Genomic imprinting in the placenta

Rescue of placental phenotype in a mechanistic model of Beckwith-Wiedemann syndrome

Background

Several imprinted genes have been implicated in the process of placentation. The distal region of mouse chromosome 7 (Chr 7) contains at least ten imprinted genes, several of which are expressed from the maternal homologue in the placenta. The corresponding paternal alleles of these genes are silenced in cis by an incompletely understood mechanism involving the formation of a repressive nuclear compartment mediated by the long non-coding RNA Kcnq1ot1 initiated from imprinting centre 2 (IC2). However, it is unknown whether some maternally expressed genes are silenced on the paternal homologue via a Kcnq1ot1-independent mechanism. We have previously reported that maternal inheritance of a large truncation of Chr7 encompassing the entire IC2-regulated domain (DelTel7 allele) leads to embryonic lethality at mid-gestation accompanied by severe placental abnormalities. Kcnq1ot1 expression can be abolished on the paternal chromosome by deleting IC2 (IC2KO allele). When the IC2KO mutation is paternally inherited, epigenetic silencing is lost in the region and the DelTel7 lethality is rescued in compound heterozygotes, leading to viable DelTel7/IC2KO mice.

Results

Considering the important functions of several IC2-regulated genes in placentation, we set out to determine whether these DelTel7/IC2KO rescued conceptuses develop normal placentae. We report no abnormalities with respect to the architecture and vasculature of the DelTel7/IC2KO rescued placentae. Imprinted expression of several of the IC2-regulated genes critical to placentation is also faithfully recapitulated in DelTel7/IC2KO placentae.

Conclusion

Taken together, our results demonstrate that all the distal chromosome 7 imprinted genes implicated in placental function are silenced by IC2 and Kcnq1ot1 on the paternal allele. Furthermore, our results demonstrate that the methylated maternal IC2 is not required for the regulation of nearby genes. The results show the potential for fully rescuing trans placental abnormalities that are caused by imprinting defects.

Nutritional developmental epigenomics: immediate and long-lasting effects

The phenotype of an individual is the result of complex interactions between genome, epigenome and current, past and ancestral environment leading to a lifelong remodelling of the epigenomes. The genetic information expression contained in the genome is controlled by labile chromatin-associated epigenetic marks. Epigenetic misprogramming during development is widely thought to have a persistent effect on the health of the offspring and may even be transmitted to the next generation. The epigenome serves as an interface between the environment and the genome. Dietary factors, including folate involved in C1 metabolism, and other social and lifestyle exposures have a profound effect on many aspects of health including ageing and do so, at least partly, through interactions with the genome, which result in altered gene expression with consequences for cell function and health throughout the life course. Depending on the nature and intensity of the environmental insult, the critical spatiotemporal windows and developmental or lifelong processes involved, epigenetic alterations can lead to permanent changes in tissue and organ structure and function or to phenotypic changes that can (or cannot) be reversed using appropriate epigenetic tools. Moreover, the flexibility of epigenetic marks may make it possible for environmental, nutritional and hormonal factors or endocrine disruptors to alter, during a particular spatiotemporal window in a sex-specific manner, the sex-specific methylation or demethylation of specific CpG and/or histone modifications underlying sex-specific expression of a substantial proportion of genes. Moreover, genetic factors, the environment and stochastic events change the epigenetic landscape during the lifetime of an individual. Epigenetic alterations leading to gene expression dysregulation accumulate during ageing and are important in tumorigenesis and age-related diseases. Several encouraging trials suggest that prevention and therapy of age- and lifestyle-related diseases by individualised tailoring to optimal epigenetic diets or drugs are conceivable. However, these interventions will require intense efforts to unravel the complexity of these epigenetic, genetic and environment interactions and to evaluate their potential reversibility with minimal side effects.

DNA methylation-mediated down-regulation of DNA methyltransferase-1 (DNMT1) is coincident with, but not essential for, global hypomethylation in human placenta

The genome of extraembryonic tissue, such as the placenta, is hypomethylated relative to that in somatic tissues. However, the origin and role of this hypomethylation remains unclear. The DNA methyltransferases DNMT1, -3A, and -3B are the primary mediators of the establishment and maintenance of DNA methylation in mammals. In this study, we investigated promoter methylation-mediated epigenetic down-regulation of DNMT genes as a potential regulator of global methylation levels in placental tissue. Although DNMT3A and -3B promoters lack methylation in all somatic and extraembryonic tissues tested, we found specific hypermethylation of the maintenance DNA methyltransferase (DNMT1) gene and found hypomethylation of the DNMT3L gene in full term and first trimester placental tissues. Bisulfite DNA sequencing revealed monoallelic methylation of DNMT1, with no evidence of imprinting (parent of origin effect). In vitro reporter experiments confirmed that DNMT1 promoter methylation attenuates transcriptional activity in trophoblast cells. However, global hypomethylation in the absence of DNMT1 down-regulation is apparent in non-primate placentas and in vitro derived human cytotrophoblast stem cells, suggesting that DNMT1 down-regulation is not an absolute requirement for genomic hypomethylation in all instances. These data represent the first demonstration of methylation-mediated regulation of the DNMT1 gene in any system and demonstrate that the unique epigenome of the human placenta includes down-regulation of DNMT1 with concomitant hypomethylation of the DNMT3L gene. This strongly implicates epigenetic regulation of the DNMT gene family in the establishment of the unique epigenetic profile of extraembryonic tissue in humans.

Chromatin mechanisms in genomic imprinting

Mammalian imprinted genes are clustered in chromosomal domains. Their mono-allelic, parent-of-origin-specific expression is regulated by imprinting control regions (ICRs), which are essential sequence elements marked by DNA methylation on one of the two parental alleles. These methylation "imprints" are established during gametogenesis and, after fertilization, are somatically maintained throughout development. Nonhistone proteins and histone modifications contribute to this epigenetic process. The way ICRs mediate imprinted gene expression differs between domains. At some domains, for instance, ICRs produce long noncoding RNAs that mediate chromatin silencing. Lysine methylation on histone H3 is involved in this developmental process and is particularly important for imprinting in the placenta and brain. Together, the newly discovered chromatin mechanisms provide further clues for addressing imprinting-related pathologies in humans.

H19 acts as a trans regulator of the imprinted gene network controlling growth in mice

The imprinted H19 gene produces a non-coding RNA of unknown function. Mice lacking H19 show an overgrowth phenotype, due to a cis effect of the H19 locus on the adjacent Igf2 gene. To explore the function of the RNA itself, we produced transgenic mice overexpressing H19. We observed postnatal growth reduction in two independent transgenic lines and detected a decrease of Igf2 expression in embryos. An extensive analysis of several other genes from the newly described imprinted gene network (IGN) was performed in both loss- and gain-of-function animals. We found that H19 deletion leads to the upregulation of several genes of the IGN. This overexpression is restored to the wild-type level by transgenic expression of H19. We therefore propose that the H19 gene participates as a trans regulator in the fine-tuning of this IGN in the mouse embryo. This is the first in vivo evidence of a functional role for the H19 RNA. Our results also bring further experimental evidence for the existence of the IGN and open new perspectives in the comprehension of the role of genomic imprinting in embryonic growth and in human imprinting pathologies.

Imprinting and epigenetic changes in the early embryo

Imprinted genes are epigenetically regulated so that only one allele is expressed in a parent-of-origin-dependent manner. Although they represent a small subset of the mammalian genome, imprinted genes are essential for normal development. The regulatory mechanisms underlying imprinting are complex and have been the subject of extensive investigation. DNA methylation is the best-established epigenetic mark that is critical for the allele-specific expression of imprinted genes. This mark must be correctly established in the germline, maintained throughout life, and erased and reestablished in the germline the next generation. These events coincide with the genome-wide epigenetic reprogramming that occurs during gametogenesis and early embryogenesis; therefore, the establishment and maintenance of DNA methylation must be tightly regulated. Studies on enzymes that participate in both de novo methylation and its maintenance (i.e., the DNMT family) have provided information on how methylation influences imprinting. However, many aspects of the regulation of DNA methylation are unknown, including how methylation complexes are targeted and the molecular mechanisms underlying DNA demethylation. In this review we focus on the epigenetic changes that occur in the germline and early embryo, with an emphasis on imprinting. We summarize recent findings on factors influencing DNA methylation establishment, maintenance, and erasure that have further elucidated the mechanisms of imprinting, while highlighting topics that require further investigation.

Unearthing the roles of imprinted genes in the placenta

Mammalian fetal survival and growth are dependent on a well-established and functional placenta. Although transient, the placenta is the first organ to be formed during pregnancy and is responsible for important functions during development, such as the control of metabolism and fetal nutrition, gas and metabolite exchange, and endocrine control. Epigenetic marks and gene expression patterns in early development play an essential role in embryo and fetal development. Specifically, the epigenetic phenomenon known as genomic imprinting, represented by the non-equivalence of the paternal and maternal genome, may be one of the most important regulatory pathways involved in the development and function of the placenta in eutherian mammals. A lack of pattern or an imprecise pattern of genomic imprinting can lead to either embryonic losses or a disruption in fetal and placental development. Genetically modified animals present a powerful approach for revealing the interplay between gene expression and placental function in vivo and allow a single gene disruption to be analyzed, particularly focusing on its role in placenta function. In this paper, we review the recent transgenic strategies that have been successfully created in order to provide a better understanding of the epigenetic patterns of the placenta, with a special focus on imprinted genes. We summarize a number of phenotypes derived from the genetic manipulation of imprinted genes and other epigenetic modulators in an attempt to demonstrate that gene-targeting studies have contributed considerably to the knowledge of placentation and conceptus development.

The function of non-coding RNAs in genomic imprinting

Non-coding RNAs (ncRNAs) that regulate gene expression in cis or in trans are a shared feature of prokaryotic and eukaryotic genomes. In mammals, cis-acting functions are associated with macro ncRNAs, which can be several hundred thousand nucleotides long. Imprinted ncRNAs are well-studied macro ncRNAs that have cis-regulatory effects on multiple flanking genes. Recent advances indicate that they employ different downstream mechanisms to regulate gene expression in embryonic and placental tissues. A better understanding of these downstream mechanisms will help to improve our general understanding of the function of ncRNAs throughout the genome.

DNA methylation analysis of the mammalian PEG3 imprinted domain

In this study, we performed the first systematic survey of DNA methylation status of the CpG islands of the PEG3 (Paternally expressed gene 3) imprinted domain in the mouse, cow, and human genomes. Previous studies have shown that the region surrounding the first exon of PEG3 contains a differentially methylated CpG island. In addition, we have discovered two previously unreported differentially methylated regions (DMR): one in the promoter region of mouse Zim3 and another in the promoter region of human USP29. In the cow, the Peg3-CpG island was the only area that showed DMR status. We have also examined the methylation status of several CpG islands in this region using human tumor-derived DNA. The CpG islands near PEG3 and USP29 both showed hypermethylation in DNA derived from breast and ovarian tumors. Overall, this study shows that the PEG3 imprinted domain of humans, cows, and mice contains differing numbers of DMRs, but the PEG3-CpG island is the only DMR that is conserved among these three species.

Genetic modification for bimaternal embryo development

Full mammalian development typically requires genomes from both the oocyte and spermatozoon. Biparental reproduction is necessary because of parent-specific epigenetic modification of the genome during gametogenesis; that is, a maternal methylation imprint imposed during the oocyte growth period and a paternal methylation imprint imposed in pregonadal gonocytes. This leads to unequivalent expression of imprinted genes from the maternal and paternal alleles in embryos and individuals. It is possible to hypothesise that the maternal methylation imprint is necessary to prevent parthenogenesis, which extinguishes the opportunity for having descendents, whereas the paternal methylation imprint prevents parthenogenesis, ensuring that a paternal contribution is obligatory for any descendants. To date, there are several lines of direct evidence that the epigenetic modifications that occur during oocyte growth have a decisive effect on mammalian development. Using bimaternal embryos with two sets of maternal genomes, the present paper illustrates how parental methylation imprints are an obstacle to the progression of parthenogenesis.

X chromosome dosage compensation: how mammals keep the balance

The development of genetic sex determination and cytologically distinct sex chromosomes leads to the potential problem of gene dosage imbalances between autosomes and sex chromosomes and also between males and females. To circumvent these imbalances, mammals have developed an elaborate system of dosage compensation that includes both upregulation and repression of the X chromosome. Recent advances have provided insights into the evolutionary history of how both the imprinted and random forms of X chromosome inactivation have come about. Furthermore, our understanding of the epigenetic switch at the X-inactivation center and the molecular aspects of chromosome-wide silencing has greatly improved recently. Here, we review various facets of the ever-expanding field of mammalian dosage compensation and discuss its evolutionary, developmental, and mechanistic components.

[Influence of the male genomic imprinting on the reproduction]

OBJECTIVE

Genomic imprinting is the epigenetic change that occurred differentially in the specific genes in spermatozoa and oocyte according to their paternal or maternal origin, thus allowing a monoallelic expression. This review is a critical analysis of the published information relating to the role of the male imprinting on the successful reproduction.

METHODS

We performed a literature search on some of the components that regulate the male genomic imprinting and the possible role on reproductive events such as spermatogenesis, and placental and embryo development.

RESULTS

The literature analysis allowed us to appreciate structural, genetic and epigenetic changes occurring during the formation of the male gamete that could have an impact on embryo development, mainly in the formation of extraembryonic tissues as the placenta.

CONCLUSION

Alterations in the molecular mechanisms involved in the sperm DNA methylation during the spermatogenesis, could induce alterations in the normal pattern of expression required in the fetal-placental components development.

Altered gene expression in cloned piglets

Studies on cloned pigs are scant compared with those in mice and cattle. Expression profiles of cloned pig embryos on full-term cloned pigs are even more limited owing to the limited availability of DNA microarray technology in the pig. We have conducted expression profile comparisons between pigs from somatic cell nuclear transfer and pigs from conventional breeding at birth and 1 month of age. Differentially expressed genes that are subjected to DNA methylation were also examined for their DNA methylation status. These data will be presented in the 2009 Annual Meeting of the International Embryo Transfer Society in San Diego. In the present review, we focus on summarising existing findings on epigenetic and other changes in cloned embryo, cloned pigs and their offspring by conventional breeding.

Epigenetic regulation of foetal development in nuclear transfer animal models

Somatic cell nuclear transfer (SCNT, 'cloning') holds great potential for agricultural applications, generation of medical model animals, transgenic farm animals or by 'therapeutic cloning' for generating human embryonic stem cells for the treatment of human diseases. However, the low survival rate of SCNT-derived pregnancies represents a serious limitation of the current technology. In order to overcome this hurdle, a deeper understanding of the epigenetic reprogramming of the somatic cell nuclei and its effect on the pregnancy is needed. Here we review the literature on nuclear reprogramming by SCNT, including studies of gene expression, DNA methylation, chromatin remodelling, genomic imprinting and X chromosome inactivation. Reprogramming of genes expressed in the inner cell mass, from which the body of the foetus is formed, seems to be highly efficient. Defects in the extra-embryonic tissues are probably the major cause of the low success rate of reproductive cloning. Methods to partially overcome such problems exist, yet more future research is needed to find practical and efficient methods to remedy this problem. Improvement of the survival of foetuses is a central issue for the future of agricultural SCNT not only for its economic viability, but also because in lack of improvements in animal welfare current regulations can block the use of the method in the EU and several other countries.

Genomic imprinting in the development and evolution of psychotic spectrum conditions

I review and evaluate genetic and genomic evidence salient to the hypothesis that the development and evolution of psychotic spectrum conditions have been mediated in part by alterations of imprinted genes expressed in the brain. Evidence from the genetics and genomics of schizophrenia, bipolar disorder, major depression, Prader-Willi syndrome, Klinefelter syndrome, and other neurogenetic conditions support the hypothesis that the etiologies of psychotic spectrum conditions commonly involve genetic and epigenetic imbalances in the effects of imprinted genes, with a bias towards increased relative effects from imprinted genes with maternal expression or other genes favouring maternal interests. By contrast, autistic spectrum conditions, including Kanner autism, Asperger syndrome, Rett syndrome, Turner syndrome, Angelman syndrome, and Beckwith-Wiedemann syndrome, commonly engender increased relative effects from paternally expressed imprinted genes, or reduced effects from genes favouring maternal interests. Imprinted-gene effects on the etiologies of autistic and psychotic spectrum conditions parallel the diametric effects of imprinted genes in placental and foetal development, in that psychotic spectrum conditions tend to be associated with undergrowth and relatively-slow brain development, whereas some autistic spectrum conditions involve brain and body overgrowth, especially in foetal development and early childhood. An important role for imprinted genes in the etiologies of psychotic and autistic spectrum conditions is consistent with neurodevelopmental models of these disorders, and with predictions from the conflict theory of genomic imprinting.

Are H19 variants associated with Silver-Russell syndrome?

Opposite (epi)mutations affecting the imprinted region 11p15 are associated with Silver-Russell (SRS) and Beckwith-Wiedemann syndrome (BWS). Apart from other disturbances more than 35% of patients with SRS show hypomethylation at the imprinting control region 1 (ICR1) in 11p15. ICR1 is paternally methylated and regulates the expression of the paternally expressed growth factor IGF2 and the maternally expressed gene H19. The exact function of the non-coding RNA H19 is still unknown. However, the finding that this gene is highly conserved in mammals indicates profound functional relevance. Due to the supposed function of H19 in the regulation of the imprinted region 11p15 we searched for mutations in the transcribed sequence and the CTCF binding sites of H19 in 44 patients with SRS. In two cases different 3 base-pair (bp) deletions in exon 1 could be identified. A third patient carried a 39 bp duplication affecting exon 2 and intron 2. These three variants were not detected in 100 controls and 42 patients with isolated growth retardation. One of the patients carrying a mutation also showed hypomethylation at the ICR1 in 11p15. Splicing studies in HEK cells transfected with constructs carrying the three different variants revealed a deviation from the normal H19 splicing pattern in two of these individuals. However, analysis of lymphocytes of one of these two patients did not verify an altered expression pattern of H19. Nevertheless, our results indicate a relevant role of H19 in the aetiology of SRS: functional effects of these variants on chromatin restructuring of the ICR1, or altered function of H19 as a posttranslational modifying factor (microRNA/antisense RNA) are conceivable.

The opossum genome: insights and opportunities from an alternative mammal

The strategic importance of the genome sequence of the gray, short-tailed opossum, Monodelphis domestica, accrues from both the unique phylogenetic position of metatherian (marsupial) mammals and the fundamental biologic characteristics of metatherians that distinguish them from other mammalian species. Metatherian and eutherian (placental) mammals are more closely related to one another than to other vertebrate groups, and owing to this close relationship they share fundamentally similar genetic structures and molecular processes. However, during their long evolutionary separation these alternative mammals have developed distinctive anatomical, physiologic, and genetic features that hold tremendous potential for examining relationships between the molecular structures of mammalian genomes and the functional attributes of their components. Comparative analyses using the opossum genome have already provided a wealth of new evidence regarding the importance of noncoding elements in the evolution of mammalian genomes, the role of transposable elements in driving genomic innovation, and the relationships between recombination rate, nucleotide composition, and the genomic distributions of repetitive elements. The genome sequence is also beginning to enlarge our understanding of the evolution and function of the vertebrate immune system, and it provides an alternative model for investigating mechanisms of genomic imprinting. Equally important, availability of the genome sequence is fostering the development of new research tools for physical and functional genomic analyses of M. domestica that are expanding its versatility as an experimental system for a broad range of research applications in basic biology and biomedically oriented research.

[Parental genomic imprinting in plants: significance for reproduction]

Parental genomic imprinting is an epigenetic phenomenon causing the expression of a gene from one of the two parental alleles. Imprinting has been identified in plants and mammals. Recent evidence shows that DNA methylation and histone modifications are responsible for this parent-of-origin dependent expression of imprinted genes. We review the mechanisms and functions of imprinting in plants. We further describe the significance of imprinting for reproduction and discuss potential models for its evolution.

Syngeneic immune-dependent abortions in mice suggest paternal alloantigen-independent mechanisms

PROBLEM

Recurrent immune-associated miscarriages in humans are thought to result from maternal immune responses to paternal alloantigens. We investigated the role of paternal alloantigens in a mouse model of immune-dependent abortion.

METHOD OF STUDY

Sib-crosses of C57Bl/6J (haplotype b/b) mice heterozygous for a targeted hypomorphic allele of the tbp gene (tbp(deltaN/+)) resulted in selective mid-gestational abortion of 88% of the tbp(deltaN/deltaN) fetuses. In dams lacking mature lymphocytes (rag1-/-), nearly all tbp(deltaN/deltaN) fetuses survived to birth, indicating abortions were immune-dependent. Allogeneic pregnancies bearing tbp(deltaN/deltaN) fetuses were established by either hybridizing the paternal lineage to BALB/cJ (haplotype d/d) and mating hybrid tbp(deltaN/+) sires to haplotype b/b tbp(deltaN/+) C57Bl/6J dams, or by transfer of haplotype b/b zygotes from tbp(deltaN/+)x tbp(deltaN/+) matings into pseudopregnant wild-type CByD2F1/J dams (haplotype d/d).

RESULTS

Neither hemizygous paternal allogeneic loci nor homozygous allogeneic loci, including a haplotype-mismatched major histocompatibility complex (MHC), increased abortion frequencies.

CONCLUSION

Results suggested that mechanisms for maternal tolerance of paternal alloantigens, including mismatched MHC antigens, were intact in these pregnancies, yet maternal immune-dependent paternal antigen-independent abortion of mutants occurred. These data indicate that, in some cases of immune-mediated abortions, the presence of paternal alloantigens can be coincidental and superfluous to the compromising rejection response.

Specific tumour-associated methylation in normal human term placenta and first-trimester cytotrophoblasts

Human placentation displays many similarities with tumourigenesis, including rapid cell division, migration and invasion, overlapping gene expression profiles and escape from immune detection. Recent data have identified promoter methylation in the Ras association factor and adenomatous polyposis coli tumour suppressor genes as part of this process. However, the extent of tumour-associated methylation in the placenta remains unclear. Using whole genome methylation data as a starting point, we have examined this phenomenon in placental tissue. We found no evidence for methylation of the majority of common tumour suppressor genes in term placentas, but identified methylation in several genes previously described in some human tumours. Notably, promoter methylation of four independent negative regulators of Wnt signalling has now been identified in human placental tissue and purified trophoblasts. Methylation is present in baboon, but not in mouse placentas. This supports a role for elevated Wnt signalling in primate trophoblast invasiveness and placentation. Examination of invasive choriocarcinoma cell lines revealed altered methylation patterns consistent with a role of methylation change in gestational trophoblastic disease. This distinct pattern of tumour-associated methylation implicates a coordinated series of epigenetic silencing events, similar to those associated with some tumours, in the distinct features of normal human placental invasion and function.

Epigenetic reprogramming of the male genome during gametogenesis and in the zygote

During post-meiotic maturation, male germ cells undergo a formidable reorganization and condensation of their genome. During this phase most histones are globally acetylated and then replaced by sperm-specific basic proteins, named protamines, which compact the genome into a very specific structure within the sperm nucleus. Several studies suggest that this sperm-specific genome packaging structure conveys an important epigenetic message to the embryo. This paper reviews what is known about this fundamental, yet poorly understood, process, which involves not only global changes of the structure of the haploid genome, but also localized specific modifications of particular genomic regions, including pericentric heterochromatin and sex chromosomes. After fertilization, the male genome undergoes a drastic decondensation, and rapidly incorporates new histones. However, it remains different from the maternal genome, bearing specific epigenetic marks, especially in the pericentric heterochromatin region. The functional implications of male post-meiotic and post-fertilization genome reprogramming are not well known, but there is experimental evidence to show that it affects early embryonic development.

Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing

Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is organized around a maternally methylated CpG island comprising the promoters of the adjacent PEG10 and SGCE imprinted genes. Examination of Dnmt3l(-/+) conceptuses shows that imprinted expression for all genes of the cluster depends upon the germline methylation at this putative "imprinting control region" (ICR). Similarly as for other ICRs, we find its DNA-methylated allele to be associated with trimethylation of lysine 9 on histone H3 (H3K9me3) and trimethylation of lysine 20 on histone H4 (H4K20me3), whereas the transcriptionally active paternal allele is enriched in H3K4me2 and H3K9 acetylation. Our study reveals a novel placenta-specific transcript, TFPI2, which is expressed from the maternal allele in both humans and mice. Deficiency for the histone methyltransferase EHMT2 (also known as G9A) or for the Polycomb group protein EED, involved in repressive H3K9me2 and H3K27me3 respectively, leads to biallelic expression of Tfpi2 in the extra-embryonic lineages, whereas the other genes in the cluster maintain correct imprinting. Apart from the putative ICR, however, no other promoter regions within the domain exhibited allele-specific repressive histone modifications. This unexpected general lack of repressive histone modifications suggests that this domain may utilize a different silencing mechanism as compared to other imprinted domains.

Expression and protein localisation of IGF2 in the marsupial placenta

Background

In eutherian mammals, genomic imprinting is critical for normal placentation and embryo survival. Insulin-like growth factor 2 (IGF2) is imprinted in the placenta of both eutherians and marsupials, but its function, or that of any imprinted gene, has not been investigated in any marsupial. This study examines the role of IGF2 in the yolk sac placenta of the tammar wallaby, Macropus eugenii.

Results

IGF2 mRNA and protein were produced in the marsupial placenta. Both IGF2 receptors were present in the placenta, and presumably mediate IGF2 mitogenic actions. IGF2 mRNA levels were highest in the vascular region of the yolk sac placenta. IGF2 increased vascular endothelial growth factor expression in placental explant cultures, suggesting that IGF2 promotes vascularisation of the yolk sac.

Conclusion

This is the first demonstration of a physiological role for any imprinted gene in marsupial placentation. The conserved imprinting of IGF2 in this marsupial and in all eutherian species so far investigated, but not in monotremes, suggests that imprinting of this gene may have originated in the placenta of the therian ancestor.

G9a histone methyltransferase contributes to imprinting in the mouse placenta

Whereas DNA methylation is essential for genomic imprinting, the importance of histone methylation in the allelic expression of imprinted genes is unclear. Imprinting control regions (ICRs), however, are marked by histone H3-K9 methylation on their DNA-methylated allele. In the placenta, the paternal silencing along the Kcnq1 domain on distal chromosome 7 also correlates with the presence of H3-K9 methylation, but imprinted repression at these genes is maintained independently of DNA methylation. To explore which histone methyltransferase (HMT) could mediate the allelic H3-K9 methylation on distal chromosome 7, and at ICRs, we generated mouse conceptuses deficient for the SET domain protein G9a. We found that in the embryo and placenta, the differential DNA methylation at ICRs and imprinted genes is maintained in the absence of G9a. Accordingly, in embryos, imprinted gene expression was unchanged at the domains analyzed, in spite of a global loss of H3-K9 dimethylation (H3K9me2). In contrast, the placenta-specific imprinting of genes on distal chromosome 7 is impaired in the absence of G9a, and this correlates with reduced levels of H3K9me2 and H3K9me3. These findings provide the first evidence for the involvement of an HMT and suggest that histone methylation contributes to imprinted gene repression in the trophoblast.

Computational selection and prioritization of candidate genes for fetal alcohol syndrome

Background

Fetal alcohol syndrome (FAS) is a serious global health problem and is observed at high frequencies in certain South African communities. Although in utero alcohol exposure is the primary trigger, there is evidence for genetic- and other susceptibility factors in FAS development. No genome-wide association or linkage studies have been performed for FAS, making computational selection and -prioritization of candidate disease genes an attractive approach.

Results

10174 Candidate genes were initially selected from the whole genome using a previously described method, which selects candidate genes according to their expression in disease-affected tissues. Hereafter candidates were prioritized for experimental investigation by investigating criteria pertinent to FAS and binary filtering. 29 Criteria were assessed by mining various database sources to populate criteria-specific gene lists. Candidate genes were then prioritized for experimental investigation using a binary system that assessed the criteria gene lists against the candidate list, and candidate genes were scored accordingly. A group of 87 genes was prioritized as candidates and for future experimental validation. The validity of the binary prioritization method was assessed by investigating the protein-protein interactions, functional enrichment and common promoter element binding sites of the top-ranked genes.

Conclusion

This analysis highlighted a list of strong candidate genes from the TGF-β, MAPK and Hedgehog signalling pathways, which are all integral to fetal development and potential targets for alcohol's teratogenic effect. We conclude that this novel bioinformatics approach effectively prioritizes credible candidate genes for further experimental analysis.

The PcG gene Sfmbt2 is paternally expressed in extraembryonic tissues

Genomic imprinting has dramatic effects on placental development, as has been clearly observed in interspecific hybrid, somatic cell nuclear transfer, and uniparental embryos. In fact, the earliest defects in uniparental embryos are evident first in the extraembryonic trophoblast. We performed a microarray comparison of gynogenetic and androgenetic mouse blastocysts, which are predisposed to placental pathologies, to identify imprinted genes. In addition to identifying a large number of known imprinted genes, we discovered that the Polycomb group (PcG) gene Sfmbt2 is imprinted. Sfmbt2 is expressed preferentially from the paternal allele in early embryos, and in later stage extraembryonic tissues. A CpG island spanning the transcriptional start site is differentially methylated on the maternal allele in e14.5 placenta. Sfmbt2 is located on proximal chromosome 2, in a region known to be imprinted, but for which no genes had been identified until now. This possibly identifies a new imprinted domain within the murine genome. We further demonstrate that murine SFMBT2 protein interacts with the transcription factor YY1, similar to the Drosophila PHO-RC.

Rapid evolution of primate ESX1, an X-linked placenta- and testis-expressed homeobox gene

Homeobox genes encode transcription factors that play important roles in various developmental processes and are usually evolutionarily conserved. Here we report a case of rapid evolution of a homeobox gene in humans and non-human primates. ESX1 is an X-linked homeobox gene primarily expressed in the placenta and testis, with physiological functions in placenta/fetus development and spermatogenesis. ESX1 is paternally imprinted in mice, but is not imprinted in humans. We provide evidence for a significantly higher non-synonymous substitution rate than synonymous rate in ESX1 between humans and chimps as well as among a total of 15 primate species. Population genetic data also show signals of recent selective sweeps within humans. Positive selection appears to be concentrated in the C-terminal non-homeodomain region, which has been implicated in regulating human male germ cell division by prohibiting the degradation of cyclins. In contrast, mouse Esx1 has a substantively different C-terminal region subject to strong purifying selection. These and other results suggest that even the fundamental process of spermatogenesis has been targeted by positive selection in primate and human evolution and that mouse may not be a suitable model for studying human reproduction.

Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning

Therapeutic cloning, whereby somatic cell nuclear transfer (SCNT) is used to generate patient-specific embryonic stem cells (ESCs) from blastocysts cloned by nuclear transfer (ntESCs), holds great promise for the treatment of many human diseases. ntESCs have been derived in mice and cattle, but thus far there are no credible reports of human ntESCs. Here we review the recent literature on nuclear reprogramming by SCNT, including studies of gene expression, DNA methylation, chromatin remodeling, genomic imprinting and X chromosome inactivation. Reprogramming of genes expressed in the inner cell mass, from which ntESCs are derived, seems to be highly efficient. Defects in the extraembryonic lineage are probably the major cause of the low success rate of reproductive cloning but are not expected to affect the derivation of ntESCs. We remain optimistic that human therapeutic cloning is achievable and that the derivation of patient-specific ntESC lines will have great potential for regenerative medicine.

Germline histone dynamics and epigenetics

Germ cells have the same DNA sequence as somatic cells, but the processes that act on their chromatin are different. Germline chromatin undergoes a series of dramatic remodeling events during the life cycle of an organism. Different aspects of germline chromatin have been dissected in recent years, such as differences between the sex chromosomes and autosomes in histone variants and modifications. Excitingly, histone dynamics have recently been implicated in imprinted X inactivation and genomic imprinting processes that are independent of DNA methylation. Taken together with observations of core histone retention in mature sperm of diverse animals, histones have become prime candidates for mediating germline epigenetic inheritance.

Convergent evolution of genomic imprinting in plants and mammals

Parental genomic imprinting is characterized by the expression of a selected panel of genes from one of the two parental alleles. Recent evidence shows that DNA methylation and histone modifications are responsible for this parent-of-origin-dependent expression of imprinted genes. Because similar epigenetic marks have been recruited independently in plants and mammals, the only organisms in which imprinted gene loci have been identified so far, this phenomenon represents a case for convergent evolution. Here we discuss the emerging parallels in imprinting in both taxa. We also describe the significance of imprinting for reproduction and discuss potential models for its evolution.

A maternal-offspring coadaptation theory for the evolution of genomic imprinting

Imprinted genes are expressed either from the maternally or paternally inherited copy only, and they play a key role in regulating complex biological processes, including offspring development and mother–offspring interactions. There are several competing theories attempting to explain the evolutionary origin of this monoallelic pattern of gene expression, but a prevailing view has emerged that holds that genomic imprinting is a consequence of conflict between maternal and paternal gene copies over maternal investment. However, many imprinting patterns and the apparent overabundance of maternally expressed genes remain unexplained and may be incompatible with current theory. Here we demonstrate that sole expression of maternal gene copies is favored by natural selection because it increases the adaptive integration of offspring and maternal genomes, leading to higher offspring fitness. This novel coadaptation theory for the evolution of genomic imprinting is consistent with results of recent studies on epigenetic effects, and it provides a testable hypothesis for the origin of previously unexplained major imprinting patterns across different taxa. In conjunction with existing hypotheses, our results suggest that imprinting may have evolved due to different selective pressures at different loci.

This theoretical paper demonstrates that maternal-offspring coadaptation (the selection for gene combinations of parents and offspring) could select for genomic imprinting of the offspring trait.

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.

Differential regulation of imprinting in the murine embryo and placenta by the Dlk1-Dio3 imprinting control region

Genomic imprinting is an epigenetic mechanism controlling parental-origin-specific gene expression. Perturbing the parental origin of the distal portion of mouse chromosome 12 causes alterations in the dosage of imprinted genes resulting in embryonic lethality and developmental abnormalities of both embryo and placenta. A 1 Mb imprinted domain identified on distal chromosome 12 contains three paternally expressed protein-coding genes and multiple non-coding RNA genes, including snoRNAs and microRNAs, expressed from the maternally inherited chromosome. An intergenic, parental-origin-specific differentially methylated region, the IG-DMR, which is unmethylated on the maternally inherited chromosome, is necessary for the repression of the paternally expressed protein-coding genes and for activation of the maternally expressed non-coding RNAs: its absence causes the maternal chromosome to behave like the paternally inherited one. Here, we characterise the developmental consequences of this epigenotype switch and compare these with phenotypes associated with paternal uniparental disomy of mouse chromosome 12. The results show that the embryonic defects described for uniparental disomy embryos can be attributed to this one cluster of imprinted genes on distal chromosome 12 and that these defects alone, and not the mutant placenta, can cause prenatal lethality. In the placenta, the absence of the IG-DMR has no phenotypic consequence. Loss of repression of the protein-coding genes occurs but the non-coding RNAs are not repressed on the maternally inherited chromosome. This indicates that the mechanism of action of the IG-DMR is different in the embryo and the placenta and suggests that the epigenetic control of imprinting differs in these two lineages.

Environmental and nutritional effects on the epigenetic regulation of genes

Major efforts have been directed towards the identification of genetic mutations, their use as biomarkers, and the understanding of their consequences on human health and well-being. There is an emerging interest, however, in the possibility that environmentally-induced changes at levels other than the genetic information could have long-lasting consequences as well. This review summarises our current knowledge of how the environment, nutrition, and ageing affect the way mammalian genes are organised and transcribed, without changes in the underlying DNA sequence. Admittedly, the link between environment and epigenetics remains largely to be explored. However, recent studies indicate that environmental factors and diet can perturb the way genes are controlled by DNA methylation and covalent histone modifications. Unexpectedly, and not unlike genetic mutations, aberrant epigenetic alterations and their phenotypic effects can sometimes be passed on to the next generation.