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Kocher AA, Dutrow EV, Uebbing S, Yim KM, Rosales Larios MF, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. Genome Biol 2024; 25:156. [PMID: 38872220 PMCID: PMC11170920 DOI: 10.1186/s13059-024-03300-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. CpG islands (CGIs) have recently been shown to influence enhancer activity, and here we test how their turnover across species contributes to enhancer evolution. RESULTS We integrate maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and find that CGI content in enhancers is strongly associated with increased histone modification levels. CGIs show widespread turnover across species and species-specific CGIs are strongly enriched for enhancers exhibiting species-specific activity across all tissues and species. Genes associated with enhancers with species-specific CGIs show concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. CONCLUSIONS Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
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Affiliation(s)
- Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Division of Molecular Genetics and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Zoetis, Inc, 333 Portage St, Kalamazoo, MI, 49007, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Kristina M Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | | | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, 06510, USA.
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2
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Shiura H, Kitazawa M, Ishino F, Kaneko-Ishino T. Roles of retrovirus-derived PEG10 and PEG11/RTL1 in mammalian development and evolution and their involvement in human disease. Front Cell Dev Biol 2023; 11:1273638. [PMID: 37842090 PMCID: PMC10570562 DOI: 10.3389/fcell.2023.1273638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
PEG10 and PEG11/RTL1 are paternally expressed, imprinted genes that play essential roles in the current eutherian developmental system and are therefore associated with developmental abnormalities caused by aberrant genomic imprinting. They are also presumed to be retrovirus-derived genes with homology to the sushi-ichi retrotransposon GAG and POL, further expanding our comprehension of mammalian evolution via the domestication (exaptation) of retrovirus-derived acquired genes. In this manuscript, we review the importance of PEG10 and PEG11/RTL1 in genomic imprinting research via their functional roles in development and human disease, including neurodevelopmental disorders of genomic imprinting, Angelman, Kagami-Ogata and Temple syndromes, and the impact of newly inserted DNA on the emergence of newly imprinted regions. We also discuss their possible roles as ancestors of other retrovirus-derived RTL/SIRH genes that likewise play important roles in the current mammalian developmental system, such as in the placenta, brain and innate immune system.
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Affiliation(s)
- Hirosuke Shiura
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Moe Kitazawa
- School of BioSciences, Faculty of Science, The University of Melbourne, Melbourne, VIC, Australia
| | - Fumitoshi Ishino
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomoko Kaneko-Ishino
- Faculty of Nursing, School of Medicine, Tokai University, Isehara, Kanagawa, Japan
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3
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Kocher AA, Dutrow EV, Uebbing S, Yim KM, Larios MFR, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540063. [PMID: 37214934 PMCID: PMC10197647 DOI: 10.1101/2023.05.09.540063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. Here we show that turnover of CpG islands (CGIs), which contribute to enhancer activation, is broadly associated with changes in enhancer activity across mammals, including humans. We integrated maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and found that CGI content in enhancers was strongly associated with increased histone modification levels. CGIs showed widespread turnover across species and species-specific CGIs were strongly enriched for enhancers exhibiting species-specific activity across all tissues and species we examined. Genes associated with enhancers with species-specific CGIs showed concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
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Affiliation(s)
- Acadia A. Kocher
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | - Emily V. Dutrow
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
- Present address: Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | - Kristina M. Yim
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | | | | | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
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4
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Al Adhami H, Bardet AF, Dumas M, Cleroux E, Guibert S, Fauque P, Acloque H, Weber M. A comparative methylome analysis reveals conservation and divergence of DNA methylation patterns and functions in vertebrates. BMC Biol 2022; 20:70. [PMID: 35317801 PMCID: PMC8941758 DOI: 10.1186/s12915-022-01270-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background Cytosine DNA methylation is a heritable epigenetic mark present in most eukaryotic groups. While the patterns and functions of DNA methylation have been extensively studied in mouse and human, their conservation in other vertebrates remains poorly explored. In this study, we interrogated the distribution and function of DNA methylation in primary fibroblasts of seven vertebrate species including bio-medical models and livestock species (human, mouse, rabbit, dog, cow, pig, and chicken). Results Our data highlight both divergence and conservation of DNA methylation patterns and functions. We show that the chicken genome is hypomethylated compared to other vertebrates. Furthermore, compared to mouse, other species show a higher frequency of methylation of CpG-rich DNA. We reveal the conservation of large unmethylated valleys and patterns of DNA methylation associated with X-chromosome inactivation through vertebrate evolution and make predictions of conserved sets of imprinted genes across mammals. Finally, using chemical inhibition of DNA methylation, we show that the silencing of germline genes and endogenous retroviruses (ERVs) are conserved functions of DNA methylation in vertebrates. Conclusions Our data highlight conserved properties of DNA methylation in vertebrate genomes but at the same time point to differences between mouse and other vertebrate species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01270-x.
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Affiliation(s)
- Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Anaïs Flore Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Elouan Cleroux
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Sylvain Guibert
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Patricia Fauque
- Université Bourgogne Franche-Comté, Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, 21000, Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction - CECOS, 14 rue Gaffarel, 21000, Dijon, France
| | - Hervé Acloque
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France. .,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France.
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Renfree MB, Shaw G. Placentation in Marsupials. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2022; 234:41-60. [PMID: 34694477 DOI: 10.1007/978-3-030-77360-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
It is sometimes implied that marsupials are "aplacental," on the presumption that the only mammals that have a placenta are the eponymous "placental" mammals. This misconception has persisted despite the interest in and descriptions of the marsupial placenta, even in Amoroso's definitive chapter. It was also said that marsupials had no maternal recognition of pregnancy and no placental hormone production. In addition, it was thought that genomic imprinting could not exist in marsupials because pregnancy was so short. We now know that none of these ideas have held true with extensive studies over the last four decades definitively showing that they are indeed mammals with a fully functional placenta, and with their own specializations.
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Affiliation(s)
- Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia.
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
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6
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Kaneko-Ishino T, Ishino F. The Evolutionary Advantage in Mammals of the Complementary Monoallelic Expression Mechanism of Genomic Imprinting and Its Emergence From a Defense Against the Insertion Into the Host Genome. Front Genet 2022; 13:832983. [PMID: 35309133 PMCID: PMC8928582 DOI: 10.3389/fgene.2022.832983] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
In viviparous mammals, genomic imprinting regulates parent-of-origin-specific monoallelic expression of paternally and maternally expressed imprinted genes (PEGs and MEGs) in a region-specific manner. It plays an essential role in mammalian development: aberrant imprinting regulation causes a variety of developmental defects, including fetal, neonatal, and postnatal lethality as well as growth abnormalities. Mechanistically, PEGs and MEGs are reciprocally regulated by DNA methylation of germ-line differentially methylated regions (gDMRs), thereby exhibiting eliciting complementary expression from parental genomes. The fact that most gDMR sequences are derived from insertion events provides strong support for the claim that genomic imprinting emerged as a host defense mechanism against the insertion in the genome. Recent studies on the molecular mechanisms concerning how the DNA methylation marks on the gDMRs are established in gametes and maintained in the pre- and postimplantation periods have further revealed the close relationship between genomic imprinting and invading DNA, such as retroviruses and LTR retrotransposons. In the presence of gDMRs, the monoallelic expression of PEGs and MEGs confers an apparent advantage by the functional compensation that takes place between the two parental genomes. Thus, it is likely that genomic imprinting is a consequence of an evolutionary trade-off for improved survival. In addition, novel genes were introduced into the mammalian genome via this same surprising and complex process as imprinted genes, such as the genes acquired from retroviruses as well as those that were duplicated by retropositioning. Importantly, these genes play essential/important roles in the current eutherian developmental system, such as that in the placenta and/or brain. Thus, genomic imprinting has played a critically important role in the evolutionary emergence of mammals, not only by providing a means to escape from the adverse effects of invading DNA with sequences corresponding to the gDMRs, but also by the acquisition of novel functions in development, growth and behavior via the mechanism of complementary monoallelic expression.
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Affiliation(s)
- Tomoko Kaneko-Ishino
- School of Medicine, Tokai University, Isehara, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
| | - Fumitoshi Ishino
- Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
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7
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Keshavarz M, Tautz D. The imprinted lncRNA Peg13 regulates sexual preference and the sex-specific brain transcriptome in mice. Proc Natl Acad Sci U S A 2021; 118:e2022172118. [PMID: 33658376 PMCID: PMC7958240 DOI: 10.1073/pnas.2022172118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian genomes include many maternally and paternally imprinted genes. Most of these are also expressed in the brain, and several have been implicated in regulating specific behavioral traits. Here, we have used a knockout approach to study the function of Peg13, a gene that codes for a fast-evolving lncRNA (long noncoding RNA) and is part of a complex of imprinted genes on chromosome 15 in mice and chromosome 8 in humans. Mice lacking the 3' half of the transcript look morphologically wild-type but show distinct behavioral differences. They lose interest in the opposite sex, instead displaying a preference for wild-type animals of the same sex. Further, they show a higher level of anxiety, lowered activity and curiosity, and a deficiency in pup retrieval behavior. Brain RNA expression analysis reveals that genes involved in the serotonergic system, formation of glutamatergic synapses, olfactory processing, and estrogen signaling-as well as more than half of the other known imprinted genes-show significant expression changes in Peg13-deficient mice. Intriguingly, these pathways are differentially affected in the sexes, resulting in male and female brains of Peg13-deficient mice differing more from each other than those of wild-type mice. We conclude that Peg13 is part of a developmental pathway that regulates the neurobiology of social and sexual interactions.
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Affiliation(s)
- Maryam Keshavarz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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8
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DNA methylome signatures of prenatal exposure to synthetic glucocorticoids in hippocampus and peripheral whole blood of female guinea pigs in early life. Transl Psychiatry 2021; 11:63. [PMID: 33462183 PMCID: PMC7813870 DOI: 10.1038/s41398-020-01186-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
Synthetic glucocorticoids (sGC) are administered to women at risk of preterm delivery, approximately 10% of all pregnancies. In animal models, offspring exposed to elevated glucocorticoids, either by administration of sGC or endogenous glucocorticoids as a result of maternal stress, show increased risk of developing behavioral, endocrine, and metabolic dysregulation. DNA methylation may play a critical role in long-lasting programming of gene regulation underlying these phenotypes. However, peripheral tissues such as blood are often the only accessible source of DNA for epigenetic analyses in humans. Here, we examined the hypothesis that prenatal sGC administration alters DNA methylation signatures in guinea pig offspring hippocampus and whole blood. We compared these signatures across the two tissue types to assess epigenetic biomarkers of common molecular pathways affected by sGC exposure. Guinea pigs were treated with sGC or saline in late gestation. Genome-wide modifications of DNA methylation were analyzed at single nucleotide resolution using reduced representation bisulfite sequencing in juvenile female offspring. Results indicate that there are tissue-specific as well as common methylation signatures of prenatal sGC exposure. Over 90% of the common methylation signatures associated with sGC exposure showed the same directionality of change in methylation. Among differentially methylated genes, 134 were modified in both hippocampus and blood, of which 61 showed methylation changes at identical CpG sites. Gene pathway analyses indicated that prenatal sGC exposure alters the methylation status of gene clusters involved in brain development. These data indicate concordance across tissues of epigenetic programming in response to alterations in glucocorticoid signaling.
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9
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Kaneko-Ishino T, Ishino F. Evolution of viviparity in mammals: what genomic imprinting tells us about mammalian placental evolution. Reprod Fertil Dev 2020; 31:1219-1227. [PMID: 30625287 DOI: 10.1071/rd18127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/01/2018] [Indexed: 01/12/2023] Open
Abstract
Genomic imprinting is an epigenetic mechanism of regulating parent-of-origin-specific monoallelic expression of imprinted genes in viviparous therian mammals such as eutherians and marsupials. In this review we discuss several issues concerning the relationship between mammalian viviparity and genomic imprinting, as well as the domestication of essential placental genes: why has the genomic imprinting mechanism been so widely conserved despite the evident developmental disadvantages originating from monoallelic expression? How have genomic imprinted regions been established in the course of mammalian evolution? What drove the evolution of mammalian viviparity and how have genomic imprinting and domesticated genes contributed to this process? In considering the regulatory mechanism of imprinted genes, reciprocal expression of paternally and maternally expressed genes (PEGs and MEGs respectively) and the presence of several essential imprinted genes for placental formation and maintenance, it is likely that complementary, thereby monoallelic, expression of PEGs and MEGs is an evolutionary trade-off for survival. The innovation in novel imprinted regions was associated with the emergence of imprinting control regions, suggesting that genomic imprinting arose as a genome defence mechanism against the insertion of exogenous DNA. Mammalian viviparity emerged in the period when the atmospheric oxygen concentration was the lowest (~12%) during the last 550 million years (the Phanerozoic eon), implying this low oxygen concentration was a key factor in promoting mammalian viviparity as a response to a major evolutionary pressure. Because genomic imprinting and gene domestication from retrotransposons or retroviruses are effective measures of changing genomic function in therian mammals, they are likely to play critical roles in the emergence of viviparity for longer gestation periods.
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Affiliation(s)
- Tomoko Kaneko-Ishino
- School of Health Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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10
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Apicella C, Ruano CSM, Méhats C, Miralles F, Vaiman D. The Role of Epigenetics in Placental Development and the Etiology of Preeclampsia. Int J Mol Sci 2019; 20:ijms20112837. [PMID: 31212604 PMCID: PMC6600551 DOI: 10.3390/ijms20112837] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022] Open
Abstract
In this review, we comprehensively present the function of epigenetic regulations in normal placental development as well as in a prominent disease of placental origin, preeclampsia (PE). We describe current progress concerning the impact of DNA methylation, non-coding RNA (with a special emphasis on long non-coding RNA (lncRNA) and microRNA (miRNA)) and more marginally histone post-translational modifications, in the processes leading to normal and abnormal placental function. We also explore the potential use of epigenetic marks circulating in the maternal blood flow as putative biomarkers able to prognosticate the onset of PE, as well as classifying it according to its severity. The correlation between epigenetic marks and impacts on gene expression is systematically evaluated for the different epigenetic marks analyzed.
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Affiliation(s)
- Clara Apicella
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Camino S M Ruano
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Céline Méhats
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Francisco Miralles
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Daniel Vaiman
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
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11
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Creeth HDJ, McNamara GI, Isles AR, John RM. Imprinted genes influencing the quality of maternal care. Front Neuroendocrinol 2019; 53:100732. [PMID: 30553874 DOI: 10.1016/j.yfrne.2018.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/15/2018] [Accepted: 12/12/2018] [Indexed: 12/20/2022]
Abstract
In mammals successful rearing imposes a cost on later reproductive fitness specifically on the mother creating the potential for parental conflict. Loss of function of three imprinted genes in the dam results in deficits in maternal care suggesting that, like maternal nutrients, maternal care is a resource over which the parental genomes are in conflict. The induction of maternal care is a complex, highly regulated process and it is unsurprising that many gene disruptions and environmental adversities result in maternal care deficits. However, recent compelling evidence for a more purposeful imprinting phenomenon comes from observing alterations in the mother's behaviour when expression of the imprinted genes Phlda2 and Peg3 has been manipulated solely in the offspring. This explicit demonstration that imprinted genes expressed in the offspring influence maternal behaviour lends significant weight to the hypothesis that maternal care is a resource that has been manipulated by the paternal genome.
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Affiliation(s)
- H D J Creeth
- Biomedicine Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - G I McNamara
- Biomedicine Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - A R Isles
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff CF24 4HQ, UK
| | - R M John
- Biomedicine Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
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12
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Suzuki S, Shaw G, Renfree MB. Identification of a novel antisense noncoding RNA, ALID, transcribed from the putative imprinting control region of marsupial IGF2R. Epigenetics Chromatin 2018; 11:55. [PMID: 30268152 PMCID: PMC6162910 DOI: 10.1186/s13072-018-0227-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/25/2018] [Indexed: 12/20/2022] Open
Abstract
Background Genomic imprinting leads to maternal expression of IGF2R in both mouse and opossum. In mouse, the antisense long noncoding (lnc) RNA Airn, which is paternally expressed from the differentially methylated region (DMR) in the second intron of Igf2r, is required to silence the paternal Igf2r. In opossum, however, intriguingly, the DMR was reported to be in a different downstream intron (intron 11) and there was no antisense lncRNA detected in previous analyses. Therefore, clarifying the imprinting mechanism of marsupial IGF2R is of great relevance for understanding the origin and evolution of genomic imprinting in the IGF2R locus. Thus, the antisense lncRNA associated with the marsupial DMR can be considered as the ‘missing link’. In this study, we identified a novel antisense lncRNA, ALID, after detailed analysis of the IGF2R locus in an Australian marsupial, the tammar wallaby, Macropus eugenii, and compared it to that of the grey short-tailed opossum, Monodelphis domestica. Results Tammar IGF2R showed maternal expression and had a maternally methylated CpG island (CGI) in intron 12 as well as a promoter CGI without differential methylation, but none in the second intron. Re-analysis of the IGF2R of opossum detected the CGI in intron 12, not intron 11, as previously reported, confirming that the DMR in intron 12 is conserved between these marsupials and so is the putative imprinting control region of marsupial IGF2R. ALID is paternally expressed from the middle of the DMR and is approximately 650 bp long with a single exon structure that is extremely short compared to Airn. Hence, the lncRNA transcriptional overlap of the IGF2R promoter, which is essential for the Igf2r silencing in the mouse, is likely absent in tammar. This suggests that fundamental differences in the lncRNA-based silencing mechanisms evolved in eutherian and marsupial IGF2R and may reflect the lack of differential methylation in the promoter CGI of marsupial IGF2R. Conclusions Our study thus provides the best candidate factor for establishing paternal silencing of marsupial IGF2R without transcriptional overlap, which is distinct from the Igf2r silencing mechanism of Airn, but which may be analogous to the mode of action for the flanking Slc22a2 and Slc22a3 gene silencing in the mouse placenta. Electronic supplementary material The online version of this article (10.1186/s13072-018-0227-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, 399-4598, Japan.,Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, ICCER, Shinshu University, Nagano, 399-4598, Japan
| | - Geoffrey Shaw
- School of BioSciences, The University of Melbourne, Victoria, 3010, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Victoria, 3010, Australia.
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Mori S, Hayashi M, Inagaki S, Oshima T, Tateishi K, Fujii H, Suzuki S. Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies. Genome Biol Evol 2016; 8:2288-96. [PMID: 27389689 PMCID: PMC5010893 DOI: 10.1093/gbe/evw156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The human genome contains thousands of retrocopies, mostly as processed pseudogenes, which were recently shown to be prevalently transcribed. In particular, those specifically acquired in the human lineage are able to modulate gene expression in a manner that contributed to the evolution of human-specific traits. Therefore, knowledge of the human-specific retrocopies that are transcribed or their full-length transcript structure contributes to better understand human genome evolution. In this study, we identified 16 human-specific retrocopies that harbor 5' CpG islands by in silico analysis and showed that 12 were transcribed in normal tissues and cancer cell lines with a variety of expression patterns, including cancer-specific expression. Determination of the structure of the transcripts associated with the retrocopies revealed that none were transcribed from their 5' CpG islands, but rather, from inside the 3' UTR and the nearby 5' flanking region of the retrocopies as well as the promoter of neighboring genes. The multiple forms of the transcripts, such as chimeric and individual transcripts in both the sense and antisense orientation, might have introduced novel post-transcriptional regulation into the genome during human evolution. These results shed light on the potential role of human-specific retrocopies in the evolution of gene regulation and genomic disorders.
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Affiliation(s)
- Saori Mori
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Masaaki Hayashi
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Shun Inagaki
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Takuji Oshima
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Ken Tateishi
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Hiroshi Fujii
- Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Kami-Ina, Nagano, Japan
| | - Shunsuke Suzuki
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Kami-Ina, Nagano, Japan
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Larriba E, del Mazo J. Role of Non-Coding RNAs in the Transgenerational Epigenetic Transmission of the Effects of Reprotoxicants. Int J Mol Sci 2016; 17:452. [PMID: 27023531 PMCID: PMC4848908 DOI: 10.3390/ijms17040452] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/14/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are regulatory elements of gene expression and chromatin structure. Both long and small ncRNAs can also act as inductors and targets of epigenetic programs. Epigenetic patterns can be transmitted from one cell to the daughter cell, but, importantly, also through generations. Diversity of ncRNAs is emerging with new and surprising roles. Functional interactions among ncRNAs and between specific ncRNAs and structural elements of the chromatin are drawing a complex landscape. In this scenario, epigenetic changes induced by environmental stressors, including reprotoxicants, can explain some transgenerationally-transmitted phenotypes in non-Mendelian ways. In this review, we analyze mechanisms of action of reprotoxicants upon different types of ncRNAs and epigenetic modifications causing transgenerationally transmitted characters through germ cells but affecting germ cells and reproductive systems. A functional model of epigenetic mechanisms of transgenerational transmission ncRNAs-mediated is also proposed.
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Affiliation(s)
- Eduardo Larriba
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain.
| | - Jesús del Mazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain.
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Abstract
A fundamental initiative for evolutionary biologists is to understand the molecular basis underlying phenotypic diversity. A long-standing hypothesis states that species-specific traits may be explained by differences in gene regulation rather than differences at the protein level. Over the past few years, evolutionary studies have shifted from mere sequence comparisons to integrative analyses in which gene regulation is key to understanding species evolution. DNA methylation is an important epigenetic modification involved in the regulation of numerous biological processes. Nevertheless, the evolution of the human methylome and the processes driving such changes are poorly understood. Here, we review the close interplay between Cytosine-phosphate-Guanine (CpG) methylation and the underlying genome sequence, as well as its evolutionary impact. We also summarize the latest advances in the field, revisiting the main literature on human and nonhuman primates. We hope to encourage the scientific community to address the many challenges posed by the field of comparative epigenomics.
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Quah S, Holland PWH. The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution. EvoDevo 2015; 6:31. [PMID: 26451238 PMCID: PMC4597612 DOI: 10.1186/s13227-015-0027-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/25/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Introns represent a potentially rich source of existing transcription for the evolution of novel microRNAs (miRNAs). Within the Hox gene clusters, a miRNA gene, miR-615, is located within the intron of the Hoxc5 gene. This miRNA has a restricted phylogenetic distribution, providing an opportunity to examine the origin and evolution of a new miRNA within the intron of a developmentally-important homeobox gene. RESULTS Alignment and structural analyses show that the sequence is highly conserved across eutherian mammals and absent in non-mammalian tetrapods. Marsupials possess a similar sequence which we predict will not be efficiently processed as a miRNA. Our analyses suggest that transcription of HOXC5 in humans is accompanied by expression of miR-615 in all cases, but that the miRNA can also be transcribed independently of its host gene through the use of an intragenic promoter. We present scenarios for the evolution of miR-615 through intronic exaptation, and speculate on the acquisition of independent transcriptional regulation. Target prediction and transcriptomic analyses suggest that the dominant product of miR-615 is involved in the regulation of growth and a range of developmental processes. CONCLUSIONS The miR-615 gene evolved within the intron of Hoxc5 in the ancestor of placental mammals. Using miR-615 as a case study, we propose a model by which a functional miRNA can emerge within an intron gradually, by selection on secondary structure followed by evolution of an independent miRNA promoter. The location within a Hox gene intron is of particular interest as the miRNA is specific to placental mammals, is co-expressed with its host gene and may share complementary functions.
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Affiliation(s)
- Shan Quah
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Peter W. H. Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
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17
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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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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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Thomas M, Pingault L, Poulet A, Duarte J, Throude M, Faure S, Pichon JP, Paux E, Probst AV, Tatout C. Evolutionary history of Methyltransferase 1 genes in hexaploid wheat. BMC Genomics 2014; 15:922. [PMID: 25342325 PMCID: PMC4223845 DOI: 10.1186/1471-2164-15-922] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Plant and animal methyltransferases are key enzymes involved in DNA methylation at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of the wheat genome recently released by the International Wheat Genome Sequencing Consortium, we identified and characterized MET1 genes in the hexaploid wheat Triticum aestivum (TaMET1). RESULTS Nine TaMET1 genes were identified and mapped on homoeologous chromosome groups 2A/2B/2D, 5A/5B/5D and 7A/7B/7D. Synteny analysis and evolution rates suggest that the genome organization of TaMET1 genes results from a whole genome duplication shared within the grass family, and a second gene duplication, which occurred specifically in the Triticeae tribe prior to the speciation of diploid wheat. Higher expression levels were observed for TaMET1 homoeologous group 2 genes compared to group 5 and 7, indicating that group 2 homoeologous genes are predominant at the transcriptional level, while group 5 evolved into pseudogenes. We show the connection between low expression levels, elevated evolution rates and unexpected enrichment in CG-dinucleotides (CG-rich isochores) at putative promoter regions of homoeologous group 5 and 7, but not of group 2 TaMET1 genes. Bisulfite sequencing reveals that these CG-rich isochores are highly methylated in a CG context, which is the expected target of TaMET1. CONCLUSIONS We retraced the evolutionary history of MET1 genes in wheat, explaining the predominance of group 2 homoeologous genes and suggest CG-DNA methylation as one of the mechanisms involved in wheat genome dynamics.
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Affiliation(s)
- Mélanie Thomas
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Lise Pingault
- />UMR INRA 1095 Blaise Pascal University, Genetics Diversity & Ecophysiology of Cereals (GDEC), Clermont-Ferrand – Theix, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex 2, France
| | - Axel Poulet
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| | - Jorge Duarte
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Mickaël Throude
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Sébastien Faure
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Jean-Philippe Pichon
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Etienne Paux
- />UMR INRA 1095 Blaise Pascal University, Genetics Diversity & Ecophysiology of Cereals (GDEC), Clermont-Ferrand – Theix, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex 2, France
| | - Aline Valeska Probst
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| | - Christophe Tatout
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
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20
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Spencer HG, Clark AG. Non-conflict theories for the evolution of genomic imprinting. Heredity (Edinb) 2014; 113:112-8. [PMID: 24398886 PMCID: PMC4105448 DOI: 10.1038/hdy.2013.129] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 01/09/2023] Open
Abstract
Theories focused on kinship and the genetic conflict it induces are widely considered to be the primary explanations for the evolution of genomic imprinting. However, there have appeared many competing ideas that do not involve kinship/conflict. These ideas are often overlooked because kinship/conflict is entrenched in the literature, especially outside evolutionary biology. Here we provide a critical overview of these non-conflict theories, providing an accessible perspective into this literature. We suggest that some of these alternative hypotheses may, in fact, provide tenable explanations of the evolution of imprinting for at least some loci.
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Affiliation(s)
- H G Spencer
- Allan Wilson Centre for Molecular Ecology & Evolution and Gravida: National Centre for Growth & Development, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - A G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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21
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Rademacher K, Schröder C, Kanber D, Klein-Hitpass L, Wallner S, Zeschnigk M, Horsthemke B. Evolutionary origin and methylation status of human intronic CpG islands that are not present in mouse. Genome Biol Evol 2014; 6:1579-88. [PMID: 24923327 PMCID: PMC4122923 DOI: 10.1093/gbe/evu125] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2014] [Indexed: 12/21/2022] Open
Abstract
Imprinting of the human RB1 gene is due to the presence of a differentially methylated CpG island (CGI) in intron 2, which is part of a retrocopy derived from the PPP1R26 gene on chromosome 9. The murine Rb1 gene does not have this retrocopy and is not imprinted. We have investigated whether the RB1/Rb1 locus is unique with respect to these differences. For this, we have compared the CGIs from human and mouse by in silico analyses. We have found that the human genome does not only contain more CGIs than the mouse, but the proportion of intronic CGIs is also higher (7.7% vs. 3.5%). At least 2,033 human intronic CGIs are not present in the mouse. Among these CGIs, 104 show sequence similarities elsewhere in the human genome, which suggests that they arose from retrotransposition. We could narrow down the time points when most of these CGIs appeared during evolution. Their methylation status was analyzed in two monocyte methylome data sets from whole-genome bisulfite sequencing and in 18 published methylomes. Four CGIs, which are located in the RB1, ASRGL1, PARP11, and PDXDC1 genes, occur as methylated and unmethylated copies. In contrast to imprinted methylation at the RB1 locus, differential methylation of the ASRGL1 and PDXDC1 CGIs appears to be sequence dependent. Our study supports the notion that the epigenetic fate of the retrotransposed DNA depends on its sequence and selective forces at the integration site.
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Affiliation(s)
- Katrin Rademacher
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Christopher Schröder
- Genominformatik, Institut für Humangenetik, Medizinische Fakultät, Universität Duisburg-Essen, Essen, Germany
| | - Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Ludger Klein-Hitpass
- BioChip Labor, Institut für Zellbiologie, Medizinische Fakultät, Universität Duisburg-Essen, Essen, Germany
| | - Stefan Wallner
- Institut für Klinische Chemie und Laboratoriumsmedizin, Universitätsklinikum Regensburg, Universität Regensburg, Germany
| | - Michael Zeschnigk
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
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22
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Post-natal imprinting: evidence from marsupials. Heredity (Edinb) 2014; 113:145-55. [PMID: 24595366 DOI: 10.1038/hdy.2014.10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 12/19/2013] [Accepted: 01/09/2014] [Indexed: 12/31/2022] Open
Abstract
Genomic imprinting has been identified in therian (eutherian and marsupial) mammals but not in prototherian (monotreme) mammals. Imprinting has an important role in optimising pre-natal nutrition and growth, and most imprinted genes are expressed and imprinted in the placenta and developing fetus. In marsupials, however, the placental attachment is short-lived, and most growth and development occurs post-natally, supported by a changing milk composition tailor-made for each stage of development. Therefore there is a much greater demand on marsupial females during post-natal lactation than during pre-natal placentation, so there may be greater selection for genomic imprinting in the mammary gland than in the short-lived placenta. Recent studies in the tammar wallaby confirm the presence of genomic imprinting in nutrient-regulatory genes in the adult mammary gland. This suggests that imprinting may influence infant post-natal growth via the mammary gland as it does pre-natally via the placenta. Similarly, an increasing number of imprinted genes have been implicated in regulating feeding and nurturing behaviour in both the adult and the developing neonate/offspring in mice. Together these studies provide evidence that genomic imprinting is critical for regulating growth and subsequently the survival of offspring not only pre-natally but also post-natally.
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Postnatal epigenetic reprogramming in the germline of a marsupial, the tammar wallaby. Epigenetics Chromatin 2013; 6:14. [PMID: 23732002 PMCID: PMC3687581 DOI: 10.1186/1756-8935-6-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/08/2013] [Indexed: 01/24/2023] Open
Abstract
Background Epigenetic reprogramming is essential to restore totipotency and to reset genomic imprints during mammalian germ cell development and gamete formation. The dynamic DNA methylation change at DMRs (differentially methylated regions) within imprinted domains and of retrotransposons is characteristic of this process. Both marsupials and eutherian mammals have genomic imprinting but these two subgroups have been evolving separately for up to 160 million years. Marsupials have a unique reproductive strategy and deliver tiny, altricial young that complete their development within their mother's pouch. Germ cell proliferation in the genital ridge continues after birth in the tammar wallaby (Macropus eugenii), and it is only after 25 days postpartum that female germ cells begin to enter meiosis and male germ cells begin to enter mitotic arrest. At least two marsupial imprinted loci (PEG10 and H19) also have DMRs. To investigate the evolution of epigenetic reprogramming in the marsupial germline, here we collected germ cells from male pouch young of the tammar wallaby and analysed the methylation status of PEG10 and H19 DMR, an LTR (long terminal repeat) and a non-LTR retrotransposons. Results Demethylation of the H19 DMR was almost completed by 14 days postpartum and de-novo methylation started from 34 days postpartum. These stages correspond to 14 days after the completion of primordial germ cell migration into genital ridge (demethylation) and 9 days after the first detection of mitotic arrest (re-methylation) in the male germ cells. Interestingly, the PEG10 DMR was already unmethylated at 7 days postpartum, suggesting that the timing of epigenetic reprogramming is not the same at all genomic loci. Retrotransposon methylation was not completely removed after the demethylation event in the germ cells, similar to the situation in the mouse. Conclusions Thus, despite the postnatal occurrence of epigenetic reprogramming and the persistence of genome-wide undermethylation for 20 days in the postnatal tammar, the relative timing and mechanism of germ cell reprogramming are conserved between marsupials and eutherians. We suggest that the basic mechanism of epigenetic reprogramming had already been established before the marsupial-eutherian split and has been faithfully maintained for at least 160 million years and may reflect the timing of the onset of mitotic arrest in the male germline.
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24
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Renfree MB, Suzuki S, Kaneko-Ishino T. The origin and evolution of genomic imprinting and viviparity in mammals. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120151. [PMID: 23166401 DOI: 10.1098/rstb.2012.0151] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genomic imprinting is widespread in eutherian mammals. Marsupial mammals also have genomic imprinting, but in fewer loci. It has long been thought that genomic imprinting is somehow related to placentation and/or viviparity in mammals, although neither is restricted to mammals. Most imprinted genes are expressed in the placenta. There is no evidence for genomic imprinting in the egg-laying monotreme mammals, despite their short-lived placenta that transfers nutrients from mother to embryo. Post natal genomic imprinting also occurs, especially in the brain. However, little attention has been paid to the primary source of nutrition in the neonate in all mammals, the mammary gland. Differentially methylated regions (DMRs) play an important role as imprinting control centres in each imprinted region which usually comprises both paternally and maternally expressed genes (PEGs and MEGs). The DMR is established in the male or female germline (the gDMR). Comprehensive comparative genome studies demonstrated that two imprinted regions, PEG10 and IGF2-H19, are conserved in both marsupials and eutherians and that PEG10 and H19 DMRs emerged in the therian ancestor at least 160 Ma, indicating the ancestral origin of genomic imprinting during therian mammal evolution. Importantly, these regions are known to be deeply involved in placental and embryonic growth. It appears that most maternal gDMRs are always associated with imprinting in eutherian mammals, but emerged at differing times during mammalian evolution. Thus, genomic imprinting could evolve from a defence mechanism against transposable elements that depended on DNA methylation established in germ cells.
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Affiliation(s)
- Marilyn B Renfree
- Department of Zoology, The University of Melbourne, Victoria 3010, Australia.
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25
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Stringer JM, Suzuki S, Pask AJ, Shaw G, Renfree MB. GRB10 imprinting is eutherian mammal specific. Mol Biol Evol 2012; 29:3711-9. [PMID: 22787282 DOI: 10.1093/molbev/mss173] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
GRB10 is an imprinted gene differently expressed from two promoters in mouse and human. Mouse Grb10 is maternally expressed from the major promoter in most tissues and paternally expressed from the brain-specific promoter within specific regions of the fetal and adult central nervous system. Human GRB10 is biallelically expressed from the major promoter in most tissues except in the placental villus trophoblast where it is maternally expressed, whereas the brain-specific promoter is paternally expressed in the fetal brain. This study characterized the ortholog of GRB10 in a marsupial, the tammar wallaby (Macropus eugenii) to investigate the origin and evolution of imprinting at this locus. The protein coding exons and predicted amino acid sequence of tammar GRB10 were highly conserved with eutherian GRB10. The putative first exon, which is located in the orthologous region to the eutherian major promoter, was found in the tammar, but no exon was found in the downstream region corresponding to the eutherian brain-specific promoter, suggesting that marsupials only have a single promoter. Tammar GRB10 was widely expressed in various tissues including the brain but was not imprinted in any of the tissues examined. Thus, it is likely that GRB10 imprinting evolved in eutherians after the eutherian-marsupial divergence approximately 160 million years ago, subsequent to the acquisition of a brain-specific promoter, which resides within the imprinting control region in eutherians.
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Affiliation(s)
- Jessica M Stringer
- ARC Centre of Excellence in Kangaroo Genomics, University of Melbourne, Melbourne, Victoria, Australia
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