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Mitake M, Hirano S, Kishino T. Imprinting analysis by droplet digital PCR coupled with locked nucleic acid TaqMan probes. Epigenetics 2020; 16:729-740. [PMID: 32970510 DOI: 10.1080/15592294.2020.1823160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Imprinted genes are differentially expressed in a parent-of-origin-specific manner. Parental origin of the alleles is discriminated by intragenic DNA polymorphisms. Comparisons of parental allelic expression have been analysed by semiquantitative RT-PCR. Here, we developed a novel quantitative method for allelic expression of the imprinted gene Ube3a, which inactivation and mutations cause Angelman syndrome and predominantly expressed by the maternal allele in neuronal tissues. In this method, cDNA was amplified by droplet digital PCR (ddPCR) coupled with allele-specific locked nucleic acid (LNA) TaqMan probes, which labelled by FAM and HEX were designed to detect the SNPs in the target regions. ddPCR assay demonstrated that the sense transcript of Ube3a was equally expressed from both parental alleles in adult tissues except neuronal tissues, where Ube3a expression from the paternal allele was about 10 to 14% of total Ube3a expression in adult brain, and 20% in spinal cord. The antisense transcript of Ube3a was expressed at 60% to 70% of the sense transcript of Ube3a in adult brain. Changes in the Ube3a transcripts during postnatal brain development were also evaluated by ddPCR. The ddPCR method is far more reliable and simpler to use than semiquantitative PCR to analyse skewed or faint allelic expression of imprinted genes.
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Affiliation(s)
- Maiko Mitake
- Division of Functional Genomics, Centre for Frontier Life Sciences, Nagasaki University, Nagasaki, Japan
| | - Shiori Hirano
- Division of Functional Genomics, Centre for Frontier Life Sciences, Nagasaki University, Nagasaki, Japan
| | - Tatsuya Kishino
- Division of Functional Genomics, Centre for Frontier Life Sciences, Nagasaki University, Nagasaki, Japan
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2
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Abstract
In 1993, Denise Barlow proposed that genomic imprinting might have arisen from a host defense mechanism designed to inactivate retrotransposons. Although there were few examples at hand, she suggested that there should be maternal-specific and paternal-specific factors involved, with cognate imprinting boxes that they recognized; furthermore, the system should build on conserved biochemical factors, including DNA methylation, and maternal control should predominate for imprints. Here, we revisit this hypothesis in the light of recent advances in our understanding of host defense and DNA methylation and in particular, the link with Krüppel-associated box–zinc finger (KRAB-ZF) proteins.
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Affiliation(s)
- Miroslava Ondičová
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Rebecca J. Oakey
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Colum P. Walsh
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
- * E-mail:
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Hillman PR, Christian SGB, Doan R, Cohen ND, Konganti K, Douglas K, Wang X, Samollow PB, Dindot SV. Genomic imprinting does not reduce the dosage of UBE3A in neurons. Epigenetics Chromatin 2017; 10:27. [PMID: 28515788 PMCID: PMC5433054 DOI: 10.1186/s13072-017-0134-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The ubiquitin protein E3A ligase gene (UBE3A) gene is imprinted with maternal-specific expression in neurons and biallelically expressed in all other cell types. Both loss-of-function and gain-of-function mutations affecting the dosage of UBE3A are associated with several neurodevelopmental syndromes and psychological conditions, suggesting that UBE3A is dosage-sensitive in the brain. The observation that loss of imprinting increases the dosage of UBE3A in brain further suggests that inactivation of the paternal UBE3A allele evolved as a dosage-regulating mechanism. To test this hypothesis, we examined UBE3A transcript and protein levels among cells, tissues, and species with different imprinting states of UBE3A. RESULTS Overall, we found no correlation between the imprinting status and dosage of UBE3A. Importantly, we found that maternal Ube3a protein levels increase in step with decreasing paternal Ube3a protein levels during neurogenesis in mouse, fully compensating for loss of expression of the paternal Ube3a allele in neurons. CONCLUSIONS Based on our findings, we propose that imprinting of UBE3A does not function to reduce the dosage of UBE3A in neurons but rather to regulate some other, as yet unknown, aspect of gene expression or protein function.
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Affiliation(s)
- Paul R. Hillman
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77845 USA
| | - Sarah G. B. Christian
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
| | - Ryan Doan
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
- Interdisciplinary Genetics Program, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77845 USA
| | - Noah D. Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX USA
| | - Kranti Konganti
- Institute for Genome Science and Society, Texas A&M University, College Station, TX 77845 USA
| | - Kory Douglas
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX USA
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Paul B. Samollow
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Scott V. Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77845 USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4467 TAMU, College Station, TX 77843 USA
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Post-transcriptional control of gene expression in mouse early embryo development: a view from the tip of the iceberg. Genes (Basel) 2011; 2:345-59. [PMID: 24710195 PMCID: PMC3924817 DOI: 10.3390/genes2020345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 02/22/2011] [Accepted: 04/02/2011] [Indexed: 11/17/2022] Open
Abstract
Fertilization is a very complex biological process that requires the perfect cooperation between two highly specialized cells: the male and female gametes. The oocyte provides the physical space where this process takes place, most of the energetic need, and half of the genetic contribution. The spermatozoon mostly contributes the other half of the chromosomes and it is specialized to reach and to penetrate the oocyte. Notably, the mouse oocyte and early embryo are transcriptionally inactive. Hence, they fully depend on the maternal mRNAs and proteins stored during oocyte maturation to drive the onset of development. The new embryo develops autonomously around the four-cell stage, when maternal supplies are exhausted and the zygotic genome is activated in mice. This oocyte-to-embryo transition needs an efficient and tightly regulated translation of the maternally-inherited mRNAs, which likely contributes to embryonic genome activation. Full understanding of post-transcriptional regulation of gene expression in early embryos is crucial to understand the reprogramming of the embryonic genome, it might help driving reprogramming of stem cells in vitro and will likely improve in vitro culturing of mammalian embryos for assisted reproduction. Nevertheless, the knowledge of the mechanism(s) underlying this fundamental step in embryogenesis is still scarce, especially if compared to other model organisms. We will review here the current knowledge on the post-transcriptional control of gene expression in mouse early embryos and discuss some of the unanswered questions concerning this fascinating field of biology.
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Chou JL, Chen LY, Lai HC, Chan MWY. TGF-β: friend or foe? The role of TGF-β/SMAD signaling in epigenetic silencing of ovarian cancer and its implication in epigenetic therapy. Expert Opin Ther Targets 2011; 14:1213-23. [PMID: 20925461 DOI: 10.1517/14728222.2010.525353] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
IMPORTANCE OF THE FIELD The TGF-β signaling pathway plays an important role in regulating numerous cellular processes including growth inhibition of ovarian surface epithelial (OSE) cells. However, epithelial ovarian cancer is refractory to the inhibitory functions of TGF-β, and yet TGF-β induces metastasis or epithelial-mesenchymal transition (EMT) in advanced ovarian cancer. How TGF-β plays a certain role in one cell but a different role in its malignant counterpart is not fully understood. AREAS COVERED IN THIS REVIEW The role of TGF-β/SMAD signaling both in normal OSE cells and ovarian cancer as well as how dysregulation of this signaling pathway leads to epigenetic silencing of its downstream targets in ovarian neoplasias are reviewed. The therapeutic implication of this signaling pathway in epigenetic therapy of ovarian cancer are also discussed. WHAT THE READER WILL GAIN The reader will gain insight on how dysregulation of TGF-β signaling alters promoter methylation and histone modifications of TGF-β downstream targets in ovarian cancer. TAKE HOME MESSAGE Disruption of TGF-β/SMAD signaling leads to epigenetic silencing of its target genes transiently through histone modifications but permanently by promoter hypermethylation. Targeting the TGF-β signaling pathway may be a novel therapeutic strategy in ovarian cancer.
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Affiliation(s)
- Jian-Liang Chou
- National Chung Cheng University, Department of Life Science, Min-Hsiung, Chia-Yi, Taiwan, ROC
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6
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Korucuoglu U, Biri AA, Konac E, Alp E, Onen IH, Ilhan MN, Turkyilmaz E, Erdem A, Erdem M, Menevse S. Expression of the imprinted IGF2 and H19 genes in the endometrium of cases with unexplained infertility. Eur J Obstet Gynecol Reprod Biol 2009; 149:77-81. [PMID: 20042264 DOI: 10.1016/j.ejogrb.2009.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 12/07/2009] [Accepted: 12/07/2009] [Indexed: 01/01/2023]
Abstract
OBJECTIVE As genomic imprinting plays a critical role in the development of the placenta, the aim of this study was to detect whether the expression levels of the imprinted genes IGF2 and H19 in the endometrium differ between infertile and fertile women. STUDY DESIGN Total RNA was extracted from 30 (15 unexplained infertile and 15 fertile) women's endometrial tissue. cDNA was synthesized from total RNAs of each sample. IGF2 and H19 mRNA expression levels were measured quantitatively using the Real Time PCR method. In order to determine the allelic expression of IGF2 and H19, genomic DNA was extracted from endometrial tissues. RESULTS When compared with the control group, increased mRNA expression of IGF2 was detected (1.5-fold change, P=0.015) in the unexplained infertility group. In contrast, H19 expression was lower in the infertility group as compared to the control group (4-fold change, P<0.0001). Restriction analysis of cDNA-derived PCR product showed that all patients and controls indicated monoallelic expression of IGF2 and H19. CONCLUSION Our results showed that altered expression of these imprinted genes might affect implantation and that their timely and appropriate activation is important for proper functioning. To understand the molecular epigenetic basis of implantation and placental development, genomic imprinted genes should be further investigated.
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Affiliation(s)
- Umit Korucuoglu
- Department of Obstetrics and Gynecology, Faculty of Medicine, Gazi University, 06500 Besevler, Ankara, Turkey
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7
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The amount of heterochromatic proteins in the egg is correlated with sex determination in Planococcus citri (Homoptera, Coccoidea). Chromosoma 2009; 118:737-46. [PMID: 19636581 DOI: 10.1007/s00412-009-0231-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 07/13/2009] [Accepted: 07/13/2009] [Indexed: 10/20/2022]
Abstract
In the mealybug Planococcus citri, there are no identifiable sex chromosomes. Early in the development of embryos destined to become males, the genome contributed by the sperm undergoes heterochromatization and, following an inverted type of meiosis, will be eliminated. Only two vital sperms are therefore produced, both carrying the same maternally derived genome. A differential distribution observed on the two spermatids during male germline cyst formation of chromatin remodeling factors such as HP1 and methylated K9 histone H3 prompted us to propose an imprinting/sex determination model in which the imprinted sperm is the one to undergo heterochromatization at syngamy. The sex ratio is normally 1:1, but aged females are known to produce almost exclusively male progeny, suggesting that the imprinting pattern of the male gamete in P. citri, though necessary, is apparently not sufficient for sex determination. We report here that egg cells of aged females show larger amounts of HP1 and Su(Var)3-9 than egg cells of young females. These data suggest that a determinant of sex may be the amount of maternally derived heterochromatic proteins.
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8
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Ting AH, McGarvey KM, Baylin SB. The cancer epigenome--components and functional correlates. Genes Dev 2007; 20:3215-31. [PMID: 17158741 DOI: 10.1101/gad.1464906] [Citation(s) in RCA: 262] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
It is increasingly apparent that cancer development not only depends on genetic alterations but on an abnormal cellular memory, or epigenetic changes, which convey heritable gene expression patterns critical for neoplastic initiation and progression. These aberrant epigenetic mechanisms are manifest in both global changes in chromatin packaging and in localized gene promoter changes that influence the transcription of genes important to the cancer process. An exciting emerging theme is that an understanding of stem cell chromatin control of gene expression, including relationships between histone modifications and DNA methylation, may hold a key to understanding the origins of cancer epigenetic changes. This possibility, coupled with the reversible nature of epigenetics, has enormous significance for the prevention and control of cancer.
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Affiliation(s)
- Angela H Ting
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21231, USA
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9
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Buglia GL, Ferraro M. Germline cyst development and imprinting in male mealybug Planococcus citri. Chromosoma 2004; 113:284-94. [PMID: 15503092 DOI: 10.1007/s00412-004-0317-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Revised: 08/27/2004] [Accepted: 09/13/2004] [Indexed: 11/28/2022]
Abstract
In the epigenetic modifications involved in the phenomenon of imprinting, which is thought to take place during gametogenesis, one of the primary roles is exerted by histone tail modifications acting on chromatin structure. What is more, in insects like mealybugs, with a lecanoid chromosome system, imprinting is strictly related to sex determination. In many diverse species gametes originate in specific, highly evolutionarily conserved structures called germline cysts. The use of staining techniques specific for fusomal components like F-actin has allowed us to describe for the first time the morphogenesis of male germline cysts in the mealybug Planococcus citri. Antibodies to anti-methylated lysine 9 of histone H3 (MeLy9-H3) and anti-heterochromatin protein 1 (HP1) were used during cyst formation to investigate the involvement of these epigenetic modifications in the phenomenon of imprinting and their possible concerted action in sex determination in P. citri. These observations indicate: (i) a specific role for F-actin in the segregation, typical of the lecanoid chromosome system, of genomes of paternal origin; (ii) that the two vital gametes originating from a given meiosis, although carrying the same genome, differ in the levels of both MeLy9-H3 and HP1, one of them being more heavily labelled by both antibodies.
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Affiliation(s)
- Giovanni Luigi Buglia
- Department of Genetics and Molecular Biology, University of Rome La Sapienza, P. le A. Moro 5, 00185 Rome, Italy
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10
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Kearns M, Preis J, McDonald M, Morris C, Whitelaw E. Complex patterns of inheritance of an imprinted murine transgene suggest incomplete germline erasure. Nucleic Acids Res 2000; 28:3301-9. [PMID: 10954598 PMCID: PMC110704 DOI: 10.1093/nar/28.17.3301] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2000] [Revised: 07/11/2000] [Accepted: 07/11/2000] [Indexed: 01/26/2023] Open
Abstract
Here we report a transgenic mouse line that exhibits significant deviations from a classic pattern of parental imprinting. When the transgene is passed through the female germline, it is completely silenced in some offspring while in others expression is reduced. This variable expressivity does not appear to be the result of differences in the presence of unlinked modifiers. Female transmission of the transgene is associated with hypermethylation. The transgene is generally reactivated on passage through the male germline. Extended pedigrees reveal complex patterns of inheritance of the phenotype. The most likely explanation for this result is that the imprint is not completely erased and reset when passed through the germline of either sex. FISH analysis reveals that the transgene has integrated into chromosome 3 band E3, a region not known to carry imprinted genes, and the integration site shows no sign of allele-specific differential methylation. These findings, in conjunction with other recent work, raise the possibility that the introduction of foreign DNA into the mammalian genome, either through retrotransposition or transgenesis, may be associated with parental imprinting that is not always erased and reset during meiosis.
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Affiliation(s)
- M Kearns
- Department of Biochemistry, University of Sydney, NSW 2006, Australia
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11
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Tanos V, Prus D, Ayesh S, Weinstein D, Tykocinski ML, De-Groot N, Hochberg A, Ariel I. Expression of the imprinted H19 oncofetal RNA in epithelial ovarian cancer. Eur J Obstet Gynecol Reprod Biol 1999; 85:7-11. [PMID: 10428315 DOI: 10.1016/s0301-2115(98)00275-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
STUDY To examine the expression of the imprinted maternally expressed H19 gene in benign, low malignant potential (borderline) and malignant surface epithelial ovarian tumors. DESIGN In situ hybridization for H19 RNA using S-labeled and digoxigenin-labeled probes was performed on paraffin sections of ovarian surface epithelial tumors. The serous tumors included nine section cystadenomas, twelve serous tumors of low malignant potential and twenty serous carcinomas, grade I-IIII (FIGO classification). A smaller group included two mucinous cystadenomas, four mucinous tumors of low malignant potential and two mucinous cystadenocarcinomas. RESULTS H19 expression was found to be positive in 6/9 (67%) serous cystadenomas, 9/12 (75%) of serous tumors of low malignant potential and 13/20 (65%) of invasive serous carcinomas. Expression in mucinous tumors was confined to the stroma beneath the epithelial lining. CONCLUSION H19 is expressed in the majority of serous epithelial tumors. Taking into consideration the high percentage of H19 expressing serous ovarian neoplasms we suggest that H19 RNA may be used as an adjuvant tumor marker for the diagnosis and mainly for staging and follow-up of patients with serous ovarian carcinoma.
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Affiliation(s)
- V Tanos
- Department of Obstetrics and Gynecology, Hadassah University Hospital, Jerusalem, Israel
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12
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Davis TL, Trasler JM, Moss SB, Yang GJ, Bartolomei MS. Acquisition of the H19 methylation imprint occurs differentially on the parental alleles during spermatogenesis. Genomics 1999; 58:18-28. [PMID: 10331941 DOI: 10.1006/geno.1999.5813] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The imprinted mouse H19 gene is hypomethylated on the expressed maternal allele and hypermethylated on the silent paternal allele. A 2-kb region of differential methylation located from -2 to -4 kb relative to the H19 transcriptional start site has been proposed to act as the imprinting mark since hypermethylation in this region is inherited from sperm and retained on the paternal allele throughout development. Here, we describe a temporal analysis of the methylation patterns at the H19 locus during postnatal male germ cell development. The 2-kb region is methylated on the paternal allele throughout spermatogenesis, suggesting that methylation is acquired in this region prior to the resumption of mitosis in postnatal male mice. Likewise, more than half of the maternal alleles are hypermethylated prior to the resumption of mitosis. However, the remaining maternal alleles are not hypermethylated until the completion of meiosis I, indicating that de novo methylation in this region is a continuous process. Sequences proximal to the H19 promoter, which are methylated in spermatozoa and on the paternal allele in somatic cells, are differentially methylated in diploid, mitotic spermatogonia. The maternal allele becomes hypermethylated in this region during meiotic prophase. Thus, the parental H19 alleles acquire methylation differentially in the male germline.
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Affiliation(s)
- T L Davis
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Jamieson RV, Tan SS, Tam PP. Retarded postimplantation development of X0 mouse embryos: impact of the parental origin of the monosomic X chromosome. Dev Biol 1998; 201:13-25. [PMID: 9733570 DOI: 10.1006/dbio.1998.8972] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
About 12-17% of the embryos obtained by mating mice carrying the In(X)1H or Paf mutations are of the 39,X (X0) genotype. Depending on the mutant mice used for mating, the monosomic X chromosome can be inherited from the paternal (XP) or the maternal (XM) parent. The XP0 embryos display developmental retardation at gastrulation and early organogenesis. XP0 embryos also display poor development of the ectoplacental cone, which is significantly smaller in size and contains fewer trophoblasts than XX siblings. In contrast, XM0 embryos develop normally and are indistinguishable from XX littermates. In both types of X0 embryos, an X-linked lacZ transgene is expressed in nearly all cells in both the embryonic and the extraembryonic tissues, suggesting that X inactivation does not occur when only one X is present. Of particular significance is the maintenance of an active XP chromosome in the extraembryonic tissues where normally the paternal X chromosome is preferentially inactivated in XX embryos. The differential impact of the inheritance of X chromosomes from different parents on the development of the X0 embryos raises the possibility that the XP is less capable than the XM in providing the appropriate dosage of X-linked activity that is necessary to support normal development of the embryo and the ectoplacental cone. Alternatively, the development of the XP0 embryo may be compromised by the lack of activity of one or several X-linked genes which are expressed only from the maternal X chromosome. Without the activity of these genes, embryonic development may be curtailed even though all other loci on the XP chromosome are actively transcribed.
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Affiliation(s)
- R V Jamieson
- Embryology Unit, Children's Medical Research Institute, Wentworthville, New South Wales, 2145, Australia
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14
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Lefebvre L, Viville S, Barton SC, Ishino F, Surani MA. Genomic structure and parent-of-origin-specific methylation of Peg1. Hum Mol Genet 1997; 6:1907-15. [PMID: 9302270 DOI: 10.1093/hmg/6.11.1907] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We previously identified Peg1/Mest as a novel paternally expressed gene in the developing mouse embryo. The human PEG1 gene was recently assigned to 7q32 and shown to be imprinted and paternally expressed. Therefore, PEG1 deficiency could participate in the aetiology of pre- and post-natal growth retardation associated with maternal uniparental disomy 7 in humans. We have now initiated the characterization of the Peg1 locus in order to identify and dissect cis-acting elements implicated in its imprinted monoallelic expression. The genomic structure of Peg1 as well as the DNA sequence of the 5'-end of the gene, including 2.4 kb of promoter sequences and covering the first 2 exons, have been determined. Important sequence elements, such as a CpG island spanning exon 1 and direct repeats, are identified and discussed. To address the role of epigenetic modifications in the imprinting of Peg1, a methylation analysis of the Peg1 gene is presented. Partially methylated cytosine residues in 13.5 d.p.c. embryos and undifferentiated ES cells were identified. Using embryos carrying a targetted mutation at the Peg1 locus, we show that this partial promoter methylation pattern reflects a strict parent-of-origin-specific differential methylation: the expressed paternal allele is unmethylated, whereas the silenced maternal allele is fully methylated at the CpG sites studied. That the gametes carry the epigenetic information necessary to lay down this allele-specific methylation pattern is suggested by analysis of DNA isolated from sperm and parthenogenetic embryos.
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Affiliation(s)
- L Lefebvre
- Wellcome/CRC Institute of Cancer and Developmental Biology and Physiological Laboratory, University of Cambridge, UK.
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15
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Ariel I, Weinstein D, Voutilainen R, Schneider T, Lustig-Yariv O, de Groot N, Hochberg A. Genomic imprinting and the endometrial cycle. The expression of the imprinted gene H19 in the human female reproductive organs. DIAGNOSTIC MOLECULAR PATHOLOGY : THE AMERICAN JOURNAL OF SURGICAL PATHOLOGY, PART B 1997; 6:17-25. [PMID: 9028733 DOI: 10.1097/00019606-199702000-00004] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
H19 is an imprinted maternally expressed gene, which is not translated to protein and functions as an RNA molecule. It is closely related to the oppositely imprinted paternally expressed insulin-like growth factor 2 (IGF-2). While the biological function of H19 is not understood IGF-2 is a growth factor that plays a role in human follicular and endometrial differentiation. We examined the expression of H19 in the endometrium and ovary during the menstrual cycle by in situ hybridization applied to paraffin sections of human endometrium and ovaries at different stages of differentiation. In the endometrium, H19 expression was confined to the stroma and fluctuated with endometrial dating to reach its peak in the late secretory stage. IGF-2 was also prominently expressed in late secretory endometrium, but its expression was evident both in the stroma and glandular epithelium. Expression of H19 was not found in primordial, primary, and preantral follicles of the ovary, but prominent expression was evident in the theca of antral and cystic atretic follicles, and focal expression was noted in the granulosa of corpora lutea. An association between H19 expression during the menstrual cycle and the differentiation state of the human female reproductive tract, which is under hormonal control, is suggested.
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Affiliation(s)
- I Ariel
- Department of Pathology, Quantitative Molecular Pathology, Hadassah Hospital, Jerusalem, Israel
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16
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Cattanach BM, Beechey CV, Rasberry C, Jones J, Papworth D. Time of initiation and site of action of the mouse chromosome 11 imprinting effects. Genet Res (Camb) 1996; 68:35-44. [PMID: 8772424 DOI: 10.1017/s0016672300033863] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Previous studies have shown that mice with paternal disomy for chromosome 11 are consistently larger at birth than their normal sibs, whereas mice with the maternal disomy are consistently smaller. An imprinting effect with monoallelic expression of some gene/s affecting growth was indicated. Here we show that the size differences become established prior to birth and are only maintained subsequently, indicating that the gene repression is limited to prenatal development. Fetal analysis was limited to 12.5-17.5 days post coitum. However by extrapolating the data backwards it could be calculated that both the maternal and paternal size effects might commence as early as 7 days post coitum, although possibly slightly later. It may be deduced that initiation of expression of the gene/s responsible may occur at about this time in development. The two disomy growth rates were mirror-images of each other, suggesting that expressed gene dosage is the underlying cause. Differential growth of the placentas of the two disomies was also found, and extrapolation of these data backwards suggested that the placental size differences were initiated later in development than those for the fetuses. The differential placental growth of the maternal and paternal disomies may therefore have developed independently or emerged as a consequence of the differential fetal growth. In either event it would seem that the expression of the responsible gene occurs in the fetus itself to cause the anomalies of growth. The data therefore provide information on the temporal and tissue specificity of the gene/s responsible for the chromosome 11 imprinting effects. Possible candidate genes are discussed.
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Affiliation(s)
- B M Cattanach
- MRC Mammalian Genetics Unit Harwell, Didcot, Oxfordshire, UK
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Nakao M, Sutcliffe JS, Beaudet AL. Advantages of RT-PCR and denaturing gradient gel electrophoresis for analysis of genomic imprinting: detection of new mouse and human expressed polymorphisms. Hum Mutat 1996; 7:144-8. [PMID: 8829631 DOI: 10.1002/(sici)1098-1004(1996)7:2<144::aid-humu8>3.0.co;2-c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Genomic imprinting, or differential expression of alleles based on parental origin, is documented for numerous mouse and human loci and is implicated in various phenotypes such as Wilms tumor, Beckwith-Wiedemann syndrome, Prader-Willi syndrome, and Angelman syndrome. Improved methods would facilitate the analysis of imprinting, and we describe a simple strategy designed to analyze transcripts for imprinting in mouse and human using reverse transcription-polymerase chain reaction (RT-PCR) in combination with GC-clamped denaturing gradient gel electrophoresis (DGGE). As a demonstration, novel polymorphisms in the untranslated portions of mRNA between CBA/NJ and Skive strains of mice were identified and used to document paternal expression of small nuclear ribonucleoprotein associated polypeptide N (Snrpn) in brain, maternal expression of H19 in liver, and biallelic expression of glyceraldehyde 3-phosphate dehydrogenease (Gapd) in liver. The method was also used to demonstrate a new polymorphism and monoallelic expression of H19 in human peripheral leukocytes. Assessment of imprinting for novel or unstudied transcripts requires identification and analysis of polymorphisms at the RNA level, and we believe that RT-PCR with DGGE is a preferred method for this application, with advantages over nuclease protection and other methods.
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Affiliation(s)
- M Nakao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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18
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Sasaki H, Ferguson-Smith AC, Shum AS, Barton SC, Surani MA. Temporal and spatial regulation of H19 imprinting in normal and uniparental mouse embryos. Development 1995; 121:4195-202. [PMID: 8575319 DOI: 10.1242/dev.121.12.4195] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mouse H19 gene is imprinted so that the paternal copy is both methylated and repressed during fetal development. However, the CpG-rich promoter region encompassing the transcription start is not methylated in sperm; this region must therefore become methylated postzygotically. We first examined the timing of DNA methylation of this region and the corresponding expression of H19. Both parental copies are initially undermethylated in blastocysts and the paternal copy then becomes fully methylated in the embryo around implantation; this methylation is more protracted in the extraembryonic lineages, especially in the trophoblast. By contrast to the lineage-dependent methylation, we observed exclusive expression of the maternal copy in preimplantation embryos and in all the lineages of early postimplantation embryos although variability may exist in cultured embryos. This indicates that methylation of the CpG-rich promoter is not a prerequisite for the paternal repression. We then examined whether methylation and expression occurs appropriately in the absence of a maternal or a paternal genome. Both H19 copies in androgenetic embryos are fully methylated while they are unmethylated in parthenogenetic embryos. This correlates with the lack of expression in androgenetic embryos but expression in parthenogenetic embryos. However, the androgenetic trophoblast was exceptional as it shows reduced methylation and expresses H19. These results suggest that promoter methylation is not the primary inactivation mechanism but is a stabilizing factor. Differential methylation in the more upstream region, which is established in the gametes, is a likely candidate for the gametic signal and may directly control H19 activity.
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Affiliation(s)
- H Sasaki
- Wellcome/CRC Institute of Cancer and Developmental Biology, University of Cambridge, UK
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19
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Walsh C, Glaser A, Fundele R, Ferguson-Smith A, Barton S, Surani MA, Ohlsson R. The non-viability of uniparental mouse conceptuses correlates with the loss of the products of imprinted genes. Mech Dev 1994; 46:55-62. [PMID: 8068549 DOI: 10.1016/0925-4773(94)90037-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Diploid parthenogenetic or androgenetic mouse conceptuses produce characteristic and opposite mutant phenotypes and are non-viable, presumably due to different contributions from the maternal and paternal genomes. This is likely to be the result of the preferential expression of only one parent's copy of certain genes in the offspring. So far, four such endogenous imprinted genes are known: the paternal alleles of Igf2 and Snrpn and the maternal alleles of Igf2r and H19 are active, while their opposite parental alleles are inactive. Here we demonstrate that the expression patterns of the Igf2 and Igf2r genes in androgenetic and parthenogenetic conceptuses correlate with which parental alleles normally express them, implying that the imprint can be maintained in the absence of the other parent's genome for these genes. This also indicates that both types of uniparental conceptuses are lacking developmentally important gene products. We did find, however, that the H19 gene was highly expressed not only in the parthenogenetic conceptus, but also in giant trophoblasts and secondary giant cells in the androgenetic placenta, in spite of the imprinting of the H19 gene in normal mouse extra embryonic tissues. We discuss these observations with respect to the non-viability of uniparental conceptuses and the reciprocal imprinting patterns of the Igf2 and H19 genes.
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Affiliation(s)
- C Walsh
- Institute for Experimental Drug Research, Karolinska Hospital, Stockholm, Sweden
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20
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Abstract
The molecular mechanisms introducing epigenetic modifications that lead to differential silencing of some autosomal alleles depending on their parental legacy are still largely unknown, but recent results from studies of endogenously imprinted genes and particular transgenes make DNA methylation a strong candidate. At the same time, these results have raised new questions about the details of the imprinting process.
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Affiliation(s)
- A Efstratiadis
- Department of Genetics and Development, Columbia University, New York, New York 10032
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21
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Madar J, Jandová L, Hraba T, Boubelík M, Holub M. Immunological properties of heterozygous nu/+ mice: changes in antibody response and inducibility of tolerance to protein antigens. Immunobiology 1994; 190:212-24. [PMID: 7522212 DOI: 10.1016/s0171-2985(11)80270-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Heterozygous nu/+ mice are not fully identical in their immunological properties with the mice of wild +/+ genotype. A colony of nu/nu, nu/+ and +/+ mice from the same breeding nucleus was established and their immune reactivity to human serum albumin, inducibility of adult immune tolerance to hen egg lysozyme (HEL), sensitivity of their lymphoid cells to stimulation by mitogens and ratio of CD3, CD4 and CD8 positive cell populations was studied. Both the numbers of antibody-forming cells in regional lymph nodes and the antibody titres in sera of nu/+ mice were highly variable, between undetectable values of nu/nu and high values of +/+ homozygotes. Intravenous pretreatment with soluble HEL, leading in +/+ mice to a deep hyporeactivity to subsequent immunization with the same antigen, did not decrease the response of nu/+ mice significantly. These results indicate that the immunological alteration of nu/+ mice is not only quantitative and that T cell subpopulations might be differentially modified by the presence of nu allele. The finding of decreased CD4:CD8 ratio in nu/+ mice also supports this idea.
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Affiliation(s)
- J Madar
- Institute of Molecular Genetics, Czech Academy of Sciences
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22
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Ohlsson R, Hedborg F, Holmgren L, Walsh C, Ekström TJ. Overlapping patterns of IGF2 and H19 expression during human development: biallelic IGF2 expression correlates with a lack of H19 expression. Development 1994; 120:361-8. [PMID: 8149914 DOI: 10.1242/dev.120.2.361] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The spatial patterns of IGF2 and H19 gene expression are strikingly similar during parts of human embryonic/fetal and early postnatal development. Notable exceptions were found with the ciliary anlage of the embryonic retina and the choroid plexus/leptomeninges, where transcripts from the IGF2 but not the H19 locus could be detected. Moreover, in contrast to the other tissue samples examined, the choroid plexus/leptomeninges expressed both parental IGF2 alleles. Whilst RNase protection analysis revealed a weak activity of the P1 promoter in the choroid plexus/leptomeninges, the P2, P3 and P4 promoters were all active wherever IGF2 was expressed. We discuss these observations with respect to a hypothesized coordinated control of the reciprocally imprinted and closely linked IGF2 and H19 loci.
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Affiliation(s)
- R Ohlsson
- Department of Drug Dependence Research, Karolinska Hospital, Stockholm, Sweden
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23
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Affiliation(s)
- D J Driscoll
- Department of Pediatrics, University of Florida College of Medicine, Gainesville 32610
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24
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Jorgensen R. Developmental significance of epigenetic impositions on the plant genome: A paragenetic function for chromosomes. ACTA ACUST UNITED AC 1994. [DOI: 10.1002/dvg.1020150611] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Abstract
This chapter can be summarized by the following main points: Genomic imprinting results in the functional nonequivalence of the maternal and paternal genomes, thereby preventing the development of viable parthenogenotes and androgenotes in eutherian mammals. Imprinting may have arisen as a result of the specialized evolutionary requirements of the parental genomes or may have been an obligatory step in the development of placentation. A substantial proportion of transgenes and a smaller number of endogenous genes demonstrate imprinted pattern of expression in mice and humans. An analysis of DNA methylation in somatic tissues and germ cells during embryonic and postnatal development reveals dynamic changes, particularly during gametogenesis and early embryogenesis. The nature and timing of these changes suggest that DNA methylation may be involved in genomic imprinting. Imprinted genes display complex methylation patterns. Many aspects of these patterns are consistent with a role for methylation in the imprinted phenotype, although it is currently unclear whether methylation functions in the establishment of imprinting or plays a secondary role in the maintenance of the imprinted pattern of expression. Studies underway to identify new imprinted genes may help elucidate both the function and mechanism of genomic imprinting.
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Affiliation(s)
- J D Gold
- Laboratory of Radiobiology and Environmental Health, University of California, San Francisco 94143
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26
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Fundele RH, Surani MA. Experimental embryological analysis of genetic imprinting in mouse development. DEVELOPMENTAL GENETICS 1994; 15:515-22. [PMID: 7834910 DOI: 10.1002/dvg.1020150610] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- R H Fundele
- Institut für Biologie III, Universität Freiburg, Germany
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27
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Abstract
An understanding of brain development and brain function at the level of the genome is developing rapidly, because of the availability of new technologies in molecular and cellular biology. This understanding can be further enhanced by an interactive exchange between the disciplines of behavioural neuroscience and molecular genetics. New genes are being cloned almost daily, but their function remains an enigma. The purpose of this review is to illustrate how reporter genes can be used to map the brain's genetic activity in developmental time and anatomical space. The production of mutants in the homozygous condition may further lead to a morphological or behavioural phenotype. A knowledge of behavioural neuroscience can provide a prescreen of the reporter distribution and thereby make predictions concerning the type of behavioural analysis required. This approach allows selective cloning and sequencing of those genes which have either a morphological or behavioural phenotype but are transcribed at low levels. It is known that genomic imprinting influences brain development, and also that human genetic mutations and deletions influence imprinting in mental retardation as well as certain behavioural disorders. Precisely how such imprinted genes influence brain development and behaviour is being pursued by the use of chimeras. The distribution of maternal or paternal disomy cells in the brain and the way they influence behaviour may reveal the phenotype and how this is brought about.
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Affiliation(s)
- E B Keverne
- Sub-Department of Animal Behaviour, University of Cambridge, Madingley, United Kingdom
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28
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de Groot N, Rachmilewitz J, Ariel I, Goshen R, Lustig O, Hochberg A. Genetic imprinting in human embryogenesis H19 and IGF2 gene expression. Placenta 1994. [DOI: 10.1016/s0143-4004(05)80352-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Affiliation(s)
- N De-Groot
- Department of Biological Chemistry, Hebrew University of Jerusalem, Israel
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30
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Ohlsson R, Nyström A, Pfeifer-Ohlsson S, Töhönen V, Hedborg F, Schofield P, Flam F, Ekström TJ. IGF2 is parentally imprinted during human embryogenesis and in the Beckwith-Wiedemann syndrome. Nat Genet 1993; 4:94-7. [PMID: 8513333 DOI: 10.1038/ng0593-94] [Citation(s) in RCA: 219] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The phenomenon of parental imprinting involves the preferential expression of one parental allele of a subset of chromosomal genes and has so far only been documented in the mouse. We show here, by exploiting sequence polymorphisms in exon nine of the human insulin-like growth factor 2 (IGF2) gene, that only the paternally-inherited allele is active in embryonic and extra-embryonic cells from first trimester pregnancies. In addition, only the paternal allele is expressed in tissues from a patient who suffered from Beckwith-Wiedemann syndrome. Thus the parental imprinting of IGF2 appears to be evolutionarily conserved from mouse to man and has implications for the generation of the Beckwith-Wiedemann syndrome.
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Affiliation(s)
- R Ohlsson
- Department of Experimental Drug Research, Karolinska Hospital, Stockholm, Sweden
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31
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Affiliation(s)
- D P Barlow
- Research Institute of Molecular Pathology, Vienna, Austria
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32
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Affiliation(s)
- W Reik
- Department of Molecular Embryology, Institute of Animal Physiology and Genetics Research, Babraham, Cambridge, UK
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33
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Hultén M, Armstrong S, Challinor P, Gould C, Hardy G, Leedham P, Lee T, McKeown C. Genomic imprinting in an Angelman and Prader-Willi translocation family. Lancet 1991; 338:638-9. [PMID: 1679180 DOI: 10.1016/0140-6736(91)90652-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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