Role Of Genomic Imprinting Research Articles

Hydatidiform mole and triploidy: the role of genomic imprinting in placental development

Genomic imprinting, the differential expression of paternal and maternal alleles, is involved in the regulation of embryonic and fetal growth and development. In this review, we focus on the genetics of a disorder caused by a global defect in genomic imprinting, the hydatidiform mole. The ratio between the maternal and paternal genomes is critical in determining the development of both the embryonic and extraembryonic tissues, with an excess of paternally derived chromosomes leading to a complete (no maternal genome) or partial (lower amount of maternal chromosomes) mole. The recent identification and molecular studies in biparental complete moles may yield more insight into the regulation of imprinting during gametogenesis.

Pharmacogénomique de l’hormone de croissance: le polymorphisme du récepteur en première ligne

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Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures

We performed a comparative genomic sequence analysis between human and mouse for 24 imprinted genes on human chromosomes 1, 6, 7, 11, 13, 14, 15, 18, 19, and 20. The MEME program was used to search for motifs within conserved sequences among the imprinted genes and we then used the MAST program to analyze for the presence or absence of motifs in the imprinted genes and 128 nonimprinted genes. Our analysis identified 15 motifs that were significantly enriched in the imprinted genes. We generated a logistic regression model by combining multiple motifs as input variables and the 24 imprinted genes and the 128 nonimprinted genes as a training set. The accuracy, sensitivity, and specificity of our model were 98, 92, and 99%, respectively. The model was further validated by an open test on 12 additional imprinted genes. The motifs identified in this study are novel imprinting signatures, which should improve our understanding of genomic imprinting and the role of genomic imprinting in human diseases.

Brain development in Turner syndrome: a magnetic resonance imaging study

Turner syndrome (TS) results from the absence of an X chromosome in females. This genetic condition is associated with specific cognitive deficits and variations in brain volumes. The goal of this study was to use high-resolution magnetic resonance imaging (MRI) to determine morphological variations in TS and to investigate the effects of parental origin of the X chromosome on brain development in TS. MRI brain scans were acquired from 26 girls with TS and 26 age- and gender-matched controls. Seventeen of the TS subjects had a maternally inherited X chromosome (Xm), and nine of the subjects had a paternally inherited X chromosome (Xp). Rater-blind morphometric analyses were conducted to compare tissue volume differences between girls with TS and controls. Three-way analyses were used to compare subgroups and controls. Subjects with TS demonstrated bilateral decreases in parietal gray and occipital white matter accompanied by increased cerebellar gray matter. Subjects with Xm showed decreased occipital white matter and increased cerebellar gray matter compared to controls. No differences were found in comparisons between subjects with Xp and controls or between subjects with Xm and Xp. Results suggest that X monosomy affects posterior cerebral and cerebellar anatomy in TS. While differences between comparisons of Xm and Xp to controls might suggest an imprinting effect, no significant differences were found when the two subgroups were directly compared to each other. Further investigation into the possible role of genomic imprinting is therefore warranted.

Shared role for differentially methylated domains of imprinted genes.

For most imprinted genes, a difference in expression between the maternal and paternal alleles is associated with a corresponding difference in DNA methylation that is localized to a differentially methylated domain (DMD). Removal of a gene's DMD leads to a loss of imprinting. These observations suggest that DMDs have a determinative role in genomic imprinting. To examine this possibility, we introduced sequences from the DMDs of the imprinted Igf2r, H19, and Snrpn genes into a nonimprinted derivative of the normally imprinted RSVIgmyc transgene, created by excising its own DMD. Hybrid transgenes with sequences from the Igf2r DMD2 were consistently imprinted, with the maternal allele being more methylated than the paternal allele. Only the repeated sequences within DMD2 were required for imprinting these transgenes. Hybrid transgenes containing H19 and Snrpn DMD sequences and ones containing sequences from the long terminal repeat of a murine intracisternal A particle retrotransposon were not imprinted. The Igf2r hybrid transgenes are comprised entirely of mouse genomic DNA and behave as endogenous imprinted genes in inbred wild-type and mutant mouse strains. These types of hybrid transgenes can be used to elucidate the functions of DMD sequences in genomic imprinting.

The non-coding Air RNA is required for silencing autosomal imprinted genes

In genomic imprinting, one of the two parental alleles of an autosomal gene is silenced epigenetically by a cis-acting mechanism. A bidirectional silencer for a 400-kilobase region that contains three imprinted, maternally expressed protein-coding genes (Igf2r/Slc22a2/Slc22a3) has been shown by targeted deletion to be located in a sequence of 3.7 kilobases, which also contains the promoter for the imprinted, paternally expressed non-coding Air RNA. Expression of Air is correlated with repression of all three genes on the paternal allele; however, Air RNA overlaps just one of these genes in an antisense orientation. Here we show, by inserting a polyadenylation signal that truncates 96% of the RNA transcript, that Air RNA is required for silencing. The truncated Air allele maintains imprinted expression and methylation of the Air promoter, but shows complete loss of silencing of the Igf2r/Slc22a2/Slc22a3 gene cluster on the paternal chromosome. Our results indicate that non-coding RNAs have an active role in genomic imprinting.

In vitro methylation of predetermined regions in recombinant DNA constructs.

DNA methylation at position 5 in the cytosine ring in the sequence CpG can be detrimental to the transcription of a variety of genes in higher eukaryotes (1,2). Although the significance of this transcriptional repression is currently under debate (3,4), there is little disagreement that it plays an important role in genomic imprinting and X-chromosome inactivation (5,6). To study the effects of DNA methylation on transcription in an experimental system, bacterial DNA methyltransferases have been used widely in order to mimic the DNA methylation pattern of eukaryotic genes. However, usually every target site in a given recombinant DNA molecule will be subject to DNA methylation by making use of those enzymes. This might result in an exaggeration of the effects of DNA methylation, as most recombinant DNA molecules contain a high degree of prokaryotic DNA, which is rich in CpGs. This methylated CpGrich DNA can contribute to the effects of DNA methylation by formation of a repressive chromatin structure (7,8). In addition, selective DNA methylation is required to distinguish the effects of DNA methylation on transcription initiation and transcript elongation (8,9). Thus, there is a requirement for a method to generate recombinant DNA molecules that are methylated in a predetermined region. The chapter following this one will describe a method that makes use of ligation of methylated DNA fragments into unmethylated vector DNA. This method relies on the availability of suitable restriction sites, which allow directional cloning of the fragment and, in addition, requires a highly efficient ligation reaction.

Endocrine Manifestations of Stimulatory G Protein -Subunit Mutations and the Role of Genomic Imprinting

Endocrine Manifestations of Stimulatory G Protein -Subunit Mutations and the Role of Genomic Imprinting

Endocrine manifestations of stimulatory G protein alpha-subunit mutations and the role of genomic imprinting.

The heterotrimeric G protein G(s) couples hormone receptors (as well as other receptors) to the effector enzyme adenylyl cyclase and is therefore required for hormone-stimulated intracellular cAMP generation. Receptors activate G(s) by promoting exchange of GTP for GDP on the G(s) alpha-subunit (G(s)alpha) while an intrinsic GTPase activity of G(s)alpha that hydrolyzes bound GTP to GDP leads to deactivation. Mutations of specific G(s)alpha residues (Arg(201) or Gln(227)) that are critical for the GTPase reaction lead to constitutive activation of G(s)-coupled signaling pathways, and such somatic mutations are found in endocrine tumors, fibrous dysplasia of bone, and the McCune-Albright syndrome. Conversely, heterozygous loss-of-function mutations may lead to Albright hereditary osteodystrophy (AHO), a disease characterized by short stature, obesity, brachydactyly, sc ossifications, and mental deficits. Similar mutations are also associated with progressive osseous heteroplasia. Interestingly, paternal transmission of GNAS1 mutations leads to the AHO phenotype alone (pseudopseudohypoparathyroidism), while maternal transmission leads to AHO plus resistance to several hormones (e.g., PTH, TSH) that activate G(s) in their target tissues (pseudohypoparathyroidism type IA). Studies in G(s)alpha knockout mice demonstrate that G(s)alpha is imprinted in a tissue-specific manner, being expressed primarily from the maternal allele in some tissues (e.g., renal proximal tubule, the major site of renal PTH action), while being biallelically expressed in most other tissues. Disrupting mutations in the maternal allele lead to loss of G(s)alpha expression in proximal tubules and therefore loss of PTH action in the kidney, while mutations in the paternal allele have little effect on G(s)alpha expression or PTH action. G(s)alpha has recently been shown to be also imprinted in human pituitary glands. The G(s)alpha gene GNAS1 (as well as its murine ortholog Gnas) has at least four alternative promoters and first exons, leading to the production of alternative gene products including G(s)alpha, XLalphas (a novel G(s)alpha isoform that is expressed only from the paternal allele), and NESP55 (a chromogranin-like protein that is expressed only from the maternal allele). A fourth alternative promoter and first exon (exon 1A) located approximately 2.5 kb upstream of the G(s)alpha promoter is normally methylated on the maternal allele and transcriptionally active on the paternal allele. In patients with isolated renal resistance to PTH (pseudohypoparathyroidism type IB), the exon 1A promoter region has a paternal-specific imprinting pattern on both alleles (unmethylated, transcriptionally active), suggesting that this region is critical for the tissue-specific imprinting of G(s)alpha. The GNAS1 imprinting defect in pseudohypoparathyroidism type IB is predicted to decrease G(s)alpha expression in renal proximal tubules. Studies in G(s)alpha knockout mice also demonstrate that this gene is critical in the regulation of lipid and glucose metabolism.

Molecular genetics of bipolar disorder.

Alteration of monoaminergic neurotransmission is implicated in the pathophysiology of bipolar disorder (manic-depressive illness). Candidate genes participating in monoaminergic neurotransmission, especially serotonin transporter and monoamine oxidase A, may be associated with bipolar disorder. And the regulating regions of these genes and the molecules participating in intracellular signal transduction are now under investigation. To date, 13 whole genome positional cloning studies have been performed and many candidate loci identified. Using patients from a pedigree in which schizophrenia, depression or bipolar disorder have been linked with a balanced translocation at 1 and 11, candidate pathogenetic genes were cloned as DISC1 (disrupted in schizophrenia-1) and DISC2. Recently, pathogenetic mutations have been identified in two genetic diseases frequently co-morbid with mood disorder; WFS1 for Wolfram syndrome and ATP2A2 (SERCA2) for Darier's disease. Transmission of bipolar disorder may be characterized by anticipation and parent-of-origin effect, and extended CTG repeat at SEF2-1B gene was identified from a bipolar patient. However, its pathogenetic role was not supported by subsequent studies. Association of bipolar disorder with mitochondrial DNA has also been suggested. The role of genomic imprinting is also possible because linkage to 18p11 is limited to paternally transmitted pedigrees. These results warrant further study of molecular genetics of bipolar disorder.

The role of genomic imprinting in human developmental disorders: lessons from Prader–Willi syndrome

Normal human development involves a delicate interplay of gene expression in specific tissues at narrow windows of time. Temporally and spatially regulated gene expression is controlled both by gene-specific factors and chromatin-specific factors. Genomic imprinting is the expression of specific genes primarily from only one allele at particular times during development, and is one mechanism implicated in the intricate control of gene expression. Two human genetic disorders, Prader-Willi syndrome (PWS, MIM 176270) and Angelman syndrome (AS, MIM 105830), result from rearrangements of chromosome 15q11-q13, an imprinted region of the human genome. Despite their rarity, disorders such as PWS and AS can give focused insight into the role of genomic imprinting and imprinted genes in human development.

X Inactivation in the Mouse Embryo Deficient for Dnmt1: Distinct Effect of Hypomethylation on Imprinted and Random X Inactivation

It has been suggested that DNA methylation plays a crucial role in genomic imprinting and X inactivation. Using DNA methyltransferase 1 (Dnmt1)-deficient mouse embryos carrying X-linked lacZ transgenes, we studied the effects of genomic demethylation on X inactivation. Based on the expression pattern of lacZ, the imprinted X inactivation in the visceral endoderm, a derivative of the extraembryonic lineage, was unaffected in Dnmt1 mutant embryos at the time other imprinted genes showed aberrant expression. Random X inactivation in the embryonic lineage of Dnmt1 mutant embryos, however, was unstable as a result of hypomethylation, causing reactivation of, at least, one lacZ transgene that had initially been repressed. Our results suggest that maintenance of imprinted X inactivation in the extraembryonic lineage can tolerate extensive demethylation while normal levels of methylation are required for stable maintenance of X inactivation in the embryonic lineage.

Beckwith-Wiedemann syndrome: imprinting in clusters revisited.

Genomic imprinting, a process that causes genes to be expressed according to their parental origin, affects a minority of human genes, probably less than 1,000. Nevertheless, this class of epigenetic modification acts on many genes with critical roles in growth and development, and disordered imprinting is implicated in genetic disease and in many cancers. Various theories have been proposed to explain the evolution of imprinting in mammals. The most popular is the Haig parental conflict model, which holds that imprinting evolved as a result of opposing interests of the maternal and paternal genomes. Thus, in polygamous species, paternally derived genes will favor fetal growth at the expense of depleting maternal resources and disadvantaging further offspring. In contrast, the maternal genes will oppose the paternal effect and conserve resources to ensure the fitness of the mother and future offspring. This model predicts that although paternally expressed imprinted genes should promote growth, maternally expressed genes should have opposite effects. Many, but not all, imprinted genes identified to date conform to these predictions (1). The mechanisms by which imprinting is established and maintained are the subject of intense investigation (2). The process must involve a reversible epigenetic marking, and a number of features of imprinted genes have been described. Thus, differential methylation of maternal and paternal alleles is a major characteristic of imprinted genes, and defects in methylation processes (e.g., methyltransferase deficiency) disrupt normal genomic imprinting. Parental allele-specific alterations in the chromosome environment of imprinted genes are revealed by the presence of asynchronous DNA replication and differences in chromatin structure and modification (e.g., histone acetylation). A striking feature of imprinted genes in mammals is their tendency to cluster in the genome. The arrangement of coordinately or oppositely imprinted genes within a cluster offers insights into the mechanisms by which cells establish and maintain appropriate imprints on functionally related genes. Here, we discuss the organization and function of a major imprinted gene cluster, occurring on human chromosome 11p15.5, that has been implicated in the imprinting disorder Beckwith-Wiedemann syndrome (BWS) and in a variety of human cancers including Wilms’ tumor (3, 4). Because the regulation of imprinted genes in the homologous region in the mouse (distal region of chromosome 7) is broadly conserved between mice and humans, experiments in mice have complemented molecular analyses of BWS pathology and have contributed greatly to our current knowledge of mammalian genomic imprinting mechanisms. In this review, we consider the mechanisms and role of genomic imprinting in human development and in BWS pathogenesis, drawing on research on the human and the mouse clusters of imprinted genes.

Improving the safety of embryo technologies: Possible role of genomic imprinting

Although developments in mammalian in vitro embryo technologies have allowed many new clinical and agricultural achievement!, their application has been hindered by limitations in the developmental potential of resulting embryos. Low efficiencies of development to the preimplantation blastocyst stage have been consistently observed in most species, including humans, rabbits, pigs and ruminants. Furthermore, in cattle and sheep a wide range of congenital abnormalities currently termed “Large Offspring syndrome” (LOS) are commonly observed as a result of several embryo culture and manipulation procedures. This paper reviews the hypothesis that at least some of the problems associated with embryo technologies may result from disruptions in imprinted genes, Several imprinted genes (i.e. genes which express only the maternal or paternal allele) are known to have significant effects on fetal size and survival in other species and are possible candidates for involvement in livestock LOS. Major changes in putative imprinting mechanisms such as DNA methylation of imprinted genes occur in the mouse embryo during pre-implantation development, Alterations in DNA methylation are stabley transmitted through repeated cell cycles such that changes in the embryo may still act at the fetal stages. Thus any disruption in establishment and/ or maintenance of imprinting during the vulnerable periods of embryo culture or manipulation is a plausible candidate mechanism for inducing fetal loss and Large Offspring Syndrome, Identification of these disruptions may provide crucial means to improve the success of current procedures.

Polymorphisms, genomic imprinting and cancer susceptibility.

Polymorphisms have been identified in proto-oncogenes and tumor suppressor genes that predispose people to cancer. Recent evidence indicates that genomic imprinting, an epigenetic form of gene regulation that results in uniparental gene expression, can also function as a cancer predisposing event. Thus, cancer susceptibility is increased by both Mendelian inherited genetic and non-Mendelian inherited epigenetic events. Consequently, chemical and physical agents cannot only induce cancer through the formation of genetic mutations but also through epigenetic changes that result in the inappropriate expression of imprinted proto-oncogenes and tumor suppressor genes. The role of genomic imprinting in carcinogenesis and cancer susceptibility is examined in this review.

Genomic imprinting and cancer.

Fifteen years have gone by since the initial demonstrations of mammalian genomic imprinting (Barton et al. 1984; McGrath andSolter 1984; Surani et al. 1984), 7 years since the identification of specific imprinted genes in mice (DeChiara et al. 1991; Barlow et al. 1991; Bartolomei et al. 1991) and 6 years since the demonstration of conservation of imprinting in humans (Zhang and Tycko 1992; Giannoukakis et al. 1993; Ohlsson et al. 1993; Rainier et al. 1993; Zhang et al. 1993). During this time our understanding of the importance of this phenomenon for human diseases has advanced in some areas but remained incomplete in others. In this chapter we review data bearing on the role of genomic imprinting and imprinted genes in human cancer. We highlight the possible relationship of the regionality of imprinting and the role of imprinted genes in controlling fetal growth to the involvement of imprinting in human neoplasia. We describe data linking three imprinted genes on chromosome 11p15.5, H19, IGF2, and p57KIP2, to the pathogenesis of Wilms’ tumor (WT) and other neoplasms, as well as to the fetal overgrowth associated with the Beckwith-Wiedemann Syndrome(BWS). We discuss evidence for epimutations at the H19 locus, causing H19 silencing and biallelic activation of IGF2, as site-specific molecular lesions with a crucial permissive role in Wilms’ tumorigenesis. We also discuss the possible roles of imprinted genes in other pediatric tumors, in other proliferative and tumor syndromes, and in high grade adult malignancies. Lastly, we consider the feasibility of designing rational anticancer therapy targeting imprinted genes.

Loss of imprinting of igf2 in renal-cell carcinomas.

Loss of imprinting (LOI) of the igf2 and h19 genes has been found not only in embryonal tumors but also in common adult cancers. To determine any possible role of genomic imprinting in the development of renal-cell carcinomas (RCCs), we examined the imprinting status of igf2 and h19 in a series of 22 such tumors, and studied its relation to their mRNA expression. Of 14 RCC specimens heterozygous for the ApaI polypmorphism, 7 (50%) showed LOI of igf2. In contrast, for h19 all 9 informative cases maintained imprinting. Furthermore, all 7 cases with LOI transcribed igf2 mRNA at elevated levels, while H19 expression was low regardless of the imprinting status compared with that of background level in each case. These results suggest that LOI of igf2, but not of h19, plays a role in the case of human RCC. However, in contrast to that in Wilms' tumor, LOI in RCC was not associated with any specific down-regulation of h19.

Role of genomic imprinting in Wilms' tumour and overgrowth disorders

Role of genomic imprinting in Wilms' tumour and overgrowth disorders

Role of genomic imprinting in Wilms' tumour and overgrowth disorders.

Activation of the silent maternal IGF2 allele has recently been found in approximately half of Wilms' tumour (WTs) examined. This process of imprint relaxation leads to biallelic expression of IGF2 and it has been suggested that this is a key event in the onset of some WTs. Although it has previously been proposed that the 11p15 chromosome region contains a growth-promoting gene and a tumour suppressor gene, the simplest explanation is that increased expression of the IGF2 gene is responsible for somatic overgrowth in the BWS and predisposition to tumours. This model explains overgrowth in BWS cases with unbalanced translocations with paternal dup(11p), and cases with balanced maternal translocations which are physically close to the IGF2 gene. Maternal translocations are envisaged to disrupt the maternal IGF2 imprint by a mechanism similar to the position-effect variegation mechanism in Drosophila. Relaxation of IGF2 imprinting has also been detected in several patients with the BWS syndrome and a patient with gigantism and Wilms' tumour. Recent gene disruption experiments have shown that inactivation of the mouse h19 gene leads to biallelic lgf2 expression and extensive proportional overgrowth. This mouse model has parallels with the BWS and WT where it has been found that biallelic IGF2 expression is accompanied by an epigenetic modification of the H19 gene. From these data it is possible to speculate that an epigenetic modification of the H19 gene may be the primary event leading to the relaxation of IGF2 imprinting.

Genomic imprinting in unstable DNA diseases.

Evidence for recombination suppression has been identified in linkage studies of several unstable DNA diseases. Also sex-specific changes in recombination frequency have been detected at the loci of Huntington's disease and myotonic dystrophy. It can be hypothesized that meiotic recombination is regulated by genome-wide genomic imprinting and that changes in meiotic recombination imply the presence of the genomic imprinting defect. If aberrant recombination at the locus of trinucleotide repeat expansion is verified, new theoretical and experimental opportunities will arise in studies on the role of genomic imprinting in the unstable DNA disease.