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Bajrami E, Spiroski M. Genomic Imprinting. Open Access Maced J Med Sci 2016; 4:181-4. [PMID: 27275355 PMCID: PMC4884243 DOI: 10.3889/oamjms.2016.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/01/2015] [Accepted: 01/09/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND: Genomic imprinting is the inheritance out of Mendelian borders. Many of inherited diseases and human development violates Mendelian law of inheritance, this way of inheriting is studied by epigenetics. AIM: The aim of this review is to analyze current opinions and options regarding to this way of inheriting. RESULTS: Epigenetics shows that gene expression undergoes changes more complex than modifications in the DNA sequence; it includes the environmental influence on the gametes before conception. Humans inherit two alleles from mother and father, both are functional for the majority of the genes, but sometimes one is turned off or “stamped” and doesn’t show in offspring, that gene is imprinted. Imprinting means that that gene is silenced, and gene from other parent is expressed. The mechanisms for imprinting are still incompletely defined, but they involve epigenetic modifications that are erased and then reset during the creation of eggs and sperm. Genomic imprinting is a process of silencing genes through DNA methylation. The repressed allele is methylated, while the active allele is unmethylated. The most well-known conditions include Prader-Willi syndrome, and Angelman syndrome. Both of these syndromes can be caused by imprinting or other errors involving genes on the long arm of chromosome 15. CONCLUSIONS: Genomic imprinting and other epigenetic mechanisms such as environment is shown that plays role in offspring neurodevelopment and autism spectrum disorder.
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Affiliation(s)
- Emirjeta Bajrami
- University Clinical Centre, Neonatology Clinic, Prishtina, Kosovo
| | - Mirko Spiroski
- Institute of Immunobiology and Human Genetics, Faculty of Medicine, Ss Cyril and Methodius University of Skopje, Skopje, Republic of Macedonia
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102
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Hanna CW, Peñaherrera MS, Saadeh H, Andrews S, McFadden DE, Kelsey G, Robinson WP. Pervasive polymorphic imprinted methylation in the human placenta. Genome Res 2016; 26:756-67. [PMID: 26769960 PMCID: PMC4889973 DOI: 10.1101/gr.196139.115] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/07/2016] [Indexed: 01/19/2023]
Abstract
The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilization. There are a large number of germline DMRs that have not yet been associated with imprinting, and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs in the human placenta and investigated the dynamics of these imprinted DMRs during development in somatic and extraembryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 134 human tissue samples, publicly available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. Forty-three known and 101 novel imprinted DMRs were identified in the human placenta by comparing methylation between diandric and digynic triploid conceptions in addition to female and male gametes. Seventy-two novel DMRs showed a pattern consistent with placental-specific imprinting, and this monoallelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation between placental samples. These data suggest that imprinting in human development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Maria S Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Heba Saadeh
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Deborah E McFadden
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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Anvar Z, Cammisa M, Riso V, Baglivo I, Kukreja H, Sparago A, Girardot M, Lad S, De Feis I, Cerrato F, Angelini C, Feil R, Pedone PV, Grimaldi G, Riccio A. ZFP57 recognizes multiple and closely spaced sequence motif variants to maintain repressive epigenetic marks in mouse embryonic stem cells. Nucleic Acids Res 2015; 44:1118-32. [PMID: 26481358 PMCID: PMC4756812 DOI: 10.1093/nar/gkv1059] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/01/2015] [Indexed: 12/15/2022] Open
Abstract
Imprinting Control Regions (ICRs) need to maintain their parental allele-specific DNA methylation during early embryogenesis despite genome-wide demethylation and subsequent de novo methylation. ZFP57 and KAP1 are both required for maintaining the repressive DNA methylation and H3-lysine-9-trimethylation (H3K9me3) at ICRs. In vitro, ZFP57 binds a specific hexanucleotide motif that is enriched at its genomic binding sites. We now demonstrate in mouse embryonic stem cells (ESCs) that SNPs disrupting closely-spaced hexanucleotide motifs are associated with lack of ZFP57 binding and H3K9me3 enrichment. Through a transgenic approach in mouse ESCs, we further demonstrate that an ICR fragment containing three ZFP57 motif sequences recapitulates the original methylated or unmethylated status when integrated into the genome at an ectopic position. Mutation of Zfp57 or the hexanucleotide motifs led to loss of ZFP57 binding and DNA methylation of the transgene. Finally, we identified a sequence variant of the hexanucleotide motif that interacts with ZFP57 both in vivo and in vitro. The presence of multiple and closely located copies of ZFP57 motif variants emerges as a distinct characteristic that is required for the faithful maintenance of repressive epigenetic marks at ICRs and other ZFP57 binding sites.
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Affiliation(s)
- Zahra Anvar
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Marco Cammisa
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Vincenzo Riso
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Harpreet Kukreja
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Angela Sparago
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Shraddha Lad
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
| | - Italia De Feis
- Istituto per le Applicazioni del Calcolo 'Mauro Picone' (IAC), CNR, 80131 Naples, Italy
| | - Flavia Cerrato
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo 'Mauro Picone' (IAC), CNR, 80131 Naples, Italy
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Giovanna Grimaldi
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Ceinge Biotecnologie Avanzate s.c.a.r.l., 80145 Naples, Italy
| | - Andrea Riccio
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
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104
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Prindull G. Potential Gene Interactions in the Cell Cycles of Gametes, Zygotes, Embryonic Stem Cells and the Development of Cancer. Front Oncol 2015; 5:200. [PMID: 26442212 PMCID: PMC4585297 DOI: 10.3389/fonc.2015.00200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/31/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This review is to explore whether potential gene interactions in the cell cycles of gametes, zygotes, and embryonic stem (ES) cells are associated with the development of cancer. METHODS MEDPILOT at the Central Library of the University of Cologne, Germany (Zentralbibliothek Köln) that covers 5,800 international medical journals and 4,300 E-journals was used to collect data. The initial searches were done in December 2012 and additional searches in October 2013-May 2015. The search terms included "cancer development," "gene interaction," and "ES cells," and the time period was between 1998 and 2015. A total of 147 articles in English language only were included in this review. RESULTS Transgenerational gene translation is implemented in the zygote through interactions of epigenetic isoforms of transcription factors (TFs) from parental gametes, predominantly during the first two zygote cleavages. Pluripotent transcription factors may provide interacting links with mutated genes during zygote-to-ES cell switches. Translation of post-transcriptional carcinogenic genes is implemented by abnormally spliced, tumor-specific isoforms of gene-encoded mRNA/non-coding RNA variants of TFs employing de novo gene synthesis and neofunctionalization. Post-translationally, mutated genes are preserved in pre-neoplastic ES cell subpopulations that can give rise to overt cancer stem cells. Thus, TFs operate as cell/disease-specific epigenetic messengers triggering clinical expression of neoplasms. CONCLUSION Potential gene interactions in the cell cycle of gametes, zygotes, and ES cells may play some roles in the development of cancer.
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Affiliation(s)
- Gregor Prindull
- Medical Faculty, University of Göttingen , Göttingen , Germany
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105
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Soellner L, Monk D, Rezwan FI, Begemann M, Mackay D, Eggermann T. Congenital imprinting disorders: Application of multilocus and high throughput methods to decipher new pathomechanisms and improve their management. Mol Cell Probes 2015; 29:282-90. [DOI: 10.1016/j.mcp.2015.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/02/2015] [Accepted: 05/05/2015] [Indexed: 12/17/2022]
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106
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Matsuzaki H, Okamura E, Takahashi T, Ushiki A, Nakamura T, Nakano T, Hata K, Fukamizu A, Tanimoto K. De novo DNA methylation through the 5'-segment of the H19 ICR maintains its imprint during early embryogenesis. Development 2015; 142:3833-44. [PMID: 26417043 DOI: 10.1242/dev.126003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 09/15/2015] [Indexed: 12/30/2022]
Abstract
Genomic imprinting is a major monoallelic gene expression regulatory mechanism in mammals, and depends on gamete-specific DNA methylation of specialized cis-regulatory elements called imprinting control regions (ICRs). Allele-specific DNA methylation of the ICRs is faithfully maintained at the imprinted loci throughout development, even in early embryos where genomes undergo extensive epigenetic reprogramming, including DNA demethylation, to acquire totipotency. We previously found that an ectopically introduced H19 ICR fragment in transgenic mice acquired paternal allele-specific methylation in the somatic cells of offspring, whereas it was not methylated in sperm, suggesting that its gametic and postfertilization modifications were separable events. We hypothesized that this latter activity might contribute to maintenance of the methylation imprint in early embryos. Here, we demonstrate that methylation of the paternally inherited transgenic H19 ICR commences soon after fertilization in a maternal DNMT3A- and DNMT3L-dependent manner. When its germline methylation was partially obstructed by insertion of insulator sequences, the endogenous paternal H19 ICR also exhibited postfertilization methylation. Finally, we refined the responsible sequences for this activity in transgenic mice and found that deletion of the 5' segment of the endogenous paternal H19 ICR decreased its methylation after fertilization and attenuated Igf2 gene expression. These results demonstrate that this segment of the H19 ICR is essential for its de novo postfertilization DNA methylation, and that this activity contributes to the maintenance of imprinted methylation at the endogenous H19 ICR during early embryogenesis.
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Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Eiichi Okamura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Takuya Takahashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Aki Ushiki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Toshinobu Nakamura
- Department of Animal Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Toru Nakano
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo 157-8535, Japan
| | - Akiyoshi Fukamizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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107
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Maupetit-Méhouas S, Montibus B, Nury D, Tayama C, Wassef M, Kota SK, Fogli A, Cerqueira Campos F, Hata K, Feil R, Margueron R, Nakabayashi K, Court F, Arnaud P. Imprinting control regions (ICRs) are marked by mono-allelic bivalent chromatin when transcriptionally inactive. Nucleic Acids Res 2015; 44:621-35. [PMID: 26400168 PMCID: PMC4737186 DOI: 10.1093/nar/gkv960] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/12/2015] [Indexed: 01/10/2023] Open
Abstract
Parental allele-specific expression of imprinted genes is mediated by imprinting control regions (ICRs) that are constitutively marked by DNA methylation imprints on the maternal or paternal allele. Mono-allelic DNA methylation is strictly required for the process of imprinting and has to be faithfully maintained during the entire life-span. While the regulation of DNA methylation itself is well understood, the mechanisms whereby the opposite allele remains unmethylated are unclear. Here, we show that in the mouse, at maternally methylated ICRs, the paternal allele, which is constitutively associated with H3K4me2/3, is marked by default by H3K27me3 when these ICRs are transcriptionally inactive, leading to the formation of a bivalent chromatin signature. Our data suggest that at ICRs, chromatin bivalency has a protective role by ensuring that DNA on the paternal allele remains unmethylated and protected against spurious and unscheduled gene expression. Moreover, they provide the proof of concept that, beside pluripotent cells, chromatin bivalency is the default state of transcriptionally inactive CpG island promoters, regardless of the developmental stage, thereby contributing to protect cell identity.
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Affiliation(s)
- Stéphanie Maupetit-Méhouas
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Bertille Montibus
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - David Nury
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Michel Wassef
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Satya K Kota
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Anne Fogli
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Fabiana Cerqueira Campos
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Robert Feil
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Raphael Margueron
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Franck Court
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Philippe Arnaud
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
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108
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A Mouse Model for Imprinting of the Human Retinoblastoma Gene. PLoS One 2015; 10:e0134672. [PMID: 26275142 PMCID: PMC4537222 DOI: 10.1371/journal.pone.0134672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/13/2015] [Indexed: 12/21/2022] Open
Abstract
The human RB1 gene is imprinted due to integration of the PPP1R26P1 pseudogene into intron 2. PPP1R26P1 harbors the gametic differentially methylated region of the RB1 gene, CpG85, which is methylated in the female germ line. The paternally unmethylated CpG85 acts as promoter for the alternative transcript 2B of RB1, which interferes with expression of full-length RB1 in cis. In mice, PPP1R26P1 is not present in the Rb1 gene and Rb1 is not imprinted. Assuming that the mechanisms responsible for genomic imprinting are conserved, we investigated if imprinting of mouse Rb1 can be induced by transferring human PPP1R26P1 into mouse Rb1. We generated humanized Rb1_PPP1R26P1 knock-in mice that pass human PPP1R26P1 through the mouse germ line. We found that the function of unmethylated CpG85 as promoter for an alternative Rb1 transcript and as cis-repressor of the main Rb1 transcript is maintained in mouse tissues. However, CpG85 is not recognized as a gametic differentially methylated region in the mouse germ line. DNA methylation at CpG85 is acquired only in tissues of neuroectodermal origin, independent of parental transmission of PPP1R26P1. Absence of CpG85 methylation in oocytes and sperm implies a failure of imprint methylation establishment in the germ line. Our results indicate that site-specific integration of a proven human gametic differentially methylated region is not sufficient for acquisition of DNA methylation in the mouse germ line, even if promoter function of the element is maintained. This suggests a considerable dependency of DNA methylation induction on the surrounding sequence. However, our model is suited to determine the cellular function of the alternative Rb1 transcript.
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109
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Environmental Impact on DNA Methylation in the Germline: State of the Art and Gaps of Knowledge. BIOMED RESEARCH INTERNATIONAL 2015; 2015:123484. [PMID: 26339587 PMCID: PMC4538313 DOI: 10.1155/2015/123484] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/03/2015] [Indexed: 12/19/2022]
Abstract
The epigenome consists of chemical changes in DNA and chromatin that without modifying the DNA sequence modulate gene expression and cellular phenotype. The epigenome is highly plastic and reacts to changing external conditions with modifications that can be inherited to daughter cells and across generations. Whereas this innate plasticity allows for adaptation to a changing environment, it also implies the potential of epigenetic derailment leading to so-called epimutations. DNA methylation is the most studied epigenetic mark. DNA methylation changes have been associated with cancer, infertility, cardiovascular, respiratory, metabolic, immunologic, and neurodegenerative pathologies. Experiments in rodents demonstrate that exposure to a variety of chemical stressors, occurring during the prenatal or the adult life, may induce DNA methylation changes in germ cells, which may be transmitted across generations with phenotypic consequences. An increasing number of human biomonitoring studies show environmentally related DNA methylation changes mainly in blood leukocytes, whereas very few data have been so far collected on possible epigenetic changes induced in the germline, even by the analysis of easily accessible sperm. In this paper, we review the state of the art on factors impinging on DNA methylation in the germline, highlight gaps of knowledge, and propose priorities for future studies.
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110
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Clarke HJ, Vieux KF. Epigenetic inheritance through the female germ-line: The known, the unknown, and the possible. Semin Cell Dev Biol 2015; 43:106-116. [DOI: 10.1016/j.semcdb.2015.07.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/04/2015] [Accepted: 07/06/2015] [Indexed: 02/06/2023]
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111
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Ross L, Normark BB. Evolutionary problems in centrosome and centriole biology. J Evol Biol 2015; 28:995-1004. [PMID: 25781035 PMCID: PMC4979663 DOI: 10.1111/jeb.12620] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 01/01/2023]
Abstract
Centrosomes have been an enigma to evolutionary biologists. Either they have been the subject of ill-founded speculation or they have been ignored. Here, we highlight evolutionary paradoxes and problems of centrosome and centriole evolution and seek to understand them in the light of recent advances in centrosome biology. Most evolutionary accounts of centrosome evolution have been based on the hypothesis that centrosomes are replicators, independent of the nucleus and cytoplasm. It is now clear, however, that this hypothesis is not tenable. Instead, centrosomes are formed de novo each cell division, with the presence of an old centrosome regulating, but not essential for, the assembly of a new one. Centrosomes are the microtubule-organizing centres of cells. They can potentially affect sensory and motor characters (as the basal body of cilia), as well as the movements of chromosomes during cell division. This latter role does not seem essential, however, except in male meiosis, and the reasons for this remain unclear. Although the centrosome is absent in some taxa, when it is present, its structure is extraordinarily conserved: in most taxa across eukaryotes, it does not appear to evolve at all. And yet a few insect groups display spectacular hypertrophy of the centrioles. We discuss how this might relate to the unusual reproductive system found in these insects. Finally, we discuss why the fate of centrosomes in sperm and early embryos might differ between different groups of animals.
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Affiliation(s)
- L Ross
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - B B Normark
- Department of Biology and Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA
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112
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O'Doherty AM, MacHugh DE, Spillane C, Magee DA. Genomic imprinting effects on complex traits in domesticated animal species. Front Genet 2015; 6:156. [PMID: 25964798 PMCID: PMC4408863 DOI: 10.3389/fgene.2015.00156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/06/2015] [Indexed: 11/13/2022] Open
Abstract
Monoallelically expressed genes that exert their phenotypic effect in a parent-of-origin specific manner are considered to be subject to genomic imprinting, the most well understood form of epigenetic regulation of gene expression in mammals. The observed differences in allele specific gene expression for imprinted genes are not attributable to differences in DNA sequence information, but to specific chemical modifications of DNA and chromatin proteins. Since the discovery of genomic imprinting some three decades ago, over 100 imprinted mammalian genes have been identified and considerable advances have been made in uncovering the molecular mechanisms regulating imprinted gene expression. While most genomic imprinting studies have focused on mouse models and human biomedical disorders, recent work has highlighted the contributions of imprinted genes to complex trait variation in domestic livestock species. Consequently, greater understanding of genomic imprinting and its effect on agriculturally important traits is predicted to have major implications for the future of animal breeding and husbandry. In this review, we discuss genomic imprinting in mammals with particular emphasis on domestic livestock species and consider how this information can be used in animal breeding research and genetic improvement programs.
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Affiliation(s)
- Alan M O'Doherty
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Ireland
| | - David E MacHugh
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Ireland ; Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, Galway Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield Ireland ; Department of Animal Science, University of Connecticut, Storrs, CT USA
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113
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Sanli I, Feil R. Chromatin mechanisms in the developmental control of imprinted gene expression. Int J Biochem Cell Biol 2015; 67:139-47. [PMID: 25908531 DOI: 10.1016/j.biocel.2015.04.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
Hundreds of protein-coding genes and regulatory non-coding RNAs (ncRNAs) are subject to genomic imprinting. The mono-allelic DNA methylation marks that control imprinted gene expression are somatically maintained throughout development, and this process is linked to specific chromatin features. Yet, at many imprinted genes, the mono-allelic expression is lineage or tissue-specific. Recent studies provide mechanistic insights into the developmentally-restricted action of the 'imprinting control regions' (ICRs). At several imprinted domains, the ICR expresses a long ncRNA that mediates chromatin repression in cis (and probably in trans as well). ICRs at other imprinted domains mediate higher-order chromatin structuration that enhances, or prevents, transcription of close-by genes. Here, we present how chromatin and ncRNAs contribute to developmental control of imprinted gene expression and discuss implications for disease. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Ildem Sanli
- Institute of Molecular Genetics (IGMM), UMR-5535, CNRS, University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), UMR-5535, CNRS, University of Montpellier, 1919 route de Mende, 34293 Montpellier, France.
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114
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Voon HPJ, Hughes JR, Rode C, De La Rosa-Velázquez IA, Jenuwein T, Feil R, Higgs DR, Gibbons RJ. ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes. Cell Rep 2015; 11:405-18. [PMID: 25865896 PMCID: PMC4410944 DOI: 10.1016/j.celrep.2015.03.036] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 01/30/2015] [Accepted: 03/14/2015] [Indexed: 11/27/2022] Open
Abstract
Histone H3.3 is a replication-independent histone variant, which replaces histones that are turned over throughout the entire cell cycle. H3.3 deposition at euchromatin is dependent on HIRA, whereas ATRX/Daxx deposits H3.3 at pericentric heterochromatin and telomeres. The role of H3.3 at heterochromatic regions is unknown, but mutations in the ATRX/Daxx/H3.3 pathway are linked to aberrant telomere lengthening in certain cancers. In this study, we show that ATRX-dependent deposition of H3.3 is not limited to pericentric heterochromatin and telomeres but also occurs at heterochromatic sites throughout the genome. Notably, ATRX/H3.3 specifically localizes to silenced imprinted alleles in mouse ESCs. ATRX KO cells failed to deposit H3.3 at these sites, leading to loss of the H3K9me3 heterochromatin modification, loss of repression, and aberrant allelic expression. We propose a model whereby ATRX-dependent deposition of H3.3 into heterochromatin is normally required to maintain the memory of silencing at imprinted loci. ATRX deposits H3.3 at heterochromatin throughout the genome ATRX and H3.3 preferentially bind the methylated allele of imprinted DMRs H3.3 deposition at imprinted DMRs is dependent on ATRX Loss of ATRX/H3.3 leads to loss of H3K9me3 modification at imprinted DMRs
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Affiliation(s)
- Hsiao P J Voon
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Thomas Jenuwein
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS), 34293 Montpellier, France
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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115
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Al Adhami H, Evano B, Le Digarcher A, Gueydan C, Dubois E, Parrinello H, Dantec C, Bouschet T, Varrault A, Journot L. A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation. Genome Res 2015; 25:353-67. [PMID: 25614607 PMCID: PMC4352888 DOI: 10.1101/gr.175919.114] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 12/08/2014] [Indexed: 11/24/2022]
Abstract
Genomic imprinting is an epigenetic mechanism that restrains the expression of ∼ 100 eutherian genes in a parent-of-origin-specific manner. The reason for this selective targeting of genes with seemingly disparate molecular functions is unclear. In the present work, we show that imprinted genes are coexpressed in a network that is regulated at the transition from proliferation to quiescence and differentiation during fibroblast cell cycle withdrawal, adipogenesis in vitro, and muscle regeneration in vivo. Imprinted gene regulation is not linked to alteration of DNA methylation or to perturbation of monoallelic, parent-of-origin-dependent expression. Overexpression and knockdown of imprinted gene expression alters the sensitivity of preadipocytes to contact inhibition and adipogenic differentiation. In silico and in cellulo experiments showed that the imprinted gene network includes biallelically expressed, nonimprinted genes. These control the extracellular matrix composition, cell adhesion, cell junction, and extracellular matrix-activated and growth factor-activated signaling. These observations show that imprinted genes share a common biological process that may account for their seemingly diverse roles in embryonic development, obesity, diabetes, muscle physiology, and neoplasm.
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Affiliation(s)
- Hala Al Adhami
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Brendan Evano
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Anne Le Digarcher
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Charlotte Gueydan
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | | | | | | | - Tristan Bouschet
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Annie Varrault
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Laurent Journot
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France; MGX-Montpellier GenomiX, Montpellier 34094, France
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116
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Abstract
Several hundred mammalian genes are expressed preferentially from one parental allele as the result of a process called genomic imprinting. Genomic imprinting is prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. We found evidence of imprinted expression for 48 genes, 31 of which had been described previously as imprinted and 17 of which we suggest as candidate imprinted genes. An equal number of maternally and paternally biased genes were detected. On average, candidate imprinted genes were more lowly expressed and had weaker parent-of-origin biases than known imprinted genes. Several known and candidate imprinted genes showed variability in parent-of-origin expression bias between the six trophoblast stem cell lines. Sixteen of the 48 known and candidate imprinted genes were previously or newly annotated noncoding RNAs and six encoded for a total of 60 annotated microRNAs. Pyrosequencing across our panel of trophoblast stem cell lines returned levels of imprinted expression that were concordant with RNA-Seq measurements for all eight genes examined. Our results solidify trophoblast stem cells as a cell culture-based experimental model to study genomic imprinting, and provide a quantitative foundation upon which to delineate mechanisms by which the process is maintained in the mouse.
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117
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Badyaev AV. Epigenetic resolution of the 'curse of complexity' in adaptive evolution of complex traits. J Physiol 2015; 592:2251-60. [PMID: 24882810 DOI: 10.1113/jphysiol.2014.272625] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The age of most genes exceeds the longevity of their genomic and physiological associations by many orders of magnitude. Such transient contexts modulate the expression of ancient genes to produce currently appropriate and often highly distinct developmental and functional outcomes. The efficacy of such adaptive modulation is diminished by the high dimensionality of complex organisms and associated vast areas of neutrality in their genotypic and developmental networks (and, thus, weak natural selection). Here I explore whether epigenetic effects facilitate adaptive modulation of complex phenotypes by effectively reducing the dimensionality of their deterministic networks and thus delineating their developmental and evolutionary trajectories even under weak selection. Epigenetic effects that link unconnected or widely dispersed elements of genotype space in ecologically relevant time could account for the rapid appearance of functionally integrated adaptive modifications. On an organismal time scale, conceptually similar processes occur during recurrent epigenetic reprogramming of somatic stem cells to produce, recurrently and reversibly, a bewildering array of differentiated and persistent cell lineages, all sharing identical genomic sequences despite strongly distinct phenotypes. I discuss whether close dependency of onset, scope and duration of epigenetic effects on cellular and genomic context in stem cells could provide insights into contingent modulation of conserved genomic material on a much longer evolutionary time scale. I review potential empirical examples of epigenetic bridges that reduce phenotype dimensionality and accomplish rapid adaptive modulation in the evolution of novelties, expression of behavioural types, and stress-induced ossification schedules.
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Affiliation(s)
- Alexander V Badyaev
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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118
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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.
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Affiliation(s)
- Susannah Varmuza
- Department of Cell and Systems Biology, University of Toronto, 611-25 Harbord Street, Toronto, M5S 3G5, Canada,
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119
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KANEKO-ISHINO T, ISHINO F. Mammalian-specific genomic functions: Newly acquired traits generated by genomic imprinting and LTR retrotransposon-derived genes in mammals. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2015; 91:511-38. [PMID: 26666304 PMCID: PMC4773580 DOI: 10.2183/pjab.91.511] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
Mammals, including human beings, have evolved a unique viviparous reproductive system and a highly developed central nervous system. How did these unique characteristics emerge in mammalian evolution, and what kinds of changes did occur in the mammalian genomes as evolution proceeded? A key conceptual term in approaching these issues is "mammalian-specific genomic functions", a concept covering both mammalian-specific epigenetics and genetics. Genomic imprinting and LTR retrotransposon-derived genes are reviewed as the representative, mammalian-specific genomic functions that are essential not only for the current mammalian developmental system, but also mammalian evolution itself. First, the essential roles of genomic imprinting in mammalian development, especially related to viviparous reproduction via placental function, as well as the emergence of genomic imprinting in mammalian evolution, are discussed. Second, we introduce the novel concept of "mammalian-specific traits generated by mammalian-specific genes from LTR retrotransposons", based on the finding that LTR retrotransposons served as a critical driving force in the mammalian evolution via generating mammalian-specific genes.
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Affiliation(s)
| | - Fumitoshi ISHINO
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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120
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Angelman syndrome imprinting center encodes a transcriptional promoter. Proc Natl Acad Sci U S A 2014; 112:6871-5. [PMID: 25378697 DOI: 10.1073/pnas.1411261111] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clusters of imprinted genes are often controlled by an imprinting center that is necessary for allele-specific gene expression and to reprogram parent-of-origin information between generations. An imprinted domain at 15q11-q13 is responsible for both Angelman syndrome (AS) and Prader-Willi syndrome (PWS), two clinically distinct neurodevelopmental disorders. Angelman syndrome arises from the lack of maternal contribution from the locus, whereas Prader-Willi syndrome results from the absence of paternally expressed genes. In some rare cases of PWS and AS, small deletions may lead to incorrect parent-of-origin allele identity. DNA sequences common to these deletions define a bipartite imprinting center for the AS-PWS locus. The PWS-smallest region of deletion overlap (SRO) element of the imprinting center activates expression of genes from the paternal allele. The AS-SRO element generates maternal allele identity by epigenetically inactivating the PWS-SRO in oocytes so that paternal genes are silenced on the future maternal allele. Here we have investigated functional activities of the AS-SRO, the element necessary for maternal allele identity. We find that, in humans, the AS-SRO is an oocyte-specific promoter that generates transcripts that transit the PWS-SRO. Similar upstream promoters were detected in bovine oocytes. This result is consistent with a model in which imprinting centers become DNA methylated and acquire maternal allele identity in oocytes in response to transiting transcription.
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121
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Pierron F, Bureau du Colombier S, Moffett A, Caron A, Peluhet L, Daffe G, Lambert P, Elie P, Labadie P, Budzinski H, Dufour S, Couture P, Baudrimont M. Abnormal ovarian DNA methylation programming during gonad maturation in wild contaminated fish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:11688-11695. [PMID: 25203663 DOI: 10.1021/es503712c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
There is increasing evidence that pollutants may cause diseases via epigenetic modifications. Epigenetic mechanisms such as DNA methylation participate in the regulation of gene transcription. Surprisingly, epigenetics research is still limited in ecotoxicology. In this study, we investigated whether chronic exposure to contaminants experienced by wild female fish (Anguilla anguilla) throughout their juvenile phase can affect the DNA methylation status of their oocytes during gonad maturation. Thus, fish were sampled in two locations presenting a low or a high contamination level. Then, fish were transferred to the laboratory and artificially matured. Before hormonal treatment, the DNA methylation levels of the genes encoding for the aromatase and the receptor of the follicle stimulating hormone were higher in contaminated fish than in fish from the clean site. For the hormone receptor, this hypermethylation was positively correlated with the contamination level of fish and was associated with a decrease in its transcription level. In addition, whereas gonad growth was associated with an increase in DNA methylation in fish from the clean site, no changes were observed in contaminated fish in response to hormonal treatment. Finally, a higher gonad growth was observed in fish from the reference site in comparison to contaminated fish.
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Affiliation(s)
- Fabien Pierron
- University of Bordeaux, EPOC, UMR 5805 , F-33400 Talence, France
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122
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Kota SK, Llères D, Bouschet T, Hirasawa R, Marchand A, Begon-Pescia C, Sanli I, Arnaud P, Journot L, Girardot M, Feil R. ICR noncoding RNA expression controls imprinting and DNA replication at the Dlk1-Dio3 domain. Dev Cell 2014; 31:19-33. [PMID: 25263792 DOI: 10.1016/j.devcel.2014.08.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 07/04/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
Imprinted genes play essential roles in development, and their allelic expression is mediated by imprinting control regions (ICRs). The Dlk1-Dio3 locus is among the few imprinted domains controlled by a paternally methylated ICR. The unmethylated maternal copy activates imprinted expression early in development through an unknown mechanism. We find that in mouse embryonic stem cells (ESCs) and in blastocysts, this function is linked to maternal, bidirectional expression of noncoding RNAs (ncRNAs) from the ICR. Disruption of ICR ncRNA expression in ESCs affected gene expression in cis, led to acquisition of aberrant histone and DNA methylation, delayed replication timing along the domain on the maternal chromosome, and changed its subnuclear localization. The epigenetic alterations persisted during differentiation and affected the neurogenic potential of the stem cells. Our data indicate that monoallelic expression at an ICR of enhancer RNA-like ncRNAs controls imprinted gene expression, epigenetic maintenance processes, and DNA replication in embryonic cells.
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Affiliation(s)
- Satya K Kota
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Tristan Bouschet
- Institute of Functional Genomics (IGF), CNRS and University of Montpellier, 141 rue de la Cardonille, Montpellier 34090, France
| | - Ryutaro Hirasawa
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Alice Marchand
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Christina Begon-Pescia
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Ildem Sanli
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Philippe Arnaud
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Laurent Journot
- Institute of Functional Genomics (IGF), CNRS and University of Montpellier, 141 rue de la Cardonille, Montpellier 34090, France
| | - Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France.
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123
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Dauncey MJ. Nutrition, the brain and cognitive decline: insights from epigenetics. Eur J Clin Nutr 2014; 68:1179-85. [PMID: 25182020 DOI: 10.1038/ejcn.2014.173] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 07/11/2014] [Indexed: 02/07/2023]
Abstract
Nutrition affects the brain throughout life, with profound implications for cognitive decline and dementia. These effects are mediated by changes in expression of multiple genes, and responses to nutrition are in turn affected by individual genetic variability. An important layer of regulation is provided by the epigenome: nutrition is one of the many epigenetic regulators that modify gene expression without changes in DNA sequence. Epigenetic mechanisms are central to brain development, structure and function, and include DNA methylation, histone modifications and non-protein-coding RNAs. They enable cell-specific and age-related gene expression. Although epigenetic events can be highly stable, they can also be reversible, highlighting a critical role for nutrition in prevention and treatment of disease. Moreover, they suggest key mechanisms by which nutrition is involved in the pathogenesis of age-related cognitive decline: many nutrients, foods and diets have both immediate and long-term effects on the epigenome, including energy status, that is, energy intake, physical activity, energy metabolism and related changes in body composition, and micronutrients involved in DNA methylation, for example, folate, vitamins B6 and B12, choline, methionine. Optimal brain function results from highly complex interactions between numerous genetic and environmental factors, including food intake, physical activity, age and stress. Future studies linking nutrition with advances in neuroscience, genomics and epigenomics should provide novel approaches to the prevention of cognitive decline, and treatment of dementia and Alzheimer's disease.
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Affiliation(s)
- M J Dauncey
- Wolfson College, University of Cambridge, Cambridge, UK
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124
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Hahn MA, Szabó PE, Pfeifer GP. 5-Hydroxymethylcytosine: a stable or transient DNA modification? Genomics 2014; 104:314-23. [PMID: 25181633 DOI: 10.1016/j.ygeno.2014.08.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 12/16/2022]
Abstract
The DNA base 5-hydroxymethylcytosine (5hmC) is produced by enzymatic oxidation of 5-methylcytosine (5mC) by 5mC oxidases (the Tet proteins). Since 5hmC is recognized poorly by DNA methyltransferases, DNA methylation may be lost at 5hmC sites during DNA replication. In addition, 5hmC can be oxidized further by Tet proteins and converted to 5-formylcytosine and 5-carboxylcytosine, two bases that can be removed from DNA by base excision repair. The completed pathway represents a replication-independent DNA demethylation cycle. However, the DNA base 5hmC is also known to be rather stable and occurs at substantial levels, for example in the brain, suggesting that it represents an epigenetic mark by itself that may regulate chromatin structure and transcription. Focusing on a few well-studied tissues and developmental stages, we discuss the opposing views of 5hmC as a transient intermediate in DNA demethylation and as a modified DNA base with an instructive role.
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Affiliation(s)
- Maria A Hahn
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA
| | - Piroska E Szabó
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA
| | - Gerd P Pfeifer
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA.
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125
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Hill PWS, Amouroux R, Hajkova P. DNA demethylation, Tet proteins and 5-hydroxymethylcytosine in epigenetic reprogramming: an emerging complex story. Genomics 2014; 104:324-33. [PMID: 25173569 DOI: 10.1016/j.ygeno.2014.08.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 12/20/2022]
Abstract
Epigenetic reprogramming involves processes that lead to the erasure of epigenetic information, reverting the chromatin template to a less differentiated state. Extensive epigenetic reprogramming occurs both naturally during mammalian development in the early embryo and the developing germ line, and artificially in various in vitro reprogramming systems. Global DNA demethylation appears to be a shared attribute of reprogramming events, and understanding DNA methylation dynamics is thus of considerable interest. Recently, the Tet enzymes, which catalyse the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have emerged as potential drivers of epigenetic reprogramming. Although some of the recent studies point towards the direct role of Tet proteins in the removal of DNA methylation, the accumulating evidence suggests that the processes underlying DNA methylation dynamics might be more complex. Here, we review the current evidence, highlighting the agreements and the discrepancies between the suggested models and the experimental evidence.
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Affiliation(s)
- Peter W S Hill
- MRC Clinical Sciences Centre, Imperial College London, Faculty of Medicine, Du Cane Road, W12 0NN London, UK
| | - Rachel Amouroux
- MRC Clinical Sciences Centre, Imperial College London, Faculty of Medicine, Du Cane Road, W12 0NN London, UK
| | - Petra Hajkova
- MRC Clinical Sciences Centre, Imperial College London, Faculty of Medicine, Du Cane Road, W12 0NN London, UK.
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126
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Ma JY, Zhang T, Shen W, Schatten H, Sun QY. Molecules and mechanisms controlling the active DNA demethylation of the mammalian zygotic genome. Protein Cell 2014; 5:827-36. [PMID: 25152302 PMCID: PMC4225482 DOI: 10.1007/s13238-014-0095-3] [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] [Received: 06/23/2014] [Accepted: 07/21/2014] [Indexed: 12/02/2022] Open
Abstract
The active DNA demethylation in early embryos is essential for subsequent development. Although the zygotic genome is globally demethylated, the DNA methylation of imprinted regions, part of repeat sequences and some gamete-specific regions are maintained. Recent evidence has shown that multiple proteins and biological pathways participate in the regulation of active DNA demethylation, such as TET proteins, DNA repair pathways and DNA methyltransferases. Here we review the recent understanding regarding proteins associated with active DNA demethylation and the regulatory networks controlling the active DNA demethylation in early embryos.
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Affiliation(s)
- Jun-Yu Ma
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
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127
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Epigenetic control of the genome-lessons from genomic imprinting. Genes (Basel) 2014; 5:635-55. [PMID: 25257202 PMCID: PMC4198922 DOI: 10.3390/genes5030635] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms modulate genome function by writing, reading and erasing chromatin structural features. These have an impact on gene expression, contributing to the establishment, maintenance and dynamic changes in cellular properties in normal and abnormal situations. Great effort has recently been undertaken to catalogue the genome-wide patterns of epigenetic marks—creating reference epigenomes—which will deepen our understanding of their contributions to genome regulation and function with the promise of revealing further insights into disease etiology. The foundation for these global studies is the smaller scale experimentally-derived observations and questions that have arisen through the study of epigenetic mechanisms in model systems. One such system is genomic imprinting, a process causing the mono-allelic expression of genes in a parental-origin specific manner controlled by a hierarchy of epigenetic events that have taught us much about the dynamic interplay between key regulators of epigenetic control. Here, we summarize some of the most noteworthy lessons that studies on imprinting have revealed about epigenetic control on a wider scale. Specifically, we will consider what these studies have revealed about: the variety of relationships between DNA methylation and transcriptional control; the regulation of important protein-DNA interactions by DNA methylation; the interplay between DNA methylation and histone modifications; and the regulation and functions of long non-coding RNAs.
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128
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Wells JCK. Adaptive variability in the duration of critical windows of plasticity: Implications for the programming of obesity. EVOLUTION MEDICINE AND PUBLIC HEALTH 2014; 2014:109-21. [PMID: 25095791 PMCID: PMC4148720 DOI: 10.1093/emph/eou019] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Developmental plasticity underlies widespread associations between early-life exposures and many components of adult phenotype, including the risk of chronic diseases. Humans take almost two decades to reach reproductive maturity, and yet the ‘critical windows’ of physiological sensitivity that confer developmental plasticity tend to close during fetal life or infancy. While several explanations for lengthy human maturation have been offered, the brevity of physiological plasticity has received less attention. I argue that offspring plasticity is only viable within the niche of maternal care, and that as this protection is withdrawn, the offspring is obliged to canalize many developmental traits in order to minimize environmental disruptions. The schedule of maternal care may therefore shape the duration of critical windows, and since the duration of this care is subject to parent–offspring conflict, the resolution of this conflict may shape the duration of critical windows. This perspective may help understand (i) why windows close at different times for different traits, and (ii) why the duration of critical windows may vary across human populations. The issue is explored in relation to population differences in the association between infant weight gain and later body composition. The occupation of more stable environments by western populations may have favoured earlier closure of the critical window during which growth in lean mass is sensitive to nutritional intake. This may paradoxically have elevated the risk of obesity following rapid infant weight gain in such populations.
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Affiliation(s)
- Jonathan C K Wells
- Childhood Nutrition Research Centre, UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
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129
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DNA methylation dynamics of the human preimplantation embryo. Nature 2014; 511:611-5. [PMID: 25079558 PMCID: PMC4178976 DOI: 10.1038/nature13581] [Citation(s) in RCA: 390] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 06/16/2014] [Indexed: 01/12/2023]
Abstract
In mammals, cytosine methylation is predominantly restricted to CpG dinucleotides and stably distributed across the genome, with local, cell-type-specific regulation directed by DNA binding factors. This comparatively static landscape is in marked contrast with the events of fertilization, during which the paternal genome is globally reprogrammed. Paternal genome demethylation includes the majority of CpGs, although methylation remains detectable at several notable features. These dynamics have been extensively characterized in the mouse, with only limited observations available in other mammals, and direct measurements are required to understand the extent to which early embryonic landscapes are conserved. We present genome-scale DNA methylation maps of human preimplantation development and embryonic stem cell derivation, confirming a transient state of global hypomethylation that includes most CpGs, while sites of residual maintenance are primarily restricted to gene bodies. Although most features share similar dynamics to those in mouse, maternally contributed methylation is divergently targeted to species-specific sets of CpG island promoters that extend beyond known imprint control regions. Retrotransposon regulation is also highly diverse, and transitions from maternally to embryonically expressed elements. Together, our data confirm that paternal genome demethylation is a general attribute of early mammalian development that is characterized by distinct modes of epigenetic regulation.
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130
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Sakashita A, Kobayashi H, Wakai T, Sotomaru Y, Hata K, Kono T. Dynamics of genomic 5-hydroxymethylcytosine during mouse oocyte growth. Genes Cells 2014; 19:629-36. [DOI: 10.1111/gtc.12164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 05/19/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Akihiko Sakashita
- Department of BioScience; Tokyo University of Agriculture; 1-1-1 Sakuragaoka Setagaya-ku Tokyo 156-8502 Japan
| | - Hisato Kobayashi
- Genome Research Center; NODAI Research Institute; Tokyo University of Agriculture; 1-1-1 Sakuragaoka Setagaya-ku Tokyo 156-8502 Japan
| | - Takuya Wakai
- Department of BioScience; Tokyo University of Agriculture; 1-1-1 Sakuragaoka Setagaya-ku Tokyo 156-8502 Japan
| | - Yusuke Sotomaru
- Natural Science Center for Basic Research and Development; Hiroshima University; 1-2-3 Kasumi, Minami-ku Hiroshima 734-8551 Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology; National Research Institute for Child Health and Development; 2-10-1 Ookura, Setagaya-ku Tokyo 157-0074 Japan
| | - Tomohiro Kono
- Department of BioScience; Tokyo University of Agriculture; 1-1-1 Sakuragaoka Setagaya-ku Tokyo 156-8502 Japan
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131
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Magee DA, Spillane C, Berkowicz EW, Sikora KM, MacHugh DE. Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits. Anim Genet 2014; 45 Suppl 1:25-39. [PMID: 24990393 DOI: 10.1111/age.12168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 12/30/2022]
Abstract
The phenomenon of genomic imprinting, whereby a subset of mammalian genes display parent-of-origin-specific monoallelic expression, is one of the most active areas of epigenetics research. Over the past two decades, more than 100 imprinted mammalian genes have been identified, while considerable advances have been made in elucidating the molecular mechanisms governing imprinting. These studies have helped to unravel the epigenome--a separate layer of regulatory information contained in eukaryotic chromosomes that influences gene expression and phenotypes without involving changes to the underlying DNA sequence. Although most studies of genomic imprinting in mammals have focussed on mouse models or human biomedical disorders, there is burgeoning interest in the phenotypic effects of imprinted genes in domestic livestock species. In particular, research has focused on imprinted genes influencing foetal growth and development, which are associated with economically important production traits in cattle, sheep and pigs. These findings, when coupled with the data emerging from the various different livestock genome projects, have major implications for the future of animal breeding, health and management. Here, we review current scientific knowledge regarding genomic imprinting in livestock species and evaluate how this information can be used in modern livestock improvement programmes.
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Affiliation(s)
- D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
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132
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Abstract
There is a worldwide epidemic of cardiovascular diseases causing not only a public health issue but also accounting for trillions of dollars of healthcare expenditure. Studies pertaining to epidemiology, pathophysiology, molecular biology, gene identification and genetic linkage maps have been able to lay a strong foundation for both the diagnosis and treatment of cardiovascular medicine. Although the concept of 'epigenetics' is not recent, the term in current usage is extended from the initial concept of 'controlling developmental gene expression and signaling pathways in undifferentiated zygotes' to include heritable changes to gene expression that are not from differences in the genetic code. The impact of epigenetics in cardiovascular disease is now emerging as an important regulatory key player at different levels from pathophysiology to therapeutics. This review focuses on the emerging role of epigenetics in major cardiovascular medicine specialties such as coronary artery disease, heart failure, cardiac hypertrophy and diabetes.
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Affiliation(s)
- Charbel Abi Khalil
- Department of Genetic Medicine and Department of Medicine, Weill Cornell Medical College - Qatar, PO Box 24144, Doha, Qatar
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133
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The specification of imprints in mammals. Heredity (Edinb) 2014; 113:176-83. [PMID: 24939713 PMCID: PMC4105455 DOI: 10.1038/hdy.2014.54] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 03/31/2014] [Indexed: 02/01/2023] Open
Abstract
At the heart of genomic imprinting in mammals are imprinting control regions (ICRs), which are the discrete genetic elements that confer imprinted monoallelic expression to several genes in imprinted gene clusters. A characteristic of the known ICRs is that they acquire different epigenetic states, exemplified by differences in DNA methylation, in the sperm and egg, and these imprint marks remain on the sperm- and oocyte-derived alleles into the next generation as a lifelong memory of parental origin. Although there has been much focus on gametic marking of ICRs as the point of imprint specification, recent mechanistic studies and genome-wide DNA methylation profiling do not support the existence of a specific imprinting machinery in germ cells. Rather, ICRs are part of more widespread methylation events that occur during gametogenesis. Instead, a decisive component in the specification of imprints is the choice of which sites of gamete-derived methylation to maintain in the zygote and preimplantation embryo at a time when much of the remainder of the genome is being demethylated. Among the factors involved in this selection, the zinc-finger protein Zfp57 can be regarded as an imprint-specific, sequence-specific DNA binding factor responsible for maintaining methylation at most ICRs. The recent insights into the balance of gametic and zygotic contributions to imprint specification should help understand mechanistic opportunities and constraints on the evolution of imprinting in mammals.
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134
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Messerschmidt DM, Knowles BB, Solter D. DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev 2014; 28:812-28. [PMID: 24736841 PMCID: PMC4003274 DOI: 10.1101/gad.234294.113] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Methylation of DNA is an essential epigenetic control mechanism in mammals. Messerschmidt et al. review the current understanding of epigenetic dynamics regulating the molecular processes that prepare the mammalian embryo for normal development. Methylation of DNA is an essential epigenetic control mechanism in mammals. During embryonic development, cells are directed toward their future lineages, and DNA methylation poses a fundamental epigenetic barrier that guides and restricts differentiation and prevents regression into an undifferentiated state. DNA methylation also plays an important role in sex chromosome dosage compensation, the repression of retrotransposons that threaten genome integrity, the maintenance of genome stability, and the coordinated expression of imprinted genes. However, DNA methylation marks must be globally removed to allow for sexual reproduction and the adoption of the specialized, hypomethylated epigenome of the primordial germ cell and the preimplantation embryo. Recent technological advances in genome-wide DNA methylation analysis and the functional description of novel enzymatic DNA demethylation pathways have provided significant insights into the molecular processes that prepare the mammalian embryo for normal development.
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Affiliation(s)
- Daniel M Messerschmidt
- Developmental Epigenetics and Disease, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), 138673 Singapore,
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135
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Abstract
"Angelman syndrome" (AS) is a neurodevelopmental disorder whose main features are intellectual disability, lack of speech, seizures, and a characteristic behavioral profile. The behavioral features of AS include a happy demeanor, easily provoked laughter, short attention span, hypermotoric behavior, mouthing of objects, sleep disturbance, and an affinity for water. Microcephaly and subtle dysmorphic features, as well as ataxia and other movement disturbances, are additional features seen in most affected individuals. AS is due to deficient expression of the ubiquitin protein ligase E3A (UBE3A) gene, which displays paternal imprinting. There are four molecular classes of AS, and some genotype-phenotype correlations have emerged. Much remains to be understood regarding how insufficiency of E6-AP, the protein product of UBE3A, results in the observed neurodevelopmental deficits. Studies of mouse models of AS have implicated UBE3A in experience-dependent synaptic remodeling.
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Affiliation(s)
- Lynne M Bird
- Department of Pediatrics, University of California, Division of Genetics, Rady Children’s Hospital, San Diego, California, USA
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136
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Eckersley-Maslin MA, Spector DL. Random monoallelic expression: regulating gene expression one allele at a time. Trends Genet 2014; 30:237-44. [PMID: 24780084 DOI: 10.1016/j.tig.2014.03.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
Abstract
Monoallelic gene expression is a remarkable process in which transcription occurs from only one of two homologous alleles in a diploid cell. Interestingly, between 0.5% and 15% of autosomal genes exhibit random monoallelic gene expression, in which different cells express only one allele independently of the underlying genomic sequence, in a cell type-specific manner. Recently, genome-wide studies have increased our understanding of the cell type-specific incidence of random monoallelic gene expression, and how the imbalance in allelic expression is distinguished within the cell and potentially maintained across cell generations. Monoallelic gene expression is likely generated through stochastic independent regulation of the two alleles upon differentiation, and has varied implications for the cell and organism, in particular with respect to disease.
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Affiliation(s)
- Mélanie A Eckersley-Maslin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - David L Spector
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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137
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Wells JCK. Commentary: Paternal and maternal influences on offspring phenotype: the same, only different. Int J Epidemiol 2014; 43:772-4. [PMID: 24651398 PMCID: PMC4052140 DOI: 10.1093/ije/dyu055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jonathan C K Wells
- Childhood Nutrition Research Centre, UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK. E-mail:
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138
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Wolf JB, Oakey RJ, Feil R. Imprinted gene expression in hybrids: perturbed mechanisms and evolutionary implications. Heredity (Edinb) 2014; 113:167-75. [PMID: 24619185 DOI: 10.1038/hdy.2014.11] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 01/24/2014] [Accepted: 01/28/2014] [Indexed: 01/21/2023] Open
Abstract
Diverse mechanisms contribute to the evolution of reproductive barriers, a process that is critical in speciation. Amongst these are alterations in gene products and in gene dosage that affect development and reproductive success in hybrid offspring. Because of its strict parent-of-origin dependence, genomic imprinting is thought to contribute to the aberrant phenotypes observed in interspecies hybrids in mammals and flowering plants, when the abnormalities depend on the directionality of the cross. In different groups of mammals, hybrid incompatibility has indeed been linked to loss of imprinting. Aberrant expression levels have been reported as well, including imprinted genes involved in development and growth. Recent studies in humans emphasize that genetic diversity within a species can readily perturb imprinted gene expression and phenotype as well. Despite novel insights into the underlying mechanisms, the full extent of imprinted gene perturbation still remains to be determined in the different hybrid systems. Here we review imprinted gene expression in intra- and interspecies hybrids and examine the evolutionary scenarios under which imprinting could contribute to hybrid incompatibilities. We discuss effects on development and reproduction and possible evolutionary implications.
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Affiliation(s)
- J B Wolf
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - R J Oakey
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - R Feil
- Institute of Molecular Genetics (IGMM), CNRS, UMR-5535 and University of Montpellier, Montpellier, France
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139
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Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL. Random monoallelic gene expression increases upon embryonic stem cell differentiation. Dev Cell 2014; 28:351-65. [PMID: 24576421 PMCID: PMC3955261 DOI: 10.1016/j.devcel.2014.01.017] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 12/21/2013] [Accepted: 01/21/2014] [Indexed: 11/23/2022]
Abstract
Random autosomal monoallelic gene expression refers to the transcription of a gene from one of two homologous alleles. We assessed the dynamics of monoallelic expression during development through an allele-specific RNA-sequencing screen in clonal populations of hybrid mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). We identified 67 and 376 inheritable autosomal random monoallelically expressed genes in ESCs and NPCs, respectively, a 5.6-fold increase upon differentiation. Although DNA methylation and nuclear positioning did not distinguish the active and inactive alleles, specific histone modifications were differentially enriched between the two alleles. Interestingly, expression levels of 8% of the monoallelically expressed genes remained similar between monoallelic and biallelic clones. These results support a model in which random monoallelic expression occurs stochastically during differentiation and, for some genes, is compensated for by the cell to maintain the required transcriptional output of these genes.
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Affiliation(s)
- Mélanie A Eckersley-Maslin
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jan H Bergmann
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David L Spector
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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140
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Azzi S, Abi Habib W, Netchine I. Beckwith-Wiedemann and Russell-Silver Syndromes: from new molecular insights to the comprehension of imprinting regulation. Curr Opin Endocrinol Diabetes Obes 2014; 21:30-8. [PMID: 24322424 DOI: 10.1097/med.0000000000000037] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW The imprinted human 11p15.5 region encompasses two imprinted domains important for the control of fetal growth: the H19/IGF2 domain in the telomeric region and the KCNQ1OT1/CDKN1C domain in the centromeric region. These two domains are differentially methylated and each is regulated by its own imprinting control region (ICR): ICR1 in the telomeric region and ICR2 in the centromeric region. Aberrant methylation of the 11p15.5 imprinted region, through genetic or epigenetic mechanisms, leads to two clinical syndromes, with opposite growth phenotypes: Russell-Silver Syndrome (RSS; with severe fetal and postnatal growth retardation) and Beckwith-Wiedemann Syndrome (BWS; an overgrowth syndrome). RECENT FINDINGS In this review, we discuss the recently identified molecular abnormalities at 11p15.5 involved in RSS and BWS, which have led to the identification of cis-acting elements and trans-acting regulatory factors involved in the regulation of imprinting in this region. We also discuss the multilocus imprinting disorders identified in various human syndromes, their clinical outcomes and their impact on commonly identified metabolism disorders. SUMMARY These new findings and progress in this field will have direct consequence for diagnostic and predictive tools, risk assessment and genetic counseling for these syndromes.
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Affiliation(s)
- Salah Azzi
- aAP-HP, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes bUPMC Paris 6, UMR_S938, Centre de Recherche de Saint-Antoine cINSERM, UMR_S938, Centre de Recherche de Saint-Antoine, Paris, France
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141
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Influencing the Social Group. EPIGENETIC SHAPING OF SOCIOSEXUAL INTERACTIONS - FROM PLANTS TO HUMANS 2014; 86:107-34. [DOI: 10.1016/b978-0-12-800222-3.00006-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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142
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Dosage-sensitivity of imprinted genes expressed in the brain: 15q11-q13 and neuropsychiatric illness. Biochem Soc Trans 2013; 41:721-6. [PMID: 23697931 DOI: 10.1042/bst20130008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Imprinted genes, those genes subject to parent-of-origin-specific epigenetic marking resulting in monoallelic parent-specific expression, are sensitive to subtle changes in expression dosage. This has been illustrated in a number of experimental models and the fact that both decreased (or complete loss) and increased imprinted gene expression can lead to human diseases. In the present paper, we discuss the consequence of increased dosage of imprinted genes for brain function, focusing on the PWS (Prader-Willi syndrome) locus on human chromosome 15q11-q13 and how predicted increases in dosage of maternally expressed imprinted genes from this interval are associated with a higher risk of developing psychotic illness. The evidence for this comes from individuals with PWS itself and also non-syndromic cases of psychosis in carriers of a maternally derived copy number variant spanning this locus. Of the known imprinted genes in this region, the prime candidate is maternally expressed UBE3A, which encodes E6-AP (E6-associated protein) ubiquitin ligase and has an influence on a number of important neurotransmitter systems. Furthermore, these findings point to the fact that brain function is exquisitely sensitive to both decreases and increases in the expression of imprinted genes.
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143
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Girardot M, Feil R, Llères D. Epigenetic deregulation of genomic imprinting in humans: causal mechanisms and clinical implications. Epigenomics 2013; 5:715-28. [DOI: 10.2217/epi.13.66] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian genes controlled by genomic imprinting play important roles in development and diverse postnatal processes. A growing number of congenital disorders have been linked to genomic imprinting. Each of these is caused by perturbed gene expression at one principal imprinted domain. Some imprinting disorders, including the Prader–Willi and Angelman syndromes, are caused almost exclusively by genetic mutations. In several others, including the Beckwith–Wiedemann and Silver–Russell growth syndromes, and transient neonatal diabetes mellitus, imprinted expression is perturbed mostly by epigenetic alterations at ‘imprinting control regions’ and at other specific regulatory sequences. In a minority of these patients, DNA methylation is altered at multiple imprinted loci, suggesting that common trans-acting factors are affected. Here, we review the epimutations involved in congenital imprinting disorders and the associated clinical features. Trans-acting factors known to be causally involved are discussed and other trans-acting factors that are potentially implicated are also presented.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
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144
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Holman L, Kokko H. The evolution of genomic imprinting: costs, benefits and long-term consequences. Biol Rev Camb Philos Soc 2013; 89:568-87. [DOI: 10.1111/brv.12069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 09/15/2013] [Accepted: 09/26/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Luke Holman
- Centre of Excellence in Biological Interactions, Division of Ecology, Evolution & Genetics; Research School of Biology, Australian National University; Daley Road, Canberra Australian Capital Territory 0200 Australia
| | - Hanna Kokko
- Centre of Excellence in Biological Interactions, Division of Ecology, Evolution & Genetics; Research School of Biology, Australian National University; Daley Road, Canberra Australian Capital Territory 0200 Australia
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145
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Dias RP, Maher ER. Genes, assisted reproductive technology and trans-illumination. Epigenomics 2013; 5:331-40. [PMID: 23750647 DOI: 10.2217/epi.13.28] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genomic imprinting is a parent-of-origin allele-specific epigenetic process that is critical for normal development and health. The establishment and maintenance of normal imprinting is dependent on both cis-acting imprinting control centers, which are marked by differentially (parental allele specific) methylated marks, and trans mechanisms, which regulate the establishment and/or maintenance of the correct methylation epigenotype at the imprinting control centers. Studies of rare human imprinting disorders such as familial hydatidiform mole, Beckwith-Wiedemann syndrome and familial transient neonatal diabetes mellitus have enabled the identification of genetic (e.g., mutations in KHDC3L [C6ORF221], NLRP2 [NALP2], NLRP7 [NALP7] and ZFP57) and environmental (assisted reproductive technologies) factors that can disturb the normal trans mechanisms for imprinting establishment and/or maintenance. Here we review the clinical and molecular aspects of these imprinting disorders in order to demonstrate how the study of rare inherited disorders can illuminate the molecular characteristics of fundamental epigenetic processes, such as genomic imprinting.
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Affiliation(s)
- Renuka P Dias
- Centre for Rare Diseases & Personalised Medicine, School of Clinical & Experimental Medicine, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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146
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Lorthongpanich C, Cheow LF, Balu S, Quake SR, Knowles BB, Burkholder WF, Solter D, Messerschmidt DM. Single-cell DNA-methylation analysis reveals epigenetic chimerism in preimplantation embryos. Science 2013; 341:1110-2. [PMID: 24009393 DOI: 10.1126/science.1240617] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Epigenetic alterations are increasingly recognized as causes of human cancers and disease. These aberrations are likely to arise during genomic reprogramming in mammalian preimplantation embryos, when their epigenomes are most vulnerable. However, this process is only partially understood because of the experimental inaccessibility of early-stage embryos. Here, we introduce a methodologic advance, probing single cells for various DNA-methylation errors at multiple loci, to reveal failed maintenance of epigenetic mark results in chimeric mice, which display unpredictable phenotypes leading to developmental arrest. Yet we show that mouse pronuclear transfer can be used to ameliorate such reprogramming defects. This study not only details the epigenetic reprogramming dynamics in early mammalian embryos but also suggests diagnostic and potential future therapeutic applications.
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147
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MacDonald WA, Mann MRW. Epigenetic regulation of genomic imprinting from germ line to preimplantation. Mol Reprod Dev 2013; 81:126-40. [PMID: 23893518 DOI: 10.1002/mrd.22220] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/20/2013] [Indexed: 01/25/2023]
Abstract
Genomic imprinting is an epigenetic process that distinguishes parental alleles, resulting in parent-specific expression of a gene or cluster of genes. Imprints are acquired during gametogenesis when genome-wide epigenetic remodeling occurs. These imprints must then be maintained during preimplantation development, when another wave of genome-wide epigenetic remodeling takes place. Thus, for imprints to persist as parent-specific epigenetic marks, coordinated factors and processes must be involved to both recognize an imprint and protect it from genome-wide remodeling. Parent-specific DNA methylation has long been recognized as a primary epigenetic mark demarcating a genomic imprint. Recent work has advanced our understanding of how and when parent-specific DNA methylation is erased and acquired in the germ line as well as maintained during preimplantation development. Epigenetic factors have also been identified that are recruited to imprinted regions to protect them from genome-wide DNA demethylation during preimplantation development. Intriguingly, asynchrony in epigenetic reprogramming appears to be a recurrent theme with asynchronous acquisition between male and female germ lines, between different imprinted genes, and between the two parental alleles of a gene. Here, we review recent advancements and discuss how they impact our current understanding of the epigenetic regulation of genomic imprinting.
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Affiliation(s)
- William A MacDonald
- Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
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148
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Brain-expressed imprinted genes and adult behaviour: the example of Nesp and Grb10. Mamm Genome 2013; 25:87-93. [PMID: 23974804 DOI: 10.1007/s00335-013-9472-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/26/2013] [Indexed: 12/21/2022]
Abstract
Imprinted genes are defined by their parent-of-origin-specific monoallelic expression. Although the epigenetic mechanisms regulating imprinted gene expression have been widely studied, their functional importance is still unclear. Imprinted genes are associated with a number of physiologies, including placental function and foetal growth, energy homeostasis, and brain and behaviour. This review focuses on genomic imprinting in the brain and on two imprinted genes in particular, Nesp and paternal Grb10, which, when manipulated in animals, have been shown to influence adult behaviour. These two genes are of particular interest as they are expressed in discrete and overlapping neural regions, recognised as key "imprinting hot spots" in the brain. Furthermore, these two genes do not appear to influence placental function and/or maternal provisioning of offspring. Consequently, by understanding their behavioural function we may begin to shed light on the evolutionary significance of imprinted genes in the adult brain, independent of the recognised role in maternal care. In addition, we discuss the potential future directions of research investigating the function of these two genes and the behavioural role of imprinted genes more generally.
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149
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Singh P, Li AX, Tran DA, Oates N, Kang ER, Wu X, Szabó PE. De novo DNA methylation in the male germ line occurs by default but is excluded at sites of H3K4 methylation. Cell Rep 2013; 4:205-19. [PMID: 23810559 DOI: 10.1016/j.celrep.2013.06.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 04/01/2013] [Accepted: 06/03/2013] [Indexed: 12/13/2022] Open
Abstract
To understand what dictates the emerging patterns of de novo DNA methylation in the male germline, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells by using methylated CpG island recovery assay (MIRA)-chip, chromatin immunoprecipitation (ChIP)-chip, and strand-specific RNA deep sequencing, respectively. Global de novo methylation occurred by default in prospermatogonia without any apparent trigger from preexisting repressive chromatin marks but was preceded by broad, low-level transcription along the chromosomes, including the four known paternally imprinted differentially methylated regions (DMRs). Default methylation was excluded only at precisely aligned constitutive or emerging peaks of H3K4me2, including most CpG islands and some intracisternal A particles (IAPs). Similarly, each maternally imprinted DMR was protected from default DNA methylation among highly methylated DNA by an H3K4me2 peak and transcription initiation at least in one strand. Our results suggest that the pattern of de novo DNA methylation in prospermatogonia is dictated by opposing actions of broad, low-level transcription and dynamic patterns of active chromatin.
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Affiliation(s)
- Purnima Singh
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
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150
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Ishino F, Shinkai Y, Whitelaw E. Mammalian epigenetics in biology and medicine. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120386. [PMID: 23166404 DOI: 10.1098/rstb.2012.0386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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