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Genomic Imprinting

C. Cristofre Martin
Fels Institute
Temple University
3307 N. Broad Street
Philadelphia, PA 10140

Genomic imprinting can be loosely defined as the gamete-of-origin dependent modification of phenotype. That is, the phenotype elicited from a locus is differentially modified by the sex of the parent contributing that particular allele. This process results in a reversible gamete-of-origin specific marking of the genome that ultimately produces a functional difference between the genetic information contributed by each parent. In mammals, the term genomic imprinting has been restricted to describing mono-allelic gene expression or the inactivation of either the maternal or paternal allele of a particular locus.

Similarly, dominance modification involves the production of phenotypic differences in the degree of penetrance of a particular locus (Fisher, 1928). This epigenetic modification is produced by the action of other, distinct modifier loci, most commonly acting in trans. Genomic imprinting is thought to be a particular sub-type of dominance modification (Sapienza, 1990), whereby imprinting would result when one or more of these modifiers is sex-linked and would therefore produce a dosage difference.

Imprinting-like phenomena have been observed in a wide range of phyla from both the plant and animal kingdoms. Some manifestations of this gamete-of-origin dependent modification include: parental dominance in hybrid plants (Heslop-Harrison, 1990); paternal chromosome elimination in Sciara (Metz, 1938; Crouse et al., 1971); inactivation of the paternal genome by heterochromatization in the scale insects (coccids) (Nur, 1990); parent-of-origin specific modification of position effect variegation in Drosophila (Spofford, 1976); phenotypic differences in progeny produced from interspecific crosses in fish (Whitt et al., 1977) and between donkey and horse; preferential inactivation of the paternally derived X chromosome in marsupials and rodent extraembryonic tissues (VandeBerg et al., 1987); parent-of-origin dependent switching of yeast mating types (Klar, 1987); and allelic exclusion of immunoglobulin genes (Holliday, 1990). Probably the most extensively studied and best understood examples of genomic imprinting are the gamete-of-origin dependent modifications of transgene methylation and expression in mice (Swain et al., 1987; Reik et al., 1987; Sapienza et al., 1987) and more recently in a line of transgenic zebrafish (Martin and McGowan, 1995a; 1995b). It is not at all clear yet whether all of the above phenomena are occurring via a similar molecular mechanism. That a parent-of-origin effect occurs in such a wide range of organisms suggests that either there is strong evolutionary conservation of this phenomenon or that it arose independently a number of times. The final result in all cases is an individual that appears to be functionally hemizygous at an imprinted locus. Some of these functionally hemizygous loci would be the result of imprinting by the male parent and some would be the result of imprinting by the female parent (Figure 1).

Figure 1: Two examples of a hypothetical imprinted gene responsible for body color. (LEFT) In this example the pigment gene is maternally imprinted (maternal allele is inactivated). Matings between a male who possesses the allele for pigment and a female who possesses the allele for no pigment produces offspring that show only the pigmented phenotype. In this example, the mother's allele is imprinted and inactivated in the offspring. Therefore, the only actively-expressing allele is the father's pigment allele, which is not imprinted in the offspring. (RIGHT) In this example the pigment gene is paternally imprinted (paternal allele is inactivated). Matings between a male who possesses the allele for pigment and a female who possesses the allele for no pigment produces offspring that show only the pigmented phenotype. In this example, the father's allele is imprinted and inactivated in the offspring. Therefore, the only actively expressing allele is the mother's no pigment allele, which is not imprinted in the offspring. (Figure courtesy of Ross McGowan, Dept. Zoology, University of Manitoba).

Because there is monoallelic parent-of-origin specific expression from an imprinted autosomal locus, genomic imprinting is counter to classical Mendelian genetic theory, which states that there is equal inheritance of parental traits. An imprinted mutant allele would appear to be recessive when inherited from one sex, because it would be inactive (and consequently invisible), whereas it would be the only active allele when inherited from the other sex and, therefore, appear to be dominant (Figure 2).

Figure 2: Schematic representation of the phenotypic effects of maternal imprinting of a mutant allele. Darkened body indicates individual that is mutant for the hypothetical imprinted locus. A cross is used to indicated the imprinted/inactive allele. (CENTER) Both parents are homozygous for the normal allele at the imprinted locus. Although only one allele is active (the paternal copy) in the offspring produced from these parents, it must be a normal allele and therefore all offspring will have a normal phenotype. (LEFT) The mother is homozygous mutant at the imprinted locus, and the father is normal. Since this hypothetical locus is maternally imprinted, the maternal mutant copy will be inactivated in their offspring and the paternal normal copy will be the only active allele. The offspring will be phenotypically normal, and the mutant allele will appear to be a recessive mutation. (RIGHT) The mother is homozygous normal at the imprinted locus, and the father is homozygous mutant. The maternal normal allele is imprinted and inactivated in the offspring of these parents. The only allele that is active is the mutant paternal copy. Therefore, all offspring produced from these parents will display the mutant phenotype, and the mutant allele will appear to be a dominant mutation. (Figure courtesy of Ross McGowan, Dept. Zoology, University of Manitoba).

As stated previously, the genome imprinting phenomenon has been most intensively studied in mammals, particularly mice. One type of epigenetic modification in mammals involves the addition of a methyl group to position 5 of cytosine and occurs most frequently at CpG dinucleotides. This type of DNA modification is significant because, in general, methylated DNA sequences are transcriptionally inactive. Furthermore, the methylation of DNA residues can be stably preserved through the replication process by the action of maintenance methylases, which use the replicated hemimethylated DNA as a template (Razin and Riggs, 1980). It has, therefore, been suggested that DNA methylation may be the epigenetic marking responsible for the imprinting phenomenon in mammals, or at least reflects the imprinted state of a locus produced during gametogenesis (reviewed in Sasaki et al., 1993). It is logical to assume that the epigenetic differences observed in the paternal and maternal genetic contributions would be established during the only time when the two genomes are segregated; i.e., during gametogenesis.

If methylase differences exist in the gametes, one would expect to find different DNA methylation patterns in sperm and eggs. These differences should be perpetuated at least through early development when the final somatic tissue methylation pattern is established. Monk et al. (1987) and Sanford et al. (1987) demonstrated in mice that sperm DNA is more methylated than oocyte DNA. In the mouse, a period of overall demethylation has been observed from fertilization, lasting until approximately the blastocyst stage, followed by extensive de novo methylation. This period begins at gastrulation and ultimately produces methylation levels higher than those observed in either of the gametes (reviewed in Monk, 1990). Similar changes in the methylation phenotype of a variety of transgenes in mice have been observed during development (Chaillet et al., 1991; Ueda et al., 1992).

A number of laboratories have demonstrated a gamete-of-origin influence on the level of methylation of a variety of transgenes in mice (Hadchouel et al., 1987; Reik et al., 1987; Sapienza et al., 1987; Swain et al., 1987). With one exception, methylation tends to increase after passage of a transgene locus through the female germline and decrease after passage through male gametogenesis. In a number of cases an accompanying effect has been found with respect to expression of the transgene: Expression is decreased after passage through a female and increased by passage through a male (Swain et al., 1987; McGowan et al., 1989; Allen et al., 1990). A mosaic pattern of transgene expression has also been found in several lines of transgenic mice, which suggests that the imprinted state may not be retained in all cells (McGowan et al., 1989) or that only a sub-set of early stem cells is affected by the imprint.

Several endogenous genes, as well as regions of many mouse chromosomes (Cattanach and Beechey, 1990), have been shown to be imprinted. To date only a small, but still growing, list of mammalian genes has been demonstrated unequivocally to be imprinted (Table 1).

Estimates of the number of imprinted genes in the mammalian genome range from less than 100 to greater than 200. Like the imprinted transgenes, these endogenous genes show high levels of DNA methylation at the imprinted/inactive allele. At present, no consensus sequences for imprinted loci have been identified at/or surrounding these imprinted genes. However, the imprint imposed at these loci is a very specific and localized process. The imprinted genes H19 (maternal) and Igf2 (paternal) are tightly linked to each other and localized to the same region of mouse chromosome 7 but are imprinted in the opposite direction.

The pronuclear transplantation experiments of McGrath and Solter (1984) and Surani et al. (1984; 1986) using mice have unequivocally demonstrated that there is an absolute requirement for a genetic contribution from both sexes in order for development to proceed normally; i.e., maternal and paternal contributions are not equivalent. Embryos containing only maternal contributions develop minimal extraembryonic tissues (trophectoderm), whereas a poorly developed embryo proper is characteristic of embryos containing only paternal genomes. The importance to the mammalian embryo of both maternal and paternal genomes is most apparent in the very low viability of mammalian parthenogenotes. The timing of developmental arrest and the phenotype of parthenogenetic mouse embryos is highly variable and is most dependent on the genetic background of the embryos. Parthenogenetic embryos produced from one inbred strain of mice may only develop to blastula or gastrula stages, whereas parthenogenetic embryos produced from another strain of mice might develop to the 40 somite stage. Understanding of the role of genomic imprinting in development has been hampered by the lack of a distinct/consistent embryonic phenotype in parthenogenetic embryos and the lack of a precise role for the presently known imprinted genes in development.

Considerable interest has been generated by the realization that the penetrance and severity of many complex human diseases can be affected by the sex of the parent contributing the allele responsible for the disease. The parent of origin effects associated with a disease suggest that imprinting may be involved. Some of these putative imprinted diseases include Huntington's disease, cystic fibrosis, Prader-Willi and Angelman syndromes (reviewed in Hall, 1990; Sapienza and Hall, 1995). Parent of origin effects are also seen for birth defects such as spina bifida (Chatkupt et al., 1992) and certain cancers. The role of imprinting in the development of cancers such as Wilm's tumour, rhabdomyosarcomas and osteosarcomas has been particularly well studied. By examining DNAs collected from tumors and normal tissues, it has been revealed that the development and proliferation of cancerous tumors may be associated with a loss of imprinting at a number of different loci. Two examples of these imprinted loci are: Igf2 (insulin-like growth factor), which is involved in beta-cell tumorigenesis, hepatoblastoma, Wilm's tumor and rhabdomyosarcomas (Christofori et al., 1995; Li et al., 1995; Pedone et al., 1994) and the gene H19, which has been shown to be involved in hepatoblastoma, lung cancer, Wilm's tumor and bladder carcinoma (Li et al., 1995; Kondo et al., 1996; Ariel, 1995). The development of these cancers is thought to be due to the relaxation of the normal monoallelic expression or 'imprinted' status of these genes resulting from the loss of DNA methylation at the imprinted allele.

Numerous investigators have presented theories regarding the evolutionary origins/advantages of genomic imprinting. Few of these theories have been able to satisfy all the disparate information from our present understanding of the phenomenon, such as: 1) broad phylogenetic distribution, 2) the different types of imprinted genes, and 3) both paternal and maternal imprinting. Chandra and Nanjundiah (1990) put forward several postulates describing in a general way the kinds of influences that could produce imprinting and suggest several roles for imprinting: 1) imprinted and non-imprinted alleles of a locus may confer different phenotypes; 2) modifiers of imprinting (so-called"imprintor genes") may have pleiotropic effects such that they are selected for reasons other than their action on the imprinted locus; and 3) imprinting could have co-evolved with other traits. Holliday (1990) suggests that the function of genomic imprinting is to produce functionally haploid gene sets in order for the cell's regulatory machinery to be able to 'fine tune' itself on just a single gene copy. It was further implied that imprinting would also serve to prevent possible detrimental cross-talk between maternal and paternal transcripts at developmentally important regulatory loci. Barlow (1993) has suggested that genome imprinting as a mechanism of gene regulation originated from the use of DNA methylation as a host defense mechanism. The same processes that inactivate incoming viruses in oocytes might also result in the inactivation of some of the organism's own (maternal) loci. Recently, Thomas (1995) proposed that imprinting acts as a mechanism of surveillance for chromosome loss and thus protects against cancers and mono- and trisomic embryos. If imprinted loci are scattered throughout the genome, loss of a chromosome or portion of a chromosome would result in the absence of an active copy of an allele producing probable detrimental effects. Other theories are based solely on genomic imprinting as it occurs is mammals. McGrath and Solter (1984) noted that there is a phenotypic difference in the developing embryos of mouse andro- and gynogenotes. More specifically, androgenetic embryos show poorly developed embryos and excessive trophectoderm (extraembryonic supportive tissue), whereas gynogenetic embryos have well developed embryos and poorly developed trophectoderm. These "imprinting" phenotypes of andro- and gynogenetic embryos seem to suggest the possibility of the male using imprinting to maximize maternal input to the embryo (Haig and Westoby,1989). Finally, Varmuza and Mann (1994) suggested that imprinting in mammals may be a means of protecting the female from ovarian germ cell tumors. Imprinting would prevent the development of malignant trophoblast disease because of the inviability of unfertilized eggs and inability of parthenogentically activated oocytes to implant and develop.

It has been the intention of this review to provide a basic understanding of the process of genomic imprinting (further review of the listed references will provide a much greater appreciation of this very complex process). Although genomic imprinting has been intensively studied in the past few years, it is still a very new field. Our present knowledge of imprinting is limited to the identification of imprinted genes and to only the very fundamental factors that contribute to the process. Researchers are now focusing their efforts on identifying the trans- acting modifiers of imprinting -(i.e., "imprintor" genes), understanding the role of DNA conformation and chromatin structure surrounding imprinted loci (ie., cis elements) and on determining the role of imprinting in development (establishment of the imprint) and human disease.

Learning Objectives

  • Define genomic imprinting.
  • What is meant by the expression "parent of origin expression"?
  • Diagram a cross showing the phenotypes and genotypes of a gene that is only active if it is derived from the maternal parent. Do the same for a gene that is only active if it is derived from the male parent.
  • What modification of DNA is thought to be responsible for genomic imprinting?
  • What is the evidence favoring this kind of modification?
  • Discuss the pronuclear transplantation experiments of McGrath and Solter.
  • What may be some consequences of the loss of imprinting? Give examples.


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Last revised Tuesday, July 14, 1998