessed the imprinting status of five of them not previously described in swine tissues: WT1, CNTN3, IMPACT, QPCT, and GRB10. DNA methylation level was then quantified in fertile and infertile boars at these 42 loci. Results from fertile boars indicated that the methylation level of the selected loci is highly conserved between pig, human, and mice, with a few exceptions, including the POU5F1 (OCT4) promoter and RTL1. Comparison between fertile and infertile boars revealed that one imprinted region, the GNAS locus, shows an increase in sperm DNA methylation in three out of eight infertile boars with low semen quality. This increase in DNA methylation is associated with an altered expression of the genes belonging to the GNAS locus, suggesting a new role for GNAS in the proper formation of functional gametes.
Collapse
Affiliation(s)
- Annabelle Congras
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| | - Martine Yerle-Bouissou
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| | - Alain Pinton
- Université de Toulouse INPT ENVT, UMR1388 Génétique Physiologie et Systèmes d'Elevage GenPhySE, Toulouse, France
| | - Florence Vignoles
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| | - Laurence Liaubet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| | - Stéphane Ferchaud
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - Hervé Acloque
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| |
Collapse
|
50
|
Cleaton MA, Edwards CA, Ferguson-Smith AC. Phenotypic Outcomes of Imprinted Gene Models in Mice: Elucidation of Pre- and Postnatal Functions of Imprinted Genes. Annu Rev Genomics Hum Genet 2014; 15:93-126. [DOI: 10.1146/annurev-genom-091212-153441] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Carol A. Edwards
- Department of Genetics, University of Cambridge, Cambridge CB2 3EG, United Kingdom;
| | | |
Collapse
|