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Moindrot B, Imaizumi Y, Feil R. Differential 3D genome architecture and imprinted gene expression: cause or consequence? Biochem Soc Trans 2024; 52:973-986. [PMID: 38775198 PMCID: PMC11346452 DOI: 10.1042/bst20230143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.
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Affiliation(s)
- Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yui Imaizumi
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
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2
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Yao S, Prates K, Freydenzon A, Assante G, McRae AF, Morris MJ, Youngson NA. Liver-specific deletion of de novo DNA methyltransferases protects against glucose intolerance in high-fat diet-fed male mice. FASEB J 2024; 38:e23690. [PMID: 38795327 DOI: 10.1096/fj.202301546rr] [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: 08/03/2023] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/27/2024]
Abstract
Alterations to gene transcription and DNA methylation are a feature of many liver diseases including fatty liver disease and liver cancer. However, it is unclear whether the DNA methylation changes are a cause or a consequence of the transcriptional changes. It is even possible that the methylation changes are not required for the transcriptional changes. If DNA methylation is just a minor player in, or a consequence of liver transcriptional change, then future studies in this area should focus on other systems such as histone tail modifications. To interrogate the importance of de novo DNA methylation, we generated mice that are homozygous mutants for both Dnmt3a and Dnmt3b in post-natal liver. These mice are viable and fertile with normal sized livers. Males, but not females, showed increased adipose depots, yet paradoxically, improved glucose tolerance on both control diet and high-fat diets (HFD). Comparison of the transcriptome and methylome with RNA sequencing and whole-genome bisulfite sequencing in adult hepatocytes revealed that widespread loss of methylation in CpG-rich regions in the mutant did not induce loss of homeostatic transcriptional regulation. Similarly, extensive transcriptional changes induced by HFD did not require de novo DNA methylation. The improved metabolic phenotype of the Dnmt3a/3b mutant mice may be mediated through the dysregulation of a subset of glucose and fat metabolism genes which increase both glucose uptake and lipid export by the liver. However, further work is needed to confirm this.
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Affiliation(s)
- S Yao
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - K Prates
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Department of Biotechnology, Genetics, and Cellular Biology, State University of Maringá, Maringá, Brazil
| | - A Freydenzon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - G Assante
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - A F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - M J Morris
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - N A Youngson
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
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3
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Moorwood K, Smith FM, Garfield AS, Ward A. Imprinted Grb10, encoding growth factor receptor bound protein 10, regulates fetal growth independently of the insulin-like growth factor type 1 receptor (Igf1r) and insulin receptor (Insr) genes. BMC Biol 2024; 22:127. [PMID: 38816743 PMCID: PMC11140863 DOI: 10.1186/s12915-024-01926-w] [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: 11/21/2023] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Optimal size at birth dictates perinatal survival and long-term risk of developing common disorders such as obesity, type 2 diabetes and cardiovascular disease. The imprinted Grb10 gene encodes a signalling adaptor protein capable of inhibiting receptor tyrosine kinases, including the insulin receptor (Insr) and insulin-like growth factor type 1 receptor (Igf1r). Grb10 restricts fetal growth such that Grb10 knockout (KO) mice are at birth some 25-35% larger than wild type. Using a mouse genetic approach, we test the widely held assumption that Grb10 influences growth through interaction with Igf1r, which has a highly conserved growth promoting role. RESULTS Should Grb10 interact with Igf1r to regulate growth Grb10:Igf1r double mutant mice should be indistinguishable from Igf1r KO single mutants, which are around half normal size at birth. Instead, Grb10:Igf1r double mutants were intermediate in size between Grb10 KO and Igf1r KO single mutants, indicating additive effects of the two signalling proteins having opposite actions in separate pathways. Some organs examined followed a similar pattern, though Grb10 KO neonates exhibited sparing of the brain and kidneys, whereas the influence of Igf1r extended to all organs. An interaction between Grb10 and Insr was similarly investigated. While there was no general evidence for a major interaction for fetal growth regulation, the liver was an exception. The liver in Grb10 KO mutants was disproportionately overgrown with evidence of excess lipid storage in hepatocytes, whereas Grb10:Insr double mutants were indistinguishable from Insr single mutants or wild types. CONCLUSIONS Grb10 acts largely independently of Igf1r or Insr to control fetal growth and has a more variable influence on individual organs. Only the disproportionate overgrowth and excess lipid storage seen in the Grb10 KO neonatal liver can be explained through an interaction between Grb10 and the Insr. Our findings are important for understanding how positive and negative influences on fetal growth dictate size and tissue proportions at birth.
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Affiliation(s)
- Kim Moorwood
- Department of Life Sciences, University of Bath, Building 4 South, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Florentia M Smith
- Department of Life Sciences, University of Bath, Building 4 South, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Alastair S Garfield
- Department of Life Sciences, University of Bath, Building 4 South, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Andrew Ward
- Department of Life Sciences, University of Bath, Building 4 South, Claverton Down, Bath, BA2 7AY, United Kingdom.
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4
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Regmi S, Giha L, Ali A, Siebels-Lindquist C, Davis TL. Methylation is maintained specifically at imprinting control regions but not other DMRs associated with imprinted genes in mice bearing a mutation in the Dnmt1 intrinsically disordered domain. Front Cell Dev Biol 2023; 11:1192789. [PMID: 37601113 PMCID: PMC10436486 DOI: 10.3389/fcell.2023.1192789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Differential methylation of imprinting control regions in mammals is essential for distinguishing the parental alleles from each other and regulating their expression accordingly. To ensure parent of origin-specific expression of imprinted genes and thereby normal developmental progression, the differentially methylated states that are inherited at fertilization must be stably maintained by DNA methyltransferase 1 throughout subsequent somatic cell division. Further epigenetic modifications, such as the acquisition of secondary regions of differential methylation, are dependent on the methylation status of imprinting control regions and are important for achieving the monoallelic expression of imprinted genes, but little is known about how imprinting control regions direct the acquisition and maintenance of methylation at these secondary sites. Recent analysis has identified mutations that reduce DNA methyltransferase 1 fidelity at some genomic sequences but not at others, suggesting that it may function differently at different loci. We examined the impact of the mutant DNA methyltransferase 1 P allele on methylation at imprinting control regions as well as at secondary differentially methylated regions and non-imprinted sequences. We found that while the P allele results in a major reduction in DNA methylation levels across the mouse genome, methylation is specifically maintained at imprinting control regions but not at their corresponding secondary DMRs. This result suggests that DNA methyltransferase 1 may work differently at imprinting control regions or that there is an alternate mechanism for maintaining methylation at these critical regulatory regions and that maintenance of methylation at secondary DMRs is not solely dependent on the methylation status of the ICR.
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Affiliation(s)
| | | | | | | | - Tamara L. Davis
- Department of Biology, Bryn Mawr College, Bryn Mawr, PA, United States
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Juan AM, Foong YH, Thorvaldsen JL, Lan Y, Leu NA, Rurik JG, Li L, Krapp C, Rosier CL, Epstein JA, Bartolomei MS. Tissue-specific Grb10/Ddc insulator drives allelic architecture for cardiac development. Mol Cell 2022; 82:3613-3631.e7. [PMID: 36108632 PMCID: PMC9547965 DOI: 10.1016/j.molcel.2022.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022]
Abstract
Allele-specific expression of imprinted gene clusters is governed by gametic DNA methylation at master regulators called imprinting control regions (ICRs). Non-gametic or secondary differentially methylated regions (DMRs) at promoters and exonic regions reinforce monoallelic expression but do not control an entire cluster. Here, we unveil an unconventional secondary DMR that is indispensable for tissue-specific imprinting of two previously unlinked genes, Grb10 and Ddc. Using polymorphic mice, we mapped an intronic secondary DMR at Grb10 with paternal-specific CTCF binding (CBR2.3) that forms contacts with Ddc. Deletion of paternal CBR2.3 removed a critical insulator, resulting in substantial shifting of chromatin looping and ectopic enhancer-promoter contacts. Destabilized gene architecture precipitated abnormal Grb10-Ddc expression with developmental consequences in the heart and muscle. Thus, we redefine the Grb10-Ddc imprinting domain by uncovering an unconventional intronic secondary DMR that functions as an insulator to instruct the tissue-specific, monoallelic expression of multiple genes-a feature previously ICR exclusive.
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Affiliation(s)
- Aimee M Juan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yee Hoon Foong
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joanne L Thorvaldsen
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicolae A Leu
- Department of Biomedical Sciences, Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Joel G Rurik
- Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li Li
- Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Krapp
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Casey L Rosier
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A Epstein
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Bonthuis PJ, Steinwand S, Stacher Hörndli CN, Emery J, Huang WC, Kravitz S, Ferris E, Gregg C. Noncanonical genomic imprinting in the monoamine system determines naturalistic foraging and brain-adrenal axis functions. Cell Rep 2022; 38:110500. [PMID: 35263575 PMCID: PMC9128000 DOI: 10.1016/j.celrep.2022.110500] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/07/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Noncanonical genomic imprinting can cause biased expression of one parental allele in a tissue; however, the functional relevance of such biases is unclear. To investigate ethological roles for noncanonical imprinting in dopa decarboxylase (Ddc) and tyrosine hydroxylase (Th), we use machine learning to decompose naturalistic foraging in maternal and paternal allele mutant heterozygous mice. We uncover distinct roles for the maternal versus paternal alleles on foraging, where maternal alleles affect sons while daughters are under paternal allelic control. Each parental allele controls specific action sequences reflecting decisions in naive or familiar contexts. The maternal Ddc allele is preferentially expressed in subsets of hypothalamic GABAergic neurons, while the paternal allele predominates in subsets of adrenal cells. Each Ddc allele affects distinct molecular and endocrine components of the brain-adrenal axis. Thus, monoaminergic noncanonical imprinting has ethological roles in foraging and endocrine functions and operates by affecting discrete subsets of cells.
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Affiliation(s)
- Paul J Bonthuis
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign College of Veterinary Medicine, Urbana, IL, USA
| | - Susan Steinwand
- Department of Neurobiology, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Cornelia N Stacher Hörndli
- Department of Neurobiology, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Jared Emery
- Department of Neurobiology, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Wei-Chao Huang
- Department of Neurobiology, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Stephanie Kravitz
- Department of Neurobiology, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Elliott Ferris
- Department of Neurobiology, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Christopher Gregg
- Department of Neurobiology, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Room 408B, Biopolymers Research Building, Bld. 570, 20 South 2030 East, Salt Lake City, UT 84112, USA.
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7
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Scagliotti V, Esse R, Willis TL, Howard M, Carrus I, Lodge E, Andoniadou CL, Charalambous M. Dynamic Expression of Imprinted Genes in the Developing and Postnatal Pituitary Gland. Genes (Basel) 2021; 12:genes12040509. [PMID: 33808370 PMCID: PMC8066104 DOI: 10.3390/genes12040509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
In mammals, imprinted genes regulate many critical endocrine processes such as growth, the onset of puberty and maternal reproductive behaviour. Human imprinting disorders (IDs) are caused by genetic and epigenetic mechanisms that alter the expression dosage of imprinted genes. Due to improvements in diagnosis, increasing numbers of patients with IDs are now identified and monitored across their lifetimes. Seminal work has revealed that IDs have a strong endocrine component, yet the contribution of imprinted gene products in the development and function of the hypothalamo-pituitary axis are not well defined. Postnatal endocrine processes are dependent upon the production of hormones from the pituitary gland. While the actions of a few imprinted genes in pituitary development and function have been described, to date there has been no attempt to link the expression of these genes as a class to the formation and function of this essential organ. This is important because IDs show considerable overlap, and imprinted genes are known to define a transcriptional network related to organ growth. This knowledge deficit is partly due to technical difficulties in obtaining useful transcriptomic data from the pituitary gland, namely, its small size during development and cellular complexity in maturity. Here we utilise high-sensitivity RNA sequencing at the embryonic stages, and single-cell RNA sequencing data to describe the imprinted transcriptome of the pituitary gland. In concert, we provide a comprehensive literature review of the current knowledge of the role of imprinted genes in pituitary hormonal pathways and how these relate to IDs. We present new data that implicate imprinted gene networks in the development of the gland and in the stem cell compartment. Furthermore, we suggest novel roles for individual imprinted genes in the aetiology of IDs. Finally, we describe the dynamic regulation of imprinted genes in the pituitary gland of the pregnant mother, with implications for the regulation of maternal metabolic adaptations to pregnancy.
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Affiliation(s)
- Valeria Scagliotti
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Ruben Esse
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Thea L. Willis
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
| | - Mark Howard
- MRC Centre for Transplantation, Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London SE19RT, UK;
| | - Isabella Carrus
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Emily Lodge
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
| | - Cynthia L. Andoniadou
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Marika Charalambous
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
- Correspondence:
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8
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Baulina N, Kiselev I, Favorova O. Imprinted Genes and Multiple Sclerosis: What Do We Know? Int J Mol Sci 2021; 22:1346. [PMID: 33572862 PMCID: PMC7866243 DOI: 10.3390/ijms22031346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neurodegenerative disease of the central nervous system that arises from interplay between non-genetic and genetic risk factors. The epigenetics functions as a link between these factors, affecting gene expression in response to external influence, and therefore should be extensively studied to improve the knowledge of MS molecular mechanisms. Among others, the epigenetic mechanisms underlie the establishment of parent-of-origin effects that appear as phenotypic differences depending on whether the allele was inherited from the mother or father. The most well described manifestation of parent-of-origin effects is genomic imprinting that causes monoallelic gene expression. It becomes more obvious that disturbances in imprinted genes at the least affecting their expression do occur in MS and may be involved in its pathogenesis. In this review we will focus on the potential role of imprinted genes in MS pathogenesis.
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Affiliation(s)
- Natalia Baulina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ivan Kiselev
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
| | - Olga Favorova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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Catusi I, Bonati MT, Mainini E, Russo S, Orlandini E, Larizza L, Recalcati MP. Recombinant Chromosome 7 Driven by Maternal Chromosome 7 Pericentric Inversion in a Girl with Features of Silver-Russell Syndrome. Int J Mol Sci 2020; 21:ijms21228487. [PMID: 33187293 PMCID: PMC7698152 DOI: 10.3390/ijms21228487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022] Open
Abstract
Maternal uniparental disomy of chromosome 7 is present in 5-10% of patients with Silver-Russell syndrome (SRS), and duplication of 7p including GRB10 (Growth Factor Receptor-Bound Protein 10), an imprinted gene that affects pre-and postnatal growth retardation, has been associated with the SRS phenotype. Here, we report on a 17 year old girl referred to array-CGH analysis for short stature, psychomotor delay, and relative macrocephaly. Array-CGH analysis showed two copy number variants (CNVs): a ~12.7 Mb gain in 7p13-p11.2, involving GRB10 and an ~9 Mb loss in 7q11.21-q11.23. FISH experiments performed on the proband's mother showed a chromosome 7 pericentric inversion that might have mediated the complex rearrangement harbored by the daughter. Indeed, we found that segmental duplications, of which chromosome 7 is highly enriched, mapped at the breakpoints of both the mother's inversion and the daughter's CNVs. We postulate that pairing of highly homologous sequences might have perturbed the correct meiotic chromosome segregation, leading to unbalanced outcomes and acting as the putative meiotic mechanism that was causative of the proband's rearrangement. Comparison of the girl's phenotype to those of patients with similar CNVs supports the presence of 7p in a locus associated with features of SRS syndrome.
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Affiliation(s)
- Ilaria Catusi
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, 20149 Milano, Italy; (I.C.); (E.M.); (S.R.); (L.L.)
| | - Maria Teresa Bonati
- Ambulatorio di Genetica Medica, Istituto Auxologico Italiano, IRCCS, 20149 Milano, Italy; (M.T.B.); (E.O.)
| | - Ester Mainini
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, 20149 Milano, Italy; (I.C.); (E.M.); (S.R.); (L.L.)
| | - Silvia Russo
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, 20149 Milano, Italy; (I.C.); (E.M.); (S.R.); (L.L.)
| | - Eleonora Orlandini
- Ambulatorio di Genetica Medica, Istituto Auxologico Italiano, IRCCS, 20149 Milano, Italy; (M.T.B.); (E.O.)
| | - Lidia Larizza
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, 20149 Milano, Italy; (I.C.); (E.M.); (S.R.); (L.L.)
| | - Maria Paola Recalcati
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, 20149 Milano, Italy; (I.C.); (E.M.); (S.R.); (L.L.)
- Correspondence:
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10
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Varrault A, Dubois E, Le Digarcher A, Bouschet T. Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain. EPIGENOMES 2020; 4:21. [PMID: 34968292 PMCID: PMC8594728 DOI: 10.3390/epigenomes4030021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Imprinted genes are a group of ~150 genes that are preferentially expressed from one parental allele owing to epigenetic marks asymmetrically distributed on inherited maternal and paternal chromosomes. Altered imprinted gene expression causes human brain disorders such as Prader-Willi and Angelman syndromes and additional rare brain diseases. Research data principally obtained from the mouse model revealed how imprinted genes act in the normal and pathological brain. However, a better understanding of imprinted gene functions calls for building detailed maps of their parent-of-origin-dependent expression and of associated epigenetic signatures. Here we review current methods for quantifying genomic imprinting at tissue and cell resolutions, with a special emphasis on methods to detect parent-of-origin dependent expression and their applications to the brain. We first focus on bulk RNA-sequencing, the main method to detect parent-of-origin-dependent expression transcriptome-wide. We discuss the benefits and caveats of bulk RNA-sequencing and provide a guideline to use it on F1 hybrid mice. We then review methods for detecting parent-of-origin-dependent expression at cell resolution, including single-cell RNA-seq, genetic reporters, and molecular probes. Finally, we provide an overview of single-cell epigenomics technologies that profile additional features of genomic imprinting, including DNA methylation, histone modifications and chromatin conformation and their combination into sc-multimodal omics approaches, which are expected to yield important insights into genomic imprinting in individual brain cells.
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Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Emeric Dubois
- Montpellier GenomiX (MGX), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France;
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
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11
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Yin Z, Zhang X, Li J, Jiao Y, Kong Q, Mu Y. Identification of Imprinted Genes and Their Differentially Methylated Regions in Porcine. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Nechin J, Tunstall E, Raymond N, Hamagami N, Pathmanabhan C, Forestier S, Davis TL. Hemimethylation of CpG dyads is characteristic of secondary DMRs associated with imprinted loci and correlates with 5-hydroxymethylcytosine at paternally methylated sequences. Epigenetics Chromatin 2019; 12:64. [PMID: 31623686 PMCID: PMC6796366 DOI: 10.1186/s13072-019-0309-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/09/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammals, the regulation of imprinted genes is controlled by differential methylation at imprinting control regions which acquire parent of origin-specific methylation patterns during gametogenesis and retain differences in allelic methylation status throughout fertilization and subsequent somatic cell divisions. In addition, many imprinted genes acquire differential methylation during post-implantation development; these secondary differentially methylated regions appear necessary to maintain the imprinted expression state of individual genes. Despite the requirement for both types of differentially methylated sequence elements to achieve proper expression across imprinting clusters, methylation patterns are more labile at secondary differentially methylated regions. To understand the nature of this variability, we analyzed CpG dyad methylation patterns at both paternally and maternally methylated imprinted loci within multiple imprinting clusters. RESULTS We determined that both paternally and maternally methylated secondary differentially methylated regions associated with imprinted genes display high levels of hemimethylation, 29-49%, in comparison to imprinting control regions which exhibited 8-12% hemimethylation. To explore how hemimethylation could arise, we assessed the differentially methylated regions for the presence of 5-hydroxymethylcytosine which could cause methylation to be lost via either passive and/or active demethylation mechanisms. We found enrichment of 5-hydroxymethylcytosine at paternally methylated secondary differentially methylated regions, but not at the maternally methylated sites we analyzed in this study. CONCLUSIONS We found high levels of hemimethylation to be a generalizable characteristic of secondary differentially methylated regions associated with imprinted genes. We propose that 5-hydroxymethylcytosine enrichment may be responsible for the variability in methylation status at paternally methylated secondary differentially methylated regions associated with imprinted genes. We further suggest that the high incidence of hemimethylation at secondary differentially methylated regions must be counteracted by continuous methylation acquisition at these loci.
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Affiliation(s)
- Julianna Nechin
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Emma Tunstall
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Naideline Raymond
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Nicole Hamagami
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Chris Pathmanabhan
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Samantha Forestier
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA
| | - Tamara L Davis
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA, 19010-2899, USA.
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13
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Millership SJ, Van de Pette M, Withers DJ. Genomic imprinting and its effects on postnatal growth and adult metabolism. Cell Mol Life Sci 2019; 76:4009-4021. [PMID: 31270580 PMCID: PMC6785587 DOI: 10.1007/s00018-019-03197-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022]
Abstract
Imprinted genes display parent-of-origin-specific expression with this epigenetic system of regulation found exclusively in therian mammals. Historically, defined imprinted gene functions were almost solely focused on pregnancy and the influence on the growth parameters of the developing embryo and placenta. More recently, a number of postnatal functions have been identified which converge on resource allocation, both for animals in the nest and in adults. While many of the prenatal functions of imprinted genes that have so far been described adhere to the "parental conflict" hypothesis, no clear picture has yet emerged on the functional role of imprints on postnatal metabolism. As these roles are uncovered, interest in the potential for these genes to influence postnatal metabolism and associated adult-onset disease outcomes when dysregulated has gathered pace. Here, we review the published data on imprinted genes and their influence on postnatal metabolism, starting in the nest, and then progressing through to adulthood. When observing the functional effects of these genes on adult metabolism, we must always be careful to acknowledge the influence both of direct expression in the relevant metabolic tissue, but also indirect metabolic programming effects caused by their modulation of both in utero and postnatal growth trajectories.
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Affiliation(s)
- Steven J Millership
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Mathew Van de Pette
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Dominic J Withers
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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14
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Generation of Bimaternal and Bipaternal Mice from Hypomethylated Haploid ESCs with Imprinting Region Deletions. Cell Stem Cell 2018; 23:665-676.e4. [PMID: 30318303 DOI: 10.1016/j.stem.2018.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/16/2018] [Accepted: 09/05/2018] [Indexed: 11/24/2022]
Abstract
Unisexual reproduction is widespread among lower vertebrates, but not in mammals. Deletion of the H19 imprinted region in immature oocytes produced bimaternal mice with defective growth; however, bipaternal reproduction has not been previously achieved in mammals. We found that cultured parthenogenetic and androgenetic haploid embryonic stem cells (haESCs) display DNA hypomethylation resembling that of primordial germ cells. Through MII oocyte injection or sperm coinjection with hypomethylated haploid ESCs carrying specific imprinted region deletions, we obtained live bimaternal and bipaternal mice. Deletion of 3 imprinted regions in parthenogenetic haploid ESCs restored normal growth of fertile bimaternal mice, whereas deletion of 7 imprinted regions in androgenetic haploid ESCs enabled production of live bipaternal mice that died shortly after birth. Phenotypic analyses of organ and body size of these mice support the genetic conflict theory of genomic imprinting. Taken together, our results highlight the factors necessary for crossing same-sex reproduction barriers in mammals.
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15
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Effects of superovulation, in vitro fertilization, and oocyte in vitro maturation on imprinted gene Grb10 in mouse blastocysts. Arch Gynecol Obstet 2018; 298:1219-1227. [DOI: 10.1007/s00404-018-4905-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/12/2018] [Indexed: 12/12/2022]
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16
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Luo L, Jiang W, Liu H, Bu J, Tang P, Du C, Xu Z, Luo H, Liu B, Xiao B, Zhou Z, Liu F. De-silencing Grb10 contributes to acute ER stress-induced steatosis in mouse liver. J Mol Endocrinol 2018; 60:285-297. [PMID: 29555819 DOI: 10.1530/jme-18-0018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/19/2018] [Indexed: 12/14/2022]
Abstract
The growth factor receptor bound protein GRB10 is an imprinted gene product and a key negative regulator of the insulin, IGF1 and mTORC1 signaling pathways. GRB10 is highly expressed in mouse fetal liver but almost completely silenced in adult mice, suggesting a potential detrimental role of this protein in adult liver function. Here we show that the Grb10 gene could be reactivated in adult mouse liver by acute endoplasmic reticulum stress (ER stress) such as tunicamycin or a short-term high-fat diet (HFD) challenge, concurrently with increased unfolded protein response (UPR) and hepatosteatosis. Lipogenic gene expression and acute ER stress-induced hepatosteatosis were significantly suppressed in the liver of the liver-specific GRB10 knockout mice, uncovering a key role of Grb10 reactivation in acute ER stress-induced hepatic lipid dysregulation. Mechanically, acute ER stress induces Grb10 reactivation via an ATF4-mediated increase in Grb10 gene transcription. Our study demonstrates for the first time that the silenced Grb10 gene can be reactivated by acute ER stress and its reactivation plays an important role in the early development of hepatic steatosis.
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Affiliation(s)
- Liping Luo
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wanxiang Jiang
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui Liu
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jicheng Bu
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ping Tang
- The State Key Laboratory of BiotherapyWest China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chongyangzi Du
- The State Key Laboratory of BiotherapyWest China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhipeng Xu
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hairong Luo
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bilian Liu
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bo Xiao
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- The State Key Laboratory of BiotherapyWest China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhiguang Zhou
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Feng Liu
- Department of Metabolism and Endocrinology and the Metabolic Syndrome Research Center of Central South UniversityThe Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of PharmacologyUniversity of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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17
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Abstract
DIO3 and DIO3OS are two imprinted genes identified in mouse and humans. The DIO3 gene, which encodes for the type 3 deiodinase, is preferentially expressed from the paternal allele, while the DIO3OS transcript is transcribed in opposite orientation to DIO3, multiple noncoding and alternatively splicing isoforms from maternal allele. In this study, the five splice variants of DIO3OS were identified in Holstein cattle and had complex, tissue-specific expression patterns observed in eight tissues, including heart, liver, spleen, lung, kidney, muscle, fat and brain. In the G+C rich region, upstream from the cattle DIO3 gene, there were three small conserved regions and some promoter elements similar to those observed in mouse and humans. An allele-specific expression analysis-based SNP method revealed that DIO3 and DIO3OS genes exhibited monoallelic expression in the eight tissues, indicating that DIO3 and DIO3OS are imprinted in cattle.
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18
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Caffrey A, Irwin RE, McNulty H, Strain JJ, Lees-Murdock DJ, McNulty BA, Ward M, Walsh CP, Pentieva K. Gene-specific DNA methylation in newborns in response to folic acid supplementation during the second and third trimesters of pregnancy: epigenetic analysis from a randomized controlled trial. Am J Clin Nutr 2018; 107:566-575. [PMID: 29635492 DOI: 10.1093/ajcn/nqx069] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/08/2017] [Indexed: 12/21/2022] Open
Abstract
Background Emerging evidence suggests that maternal folate status can impact cognitive development in childhood. Folate-dependent DNA methylation may provide a biological mechanism to link folate status during pregnancy with cognition in the offspring. Objective The objective was to investigate the effect of continued folic acid (FA) supplementation beyond the first trimester of pregnancy on DNA methylation in cord blood of epigenetically controlled genes related to brain development and function. Design Using available cord blood samples (n = 86) from the Folic Acid Supplementation in the Second and Third Trimesters (FASSTT) trial in pregnancy, we applied pyrosequencing techniques to analyze cord blood DNA at 9 candidate loci known to be regulated by methylation, including some previously implicated in observational studies: the widely dispersed retrotransposon long interspersed nuclear element-1 (LINE-1) and 8 single-copy loci (RBM46, PEG3, IGF2, GRB10, BDNF, GRIN3B, OPCML, and APC2). Results The newborns of mothers who received ongoing FA (400 µg/d) through the second and third trimesters, compared with placebo, had significantly lower overall DNA methylation levels at LINE-1 (56.3% ± 1.7% compared with 57.2% ± 2.1%; P = 0.024), IFG2 (48.9% ± 4.4% compared with 51.2% ± 5.1%; P = 0.021), and BDNF (2.7% ± 0.7% compared with 3.1% ± 0.8%; P = 0.003). The effect of FA treatment on DNA methylation was significant only in female offspring for IGF2 (P = 0.028) and only in males for BDNF (P = 0.012). For GRB10 and GRIN3B, we detected no effect on overall methylation; however, individual cytosine-phosphate-guanine sites showed significant DNA methylation changes in response to FA. Conclusions Continued supplementation with FA through trimesters 2 and 3 of pregnancy results in significant changes in DNA methylation in cord blood of genes related to brain development. The findings offer a potential biological mechanism linking maternal folate status with neurodevelopment of the offspring, but this requires further investigation using a genome-wide approach. This trial was registered at www.isrctn.com as ISRCTN19917787.
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Affiliation(s)
- Aoife Caffrey
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Rachelle E Irwin
- Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - J J Strain
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Diane J Lees-Murdock
- Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Breige A McNulty
- School of Agriculture & Food Science, University College Dublin, Dublin, Ireland
| | - Mary Ward
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Colum P Walsh
- Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Kristina Pentieva
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
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19
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Impulsive Choice in Mice Lacking Paternal Expression of Grb10 Suggests Intragenomic Conflict in Behavior. Genetics 2018; 209:233-239. [PMID: 29563147 PMCID: PMC5937175 DOI: 10.1534/genetics.118.300898] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/19/2018] [Indexed: 12/21/2022] Open
Abstract
The imprinted gene Grb10 is expressed in the brain from the paternal copy only. Here, Dent et al. show that paternal Grb10 regulates impulsive choices, i.e. whether an animal chooses a smaller food reward... Imprinted genes are expressed from one parental allele only as a consequence of epigenetic events that take place in the mammalian germ line and are thought to have evolved through intragenomic conflict between parental alleles. We demonstrate, for the first time, oppositional effects of imprinted genes on brain and behavior. Specifically, we show that mice lacking paternal Grb10 make fewer impulsive choices, with no dissociable effects on a separate measure of impulsive action. Taken together with previous work showing that mice lacking maternal Nesp55 make more impulsive choices, this suggests that impulsive choice behavior is a substrate for the action of genomic imprinting. Moreover, the contrasting effect of these two genes suggests that impulsive choices are subject to intragenomic conflict and that maternal and paternal interests pull this behavior in opposite directions. Finally, these data may also indicate that an imbalance in expression of imprinted genes contributes to pathological conditions such as gambling and drug addiction, where impulsive behavior becomes maladaptive.
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20
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de Sá Machado Araújo G, da Silva Francisco Junior R, Dos Santos Ferreira C, Mozer Rodrigues PT, Terra Machado D, Louvain de Souza T, Teixeira de Souza J, Figueiredo Osorio da Silva C, Alves da Silva AF, Andrade CCF, da Silva AT, Ramos V, Garcia AB, Machado FB, Medina-Acosta E. Maternal 5 mCpG Imprints at the PARD6G-AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. Front Genet 2018; 9:36. [PMID: 29545821 PMCID: PMC5838017 DOI: 10.3389/fgene.2018.00036] [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: 09/28/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
A hallmark of imprinted genes in mammals is the occurrence of parent-of-origin-dependent asymmetry of DNA cytosine methylation (5mC) of alleles at CpG islands (CGIs) in their promoter regions. This 5mCpG asymmetry between the parental alleles creates allele-specific imprinted differentially methylated regions (iDMRs). iDMRs are often coupled to the transcriptional repression of the methylated allele and the activation of the unmethylated allele in a tissue-specific, developmental-stage-specific and/or isoform-specific fashion. iDMRs function as regulatory platforms, built through the recruitment of chemical modifications to histones to achieve differential, parent-of-origin-dependent chromatin segmentation states. Here, we used a comparative computational data mining approach to identify 125 novel constitutive candidate iDMRs that integrate the maximal number of allele-specific methylation region records overlapping CGIs in human methylomes. Twenty-nine candidate iDMRs display gametic 5mCpG asymmetry, and another 96 are candidate secondary iDMRs. We established the maternal origin of the 5mCpG imprints of one gametic (PARD6G-AS1) and one secondary (GCSAML) iDMRs. We also found a constitutively hemimethylated, nonimprinted domain at the PWWP2AP1 promoter CGI with oocyte-derived methylation asymmetry. Given that the 5mCpG level at the iDMRs is not a sufficient criterion to predict active or silent locus states and that iDMRs can regulate genes from a distance of more than 1 Mb, we used RNA-Seq experiments from the Genotype-Tissue Expression project and public archives to assess the transcriptional expression profiles of SNPs across 4.6 Mb spans around the novel maternal iDMRs. We showed that PARD6G-AS1 and GCSAML are expressed biallelically in multiple tissues. We found evidence of tissue-specific monoallelic expression of ZNF124 and OR2L13, located 363 kb upstream and 419 kb downstream, respectively, of the GCSAML iDMR. We hypothesize that the GCSAML iDMR regulates the tissue-specific, monoallelic expression of ZNF124 but not of OR2L13. We annotated the non-coding epigenomic marks in the two maternal iDMRs using data from the Roadmap Epigenomics project and showed that the PARD6G-AS1 and GCSAML iDMRs achieve contrasting activation and repression chromatin segmentations. Lastly, we found that the maternal 5mCpG imprints are perturbed in several hematopoietic cancers. We conclude that the maternal 5mCpG imprints at PARD6G-AS1 and GCSAML iDMRs are decoupled from parent-of-origin transcriptional expression effects in multiple tissues.
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Affiliation(s)
- Graziela de Sá Machado Araújo
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Ronaldo da Silva Francisco Junior
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Cristina Dos Santos Ferreira
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Pedro Thyago Mozer Rodrigues
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thais Louvain de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade de Medicina de Campos, Campos dos Goytacazes, Brazil
| | - Jozimara Teixeira de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Cleiton Figueiredo Osorio da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Antônio Francisco Alves da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Claudia Caixeta Franco Andrade
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade Metropolitana São Carlos, Bom Jesus do Itabapoana, Brazil
| | - Alan Tardin da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Victor Ramos
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ana Beatriz Garcia
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Filipe Brum Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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21
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Guntrum M, Vlasova E, Davis TL. Asymmetric DNA methylation of CpG dyads is a feature of secondary DMRs associated with the Dlk1/ Gtl2 imprinting cluster in mouse. Epigenetics Chromatin 2017. [PMID: 28649282 PMCID: PMC5480104 DOI: 10.1186/s13072-017-0138-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development. To investigate the nature of these more variably methylated secondary differentially methylated regions, we adopted a hairpin linker bisulfite mutagenesis approach to examine CpG dyad methylation at differentially methylated regions associated with the murine Dlk1/Gtl2 imprinting cluster on both complementary strands. Results We observed homomethylation at greater than 90% of the methylated CpG dyads at the IG-DMR, which serves as the imprinting control element. In contrast, homomethylation was only observed at 67–78% of the methylated CpG dyads at the secondary differentially methylated regions; the remaining 22–33% of methylated CpG dyads exhibited hemimethylation. Conclusions We propose that this high degree of hemimethylation could explain the variability in DNA methylation patterns at secondary differentially methylated regions associated with imprinted loci. We further suggest that the presence of 5-hydroxymethylation at secondary differentially methylated regions may result in hemimethylation and methylation variability as a result of passive and/or active demethylation mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0138-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Megan Guntrum
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899 USA
| | - Ekaterina Vlasova
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899 USA
| | - Tamara L Davis
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899 USA
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22
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Patten MM, Cowley M, Oakey RJ, Feil R. Regulatory links between imprinted genes: evolutionary predictions and consequences. Proc Biol Sci 2017; 283:rspb.2015.2760. [PMID: 26842569 PMCID: PMC4760173 DOI: 10.1098/rspb.2015.2760] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.
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Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, DC 20057, USA
| | - Michael Cowley
- Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Robert Feil
- Centre National de Recherche Scientifique (CNRS), Institute of Molecular Genetics (IGMM), 1919 route de Mende, Montpellier 34293, France University of Montpellier, 163 rue Auguste Broussonnet, Montpellier 34090, France Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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23
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Kai M, Niinuma T, Kitajima H, Yamamoto E, Harada T, Aoki H, Maruyama R, Toyota M, Sasaki Y, Sugai T, Tokino T, Nakase H, Suzuki H. TET1 Depletion Induces Aberrant CpG Methylation in Colorectal Cancer Cells. PLoS One 2016; 11:e0168281. [PMID: 27977763 PMCID: PMC5158030 DOI: 10.1371/journal.pone.0168281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/29/2016] [Indexed: 01/02/2023] Open
Abstract
Aberrant DNA methylation is commonly observed in colorectal cancer (CRC), but the underlying mechanism is not fully understood. 5-hydroxymethylcytosine levels and TET1 expression are both reduced in CRC, while epigenetic silencing of TET1 is reportedly associated with the CpG island methylator phenotype. In the present study, we aimed to clarify the relationship between loss of TET1 and aberrant DNA methylation in CRC. Stable TET1 knockdown clones were established using Colo320DM cells, which express high levels of TET1, and HCT116 cells, which express TET1 at a level similar to that in normal colonic tissue. Infinium HumanMethylation450 BeadChip assays revealed increased levels of 5-methylcytosine at more than 10,000 CpG sites in TET1-depleted Colo320DM cells. Changes in DNA methylation were observed at various positions within the genome, including promoters, gene bodies and intergenic regions, and the altered methylation affected expression of a subset of genes. By contrast, TET1 knockdown did not significantly affect DNA methylation in HCT116 cells. However, TET1 depletion was associated with attenuated effects of 5-aza-2’-deoxycytidine on gene expression profiles in both cell lines. These results suggest that loss of TET1 may induce aberrant DNA methylation and may attenuate the effect of 5-aza-2’-deoxycytidine in CRC cells.
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Affiliation(s)
- Masahiro Kai
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Niinuma
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Kitajima
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Eiichiro Yamamoto
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Taku Harada
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hironori Aoki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Reo Maruyama
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mutsumi Toyota
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasushi Sasaki
- Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, Iwate Medical University, Morioka, Japan
| | - Takashi Tokino
- Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
- * E-mail:
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24
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Tsanov N, Samacoits A, Chouaib R, Traboulsi AM, Gostan T, Weber C, Zimmer C, Zibara K, Walter T, Peter M, Bertrand E, Mueller F. smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Res 2016; 44:e165. [PMID: 27599845 PMCID: PMC5159540 DOI: 10.1093/nar/gkw784] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/26/2016] [Indexed: 11/12/2022] Open
Abstract
Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification approach that uses unlabelled primary probes and a fluorescently labelled secondary detector oligonucleotide. The gene-specific probes are unlabelled and can therefore be synthesized at low cost, thus allowing to use more probes per mRNA resulting in a substantial increase in detection efficiency. smiFISH is also flexible since differently labelled secondary detector probes can be used with the same primary probes. We demonstrate that this flexibility allows multicolor labelling without the need to synthesize new probe sets. We further demonstrate that the use of a specific acrydite detector oligonucleotide allows smiFISH to be combined with expansion microscopy, enabling the resolution of transcripts in 3D below the diffraction limit on a standard microscope. Lastly, we provide improved, fully automated software tools from probe-design to quantitative analysis of smFISH images. In short, we provide a complete workflow to obtain automatically counts of individual RNA molecules in single cells.
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Affiliation(s)
- Nikolay Tsanov
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Aubin Samacoits
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France.,C3BI, USR 3756 IP CNRS - Paris, France
| | - Racha Chouaib
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France.,ER045, Laboratory of Stem Cells, DSST, PRASE, Lebanese University, Beirut, Lebanon
| | - Abdel-Meneem Traboulsi
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Christian Weber
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France.,C3BI, USR 3756 IP CNRS - Paris, France
| | - Christophe Zimmer
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France.,C3BI, USR 3756 IP CNRS - Paris, France
| | - Kazem Zibara
- ER045, Laboratory of Stem Cells, DSST, PRASE, Lebanese University, Beirut, Lebanon.,Biology Department, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Thomas Walter
- MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 77300 Fontainebleau, France.,Institut Curie, 75248 Paris Cedex, France.,INSERM, U900, 75248 Paris Cedex, France
| | - Marion Peter
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France .,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France .,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, 28 rue du Docteur Roux, 75015 Paris, France .,C3BI, USR 3756 IP CNRS - Paris, France
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25
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Boot A, Oosting J, de Miranda NFCC, Zhang Y, Corver WE, van de Water B, Morreau H, van Wezel T. Imprinted survival genes preclude loss of heterozygosity of chromosome 7 in cancer cells. J Pathol 2016; 240:72-83. [DOI: 10.1002/path.4756] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/21/2016] [Accepted: 05/24/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Arnoud Boot
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Jan Oosting
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Noel FCC de Miranda
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Yinghui Zhang
- Division of Toxicology, Leiden Academic Center for Drug Research; Leiden University; The Netherlands
| | - Willem E Corver
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Center for Drug Research; Leiden University; The Netherlands
| | - Hans Morreau
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
| | - Tom van Wezel
- Department of Pathology; Leiden University Medical Center; Leiden The Netherlands
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26
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Genomic imprinting of DIO3, a candidate gene for the syndrome associated with human uniparental disomy of chromosome 14. Eur J Hum Genet 2016; 24:1617-1621. [PMID: 27329732 DOI: 10.1038/ejhg.2016.66] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/29/2016] [Accepted: 05/20/2016] [Indexed: 12/18/2022] Open
Abstract
Individuals with uniparental disomy of chromosome 14 (Temple and Kagami-Ogata syndromes) exhibit a number of developmental abnormalities originating, in part, from aberrant developmental expression of imprinted genes in the DLK1-DIO3 cluster. Although genomic imprinting has been reported in humans for some genes in the cluster, little evidence is available about the imprinting status of DIO3, which modulates developmental exposure to thyroid hormones. We used pyrosequencing to evaluate allelic expression of DLK1 and DIO3 in cDNAs prepared from neonatal foreskins carrying single-nucleotide polymorphisms (SNPs) in the exonic sequence of those genes, and hot-stop PCR to quantify DIO3 allelic expression in cDNA obtained from a skin specimen collected from an adult individual with known parental origin of the DIO3 SNP. In neonatal skin, DLK1 and DIO3 both exhibited a high degree of monoallelic expression from the paternal allele. In the adult skin sample, the allele preferentially expressed is that inherited from the mother, although a different, larger DIO3 mRNA transcript appears the most abundant at this stage. We conclude that DIO3 is an imprinted gene in humans, suggesting that alterations in thyroid hormone exposure during development may partly contribute to the phenotypes associated with uniparental disomy of chromosome 14.
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27
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Wilkins JF, Úbeda F, Van Cleve J. The evolving landscape of imprinted genes in humans and mice: Conflict among alleles, genes, tissues, and kin. Bioessays 2016; 38:482-9. [PMID: 26990753 DOI: 10.1002/bies.201500198] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Three recent genome-wide studies in mice and humans have produced the most definitive map to date of genomic imprinting (gene expression that depends on parental origin) by incorporating multiple tissue types and developmental stages. Here, we explore the results of these studies in light of the kinship theory of genomic imprinting, which predicts that imprinting evolves due to differential genetic relatedness between maternal and paternal relatives. The studies produce a list of imprinted genes with around 120-180 in mice and ~100 in humans. The studies agree on broad patterns across mice and humans including the complex patterns of imprinted expression at loci like Igf2 and Grb10. We discuss how the kinship theory provides a powerful framework for hypotheses that can explain these patterns. Finally, since imprinting is rare in the genome despite predictions from the kinship theory that it might be common, we discuss evolutionary factors that could favor biallelic expression.
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Affiliation(s)
| | - Francisco Úbeda
- School of Biological Sciences, Royal Holloway, University of London, Egham, UK
| | - Jeremy Van Cleve
- Department of Biology, University of Kentucky, Lexington, KY, USA
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28
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Marzi SJ, Meaburn EL, Dempster EL, Lunnon K, Paya-Cano JL, Smith RG, Volta M, Troakes C, Schalkwyk LC, Mill J. Tissue-specific patterns of allelically-skewed DNA methylation. Epigenetics 2016; 11:24-35. [PMID: 26786711 PMCID: PMC4846124 DOI: 10.1080/15592294.2015.1127479] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with > 4% of the ∼220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are tissue-specific. These findings contribute to our understanding of the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood.
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Affiliation(s)
- Sarah J Marzi
- a Institute of Psychiatry, Psychology and Neuroscience, King's College London , London , UK
| | - Emma L Meaburn
- b Department of Psychological Sciences , Birkbeck, University of London , London , UK
| | - Emma L Dempster
- c University of Exeter Medical School, University of Exeter , Exeter , UK
| | - Katie Lunnon
- c University of Exeter Medical School, University of Exeter , Exeter , UK
| | - Jose L Paya-Cano
- a Institute of Psychiatry, Psychology and Neuroscience, King's College London , London , UK
| | - Rebecca G Smith
- c University of Exeter Medical School, University of Exeter , Exeter , UK
| | - Manuela Volta
- a Institute of Psychiatry, Psychology and Neuroscience, King's College London , London , UK
| | - Claire Troakes
- a Institute of Psychiatry, Psychology and Neuroscience, King's College London , London , UK
| | | | - Jonathan Mill
- a Institute of Psychiatry, Psychology and Neuroscience, King's College London , London , UK.,c University of Exeter Medical School, University of Exeter , Exeter , UK
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29
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Perez JD, Rubinstein ND, Fernandez DE, Santoro SW, Needleman LA, Ho-Shing O, Choi JJ, Zirlinger M, Chen SK, Liu JS, Dulac C. Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain. eLife 2015; 4:e07860. [PMID: 26140685 PMCID: PMC4512258 DOI: 10.7554/elife.07860] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/02/2015] [Indexed: 12/14/2022] Open
Abstract
The maternal and paternal genomes play different roles in mammalian brains as a result of genomic imprinting, an epigenetic regulation leading to differential expression of the parental alleles of some genes. Here we investigate genomic imprinting in the cerebellum using a newly developed Bayesian statistical model that provides unprecedented transcript-level resolution. We uncover 160 imprinted transcripts, including 41 novel and independently validated imprinted genes. Strikingly, many genes exhibit parentally biased--rather than monoallelic--expression, with different magnitudes according to age, organ, and brain region. Developmental changes in parental bias and overall gene expression are strongly correlated, suggesting combined roles in regulating gene dosage. Finally, brain-specific deletion of the paternal, but not maternal, allele of the paternally-biased Bcl-x, (Bcl2l1) results in loss of specific neuron types, supporting the functional significance of parental biases. These findings reveal the remarkable complexity of genomic imprinting, with important implications for understanding the normal and diseased brain.
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Affiliation(s)
- Julio D Perez
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Nimrod D Rubinstein
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | | | - Stephen W Santoro
- Neuroscience Program, Department of Zoology and Physiology, University of Wyoming, Laramie, United States
| | - Leigh A Needleman
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Olivia Ho-Shing
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - John J Choi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | | | | | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, United States
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
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30
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Mroue R, Huang B, Braunstein S, Firestone AJ, Nakamura JL. Monoallelic loss of the imprinted gene Grb10 promotes tumor formation in irradiated Nf1+/- mice. PLoS Genet 2015; 11:e1005235. [PMID: 26000738 PMCID: PMC4441450 DOI: 10.1371/journal.pgen.1005235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/22/2015] [Indexed: 12/26/2022] Open
Abstract
Imprinted genes are expressed from only one parental allele and heterozygous loss involving the expressed allele is sufficient to produce complete loss of protein expression. Genetic alterations are common in tumorigenesis but the role of imprinted genes in this process is not well understood. In earlier work we mutagenized mice heterozygous for the Neurofibromatosis I tumor suppressor gene (NF1) to model radiotherapy-associated second malignant neoplasms that arise in irradiated NF1 patients. Expression analysis of tumor cell lines established from our mouse models identified Grb10 expression as widely absent. Grb10 is an imprinted gene and polymorphism analysis of cell lines and primary tumors demonstrates that the expressed allele is commonly lost in diverse Nf1 mutant tumors arising in our mouse models. We performed functional studies to test whether Grb10 restoration or loss alter fundamental features of the tumor growth. Restoring Grb10 in Nf1 mutant tumors decreases proliferation, decreases soft agar colony formation and downregulates Ras signaling. Conversely, Grb10 silencing in untransformed mouse embryo fibroblasts significantly increased cell proliferation and increased Ras-GTP levels. Expression of a constitutively activated MEK rescued tumor cells from Grb10-mediated reduction in colony formation. These studies reveal that Grb10 loss can occur during in vivo tumorigenesis, with a functional consequence in untransformed primary cells. In tumors, Grb10 loss independently promotes Ras pathway hyperactivation, which promotes hyperproliferation, an early feature of tumor development. In the context of a robust Nf1 mutant mouse model of cancer this work identifies a novel role for an imprinted gene in tumorigenesis. Cancer-causing mutations typically involve either allele inherited from parents, and the parental source of a mutant allele is not known to influence the cancer phenotype. Imprinted genes are a class of genes whose expression is determined by a specific parental allele, either maternally or paternally derived. Thus, in contrast to most genes, the pattern of inheritance (maternal or paternal-derived) strongly influences the expression of an imprinted gene. Furthermore, imprinted genes can be differentially expressed in different tissue types. This work identifies a novel link between cancer and Grb10, an imprinted gene involved in organismal metabolism and growth. In our mouse model of radiation-induced tumors, we found monoallelic Grb10 gene loss involving the parental allele responsible for protein expression. Tumors harboring genetic loss of the expressed Grb10 allele showed absent transcript and total protein levels, despite an intact remaining wildtype Grb10 allele identified by sequencing. When restored, Grb10 suppressed tumor growth by down-regulating Ras signaling. This work demonstrates a new role for an imprinted gene in tumor formation, and shows that Grb10 functions to negatively regulate Ras signaling and suppress hyperproliferation.
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Affiliation(s)
- Rana Mroue
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, United States of America
| | - Brian Huang
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, United States of America
| | - Steve Braunstein
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, United States of America
| | - Ari J Firestone
- Department of Pediatrics, University of California, San Francisco, San Francisco, California, United States of America
| | - Jean L Nakamura
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, United States of America
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31
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32
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Tissue-specific regulation and function of Grb10 during growth and neuronal commitment. Proc Natl Acad Sci U S A 2014; 112:6841-7. [PMID: 25368187 DOI: 10.1073/pnas.1411254111] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Growth-factor receptor bound protein 10 (Grb10) is a signal adapter protein encoded by an imprinted gene that has roles in growth control, cellular proliferation, and insulin signaling. Additionally, Grb10 is critical for the normal behavior of the adult mouse. These functions are paralleled by Grb10's unique tissue-specific imprinted expression; the paternal copy of Grb10 is expressed in a subset of neurons whereas the maternal copy is expressed in most other adult tissues in the mouse. The mechanism that underlies this switch between maternal and paternal expression is still unclear, as is the role for paternally expressed Grb10 in neurons. Here, we review recent work and present complementary data that contribute to the understanding of Grb10 gene regulation and function, with specific emphasis on growth and neuronal development. Additionally, we show that in vitro differentiation of mouse embryonic stem cells into alpha motor neurons recapitulates the switch from maternal to paternal expression observed during neuronal development in vivo. We postulate that this switch in allele-specific expression is related to the functional role of Grb10 in motor neurons and other neuronal tissues.
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33
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Li J, Meltzer HY. A genetic locus in 7p12.2 associated with treatment resistant schizophrenia. Schizophr Res 2014; 159:333-9. [PMID: 25223841 DOI: 10.1016/j.schres.2014.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/20/2014] [Accepted: 08/23/2014] [Indexed: 11/29/2022]
Abstract
Approximately 30% of patients with schizophrenia are treatment resistant (TRS), i.e. have persistent psychotic symptoms despite adequate trials of at least two antipsychotic drugs (APDs). Most TRS patients are candidates for clozapine treatment which is underutilized because of its side effects and difficulty in identifying TRS. We conducted a genome-wide association study (GWAS) of 79 TRS and 95 non-treatment resistant (NTRS) Caucasian schizophrenia patients to identify possible biomarkers for TRS, which might also provide insight into the pathobiology of TRS. The single nucleotide polymorphism, rs2237457, located in 7p12.2, a region reported to have imprinted inheritance, was found to have the lowest p value in an allelic association test (unadjusted p = 5.53 × 10(-6)). Haploview disclosed a 30 kb block flanking this SNP within GRB10, 70 kb upstream of l-dopa decarboxylase (DDC), an enzyme which is rate-limiting in the synthesis of trace amines and neurotransmitters implicated in schizophrenia and the action of APDs. This SNP or haplotype was identified as an exclusive cis-acting eQTL for DDC in human dorsolateral prefrontal cortex by BrainCloud®. A replication sample genotyped for this SNP produced a weaker result, but in the same direction. After combining the two samples, rs2237457 remained significantly associated with TRS (unadjusted p = 5.66 × 10(-7) in recessive mode; 9.42 × 10(-5) in allelic association). If replicated in an independent sample, rs2237457 may provide a biomarker to identify a significant proportion of Caucasian TRS. The results implicate trace amines and their synthesis in the pathophysiology of TRS.
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Affiliation(s)
- Jiang Li
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, United States
| | - Herbert Y Meltzer
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, United States.
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34
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Hu M, TuanMu LC, Wei H, Gao F, Li L, Zhang S. Development and imprinted gene expression in uniparental preimplantation mouse embryos in vitro. Mol Biol Rep 2014; 42:345-53. [PMID: 25270250 DOI: 10.1007/s11033-014-3774-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 09/20/2014] [Indexed: 01/15/2023]
Abstract
Increasing numbers of reports show that imprinted genes play a crucial role in fetal development, and uniparental embryos, which possess two paternally or two maternally derived pronuclei, are excellent tools for investigating the biological significance of imprinted genes. In the present study, to examine the in vitro developmental ability and expression pattern of eight imprinted genes in uniparental embryos, we produced androgenones, gynogenones, and parthenogenones using enucleation. Our data confirmed the previously observed restriction in haploid androgenetic development potential and first indicated that diploid androgenetic embryos were arrested in the 3/4-cell stage. Some imprinted genes were expressed in androgenetic, gynogenetic, and parthenogenetic blastocysts, suggesting that they were unable to maintain their imprinted expression status in uniparental embryos and that both paternal and maternal alleles are required for the specific expression of some imprinted genes.
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Affiliation(s)
- Minhua Hu
- Agricultural Animal Genomics and Molecular Breeding Key Lab of Guangdong Province, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
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Martinez ME, Charalambous M, Saferali A, Fiering S, Naumova AK, St Germain D, Ferguson-Smith AC, Hernandez A. Genomic imprinting variations in the mouse type 3 deiodinase gene between tissues and brain regions. Mol Endocrinol 2014; 28:1875-86. [PMID: 25232934 PMCID: PMC4213365 DOI: 10.1210/me.2014-1210] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Dio3 gene, which encodes for the type 3 deiodinase (D3), controls thyroid hormone (TH) availability. The lack of D3 in mice results in tissue overexposure to TH and a broad neuroendocrine phenotype. Dio3 is an imprinted gene, preferentially expressed from the paternally inherited allele in the mouse fetus. However, heterozygous mice with paternal inheritance of the inactivating Dio3 mutation exhibit an attenuated phenotype when compared with that of Dio3 null mice. To investigate this milder phenotype, the allelic expression of Dio3 was evaluated in different mouse tissues. Preferential allelic expression of Dio3 from the paternal allele was observed in fetal tissues and neonatal brain regions, whereas the biallelic Dio3 expression occurred in the developing eye, testes, and cerebellum and in the postnatal brain neocortex, which expresses a larger Dio3 mRNA transcript. The newborn hypothalamus manifests the highest degree of Dio3 expression from the paternal allele, compared with other brain regions, and preferential allelic expression of Dio3 in the brain relaxed in late neonatal life. A methylation analysis of two regulatory regions of the Dio3 imprinted domain revealed modest but significant differences between tissues, but these did not consistently correlate with the observed patterns of Dio3 allelic expression. Deletion of the Dio3 gene and promoter did not result in significant changes in the tissue-specific patterns of Dio3 allelic expression. These results suggest the existence of unidentified epigenetic determinants of tissue-specific Dio3 imprinting. The resulting variation in the Dio3 allelic expression between tissues likely explains the phenotypic variation that results from paternal Dio3 haploinsufficiency.
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Affiliation(s)
- M Elena Martinez
- Department of Molecular Medicine (M.E.M., D.S.G., A.H.), Maine Medical Center Research Institute, Scarborough, Maine 04074; Centre for Endocrinology (M.C.), William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 1BB, United Kingdom; Department of Obstetrics and Gynecology and Human Genetics (A.S., A.K.N.), McGill University, Montréal, Québec, Canada H9X 3V9; Department of Microbiology and Immunology (S.F.), Dartmouth Medical School, Lebanon, New Hampshire 03756; and Department of Genetics (A.C.F.-S.), University of Cambridge, Cambridge CB2 1TN, United Kingdom
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Cleaton MA, Edwards CA, Ferguson-Smith AC. Phenotypic Outcomes of Imprinted Gene Models in Mice: Elucidation of Pre- and Postnatal Functions of Imprinted Genes. Annu Rev Genomics Hum Genet 2014; 15:93-126. [DOI: 10.1146/annurev-genom-091212-153441] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Carol A. Edwards
- Department of Genetics, University of Cambridge, Cambridge CB2 3EG, United Kingdom;
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Lorenc A, Linnenbrink M, Montero I, Schilhabel MB, Tautz D. Genetic differentiation of hypothalamus parentally biased transcripts in populations of the house mouse implicate the Prader-Willi syndrome imprinted region as a possible source of behavioral divergence. Mol Biol Evol 2014; 31:3240-9. [PMID: 25172960 PMCID: PMC4245819 DOI: 10.1093/molbev/msu257] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Parentally biased expression of transcripts (genomic imprinting) in adult tissues, including the brain, can influence and possibly drive the evolution of behavioral traits. We have previously found that paternally determined cues are involved in population-specific mate choice decisions between two populations of the Western house mouse (Mus musculus domesticus). Here, we ask whether this could be mediated by genomically imprinted transcripts that are subject to fast differentiation between these populations. We focus on three organs that are of special relevance for mate choice and behavior: The vomeronasal organ (VNO), the hypothalamus, and the liver. To first identify candidate transcripts at a genome-wide scale, we used reciprocal crosses between M. m. domesticus and M. m. musculus inbred strains and RNA sequencing of the respective tissues. Using a false discovery cutoff derived from mock reciprocal cross comparisons, we find a total of 66 imprinted transcripts, 13 of which have previously not been described as imprinted. The largest number of imprinted transcripts were found in the hypothalamus; fewer were found in the VNO, and the least were found in the liver. To assess molecular differentiation and imprinting in the wild-derived M. m. domesticus populations, we sequenced the RNA of the hypothalamus from individuals of these populations. This confirmed the presence of the above identified transcripts also in wild populations and allowed us to search for those that show a high genetic differentiation between these populations. Our results identify the Ube3a–Snrpn imprinted region on chromosome 7 as a region that encompasses the largest number of previously not described transcripts with paternal expression bias, several of which are at the same time highly differentiated. For four of these, we confirmed their imprinting status via single nucleotide polymorphism-specific pyrosequencing assays with RNA from reciprocal crosses. In addition, we find the paternally expressed Peg13 transcript within the Trappc9 gene region on chromosome 15 to be highly differentiated. Interestingly, both regions have been implicated in Prader–Willi nervous system disorder phenotypes in humans. We suggest that these genomically imprinted regions are candidates for influencing the population-specific mate-choice in mice.
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Affiliation(s)
- Anna Lorenc
- Max-Planck Institute for Evolutionary Biology, Department Evolutionary Genetics, Plön, Germany
| | - Miriam Linnenbrink
- Max-Planck Institute for Evolutionary Biology, Department Evolutionary Genetics, Plön, Germany
| | - Inka Montero
- Max-Planck Institute for Evolutionary Biology, Department Evolutionary Genetics, Plön, Germany
| | - Markus B Schilhabel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, Department Evolutionary Genetics, Plön, Germany
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Prokopenko I, Poon W, Mägi R, Prasad B R, Salehi SA, Almgren P, Osmark P, Bouatia-Naji N, Wierup N, Fall T, Stančáková A, Barker A, Lagou V, Osmond C, Xie W, Lahti J, Jackson AU, Cheng YC, Liu J, O'Connell JR, Blomstedt PA, Fadista J, Alkayyali S, Dayeh T, Ahlqvist E, Taneera J, Lecoeur C, Kumar A, Hansson O, Hansson K, Voight BF, Kang HM, Levy-Marchal C, Vatin V, Palotie A, Syvänen AC, Mari A, Weedon MN, Loos RJF, Ong KK, Nilsson P, Isomaa B, Tuomi T, Wareham NJ, Stumvoll M, Widen E, Lakka TA, Langenberg C, Tönjes A, Rauramaa R, Kuusisto J, Frayling TM, Froguel P, Walker M, Eriksson JG, Ling C, Kovacs P, Ingelsson E, McCarthy MI, Shuldiner AR, Silver KD, Laakso M, Groop L, Lyssenko V. A central role for GRB10 in regulation of islet function in man. PLoS Genet 2014; 10:e1004235. [PMID: 24699409 PMCID: PMC3974640 DOI: 10.1371/journal.pgen.1004235] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 01/20/2014] [Indexed: 01/03/2023] Open
Abstract
Variants in the growth factor receptor-bound protein 10 (GRB10) gene were in a GWAS meta-analysis associated with reduced glucose-stimulated insulin secretion and increased risk of type 2 diabetes (T2D) if inherited from the father, but inexplicably reduced fasting glucose when inherited from the mother. GRB10 is a negative regulator of insulin signaling and imprinted in a parent-of-origin fashion in different tissues. GRB10 knock-down in human pancreatic islets showed reduced insulin and glucagon secretion, which together with changes in insulin sensitivity may explain the paradoxical reduction of glucose despite a decrease in insulin secretion. Together, these findings suggest that tissue-specific methylation and possibly imprinting of GRB10 can influence glucose metabolism and contribute to T2D pathogenesis. The data also emphasize the need in genetic studies to consider whether risk alleles are inherited from the mother or the father. In this paper, we report the first large genome-wide association study in man for glucose-stimulated insulin secretion (GSIS) indices during an oral glucose tolerance test. We identify seven genetic loci and provide effects on GSIS for all previously reported glycemic traits and obesity genetic loci in a large-scale sample. We observe paradoxical effects of genetic variants in the growth factor receptor-bound protein 10 (GRB10) gene yielding both reduced GSIS and reduced fasting plasma glucose concentrations, specifically showing a parent-of-origin effect of GRB10 on lower fasting plasma glucose and enhanced insulin sensitivity for maternal and elevated glucose and decreased insulin sensitivity for paternal transmissions of the risk allele. We also observe tissue-specific differences in DNA methylation and allelic imbalance in expression of GRB10 in human pancreatic islets. We further disrupt GRB10 by shRNA in human islets, showing reduction of both insulin and glucagon expression and secretion. In conclusion, we provide evidence for complex regulation of GRB10 in human islets. Our data suggest that tissue-specific methylation and imprinting of GRB10 can influence glucose metabolism and contribute to T2D pathogenesis. The data also emphasize the need in genetic studies to consider whether risk alleles are inherited from the mother or the father.
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Affiliation(s)
- Inga Prokopenko
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Wenny Poon
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Reedik Mägi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Rashmi Prasad B
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - S Albert Salehi
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Peter Almgren
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Peter Osmark
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Nabila Bouatia-Naji
- University of Lille Nord de France, Lille, France; CNRS UMR8199, Institut Pasteur de Lille, Lille, France; INSERM U970, Paris Cardiovascular Research Center PARCC, Paris, France
| | - Nils Wierup
- Department of Clinical Science, Neuroendocrine Cell Biology, Lund University Diabetes Centre, Malmö, Sweden
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alena Stančáková
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Adam Barker
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Vasiliki Lagou
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Clive Osmond
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Weijia Xie
- Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, United Kingdom
| | - Jari Lahti
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland; Folkhälsan Research Centre, Helsinki, Finland
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yu-Ching Cheng
- Division of Endocrinology Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jie Liu
- Division of Endocrinology Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jeffrey R O'Connell
- Division of Endocrinology Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Paul A Blomstedt
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland; Department of Mathematics, Åbo Akademi University, Turku, Finland
| | - Joao Fadista
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Sami Alkayyali
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Tasnim Dayeh
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Emma Ahlqvist
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Jalal Taneera
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Cecile Lecoeur
- University of Lille Nord de France, Lille, France; CNRS UMR8199, Institut Pasteur de Lille, Lille, France
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Ola Hansson
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Karin Hansson
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Benjamin F Voight
- Department of Pharmacology and Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Claire Levy-Marchal
- INSERM - Institut de Santé Publique, Paris, France; INSERM CIC EC 05, Hôpital Robert Debré, Paris, France
| | - Vincent Vatin
- University of Lille Nord de France, Lille, France; CNRS UMR8199, Institut Pasteur de Lille, Lille, France
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland; Program in Medical and Population Genetics and Genetics Analysis Platform, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusettes, United States of America
| | - Ann-Christine Syvänen
- Molecular Medicine, Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andrea Mari
- CNR Institute of Biomedical Engineering, Padova, Italy
| | - Michael N Weedon
- Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, United Kingdom
| | - Ruth J F Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Peter Nilsson
- Department of Clinical Science, Internal Medicine, Skåne University Hospital Malmö, Malmö, Sweden
| | - Bo Isomaa
- Folkhälsan Research Centre, Helsinki, Finland; Department of Social Service and Health Care, Jakobstad, Finland
| | - Tiinamaija Tuomi
- Folkhälsan Research Centre, Helsinki, Finland; Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Michael Stumvoll
- University of Leipzig, Department of Medicine, Leipzig, Germany; University of Leipzig, IFB Adiposity Diseases, Leipzig, Germany
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Timo A Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland; Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Anke Tönjes
- University of Leipzig, Department of Medicine, Leipzig, Germany; University of Leipzig, IFB Adiposity Diseases, Leipzig, Germany
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland; Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timothy M Frayling
- Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, United Kingdom
| | - Philippe Froguel
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, United Kingdom; University of Lille Nord de France, Lille, France; CNRS UMR8199, Institut Pasteur de Lille, Lille, France
| | - Mark Walker
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Johan G Eriksson
- Folkhälsan Research Centre, Helsinki, Finland; Helsinki University, Department of General Practice and Primary Health Care, Helsinki, Finland; Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Peter Kovacs
- University of Leipzig, Department of Medicine, Leipzig, Germany; University of Leipzig, IFB Adiposity Diseases, Leipzig, Germany
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, United Kindom
| | - Alan R Shuldiner
- Division of Endocrinology Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America; Baltimore Geriatric Research, Education and Clinical Center, Baltimore, Maryland, United States of America
| | - Kristi D Silver
- Division of Endocrinology Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America; Baltimore Geriatric Research, Education and Clinical Center, Baltimore, Maryland, United States of America
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Leif Groop
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Valeriya Lyssenko
- Department of Clinical Science, Diabetes & Endocrinology, Lund University Diabetes Centre, Malmö, Sweden; Steno Diabetes Center A/S, Gentofte, Denmark
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Hannula-Jouppi K, Muurinen M, Lipsanen-Nyman M, Reinius LE, Ezer S, Greco D, Kere J. Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7. Epigenetics 2013; 9:351-65. [PMID: 24247273 PMCID: PMC4053454 DOI: 10.4161/epi.27160] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is a hallmark of genomic imprinting and differentially methylated regions (DMRs) are found near and in imprinted genes. Imprinted genes are expressed only from the maternal or paternal allele and their normal balance can be disrupted by uniparental disomy (UPD), the inheritance of both chromosomes of a chromosome pair exclusively from only either the mother or the father. Maternal UPD for chromosome 7 (matUPD7) results in Silver-Russell syndrome (SRS) with typical features and growth retardation, but no gene has been conclusively implicated in SRS. In order to identify novel DMRs and putative imprinted genes on chromosome 7, we analyzed eight matUPD7 patients, a segmental matUPD7q31-qter, a rare patUPD7 case and ten controls on the Infinium HumanMethylation450K BeadChip with 30 017 CpG methylation probes for chromosome 7. Genome-scale analysis showed highly significant clustering of DMRs only on chromosome 7, including the known imprinted loci GRB10, SGCE/PEG10, and PEG/MEST. We found ten novel DMRs on chromosome 7, two DMRs for the predicted imprinted genes HOXA4 and GLI3 and one for the disputed imprinted gene PON1. Quantitative RT-PCR on blood RNA samples comparing matUPD7, patUPD7, and controls showed differential expression for three genes with novel DMRs, HOXA4, GLI3, and SVOPL. Allele specific expression analysis confirmed maternal only expression of SVOPL and imprinting of HOXA4 was supported by monoallelic expression. These results present the first comprehensive map of parent-of-origin specific DMRs on human chromosome 7, suggesting many new imprinted sites.
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Affiliation(s)
- Katariina Hannula-Jouppi
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Dermatology and Allergology; Skin and Allergy Hospital; Helsinki University Central Hospital; Helsinki University Hospital; Helsinki, Finland
| | - Mari Muurinen
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland
| | - Marita Lipsanen-Nyman
- Children's Hospital; University of Helsinki and Helsinki University Central Hospital; Helsinki University Hospital; Helsinki, Finland
| | - Lovisa E Reinius
- Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden
| | - Sini Ezer
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland
| | - Dario Greco
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden; Unit of Systems Toxicology; Finnish Institute of Occupational Health (FIOH); Helsinki, Finland
| | - Juha Kere
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden; Science for Life Laboratory; Karolinska Institutet; Solna, Sweden
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40
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Reintroducing domesticated wild mice to sociality induces adaptive transgenerational effects on MUP expression. Proc Natl Acad Sci U S A 2013; 110:19848-53. [PMID: 24248373 DOI: 10.1073/pnas.1310427110] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
When brought into captivity, wild animals can adapt to domestication within 10 generations. Such adaptations may decrease fitness in natural conditions. Many selective pressures are disrupted in captivity, including social behavioral networks. Although lack of sociality in captivity appears to mediate domestication, the underlying mechanisms are not well understood. Additionally, determining the contribution of genetic inheritance vs. transgenerational effects during relaxed selection may provide insight into the flexibility of adaptation. When wild-derived mice kept under laboratory conditions for eight generations were reintroduced to sociality and promiscuity (free mate choice), they adapted within two generations. Fitness assessments between this promiscuous lineage and a monogamous laboratory lineage revealed male-specific effects. Promiscuous-line males had deficits in viability, but a striking advantage in attracting mates, and their scent marks were also more attractive to females. Here, we investigate mechanistic details underlying this olfactory signal and identify a role of major urinary protein (MUP) pheromones. Promiscuous-line males inherit higher MUP expression than monogamous-line males through transgenerational inheritance. Sociality-driven maternal and paternal effects reveal intriguing conflicts among parents and offspring over pheromone expression. MUP up-regulation is not driven by hormone-driven transduction pathways, but rather is associated with reduction in DNA methylation of a CpG dinucleotide in the promoter. This reduction in methylation could enhance transcription by promoting the binding of transcription factor USF1 (upstream stimulatory factor 1). Finally, we experimentally demonstrate that increased MUP expression is a female attractant. These results identify molecular mechanisms guiding domestication and adaptive responses to fluctuating sociality.
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Das R, Lee YK, Strogantsev R, Jin S, Lim YC, Ng PY, Lin XM, Chng K, Yeo GSH, Ferguson-Smith AC, Ding C. DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation. BMC Genomics 2013; 14:685. [PMID: 24094292 PMCID: PMC3829101 DOI: 10.1186/1471-2164-14-685] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 09/25/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genomic imprinting is an epigenetically regulated process wherein genes are expressed in a parent-of-origin specific manner. Many imprinted genes were initially identified in mice; some of these were subsequently shown not to be imprinted in humans. Such discrepancy reflects developmental, morphological and physiological differences between mouse and human tissues. This is particularly relevant for the placenta. Study of genomic imprinting thus needs to be carried out in a species and developmental stage-specific manner. We describe here a new strategy to study allele-specific DNA methylation in the human placenta for the discovery of novel imprinted genes. RESULTS Using this methodology, we confirmed 16 differentially methylated regions (DMRs) associated with known imprinted genes. We chose 28 genomic regions for further testing and identified two imprinted genes (DNMT1 and AIM1). Both genes showed maternal allele-specific methylation and paternal allele-specific transcription. Imprinted expression for AIM1 was conserved in the cynomolgus macaque placenta, but not in other macaque tissues or in the mouse. CONCLUSIONS Our study indicates that while there are many genomic regions with allele-specific methylation in tissues like the placenta, only a small sub-set of them are associated with allele-specific transcription, suggesting alternative functions for such genomic regions. Nonetheless, novel tissue-specific imprinted genes remain to be discovered in humans. Their identification may help us better understand embryonic and fetal development.
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Affiliation(s)
- Radhika Das
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yew Kok Lee
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ruslan Strogantsev
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, UK
| | - Shengnan Jin
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yen Ching Lim
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Poh Yong Ng
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xueqin Michelle Lin
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Keefe Chng
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - George SH Yeo
- Department of Maternal Fetal Medicine, K.K. Women’s and Children’s Hospital, Singapore, Singapore
| | - Anne C Ferguson-Smith
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, UK
| | - Chunming Ding
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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42
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Kedia-Mokashi NA, Kadam L, Ankolkar M, Dumasia K, Balasinor NH. Aberrant methylation of multiple imprinted genes in embryos of tamoxifen-treated male rats. Reproduction 2013; 146:155-68. [DOI: 10.1530/rep-12-0439] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genomic imprinting is an epigenetic phenomenon known to regulate fetal growth and development. Studies from our laboratory have demonstrated that treatment of adult male rats with tamoxifen increased postimplantation loss around mid gestation. Further studies demonstrated the aberrant expression of transcripts of several imprinted genes in the resorbing embryos at days 11 and 13 of gestation including IGF2. In addition, decreased methylation at theIgf2–H19imprint control region was observed in spermatozoa and in resorbing embryos sired by tamoxifen-treated males. In this study, methylation analysis of the imprinted genes, which were found to be differentially expressed, was done using EpiTYPER in the spermatozoa of tamoxifen-treated rats and in postimplantation embryos sired by tamoxifen-treated rats. Differentially methylated regions (DMRs) for most imprinted genes have not been identified in the rats. Hence, initial experiments were performed to identify the putative DMRs in the genes selected for the study. Increased methylation at CpG islands present in the putative DMRs of a number of imprinted genes was observed in the resorbing embryos sired by tamoxifen-treated male rats. This increase in methylation is associated with the downregulation of most of these genes at the transcript level in resorbing embryos. No change in the methylation status of these genes was observed in spermatozoa. These observations suggest that a deregulation of mechanisms protecting unmethylated alleles from a wave ofde novomethylation occurs following implantation.
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Epigenetic modifications and mRNA levels of the imprinted gene Grb10 in serially passaged fibroblast cells. Biochimie 2012; 94:2699-705. [DOI: 10.1016/j.biochi.2012.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/09/2012] [Indexed: 11/18/2022]
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Hoekstra EJ, von Oerthel L, van der Linden AJA, Schellevis RD, Scheppink G, Holstege FCP, Groot-Koerkamp MJ, van der Heide LP, Smidt MP. Lmx1a is an activator of Rgs4 and Grb10 and is responsible for the correct specification of rostral and medial mdDA neurons. Eur J Neurosci 2012; 37:23-32. [PMID: 23106268 DOI: 10.1111/ejn.12022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 11/26/2022]
Abstract
The LIM homeodomain transcription factor Lmx1a is a very potent inducer of stem cells towards dopaminergic neurons. Despite several studies on the function of this gene, the exact in vivo role of Lmx1a in mesodiencephalic dopamine (mdDA) neuronal specification is still not understood. To analyse the genes functioning downstream of Lmx1a, we performed expression microarray analysis of LMX1A-overexpressing MN9D dopaminergic cells. Several interesting regulated genes were identified, based on their regulation in other previously generated expression arrays and on their expression pattern in the developing mdDA neuronal field. Post analysis through in vivo expression analysis in Lmx1a mouse mutant (dr/dr) embryos demonstrated a clear decrease in expression of the genes Grb10 and Rgs4, in and adjacent to the rostral and dorsal mdDA neuronal field and within the Lmx1a expression domain. Interestingly, the DA marker Vmat2 was significantly up-regulated as a consequence of increased LMX1A dose, and subsequent analysis on Lmx1a-mutant E14.5 and adult tissue revealed a significant decrease in Vmat2 expression in mdDA neurons. Taken together, microarray analysis of an LMX1A-overexpression cell system resulted in the identification of novel direct or indirect downstream targets of Lmx1a in mdDA neurons: Grb10, Rgs4 and Vmat2.
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Affiliation(s)
- Elisa J Hoekstra
- Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
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Ivanova E, Chen JH, Segonds-Pichon A, Ozanne SE, Kelsey G. DNA methylation at differentially methylated regions of imprinted genes is resistant to developmental programming by maternal nutrition. Epigenetics 2012; 7:1200-10. [PMID: 22968513 PMCID: PMC3469461 DOI: 10.4161/epi.22141] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The nutritional environment in which the mammalian fetus or infant develop is recognized as influencing the risk of chronic diseases, such as type 2 diabetes and hypertension, in a phenomenon that has become known as developmental programming. The late onset of such diseases in response to earlier transient experiences has led to the suggestion that developmental programming may have an epigenetic component, because epigenetic marks such as DNA methylation or histone tail modifications could provide a persistent memory of earlier nutritional states. One class of genes that has been considered a potential target or mediator of programming events is imprinted genes, because these genes critically depend upon epigenetic modifications for correct expression and because many imprinted genes have roles in controlling fetal growth as well as neonatal and adult metabolism. In this study, we have used an established model of developmental programming-isocaloric protein restriction to female mice during gestation or lactation-to examine whether there are effects on expression and DNA methylation of imprinted genes in the offspring. We find that although expression of some imprinted genes in liver of offspring is robustly and sustainably changed, methylation of the differentially methylated regions (DMRs) that control their monoallelic expression remains largely unaltered. We conclude that deregulation of imprinting through a general effect on DMR methylation is unlikely to be a common factor in developmental programming.
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Affiliation(s)
- Elena Ivanova
- Epigenetics Programme; The Babraham Institute; Cambridge, UK
| | - Jian-Hua Chen
- Metabolic Research Laboratories; Institute of Metabolic Science; University of Cambridge; Cambridge UK
| | | | - Susan E. Ozanne
- Metabolic Research Laboratories; Institute of Metabolic Science; University of Cambridge; Cambridge UK
- MRC Centre for Obesity and Related Metabolic Diseases; Cambridge, UK
| | - Gavin Kelsey
- Epigenetics Programme; The Babraham Institute; Cambridge, UK
- Centre for Trophoblast Research; University of Cambridge; Cambridge, UK
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A survey of tissue-specific genomic imprinting in mammals. Mol Genet Genomics 2012; 287:621-30. [PMID: 22821278 DOI: 10.1007/s00438-012-0708-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/03/2012] [Indexed: 01/20/2023]
Abstract
In mammals, most somatic cells contain two copies of each autosomal gene, one inherited from each parent. When a gene is expressed, both parental alleles are usually transcribed. However, a subset of genes is subject to the epigenetic silencing of one of the parental copies by genomic imprinting. In this review, we explore the evidence for variability in genomic imprinting between different tissue and cell types. We also consider why the imprinting of particular genes may be restricted to, or lost in, specific tissues and discuss the potential for high-throughput sequencing technologies in facilitating the characterisation of tissue-specific imprinting and assaying the potentially functional variations in epigenetic marks.
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Cowley M, Wood AJ, Böhm S, Schulz R, Oakey RJ. Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic Acids Res 2012; 40:8917-26. [PMID: 22790983 PMCID: PMC3467052 DOI: 10.1093/nar/gks654] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Alternative polyadenylation increases transcriptome diversity by generating multiple transcript isoforms from a single gene. It is thought that this process can be subject to epigenetic regulation, but few specific examples of this have been reported. We previously showed that the Mcts2/H13 locus is subject to genomic imprinting and that alternative polyadenylation of H13 transcripts occurs in an allele-specific manner, regulated by epigenetic mechanisms. Here, we demonstrate that allele-specific polyadenylation occurs at another imprinted locus with similar features. Nap1l5 is a retrogene expressed from the paternally inherited allele, is situated within an intron of a 'host' gene Herc3, and overlaps a CpG island that is differentially methylated between the parental alleles. In mouse brain, internal Herc3 polyadenylation sites upstream of Nap1l5 are used on the paternally derived chromosome, from which Nap1l5 is expressed, whereas a downstream site is used more frequently on the maternally derived chromosome. Ablating DNA methylation on the maternal allele at the Nap1l5 promoter increases the use of an internal Herc3 polyadenylation site and alters exon splicing. These changes demonstrate the influence of epigenetic mechanisms in regulating Herc3 alternative mRNA processing. Internal Herc3 polyadenylation correlates with expression levels of Nap1l5, suggesting a possible role for transcriptional interference. Similar mechanisms may regulate alternative polyadenylation elsewhere in the genome.
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Affiliation(s)
- Michael Cowley
- Department of Medical & Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, London SE1 9RT, UK
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Fedoriw A, Mugford J, Magnuson T. Genomic imprinting and epigenetic control of development. Cold Spring Harb Perspect Biol 2012; 4:a008136. [PMID: 22687277 PMCID: PMC3385953 DOI: 10.1101/cshperspect.a008136] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epigenetic mechanisms are extensively utilized during mammalian development. Specific patterns of gene expression are established during cell fate decisions, maintained as differentiation progresses, and often augmented as more specialized cell types are required. Much of what is known about these mechanisms comes from the study of two distinct epigenetic phenomena: genomic imprinting and X-chromosome inactivation. In the case of genomic imprinting, alleles are expressed in a parent-of-origin-dependent manner, whereas X-chromosome inactivation in females requires that only one X chromosome is active in each somatic nucleus. As model systems for epigenetic regulation, genomic imprinting and X-chromosome inactivation have identified and elucidated the numerous regulatory mechanisms that function throughout the genome during development.
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Affiliation(s)
- Andrew Fedoriw
- The University of North Carolina at Chapel Hill School of Medicine, Department of Genetics, Chapel Hill, North Carolina 27599, USA
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Radford EJ, Isganaitis E, Jimenez-Chillaron J, Schroeder J, Molla M, Andrews S, Didier N, Charalambous M, McEwen K, Marazzi G, Sassoon D, Patti ME, Ferguson-Smith AC. An unbiased assessment of the role of imprinted genes in an intergenerational model of developmental programming. PLoS Genet 2012; 8:e1002605. [PMID: 22511876 PMCID: PMC3325178 DOI: 10.1371/journal.pgen.1002605] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 02/03/2012] [Indexed: 11/18/2022] Open
Abstract
Environmental factors during early life are critical for the later metabolic health of the individual and of future progeny. In our obesogenic environment, it is of great socioeconomic importance to investigate the mechanisms that contribute to the risk of metabolic ill health. Imprinted genes, a class of functionally mono-allelic genes critical for early growth and metabolic axis development, have been proposed to be uniquely susceptible to environmental change. Furthermore, it has also been suggested that perturbation of the epigenetic reprogramming of imprinting control regions (ICRs) may play a role in phenotypic heritability following early life insults. Alternatively, the presence of multiple layers of epigenetic regulation may in fact protect imprinted genes from such perturbation. Unbiased investigation of these alternative hypotheses requires assessment of imprinted gene expression in the context of the response of the whole transcriptome to environmental assault. We therefore analyse the role of imprinted genes in multiple tissues in two affected generations of an established murine model of the developmental origins of health and disease using microarrays and quantitative RT–PCR. We demonstrate that, despite the functional mono-allelicism of imprinted genes and their unique mechanisms of epigenetic dosage control, imprinted genes as a class are neither more susceptible nor protected from expression perturbation induced by maternal undernutrition in either the F1 or the F2 generation compared to other genes. Nor do we find any evidence that the epigenetic reprogramming of ICRs in the germline is susceptible to nutritional restriction. However, we propose that those imprinted genes that are affected may play important roles in the foetal response to undernutrition and potentially its long-term sequelae. We suggest that recently described instances of dosage regulation by relaxation of imprinting are rare and likely to be highly regulated. Environmental perturbations during early life are known to affect one's risk of metabolic disease many years later. Furthermore, that risk can be inherited by future generations, although the mechanisms responsible are poorly understood. Imprinted genes are unusual as only one of the two copies is expressed in a parent-of-origin–specific manner. As only one copy is active, imprinted gene dosage has been hypothesised to be uniquely vulnerable to environmental change. Therefore, it has been suggested that imprinted genes may play an important role in the developmental origins of health and disease. Alternatively, the opposite may be true—imprinted genes may be more tightly safeguarded from perturbation. To test these two hypotheses, we analysed the expression of imprinted genes in the context of all active genes in two affected generations of a mouse model of the developmental origins of health and disease. Our data show that imprinted genes as a class are neither more nor less susceptible to expression change, but a subset of imprinted genes may be involved in the adaptation of the conceptus. Furthermore, imprints in the developing germline are not affected and imprinted genes are largely stable in the second generation. This is important, as it is the first time that this hypothesis has been tested in an unbiased fashion.
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Affiliation(s)
- Elizabeth J. Radford
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Elvira Isganaitis
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Josep Jimenez-Chillaron
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joshua Schroeder
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Molla
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Nathalie Didier
- Myology Group-UMR S 787, INSERM and Université Paris VI/Pierre et Marie Curie, Paris, France
| | - Marika Charalambous
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Kirsten McEwen
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Giovanna Marazzi
- Myology Group-UMR S 787, INSERM and Université Paris VI/Pierre et Marie Curie, Paris, France
| | - David Sassoon
- Myology Group-UMR S 787, INSERM and Université Paris VI/Pierre et Marie Curie, Paris, France
| | - Mary-Elizabeth Patti
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ACF-S); (M-EP)
| | - Anne C. Ferguson-Smith
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (ACF-S); (M-EP)
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Charalambous M, Hernandez A. Genomic imprinting of the type 3 thyroid hormone deiodinase gene: regulation and developmental implications. Biochim Biophys Acta Gen Subj 2012; 1830:3946-55. [PMID: 22498139 DOI: 10.1016/j.bbagen.2012.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/08/2012] [Accepted: 03/23/2012] [Indexed: 02/03/2023]
Abstract
BACKGROUND In recent years, findings in a number of animal and human models have ignited renewed interest in the type 3 deiodinase (D3), the main enzyme responsible for the inactivation of thyroid hormones. The induction of D3 in models of illness and injury has raised critical questions about the physiological significance of reduced thyroid hormone availability in those states. Phenotypes in transgenic mice lacking this enzyme also point to important developmental roles for D3. A critical determinant of D3 expression is genomic imprinting, an epigenetic phenomenon that regulates a small number of dosage-critical genes in the mammalian genome. The D3 gene (Dio3) is imprinted and preferentially expressed from one of the alleles in most tissues. SCOPE OF REVIEW In the context of the physiological significance of D3 and the characteristics and purported origins of genomic imprinting, we review the current knowledge about the epigenetic mechanisms specifying gene dosage in the Dio3 locus. MAJOR CONCLUSIONS Altered Dio3 dosage is detrimental to development, suggesting that the level of thyroid hormone action needs to be exquisitely tailored in a timely fashion to the requirements of particular tissues. An appropriate Dio3 dosage is the result of the coordinated action of certain genomic elements and epigenetic marks in the Dlk1-Dio3 domain. GENERAL SIGNIFICANCE The imprinting of Dio3 prompts intriguing questions about why the level of thyroid hormone signaling should be regulated in this rare epigenetic manner, and to what extent altered Dio3 expression due to aberrant imprinting may be implicated in human conditions. This article is part of a Special Issue entitled Thyroid hormone signalling.
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Affiliation(s)
- Marika Charalambous
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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