Mechanisms Of Genomic Imprinting Research Articles

Genomic imprinting mechanisms in mammals

Genomic imprinting mechanisms in mammals

Imprinting of mammalian male gametes is gene specific and does not occur at a single stage of differentiation

Epigenetic modifications such as DNA methylation and alterations to chromatin structure have been proposed as hallmarks of imprinting in somatic cells after fertilization. In the germ cell line, gene imprinting needs to be reset in order to transmit the correct sex-specific imprinting pattern to the next generation. The precise timing of imprint erasure and re-establishment for many genes remains to be determined and precise molecular mechanisms of genomic imprinting have not yet been fully characterized. Here, we have analysed the methylation state and DNase-I sensitivity of two genes with reciprocal genomic imprinting (U2af1-rs1 and H19 genes) in a male mouse primordial germ cell (PGC) derived cell line (EG-1), isolated post-natal spermatogonia and mature sperm cells. Our results show that establishment of imprinting of the U2af1-rs1 and H19 genes during male germ cell differentiation occurs at different stages of differentiation. Furthermore, the presence of DNase-I hypersensitive sites may constitute a molecular marker to identify alleles and subsequently acquire the appropriate methylation imprint. We propose that this molecular identifier may be present or absent for a specific gene according to the sex of the gamete.

The Transcriptional Status but Not the Imprinting Control Region Determines Allele-Specific Histone Modifications at the Imprinted H19 Locus

Genomic imprinting governs allele-specific gene expression in an epigenetically heritable manner. The characterization of histone modifications at imprinted gene loci is incomplete, and whether specific histone marks determine transcription or are dependent on it is not understood. Using chromatin immunoprecipitations, we examined in multiple cell types and in an allele-specific manner the active and repressive histone marks of several imprinted loci, including H19, KvDMR1, Snrpn promoter/exon 1, and IG-DMR imprinting control regions. Expressed alleles are enriched for specific actively modified histones, including H3 di- and trimethylated at Lys4 and acetylated histones H3 and H4, while their silent counterparts are associated with repressive marks such as H3 trimethylated at Lys9 alone or in combination with H3 trimethylated at Lys27 and H4/H2A symmetrically dimethylated at Arg3. At H19, allele-specific histone modifications occur throughout the entire locus, including nontranscribed regions such as the differentially methylated domain (DMD) as well as sequences in the H19 gene body that are not differentially methylated. Significantly, the presence of active marks at H19 depends on transcriptional activity and occurs even in the absence of the DMD. These findings suggest that histone modifications are dependent on the transcriptional status of imprinted alleles and illuminate epigenetic mechanisms of genomic imprinting.

Monoallelic expression of nine imprinted genes in the sheep embryo occurs after the blastocyst stage

The preimplantation embryos of a range of mammals can be susceptible to disruptions in genomic imprinting mechanisms, resulting in loss of imprinting. Such disruptions can have developmental consequences involving foetal and placental growth such as Beckwith-Wiedemann syndrome in humans and large offspring syndrome in sheep. Our objective was to investigate the dynamics of establishing monoallelic expression of individual sheep imprinted genes post-fertilisation. Semi-quantitative RT-PCR was used to amplify cDNA from the sheep blastocyst, day 21 foetus and day 21 chorioallantois, to compare expression levels between biparental and parthenogenetic embryos in order to indicate allelic expression status. In common with other mammals, IGF2, PEG1 and PEG3 were paternally expressed in the day 21 conceptus, while H19, IGF2R, GRB10 and p57KIP were maternally expressed. Interestingly, GNAS was maternally expressed in the foetus, but paternally expressed in the chorioallantois at day 21. Overall, the imprinting of ovine GRB10 and IGF2R was comparable with mouse but not with human. Contrary to the trophoblast-restricted maternal expression in both mouse and human, SASH2 (sheep homologue of Mash2/HASH2) was expressed in the ovine foetus and was biallelically expressed in the chorioallantois. Differential methylation of the H19 CTCF III upstream region and IGF2R DMR2 in the chorioallantois revealed predominantly paternal and maternal methylation respectively, indicating conservation of these imprinting regulatory regions. In blastocysts, IGF2R, GRB10 and SASH2 were expressed biallelically, while the other genes were not detected. Thus, for the majority of ovine imprinted genes examined, monoallelic expression does not occur until after the blastocyst stage.

Genomic Imprinting in Mammals

ABSTRACT Genomic imprinting describes the epigenetic phenomenon is that the parent's origin is marked on genome. The phenomenon is unique to placental mammals, and causes parent-of-origin-specific monoallelic expression of most of imprinted genes. The previous studies on mice clarified that these gene expression control required the sex-specific differences of DNA methylation which were established in oogenesis or spermatogenesis. In this paper, we review the relevance of genomic imprinting mechanism and DNA methylation.

The evolutionary biology of cryptic pregnancy: A re-appraisal of the “denied pregnancy” phenomenon

Previous research on 'denied pregnancy', i.e. lack of subjective awareness of pregnancy until the end of gestation in pregnant women, is reviewed and reinterpreted in an evolutionary biological framework. Recent epidemiological studies show that this condition has a much higher incidence than previously thought (about 1:475). Very often, bodily symptoms of pregnancy (nausea, amenorrhea and abdomen swelling) are absent or greatly reduced, and neonates tend to be underweight; in many cases, pregnancy goes undetected also by relatives and physicians. Current explanations in the clinical literature are based on psychodynamic hypotheses about pregnancy-related unconscious conflicts; the lack of symptoms is accounted for by 'somatic denial'. I argue that such psychodynamic accounts are misguided for two reasons: (1) they rest on a failure to recognize the active biological role of the fetus in determining the course of pregnancy, and (2) they ignore the many levels of mother-fetus conflict over resource allocation described by biological theories of parent-offspring conflict. Here I propose to redefine this condition as 'cryptic pregnancy', and begin to explore its possible physiological correlates and evolutionary significance. In the light of parent-offspring conflict theory, cryptic pregnancy appears to reduce the costs of pregnancy, both energetic and ecological (mobility, dependence on kin/mate, etc.), thus favoring the mother at the expense of the fetus. Reduced hCG production and/or effectiveness is likely to be involved in the process. I propose and discuss three nonexclusive evolutionary hypotheses to account for this phenomenon: (1) cryptic pregnancy could be a nonadaptive outcome of conflict resolution processes over resource allocation in pregnancy, possibly related to minor disruptions of genomic imprinting mechanisms. (2) Cryptic pregnancy could result from missed spontaneous abortions of low-quality fetuses. (3) Finally, cryptic pregnancy could be an adaptive pattern of 'forced cooperation' between mother and fetus in stressful or threatening ecological circumstances, as suggested by the reported association with elevated psychosocial stress. In case of reduced survival probability, both mother and fetus would benefit if the mother reduced investment in pregnancy in order to maximize her chances of surviving and reaching delivery.

Genomic imprinting in epigenetic of mammals

Genomic imprinting is one of the most remarkable and important epigenetic phenomena. A biological ban on parthenogenetic and androgenetic development of mammals is an obvious consequence of genomic imprinting. Genomic imprinting defects may cause malformations, clinical syndromes, and tumor growth in humans and to the large offspring syndrome and an increased mortality after in vitro manipulations with early embryos in mammals. Differential expression of parental alleles during ontogeny implies a mechanism of reversible, selective marking of gene alleles. These relatively stable epigenetic modifications, which do not affect the primary nucleotide sequence of DNA, may be transmitted in somatic cell lines and reproduced in the germ line. The genomic imprinting mechanism may be involved in other epigenetic processes, such as epigenetic inheritance, nonrandom allele segregation, meiotic drive, etc. Artificial modulation of genomic imprinting effects with the use of growth factors and demethylating agents permits partial “normocoping” during the development of parthenogenetic mouse embryos. Targeted changes in the transcriptional activity of imprinted genes provide prerequisites for epigenetic correction of syndromes and diseases caused by genomic impriting defects.

Additional evidence for the genomic imprinting model of sex determination in the haplodiploid wasp Nasonia vitripennis: isolation of biparental diploid males after X-ray mutagenesis

The primary sex-determining signal in the haplodiploid wasp Nasonia vitripennis is not known. In haplodiploid reproduction, unfertilized eggs typically develop into uniparental haploid males and fertilized eggs into biparental diploid females. Although this reproductive strategy is common to all Hymenoptera, sex-determination is not strictly specified by the number of genome copies inherited. Furthermore, primary sex-determining signals differ among haplodiploid species. In the honeybee, for example, the primary signal is the genotype at a single, polymorphic locus: diploid animals that are homozygous develop into males while heterozygotes develop into females. Sex determination in Nasonia cannot be explained by this mechanism. Various lines of evidence show that the inheritance of a paternal genome is required for female sexual development and suggest a genomic imprinting mechanism involving an imprinted gene, expressed only from a paternal copy, that triggers female sexual development. In this model, haploid or diploid uniparental embryos develop into males due to a maternal imprint that silences this locus. The genomic imprinting model predicts that a loss-of-function mutation in the paternal copy of the imprinted gene would result in male sexual development in a biparental diploid embryo. In support of this model, we have identified rare biparental diploid males in the F1 progeny of X-ray mutagenized haploid males. Although uniparental diploid male progeny of virgin triploid females have been previously described, this is the first report of biparental diploid males in Nasonia. Our work provides a new, independent line of evidence for the genomic imprinting model of Nasonia sex determination.

Genomic imprinting in the mealybugs

The coccid insects (Hemiptera; Sternorrhyncha; Aphidiformes; Coccoidea; Pseudococcidae) are well suited to study not only the mechanisms of genomic imprinting but also facultative heterochromatization, a phenomenon well exemplified by inactivation of the X chromosome in female mammals. Coccids show sex-specific heterochromatization of an entire set of chromosomes and transcriptional silencing of all the paternally contributed chromosomes in males. Thus, genomic imprinting and the resultant differential regulation operate on 50% of the genome in contrast to the single X chromosome in female mammals. A significant insight into the phenomenon of genomic imprinting has come from very elegant cytological analysis of the coccid system. Recently, efforts have been made to dissect out at the molecular level the phenomenon of genomic imprinting in these insects. The present review summarizes both of these aspects. In light of the accruing experimental evidence for chromatin-based differences in the maternal and paternal genomes, it appears that the mealybug system may provide evidence for stable maintenance of chromatin code not only through mitosis but also through meiosis.

Detection of Parent-of-Origin Effects in Nuclear Families Using Haplotype Analysis

Despite the potential pitfalls of stratification, population-based association studies nowadays are being conducted more often than family-based association studies. However, the mechanism of genomic imprinting has lately been implicated in the etiology of genetic complex diseases and can be detected using statistics only in family-based designs. Powerful tests for association and imprinting have been proposed previously for case-parent trios and single markers. Since the power of association studies can be improved if multiple affected children and haplotypes are considered, we extended the parental asymmetry test (PAT) for imprinting to a test that is suited for both general nuclear families and haplotypes, called HAP-PAT. Significance of the HAP-PAT is determined via a Monte-Carlo simulation procedure. In addition to the HAP-PAT, we modified a haplotype-based association test, proposed by us before, in such a way that either only paternal or maternal transmissions contribute to the test statistic. The approaches were implemented in FAMHAP and we evaluated their performance under a variety of disease models. We were able to demonstrate the usefulness of our haplotype-based approaches to detect parent-of-origin effects. Furthermore, we showed that also in the presence of imprinting it is more reasonable to consider all affected children of a nuclear family, than to randomly select one affected child from each family and to conduct a trio study using the selected individuals.

Genomic imprinting and reproduction

Genomic imprinting is the parent-of-origin specific gene expression which is a vital mechanism through both development and adult life. One of the key elements of the imprinting mechanism is DNA methylation, controlled by DNA methyltransferase enzymes. Germ cells undergo reprogramming to ensure that sex-specific genomic imprinting is initiated, thus allowing normal embryo development to progress after fertilisation. In some cases, errors in genomic imprinting are embryo lethal while in others they lead to developmental disorders and disease. Recent studies have suggested a link between the use of assisted reproductive techniques and an increase in normally rare imprinting disorders. A greater understanding of the mechanisms of genomic imprinting and the factors that influence them are important in assessing the safety of these techniques.

Genomic Imprinting and Assisted Reproductive Technology: Connections and Potential Risks

Assisted reproductive technology (ART) has become the standard of care for the treatment of many types of infertility. As a result, the numbers of children born after ART worldwide has escalated dramatically, and attention has turned to the potential risks of these procedures to the health and development of the children. In addition to the well-established risks of multiple gestations, recent reports have suggested a link between ART and rare disorders of imprinting including Beckwith-Wiedemann syndrome and Angelman syndrome. Here we review molecular mechanisms of genomic imprinting, consider how ART procedures could influence imprinting of gametes and embryos, and review the reports connecting imprinting disorders to ART. We highlight the importance of long-term follow-up of children born after ART, and emphasize the need for an improved understanding of the mechanisms of imprinting at the molecular level so that methods to prevent disruption of this critical epigenetic process can be developed.

Chicken orthologues of mammalian imprinted genes are clustered on macrochromosomes and replicate asynchronously

In the chicken genome, most orthologues of mouse imprinted genes are clustered on macrochromosomes. Only a few orthologues are located in the microchromosome complement. Macrochromosomal and, to a lesser extent, microchromosomal regions containing imprinted gene orthologues exhibit asynchronous DNA replication. We conclude that highly conserved arrays of imprinted gene orthologues were selected during vertebrate evolution, long before these genes were recruited for parent-specific gene expression by genomic imprinting mechanisms. Evidently, the macrochromosome complement provides a better chromatin environment for the establishment of asynchronous DNA replication and imprinted gene expression later in evolution than microchromosomes.

Male correlated non-matroclinal character inheritance in reciprocal hybrids of Rosa section Caninae (DC.) Ser. (Rosaceae)

Artificial F1 hybrids within dog-roses (Rosa section Caninae (DC.) Ser.) have been assessed for expression of morphological characters with regards to the actual taxonomy applied. In the mostly pentaploid members of the section the unique heterogamous Canina-meiosis leads to matroclinal inheritance of characters by transmitting 4/5 of the genetic information via seed donor whereas 1/5 is provided by the pollen donor. Evaluation of phenotypic variability revealed that the two taxonomically relevant characters “widening of the orifice” and “persistence of the sepals” are statistically significant controlled by the pollen donor. Reciprocal crossings confirmed the same pattern. One possible explanation is that this phenomenon might be subject to genomic imprinting mechanisms. The morphological analysis gives clear evidence that conventional taxonomical concept is artificial and does not reflect the evolutionary patterns among dog-roses.

Beckwith-Wiedemann syndrome demonstrates a role for epigenetic control of normal development.

The Beckwith-Wiedemann syndrome (BWS) is characterized by somatic overgrowth and a predisposition to pediatric embryonal tumors. It is associated with genetic or epigenetic abnormalities in a cluster of imprinted genes found within a genomic region of approximately one megabase on human chromosome 11p15. Imprinted genes are expressed preferentially or exclusively from either the paternal or maternal allele. The 11p15 region is organized into two imprinted domains in which genomic imprinting is controlled by separate 'imprinting control regions'. Twenty-five to 50% of BWS patients have biallelic rather than monoallelic expression of the insulin-like growth factor 2 (IGF2) gene. Another 50% of patients have an epigenetic mutation resulting in loss of imprinting of a transcript called KCNQ1OT1. Each of these genes resides in one of the two imprinted domains that appear to be subject to developmental dysregulation in BWS. In this review, we discuss the insights that the study of BWS have contributed to our understanding of the mechanisms of growth control, oncogenesis and genomic imprinting. Specifically, methylation and chromatin modification may coordinate the expression of closely linked imprinted genes. Finally, we discuss how knowledge of epigenetic mechanisms associated with the early stages of embryogenesis suggest caution in the current debate surrounding assisted reproductive and cloning technologies.

Gene silencing-based disease resistance.

The definition of a disease is fundamentally difficult, even if one considers only genetically based diseases. In its broadest sense, disease can be defined as any deviation from the norm that results in a physiological disadvantage. Natural selection ensures that the norm for any given species is constantly changing. In addition, some disadvantages are latent and might only manifest under certain environmental conditions. Conversely, an apparent disadvantage can carry a benefit, for example, the disease sickle-cell anemia that is an advantage in malarial areas. Because of the difficulties in giving disease a precise definition, in this review, gene silencing-based disease resistance will be restricted to the description of gene inactivation processes that contribute to maintain the physical fitness of an organism. In this sense, we are concerned with the elimination of invasive nucleic acid expressing. In numerous organisms, a variety of severe diseases are caused by the attack of invasive nucleic acids such as viruses and retroviral or transposable elements. Organisms have developed diverse mechanisms to defend themselves against such attack that include immune responses and apoptosis. Fungi, plants, invertebrates and vertebrates also enlist gene silencing systems to counteract the harmful effects of invasive nucleic acids. In particular, plants that lack interferon and immune responses have established efficient transcriptional and post-transcriptional gene silencing systems. In this review, we describe how plants defend against invasive nucleic acids and focus on the continual evolutionary battle between plants and viruses. In addition, the importance of controlling transposon activity is outlined. Finally, gene silencing-related mechanisms of genomic imprinting and X-chromosome inactivation are discussed in the context of disease resistance.

Inheritance patterns of maternal alleles in imprinted regions of the mouse genome at different stages of development.

Deviations from Mendelian 1:1 transmission ratio have been observed in mice and humans. With few exceptions, the mechanism leading to transmission-ratio distortion (TRD) remains obscure. We proposed that a genomic imprinting mechanism plays a key role in the genesis of grandparental origin-dependent TRD (Naumova et al. 2001). To further test this hypothesis, we analyzed the transmission of grandparental alleles at three imprinted regions of the mouse genome known to contain genes required for embryo development. We found and replicated moderate (58%: 42%) TRD in favor of grandmaternal alleles in the imprinted region of maternal distal Chromosome (Chr) 12 among female offspring. Comparison of transmission ratios at the distorted region of Chr 12 among 3-week-old mice with those in embryos suggests that the distortion in favor of grandmaternal alleles is owing to postimplantation embryo loss. The absence of grandparental origin-dependent TRD for maternal Chr 6 and 7 implies that the relationship between TRD and imprinting is complex. Most likely, multiple conditions are required for TRD to occur.

Hereditary paragangliomas caused by mutations in the SDHD gene

Introduction. Identification of the gene involved with hereditary paragangliomas (PGL1) was the objective. At least 50% of all glomus tumours have a positive family history via an autosomal dominant inheritance with genomic imprinting linked to chromosome 11q 23. Methods. DNA sequences revealed the presence of the SDHD gene in the PGL1 gene-related glomus families. Results. In almost all PGL-1-related glomus families, four germline mutations were found in the SDHD gene (Succinate dehydrogenase, subunit D). This is a special (tumour-suppressor) gene, encoding a mitochondrial protein that takes part in the respiratory chain complex. Surprisingly, the SDHD mutation was found in 40% of non-familial cases. Conclusion. The discovery of the SDHD gene encoding for hereditary paragangliomas offers both clinical and scientific possibilities of presymptomatic DNA research for optimal genetic counselling, efficient clinical examination, radiodiagnostics and follow-up, insight into the mechanism of genomic imprinting and into the molecular process from mutation to tumour in extremely slow-growing paragangliomas.

A view through the clouds of imprinting.

The purpose of this review is to examine whether our current knowledge of the higher order control of gene expression and nuclear organization can help us understand the mechanisms of genomic imprinting. Imprinting involves the inheritance of a silenced allele of a gene through either a paternal or maternal germline. We have approached the problem of imprinting using a model based on the dynamic attachment of chromatin loops to immobilized RNA polymerases and control elements. We have combined the information from different experimental approaches, examining primarily the IGF2-H19 locus, in an attempt to simplify the complexity of the imprinting data that has accumulated. It is hoped that a unified model may generate predictions amenable to experimental testing and contribute to the interpretation of future experiments.

Clinical aspects and genetics of Prader-Willi syndrome

Prader-Willi syndrome (PWS) is considered to be a rare neurogenetic disorder, nevertheless it represents the most common syndromatic obesity. Main features are severe hypotonia in the newborn period with feeding difficulty and failure to thrive in the first few months, and improvement in later infancy. Between 1 and 6 years the development of a marked truncal obesity is observed, sometimes later on reaching a life-threatening degree. Apart from retarded motor development speech ability is also hampered due to dysfunction of oropharyngeal muscles. Moreover, intellectual impairment is observed that leads to mostly moderate learning difficulty due to deficits in short term memory and abstract thinking. The genetic background of PWS is loss of function of a paternally inherited gene cluster on chromosome 15q11.2, therefore representing a paradigm of an epigenetic phenomenon with silencing and activating of genes depending on their parental origin. Together with the Angelman-Syndrome (AS), genetically located in the same region but clinically different PWS was identified as one of the first human disorders to be caused by the mechanism of genomic imprinting. There are some different genotypes in PWS leading to a quite similar phenotype with small differences e.g. in the pigment expression. An early diagnosis is important because the neuromuscular dysfunction improves with appropriate physiotherapy. Even more, dietary programs with periodical calorie restricted meals can counteract development of morbid obesity with subsequent complications of cardiovascular disorders and diabetes. Clinical diagnosis remains difficult especially in the newborn period and is considered mostly because of the marked hypotonia. Today, the availability of molecular testing of loss of function in the paternal inherited PWS candidate gene makes a definitive diagnosis possible as a prerequisite of symptomatic therapy. One of the most recommended therapeutic interventions is the application of recombinant human growth hormone (rhGH) which has been shown to be useful for improvement of length, physical ability and favourable influence on respiratory problems by a lot of clinical studies. Early diagnosis by means of molecular methods is helpful for comprehensive genetic counseling. It may avoid unnecessary investigations like computed tomography of the brain and muscle biopsy and it enables parents and professionals to start a purposeful therapy. Although it remains a symptomatic tool, GH therapy appears to be useful for most of the patients. Considering the multimorbidity in PWS a multidisciplinary approach seems appropriate for this still mystical condition.