Growth effects of uniparental disomies and the conflict theory of genomic imprinting

Molecular investigation of uniparental disomy (UPD) in spontaneous abortions

OBJECTIVE

About 10-15% of all clinically recognized pregnancies end as spontaneous abortions while at least 50% of pregnancies are lost before reaching term gestation. Genetic abnormalities are responsible for ≥50% of all early miscarriages. The aim is to indentify associations between UPD and abortions and regarding UPD as pathogenetic mechanism possibly to understand the role of imprinted genes or recessive mutations in abortions.

STUDY DESIGN

To determine additional factors causing spontaneous abortions we searched for uniparental disomies (UPD) which is known to be associated with distinct birth defects as per the chromosome involved and parental origin. Studies were carried on DNA of 68 cases of first trimester spontaneous abortions and DNA of their parents. We examined tissue from aborted fetuses, especially in the first trimester, with molecular techniques to detect UPD to chromosomes that contain imprinting genes.The inheritance of each region of the chromosome was determined by comparing the genotypes obtained from abortion and parental DNA.

RESULTS

Of the 68 cases of spontaneous abortions investigated, 324% were found to be biparental inheritance or were uninformative in locus that they were examined, 4118% were matUPD, 147% trisomy for a chromosome, 8,8% patUPD and 294% matUPD and trisomy for a certain chromosome. Most cases of UPD found on chromosomes 21 and 14. Many of those are found in combination with chromosomes 13, 20 and 22.

CONCLUSIONS

UPD might be a common finding among spontaneous abortuses. UPD can be a cause of miscarriage if localized to regions of chromosomes with imprinted genes which control embryogenesis and fetal development and or can activate a recessive mutation in genes which are essential for early embryogenesis.

Temple syndrome: comprehensive molecular and clinical findings in 32 Japanese patients

Purpose

Temple syndrome (TS14) is a rare imprinting disorder caused by aberrations at the 14q32.2 imprinted region. Here, we report comprehensive molecular and clinical findings in 32 Japanese patients with TS14.

Methods

We performed molecular studies for TS14 in 356 patients with variable phenotypes, and clinical studies in all TS14 patients, including 13 previously reported.

Results

We identified 19 new patients with TS14, and the total of 32 patients was made up of 23 patients with maternal uniparental disomy (UPD(14)mat), six patients with epimutations, and three patients with microdeletions. Clinical studies revealed both Prader-Willi syndrome (PWS)-like marked hypotonia and Silver-Russell syndrome (SRS)-like phenotype in 50% of patients, PWS-like hypotonia alone in 20% of patients, SRS-like phenotype alone in 20% of patients, and nonsyndromic growth failure in the remaining 10% of patients in infancy, and gonadotropin-dependent precocious puberty in 76% of patients who were pubescent or older.

Conclusion

These results suggest that TS14 is not only a genetically diagnosed entity but also a clinically recognizable disorder. Genetic testing for TS14 should be considered in patients with growth failure plus both PWS-like hypotonia and SRS-like phenotypes in infancy, and/or precocious puberty, as well as a familial history of Kagami-Ogata syndrome due to maternal microdeletion at 14q32.2.

The omniscient placenta: Metabolic and epigenetic regulation of fetal programming

Fetal development could be considered a sensitive period wherein exogenous insults and changes to the maternal milieu can have long-term impacts on developmental programming. The placenta provides the fetus with protection and necessary nutrients for growth, and responds to maternal cues and changes in nutrient signaling through multiple epigenetic mechanisms. The X-linked enzyme O-linked-N-acetylglucosamine transferase (OGT) acts as a nutrient sensor that modifies numerous proteins to alter various cellular signals, including major epigenetic processes. This review describes epigenetic alterations in the placenta in response to insults during pregnancy, the potential links of OGT as a nutrient sensor to placental epigenetics, and the implications of placental epigenetics in long-term neurodevelopmental programming. We describe the role of placental OGT in the sex-specific programming of hypothalamic-pituitary-adrenal (HPA) axis programming deficits by early prenatal stress as an example of how placental signaling can have long-term effects on neurodevelopment.

Comprehensive clinical studies in 34 patients with molecularly defined UPD(14)pat and related conditions (Kagami-Ogata syndrome)

Paternal uniparental disomy 14 (UPD(14)pat) and epimutations and microdeletions affecting the maternally derived 14q32.2 imprinted region lead to a unique constellation of clinical features such as facial abnormalities, small bell-shaped thorax with a coat-hanger appearance of the ribs, abdominal wall defects, placentomegaly, and polyhydramnios. In this study, we performed comprehensive clinical studies in patients with UPD(14)pat (n=23), epimutations (n=5), and microdeletions (n=6), and revealed several notable findings. First, a unique facial appearance with full cheeks and a protruding philtrum and distinctive chest roentgenograms with increased coat-hanger angles to the ribs constituted the pathognomonic features from infancy through childhood. Second, birth size was well preserved, with a median birth length of ±0 SD (range, -1.7 to +3.0 SD) and a median birth weight of +2.3 SD (range, +0.1 to +8.8 SD). Third, developmental delay and/or intellectual disability was invariably present, with a median developmental/intellectual quotient of 55 (range, 29-70). Fourth, hepatoblastoma was identified in three infantile patients (8.8%), and histological examination in two patients showed a poorly differentiated embryonal hepatoblastoma with focal macrotrabecular lesions and well-differentiated hepatoblastoma, respectively. These findings suggest the necessity of an adequate support for developmental delay and periodical screening for hepatoblastoma in the affected patients, and some phenotypic overlap between UPD(14)pat and related conditions and Beckwith-Wiedemann syndrome. On the basis of our previous and present studies that have made a significant contribution to the clarification of underlying (epi)genetic factors and the definition of clinical findings, we propose the name 'Kagami-Ogata syndrome' for UPD(14)pat and related conditions.

Epigenetic processes in the male germline

Sperm undergo some of the most extensive chromatin modifications seen in mammalian biology. During male germline development, paternal DNA methylation marks are erased and established on a global scale through waves of demethylation and de novo methylation. As spermatogenesis progresses, the majority of the histones are removed and replaced by protamines, enabling a tighter packaging of the DNA and transcriptional shutdown. Following fertilisation, the paternal genome is rapidly reactivated, actively demethylated, the protamines are replaced with histones and the embryonic genome is activated. The development of new assays, made possible by high-throughput sequencing technology, has resulted in the revisiting of what was considered settled science regarding the state of DNA packaging in mammalian spermatozoa. Researchers have discovered that not all histones are replaced by protamines and, in certain experiments, various species of RNA have been detected in what was previously considered transcriptionally quiescent spermatozoa. Most controversially, several groups have suggested that environmental modifications of the epigenetic state of spermatozoa may operate as a non-DNA-based form of inheritance, a process known as ‘transgenerational epigenetic inheritance’. Other developments in the field include the increased focus on the involvement of short RNAs, such as microRNAs, long non-coding RNAs and piwi-interacting RNAs. There has also been an accumulation of evidence illustrating associations between defects in sperm DNA packaging and disease and fertility. In this paper we review the literature, recent findings and areas of controversy associated with epigenetic processes in the male germline, focusing on DNA methylation dynamics, non-coding RNAs, the biology of sperm chromatin packaging and transgenerational inheritance.

Haploid genomes illustrate epigenetic constraints and gene dosage effects in mammals

Sequencing projects have revealed the information of many animal genomes and thereby enabled the exploration of genome evolution. Insights into how genomes have been repeatedly modified provide a basis for understanding evolutionary innovation and the ever increasing complexity of animal developmental programs. Animal genomes are diploid in most cases, suggesting that redundant information in two copies of the genome increases evolutionary fitness. Genomes are well adapted to a diploid state. Changes of ploidy can be accommodated early in development but they rarely permit successful development into adulthood. In mammals, epigenetic mechanisms including imprinting and X inactivation restrict haploid development. These restrictions are relaxed in an early phase of development suggesting that dosage regulation appears less critical. Here we review the recent literature on haploid genomes and dosage effects and try to embed recent findings in an evolutionary perspective.

Evolution of genomic imprinting as a coordinator of coadapted gene expression

Genomic imprinting is an epigenetic phenomenon in which the expression of a gene copy inherited from the mother differs from that of the copy inherited from the father. Many imprinted genes appear to be highly interconnected through interactions mediated by proteins, RNA, and DNA. These kinds of interactions often favor the evolution of genetic coadaptation, where beneficially interacting alleles evolve to become coinherited. Here I demonstrate theoretically that the presence of gene interactions that favor coadaptation can also favor the evolution of genomic imprinting. Selection favors genomic imprinting because it coordinates the coexpression of positively interacting alleles at different loci. Evolution is expected to proceed through a scenario where selection builds associations between beneficial combinations of alleles and, if one locus evolves to become imprinted, it leads to selection for its interacting partners to match its pattern of imprinting. This process should favor the evolution of physical linkage between interacting genes and therefore may help explain why imprinted genes tend to be found in clusters. The model suggests that, whereas some genes are expected to evolve their imprinting status because selection directly favors a specific pattern of parent-of-origin-dependent expression, other genes may evolve imprinting as a coevolutionary response to match the expression pattern of their interacting partners. As a result, some genes will show phenotypic effects consistent with the predictions of models for the evolution of genomic imprinting (e.g., conflict models), but other genes may not, having simply evolved imprinting to follow the lead of their interacting partners.

Mealybug chromosome cycle as a paradigm of epigenetics

Recently, epigenetics has had an ever-growing impact on research not only for its intrinsic interest but also because it has been implied in biological phenomena, such as tumor emergence and progression. The first epigenetic phenomenon to be described in the early 1960s was chromosome imprinting in some insect species (sciaridae and coccoideae). Here, we discuss recent experimental results to dissect the phenomenon of imprinted facultative heterochromatinization in Lecanoid coccids (mealybugs). In these insect species, the entire paternally derived haploid chromosome set becomes heterochromatic during embryogenesis in males. We describe the role of known epigenetic marks, such as DNA methylation and histone modifications, in this phenomenon. We then discuss the models proposed to explain the noncanonical chromosome cycle of these species.

Differential differences in methylation status of putative imprinted genes among cloned swine genomes

DNA methylation is a major epigenetic modification in the mammalian genome that regulates crucial aspects of gene function. Mammalian cloning by somatic cell nuclear transfer (SCNT) often results in gestational or neonatal failure with only a small proportion of manipulated embryos producing live births. Many of the embryos that survive to term later succumb to a variety of abnormalities that are likely due to inappropriate epigenetic reprogramming. Aberrant methylation patterns of imprinted genes in cloned cattle and mice have been elucidated, but few reports have analyzed the cloned pig genome. Four surviving cloned sows that were created by ear fibroblast nuclear transfer, each with a different life span and multiple organ defects, such as heart defects and bone growth delay, were used as epigenetic study materials. First, we identified four putative differential methylation regions (DMR) of imprinted genes in the wild-type pig genome, including two maternally imprinted loci (INS and IGF2) and two paternally imprinted loci (H19 and IGF2R). Aberrant DNA methylation, either hypermethylation or hypomethylation, commonly appeared in H19 (45% of imprinted loci hypermethylated vs. 30% hypomethylated), IGF2 (40% vs. 0%), INS (50% vs. 5%), and IGF2R (15% vs. 45%) in multiple tissues from these four cloned sows compared with wild-type pigs. Our data suggest that aberrant epigenetic modifications occur frequently in the genome of cloned swine. Even with successful production of cloned swine that avoid prenatal or postnatal death, the perturbation of methylation in imprinted genes still exists, which may be one of reason for their adult pathologies and short life. Understanding the aberrant pattern of gene imprinting would permit improvements in future cloning techniques.

Demography, kinship, and the evolving theory of genomic imprinting

Genomic imprinting is the differential expression of an allele based on the parent of origin. Recent transcriptome-wide evaluations of the number of imprinted genes reveal complex patterns of imprinted expression among developmental stages and cell types. Such data demand a comprehensive evolutionary framework in which to understand the effect of natural selection on imprinted gene expression. We present such a framework for how asymmetries in demographic parameters and fitness effects can lead to the evolution of genomic imprinting and place recent theoretical advances in this framework. This represents a modern interpretation of the kinship theory, is well suited to studying populations with complex social interactions, and provides predictions which can be tested with forthcoming transcriptomic data. To understand the intricate phenotypic patterns that are emerging from the recent deluge of data, future investigations of genomic imprinting will require integrating evolutionary theory, transcriptomic data, developmental and functional genetics, and natural history.

Genomic imprinting and mammalian reproduction

Among animals, genomic imprinting is a uniquely mammalian phenomenon in which certain genes are monoallelically expressed according to their parent of origin. This silencing of certain alleles often involves differential methylation at regulatory regions associated with imprinted genes and must be recapitulated at every generation with the erasure and reapplication of these epigenetic marks in the germline. Imprinted genes encode regulatory proteins that play key roles in fetal growth and development, but they also exert wider effects on mammalian reproduction. Genetic knockout experiments have shown that certain paternally expressed imprinted genes regulate post-natal behavior in offspring as well as reproductive behaviors in males and females. These deficits involve changes in hypothalamic function affecting multiple areas and different neurochemical pathways. Paternally expressed genes are highly expressed in the hypothalamus which regulates growth, metabolism and reproduction and so are well placed to influence all aspects of reproduction from adults to the resultant offspring. Coadaptation between offspring and mother appears to have played an important role in the evolution of some paternally expressed genes, but the influence of these genes on male reproductive behavior also suggests that they have evolved to regulate their own transmission to successive generations via the male germline.

Matrisibs, patrisibs, and the evolution of imprinting on autosomes and sex chromosomes

The conflict theory of genomic imprinting argues that parent-of-origin effects on allelic expression evolve as a consequence of conflict between maternally and paternally derived genomes. I derive explicit population-genetic models of this theory when individuals in a cohort with an arbitrary and variable number of sires and dams interact. I show that the evolution of imprinting is governed by the reciprocal of the harmonic mean number of fathers but the reciprocal of the arithmetic mean number of mothers per cohort. Thus, a few monandrous females in a polyandrous population decrease the strength of the genetic conflict and the opportunity for conflict-driven paternal imprinting. In contrast, in populations in which few males control large harems, rare males with small harems do not have such a disproportionate effect on genetic conflicts and maternal imprinting. Additionally, I demonstrate that under the conflict theory, selection for imprinted expression on paternally derived X chromosomes is much weaker than it is on maternally derived X chromosomes or autosomes.

Paternal uniparental isodisomy of chromosome 6 causing a complex syndrome including complete IFN-gamma receptor 1 deficiency

Mendelian susceptibility to mycobacterial disease (MSMD) is a rare primary immunodeficiency associated with clinical disease caused by weakly virulent mycobacterial species. Interferon gamma receptor 1 (IFN-gammaR1) deficiency is a genetic etiology of MSMD. We describe the clinical and genetic features of a 7-year-old Italian boy suffering from MSMD associated with a complex phenotype, including neonatal hyperglycemia, neuromuscular disease, and dysmorphic features. The child also developed necrotizing pneumonia caused by Rhodococcus equi. The child is homozygous for a nonsense mutation in exon 3 of IFNGR1 as a result of paternal uniparental disomy (UPD) of the entire chromosome 6. This is the first reported case of uniparental disomy resulting in a complex phenotype including MSMD.

Evolution of genomic imprinting in humans: does bipedalism have a role?

Recent studies have indicated that genomic imprinting is less conserved in human placenta and fetuses than in mice. Studies in mice confirm evolutionary predictions that imprinted genes have an important role in fetal growth via their effects on placental function, nutrient demand and transfer. Here, I argue that the development of bipedalism in humans might have contributed to a reduced role for imprinted genes in fetal growth. As a consequence of bipedalism, the shape of the human pelvis has changed, leading to a reduced gestation period and smaller 'premature' babies. This overarching selective pressure could, in turn, lead to a relaxation of the silencing of those imprinted genes that reduce fetal growth, a prediction borne out by current data.

Parental and perinatal factors affecting childhood anthropometry of very-low-birth-weight premature infants: a population-based survey

BACKGROUND

The perinatal-neonatal course of very-low-birth-weight (VLBW) infants might affect their childhood growth. We evaluated the effect of parental anthropometry and perinatal and neonatal morbidity of VLBW neonates on their childhood growth.

METHODS

We obtained parental anthropometry, height and weight at age 6-10.5 years of 334 children born as VLBW infants. Parental, perinatal and neonatal data of these children were tested for association with childhood anthropometry.

RESULTS

(1) Maternal and paternal weight standard deviation score (SDS) and discharge weight (DW) SDS were associated with childhood weight SDS (R(2)= 0.111, p < 0.00001); (2) Maternal and paternal height SDS, corrected gestational age (GA) at discharge, maternal assisted reproduction and SGA status were associated with childhood height SDS (R(2)= 0.208, p < 0.00001); (3) paternal weight SDS, DW SDS and surfactant therapy were associated with childhood body mass index (BMI) SDS (R(2)= 0.096, p < 0.00001). 31.1% of VLBW infants had DW SDS < -1.88, and are to be considered small for gestational age ('SGA'). One quarter of these infants did not catch up by age 6-10.5 years.

CONCLUSION

Childhood anthropometry of VLBW infants depends on parental anthropometry, postnatal respiratory morbidity and growth parameters at birth and at discharge. Almost one-third of VLBW premature infants had growth restriction at discharge from neonatal intensive care unit (NICU), a quarter of whom did not catch up by age 6-10.5 years.

Possible diversifying selection in the imprinted gene, MEDEA, in Arabidopsis

Coevolutionary conflict among imprinted genes that influence traits such as offspring growth may arise when maternal and paternal genomes have different evolutionary optima. This conflict is expected in outcrossing taxa with multiple paternity, but not self-fertilizing taxa. MEDEA (MEA) is an imprinted plant gene that influences seed growth. Disagreement exists regarding the type of selection acting on this gene. We present new data and analyses of sequence diversity of MEA in self-fertilizing and outcrossing Arabidopsis and its relatives, to help clarify the form of selection acting on this gene. Codon-based branch analysis among taxa (PAML) suggests that selection on the coding region is changing over time, and nonsynonymous substitution is elevated in at least one outcrossing branch. Codon-based analysis of diversity within outcrossing Arabidopsis lyrata ssp. petraea (OmegaMap) suggests that diversifying selection is acting on a portion of the gene, to cause elevated nonsynonymous polymorphism. Providing further support for balancing selection in A. lyrata, Hudson, Kreitman and Aguadé analysis indicates that diversity/divergence at silent sites in the MEA promoter and genic region is elevated relative to reference genes, and there are deviations from the neutral frequency spectrum. This combination of positive selection as well as balancing and diversifying selection in outcrossing lineages is consistent with other genes influence by evolutionary conflict, such as disease resistance genes. Consistent with predictions that conflict would be eliminated in self-fertilizing taxa, we found no evidence of positive, balancing, or diversifying selection in A. thaliana promoter or genic region.

Evolution of genomic imprinting with biparental care: implications for Prader-Willi and Angelman syndromes

The term "imprinted gene" refers to genes whose expression is conditioned by their parental origin. Among theories to unravel the evolution of genomic imprinting, the kinship theory prevails as the most widely accepted, because it sheds light on many aspects of the biology of imprinted genes. While most assumptions underlying this theory have not escaped scrutiny, one remains overlooked: mothers are the only source of parental investment in mammals. But, is it reasonable to assume that fathers' contribution of resources is negligible? It is not in some key mammalian orders including humans. In this research, I generalize the kinship theory of genomic imprinting beyond maternal contribution only. In addition to deriving new conditions for the evolution of imprinting, I have found that the same gene may show the opposite pattern of expression when the investment of one parent relative to the investment of the other changes; the reversion, interestingly, does not require that fathers contribute more resources than mothers. This exciting outcome underscores the intimate connection between the kinship theory and the social structure of the organism considered. Finally, the insight gained from my model enabled me to explain the clinical phenotype of Prader-Willi syndrome. This syndrome is caused by the paternal inheritance of a deletion of the PWS/AS cluster of imprinted genes in human Chromosome 15. As such, children suffering from this syndrome exhibit a striking biphasic phenotype characterized by poor sucking and reduced weight before weaning but by voracious appetite and obesity after weaning. Interest in providing an evolutionary explanation to such phenotype is 2-fold. On the one hand, the kinship theory has been doubted as being able to explain the symptoms of patients with Prader-Willi. On the other hand, the post-weaning symptoms remain as one of the primary concern of pediatricians treating children with Prader-Willi. In this research, I reconcile the clinical phenotype of Prader-Willi syndrome with the kinship theory, contending that paternal investment relative to maternal investment increases after weaning. I also propose a genetic composition of the PWS/AS cluster, discuss the effects of new types of mutations, and contemplate the potential side effects of reactivating silent genes for medical purposes.

Imprinted genes and neuroendocrine function

Imprinted genes are monoallelically expressed in a parent-of-origin dependent manner. Whilst the full functional repertoire of these genes remains obscure, they are generally highly expressed in the brain and are often involved in fundamental neural processes. Besides influencing brain neurochemistry, imprinted genes are important in the development and function of the hypothalamus and pituitary gland, key sites of neuroendocrine regulation. Moreover, imprinted genes may directly modulate hormone-dependent signalling cascades, both in the brain and elsewhere. Much of our knowledge about imprinted gene function has come from studying knockout mice and human disorders of imprinting. One such disorder is Prader-Willi syndrome, a neuroendocrine disorder characterised by hypothalamic abnormalities and aberrant feeding behaviour. Through examining the role of imprinted genes in neuroendocrine function, it may be possible to shed light on the neurobiological basis of feeding and aspects of social behaviour and underlying cognition, and to provide insights into disorders where these functions go awry.

Silver-Russell syndrome in a girl born after in vitro fertilization: partial hypermethylation at the differentially methylated region of PEG1/MEST

PURPOSE

The prevalence of low birth weight (LBW) is increased in subjects born after assisted reproduction technology (ART), and defective imprinting has frequently been identified in patients with Beckwith-Wiedermann and Angelman syndromes conceived by ART. Thus, we examined methylation pattern in a girl born after ART who had Silver-Russell syndrome (SRS) which can be caused by maternal uniparental disomy for chromosome 7 and by hypomethylation of the differentially methylated region (DMR) of H19.

METHODS

We examined methylation status of 31 cytosines at the CpG dinucleotides in the DMR of PEG1/MEST on 7q32.2 and 23 cytosines at the CpG dinucleotides in the DMR of H19 on 11p15, using leukocyte genomic DNA.

RESULTS

Eight of the 31 cytosines in the patient and four of the 31 cytosines in the father were hypermethylated in the PEG1/MEST-DMR. In the H19-DMR, no abnormal methylation pattern was identified in the patient.

CONCLUSION

The results suggest that hypermethylation of paternally expressed genes including PEG1/MEST, which usually have growth-promoting effects, may be relevant to LBW in subjects conceived by ART.

Genomic imprinting in mammals: emerging themes and established theories

The epigenetic events that occur during the development of the mammalian embryo are essential for correct gene expression and cell-lineage determination. Imprinted genes are expressed from only one parental allele due to differential epigenetic marks that are established during gametogenesis. Several theories have been proposed to explain the role that genomic imprinting has played over the course of mammalian evolution, but at present it is not clear if a single hypothesis can fully account for the diversity of roles that imprinted genes play. In this review, we discuss efforts to define the extent of imprinting in the mouse genome, and suggest that different imprinted loci may have been wrought by distinct evolutionary forces. We focus on a group of small imprinted domains, which consist of paternally expressed genes embedded within introns of multiexonic transcripts, to discuss the evolution of imprinting at these loci.

Imbalanced genomic imprinting in brain development: an evolutionary basis for the aetiology of autism

We describe a new hypothesis for the development of autism, that it is driven by imbalances in brain development involving enhanced effects of paternally expressed imprinted genes, deficits of effects from maternally expressed genes, or both. This hypothesis is supported by: (1) the strong genomic-imprinting component to the genetic and developmental mechanisms of autism, Angelman syndrome, Rett syndrome and Turner syndrome; (2) the core behavioural features of autism, such as self-focused behaviour, altered social interactions and language, and enhanced spatial and mechanistic cognition and abilities, and (3) the degree to which relevant brain functions and structures are altered in autism and related disorders. The imprinted brain theory of autism has important implications for understanding the genetic, epigenetic, neurological and cognitive bases of autism, as ultimately due to imbalances in the outcomes of intragenomic conflict between effects of maternally vs. paternally expressed genes.

Genomic imprinting in the placenta

Genomic imprinting is an epigenetic mechanism that is important for the development and function of the extra-embryonic tissues in the mouse. Remarkably all the autosomal genes which were found to be imprinted in the trophoblast (placenta) only are active on the maternal and repressed on the paternal allele. It was shown for several of these genes that their paternal silencing is not dependent on DNA methylation, at least not in its somatic maintenance. Rather, recent studies in the mouse suggest that placenta-specific imprinting involves repressive histone modifications and non-coding RNAs. This mechanism of autosomal imprinting is similar to imprinted X chromosome inactivation in the placenta. Although the underlying reasons remain to be explored, this suggests that imprinting in the placenta and imprinted X inactivation are evolutionarily related.

Insulin-like growth factor 2 as a candidate gene influencing growth and carcass traits and its bialleleic expression in chicken

We have identified DNA polymorphisms in the gene of insulin-like growth factor 2 by PCR-SSCP in a resource population, which was generated by Silky reciprocally crossing to Broilers. A C --> G mutation was detected in the exon 2 (at position 71) by sequencing. This single nucleotide polymorphism (SNP) was found to be associated with production traits. Chicken with BB genotype showed more chest angle width but less 3 week body weight and glandular stomach weight than chicken with AA genotype (P < 0.05); while the heterozygote (AB genotype) chicken had more abdominal fat weight, eviscerated yield with giblet than AA homozygote chicken. Further analysis showed that there were different genetic effects on some traits between heterozygote AB (paternal allele given first) and heterozygote BA: chickens with genotype BA had more birth weight and breast weight but less abdominal fat weight than chickens with genotype AB (P < 0.05), which could be hypothetically contributed by genome imprinting. Therefore, Silky chickens were selected for production of heterozygotes to confirm whether IGF2 locus was imprinting. Progeny from heterozygote x homozygote reciprocal cross was assayed for expression after the genotype was determined. The transcription of IGF2 was detected by RT-PCR-SSCP. IGF2 gene was expressed bialleleically in 1-day-old neonatal liver and 90-day-old liver, kidney, heart, and muscle of both heterozygote AB and BA chickens. Therefore, IGF2 was not an imprinting gene in chicken. The different genetic effects between the heterozygote AB and BA remain to be elucidated.

Genomic Imprinting and Kinship: How Good is the Evidence?

The kinship theory of genomic imprinting proposes that parent-specific gene expression evolves at a locus because a gene's level of expression in one individual has fitness effects on other individuals who have different probabilities of carrying the maternal and paternal alleles of the individual in which the gene is expressed. Therefore, natural selection favors different levels of expression depending on an allele's sex-of-origin in the previous generation. This review considers the strength of evidence in support of this hypothesis for imprinted genes in four "clusters," associated with the imprinted loci Igf2, Igf2r, callipyge, and Gnas. The clusters associated with Igf2 and Igf2r both contain paternally expressed transcripts that act as enhancers of prenatal growth and maternally expressed transcripts that act as inhibitors of prenatal growth. This is consistent with predictions of the kinship theory. However, the clusters also contain imprinted genes whose phenotypes as yet remain unexplained by the theory. The principal effects of imprinted genes in the callipyge and Gnas clusters appear to involve lipid and energy metabolism. The kinship theory predicts that maternally expressed transcripts will favor higher levels of nonshivering thermogenesis (NST) in brown adipose tissue (BAT) of animals that huddle for warmth as offspring. The phenotypes of reciprocal heterozygotes for Gnas knockouts provide provisional support for this hypothesis, as does some evidence from other imprinted genes (albeit more tentatively). The diverse effects of imprinted genes on the development of white adipose tissue (WAT) have so far defied a unifying hypothesis in terms of the kinship theory.

Mouse biodiversity in the genomic era

Comparative genomics has developed by comparison of distantly related genomes, for which the link between the reported evolutionary changes and species development/physiology/ecology is not obvious. It is argued that the mouse (genus Mus) is an optimal model for microevolutionary genomics in vertebrates. This is because the mouse genome sequence, physical and genetic map have been completed, because mouse genetics, morpho-anatomy, pathology, behavior and ecology are well-studied, and because the Mus genus is a diverse, well- documented taxon, allowing comparative studies at the level of individual, population, subspecies, and species. The potential of the interaction between mouse genome and mouse biodiversity is illustrated by recent studies of speciation in the house mouse Mus musculus, and studies about the evolution of isochores, the peculiar pattern of GC-content variation across mammalian genomes.

Natural Selection and the Evolution of Genome Imprinting

Sexual reproduction results from the fusion of gametes in which the chromatin configuration of maternal and paternal chromosomes is distinct at fertilization. Although many of the differences are erased during successive cellular divisions and chromatin modifications, some are retained in both somatic and germline cells. These epigenetic modifications can confer different characteristics on maternal and paternal chromosomes and such differences can be selected during any process that has the ability to distinguish between homologues. The end result of these selective forces are parental origin effects, writ large. The range of effects observed, including transcriptional imprinting and effects on chromosome segregation and heterochromatization, reflects the diversity of selective forces in operation. However, a closer look at these effects suggests that parental origin-dependent differences in chromatin structure might be subject to some common forces and that these forces may explain many of the "nontranscriptional" parental origin effects observed in mammals.

Genomic imprinting: could the chromatin structure be the driving force?

Genomic imprinting is traditionally defined as an epigenetic process leading to parental origin-dependent monoallelic expression of some genes. The current paradigm considers this unusual expression mode as the biological raison d être of imprinting. The present chapter proposes a critical review of our ideas about genomic imprinting in light of more recent investigatory progress. Many observations are difficult to explain on the basis of the current paradigm. Studies of allelic expression of many imprinted genes and other characteristics of chromatin domains containing clustered imprinted genes, such as replication and chromatin structure, revealed an unexpectedly complex situation that challenged the role of genomic imprinting as a mechanism of transcriptional regulation. The emerging picture is that parental imprinting is a feature of large chromatin domains with their own domain-wide characteristics. The primary biological function of imprinting may reside in the differential chromatin structure of the parental chromosomal regions and not in the monoallelic expression of some of the genes contained within them.

What good is genomic imprinting: the function of parent-specific gene expression

Parent-specific gene expression (genomic imprinting) is an evolutionary puzzle because it forgoes an important advantage of diploidy--protection against the effects of deleterious recessive mutations. Three hypotheses claim to have found a countervailing selective advantage of parent-specific expression. Imprinting is proposed to have evolved because it enhances evolvability in a changing environment, protects females against the ravages of invasive trophoblast, or because natural selection acts differently on genes of maternal and paternal origin in interactions among kin. The last hypothesis has received the most extensive theoretical development and seems the best supported by the properties of known imprinted genes. However, the hypothesis is yet to provide a compelling explanation for many examples of imprinting.

Regulation of supply and demand for maternal nutrients in mammals by imprinted genes

The placenta has evolved in eutherian mammals primarily to provide nutrients for the developing fetus. The genetic control of the regulation of supply and demand for maternal nutrients is not understood. In this review we argue that imprinted genes have central roles in controlling both the fetal demand for, and the placental supply of, maternal nutrients. Recent studies on Igf2 (insulin-like growth factor 2) knockout mouse models provide experimental support for this hypothesis. These show effects on placental transport capacity consistent with a role of IGF-II in modulating both the placental supply and fetal demand for nutrients. Imprinting of genes with such functions may have coevolved with the placenta and new evidence suggests that transporter proteins, as well as the regulators themselves, may also be imprinted. These data and hypotheses are important, as deregulation of supply and demand affects fetal growth and has long term consequences for health in mammals both in the neonatal period and, as a result of fetal programming, in adulthood.

Maternal isodisomy for 14q21-q24 in a man with diabetes mellitus

We report a 20-year-old man with maternal uniparental disomy for chromosome 14 (UPD14) and maturity-onset diabetes mellitus (DM). He had pre- and postnatal growth retardation, developed DM at age 20 years without any autoimmune antibodies, and had a mosaic 45,XY,der(14;14)(q10;q10)[129]/46,XY,+14,der(14;14)(q10;q10)[1] karyotype. Allelotyping using microsatellite markers covering the entire 14q indicated segmental maternal isodisomy for 14q21-q24 and maternal heterodisomy of the remaining regions of the chromosome. It is thus tempting to speculate that the segmental isodisomy led to reduction to homozygosity for a mutant gene and thus caused his DM, although the possibility of coincidental occurrence of the two events cannot totally be ruled out. Fluorescence in situ hybridization (FISH) analysis using BAC clone probes revealed that the isodisomic segment did not overlap any known IDDM or NIDDM susceptibility loci on chromosome 14, suggesting a novel locus for a subset of DM at the isodisomic segment.

Genetic screening for maternal uniparental disomy of chromosome 7 in prenatal and postnatal growth retardation of unknown cause

OBJECTIVE

Many short-statured children lack an etiologic explanation for their retarded growth. Recently, uniparental disomy (UPD), the inheritance of both chromosomes of a chromosome pair from only 1 parent, has been associated with short stature for many chromosomes. Silver-Russell syndrome (SRS) represents an extreme syndrome of intrauterine growth retardation (IUGR) and slight dysmorphic signs, and maternal UPD of human chromosome 7 (matUPD7) has been observed in approximately 10% of SRS cases. In addition, matUPD7 has been reported in patients with only slight dysmorphic features and prenatal or postnatal growth retardation. The objectives of this study were to study the role of matUPD7 in growth failure of unknown cause and in cases of SRS, and to evaluate the efficiency of genetic testing for matUPD7 as a diagnostic tool.

METHODS

DNA samples were studied from 205 children, 92 girls and 113 boys, with short stature of unknown cause and their parents. The patient cohort included 39 cases of SRS, 91 patients with IUGR and subsequent postnatal short stature, and 75 patients with postnatal growth retardation only. MatUPD7 was screened for by genotyping DNA samples from the patient, mother, and father with 13 chromosome-7-specific polymorphic microsatellite markers.

RESULTS

Six (3%) of 205 matUPD7 cases were observed exclusively among 39 (15%) SRS patients studied. Patients with IUGR and/or postnatal growth retardation and with dysmorphic features did not reveal cases of matUPD7.

CONCLUSIONS

Our results indicate that matUPD7 cases are predominantly observed among patients meeting the criteria of SRS, and matUPD7 is not a common cause for growth retardation. Genetic screening for cases of matUPD7 among growth-retarded patients should be focused on patients with severe IUGR and features of SRS. In addition, matUPD7 screening is advisable in individuals with cystic fibrosis and other recessive disorders mapped to chromosome 7 who have unusually short stature.

Genomic imprinting: parental influence on the genome

Genomic imprinting affects several dozen mammalian genes and results in the expression of those genes from only one of the two parental chromosomes. This is brought about by epigenetic instructions--imprints--that are laid down in the parental germ cells. Imprinting is a particularly important genetic mechanism in mammals, and is thought to influence the transfer of nutrients to the fetus and the newborn from the mother. Consistent with this view is the fact that imprinted genes tend to affect growth in the womb and behaviour after birth. Aberrant imprinting disturbs development and is the cause of various disease syndromes. The study of imprinting also provides new insights into epigenetic gene modification during development.

Genetic control of intra-uterine growth

The expression of a few genes in the human genome depends on whether they are located on the maternal or on the paternal chromosome. This phenomenon is called genomic imprinting. Several of these genes have a role in normal embryonic and fetal growth, as indicated by an abnormal development associated with disturbed genomic imprinting. This has lead to the suggestion that the genomic imprinting has evolved as a mechanism to regulate embryonic and fetal growth.

Genomic imprinting, uniparental disomy and foetal growth

Genomic imprinting is an epigenetic phenomenon identified in the past 15 years. Thus, maternally imprinted genes are only expressed from the paternal allele and vice versa. The mechanism of imprinting is still far from certain, but most probably it involves differential methylation of specific sites in or near imprinted genes. Disrupted imprinting can lead to phenotypic changes, and an increasing number of resultant clinical disorders are being identified. Many of these conditions involve disordered growth and/or development, particularly prenatal.

Monoalleleic transcription of the insulin-like growth factor-II gene (Igf2) in chick embryos

A polymorphism in the igf2 gene of chickens was identified using NlaIII (GenBank accession number AF218827). In some embryos, the igf2 alleles were expressed monoallelically from either maternal or paternal alleles. These data demonstrate that genomic imprinting is not confined to mammalian vertebrates and suggest that genomic imprinting evolved at an early stage of vertebrate evolution. The observations that the igf2 gene is imprinted in a minority of embryos suggest that the imprinting in birds is unrelated to embryonic growth. Genome imprinting may provide opportunities for evolution of genes in a nonexpressed state. In poultry breeding, the presence of imprinted genes may make a major contribution to unequal performance in reciprocal matings between commercial lines.

[Genes and intra-uterine growth retardation]

Genetic analysis of growth from birth to adulthood shows the existence of a strong genetic component in the variance of size at particular milestones in the growth process, such as height at take-off, at peak velocity and at adulthood. While it is well known that postnatal growth is strongly genetically determined, the importance of genes in normal variations of prenatal growth is less known. Genetic analysis of prenatal growth in human is not an easy problem and weighing the genetic and non-genetic component in intra-uterine growth retardation an almost impossible task. It is now well known that adults who had a low birthweight or who were thin at birth, with a low ponderal index, tend to be insulin resistant and have an increased risk of developing non-insulin-dependent diabetes mellitus later in life. According to the thrifty genotype hypothesis, genes predisposing to type 2 diabetes mellitus are very likely to have been survival genes for our ancestors, helping them to store energy during long periods of starvation. Both epidemiological surveys of adults born after prenatal exposure to exposure to famine and biochemical investigations of insulin resistance in low birthweight children show that the association between a low birthweight and an increased risk of developing type 2 diabetes mellitus later in life has a genetic basis. While low birthweight infants have a decreased survival probability in infancy, having a small baby may have been a selective advantage during long periods of starvation. This could explain why the same genetic variants cause low birthweight phenotype and insulin resistance predisposing to non-insulin-dependent diabetes.

Varied expression of a Y-linked P[w+] insert due to imprinting in Drosophila melanogaster

During gametogenesis, a gene can become imprinted affecting its expression in progeny. We have used the expression of a Y-linked P[w+]YAL transposable DNA element as a reporter system to investigate the effect of parental origination on the expression of the w+ insert. Expression of w+ was greater in male progeny when the Y chromosome, harboring the insert, was inherited from the parental male rather than from the parental female. Imprinting was not due to a genetic background influence in the males, since the only difference among the males was the parental origin of the Y chromosome. It was also observed that the genetic background can affect imprinting, since w+ expression was also higher in males when the Y was derived from C(1)DX attached-X parental females rather than from C(1)RM attached-X parental females. Though the heterochromatic imprinting mechanism is unknown, a mutated Heterochromatin Protein 1 (HP1) gene, which is associated with suppression of position-effect variegation, increases expression of the w+ locus in the P[w+]YAL insert, indicating that HP1 may play a role in Y chromosome packaging.

Paternal versus maternal transmission of a stimulatory G-protein alpha subunit knockout produces opposite effects on energy metabolism

Heterozygous disruption of Gnas, the gene encoding the stimulatory G-protein alpha subunit (G(s)alpha), leads to distinct phenotypes depending on whether the maternal (m-/+) or paternal (+/p-) allele is disrupted. G(s)alpha is imprinted, with the maternal allele preferentially expressed in adipose tissue. Hence, expression is decreased in m-/+ mice but normal in +/p- mice. M-/+ mice become obese, with increased lipid per cell in white and brown adipose tissue, whereas +/p- mice are thin, with decreased lipid in adipose tissue. These effects are not due to abnormalities in thyroid hormone status, food intake, or leptin secretion. +/p- mice are hypermetabolic at both ambient temperature (21 degrees C) and thermoneutrality (30 degrees C). In contrast, m-/+ mice are hypometabolic at ambient temperature and eumetabolic at thermoneutrality M-/+ and wild-type mice have similar dose-response curves for metabolic response to a beta(3)-adrenergic agonist, CL316243, indicating normal sensitivity of adipose tissue to sympathetic stimulation. Measurement of urinary catecholamines suggests that +/p- and m-/+ mice have increased and decreased activation of the sympathetic nervous system, respectively. This is to our knowledge the first animal model in which a single genetic defect leads to opposite effects on energy metabolism depending on parental inheritance. This probably results from deficiency of maternal- and paternal-specific Gnas gene products, respectively.

Population models of genomic imprinting. I. Differential viability in the sexes and the analogy with genetic dominance

Many single-locus, two-allele selection models of genomic imprinting have been shown to reduce formally to one-locus Mendelian models with a modified parameter for genetic dominance. One exception is the model where selection at the imprinted locus affects the sexes differently. We present two models of maternal inactivation with differential viability in the sexes, one with complete inactivation, and the other with a partial penetrance for inactivation. We show that, provided dominance relations at the imprintable locus are the same in both sexes, a globally stable polymorphism exists for a range of viabilities that is independent of the penetrance of imprinting. The conditions for a polymorphism are the same as in previous models with differential viability in the sexes but without imprinting and in a model of the paternal X-inactivation system in marsupials. The model with incomplete inactivation is used to illustrate the analogy between imprinting and dominance by comparing equilibrium bifurcation plots for fixed values of dominance and penetrance. We also derive a single expression for the dominance parameter that leaves the frequency and stability of equilibria unchanged for all levels of inactivation. Although an imprinting model with sex differences does not formally reduce to a nonimprinting scheme, close theoretical parallels clearly exist.

gamma2-COP, a novel imprinted gene on chromosome 7q32, defines a new imprinting cluster in the human genome

We describe a novel imprinted gene, gamma 2-COP (nonclathrincoatprotein), identified in a search for expressed sequences in human chromosome 7q32 where the paternally expressed MEST gene is located. gamma 2-COP contains 24 exons and spans >50 kb of genomic DNA. Like MEST, gamma 2-COP is ubiquitously transcribed in fetal and adult tissues. In fetal tissues, including skeletal muscle, skin, kidney, adrenal, placenta, intestine, lung, chorionic plate and amnion, gamma 2-COP is imprinted and expressed from the paternal allele. In contrast to the monoallelic expression observed in these fetal tissues, biallelic expression was evident in fetal brain and liver and in adult peripheral blood. Biallelic expression in blood is supported by the demonstration of gamma 2-COP transcripts in lymphoblastoid cell lines with maternal uniparental disomy 7. Absence of paternal gamma 2-COP transcripts during embryonic development may contribute to Silver-Russell syndrome. However, on mutation scanning the only gamma 2-COP mutation detected was maternally derived. Amino acid comparison of gamma2-COP protein revealed close relation to gamma-COP, a subunit of the coatomer complex COPI, suggesting a role of gamma2-COP in cellular vesicle traffic. The existence of distinct coatomer complexes could be the basis for the functional heterogeneity of COPI vesicles in retrograde and anterograde transport and/or in cargo selection. Together, gamma 2-COP and MEST constitute a novel imprinting cluster in the human genome that may contain other, as yet unknown, imprinted genes.