Co-evolution of X-chromosome inactivation and imprinting in mammals

Genomic imprinting, growth control and the allocation of nutritional resources: consequences for postnatal life

PURPOSE OF REVIEW

Genes subject to genomic imprinting are predominantly expressed from one of the two parental chromosomes, are often clustered in the genome, and their activity and repression are epigenetically regulated. The role of imprinted genes in growth control has been apparent since the discovery of imprinting in the early 1980s.

RECENT FINDINGS

Drawing from studies in the mouse, we propose three distinct classes of imprinted genes - those expressed, imprinted and acting predominantly within the placenta, those with no associated foetal growth effects that act postnatally to regulate metabolic processes, and those expressed in the embryo and placenta that programme the development of organs participating in metabolic processes. Members of this latter class may interact in functional networks regulating the interaction between the mother and the foetus, affecting generalized foetal well-being, growth and organ development; they may also coordinately regulate the development of particular organ systems.

SUMMARY

The mono-allelic behaviour and sensitivity to changes in regional epigenetic states renders imprinted genes adaptable and vulnerable; in all cases, their perturbed dosage can compromise prenatal and/or postnatal control of nutritional resources. This finding has implications for understanding the relationships between prenatal events and diseases later in life.

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.

Society for Reproductive Biology Founders' Lecture 2006 - life in the pouch: womb with a view

Marsupials give birth to an undeveloped altricial young after a relatively short gestation period, but have a long and sophisticated lactation with the young usually developing in a pouch. Their viviparous mode of reproduction trades placentation for lactation, exchanging the umbilical cord for the teat. The special adaptations that marsupials have developed provide us with unique insights into the evolution of all mammalian reproduction. Marsupials hold many mammalian reproductive 'records', for example they have the shortest known gestation but the longest embryonic diapause, the smallest neonate but the longest sperm. They have contributed to our knowledge of many mammalian reproductive events including embryonic diapause and development, birth behaviour, sex determination, sexual differentiation, lactation and seasonal breeding. Because marsupials have been genetically isolated from eutherian mammals for over 125 million years, sequencing of the genome of two marsupial species has made comparative genomic biology an exciting and important new area of investigation. This review will show how the study of marsupials has widened our understanding of mammalian reproduction and development, highlighting some mechanisms that are so fundamental that they are shared by all today's marsupial and eutherian mammals.

Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth

Genomic imprinting is an epigenetic mechanism of regulation that restrains the expression of a small subset of mammalian genes to one parental allele. The reason for the targeting of these approximately 80 genes by imprinting remains uncertain. We show that inactivation of the maternally repressed Zac1 transcription factor results in intrauterine growth restriction, altered bone formation, and neonatal lethality. A meta-analysis of microarray data reveals that Zac1 is a member of a network of coregulated genes comprising other imprinted genes involved in the control of embryonic growth. Zac1 alters the expression of several of these imprinted genes, including Igf2, H19, Cdkn1c, and Dlk1, and it directly regulates the Igf2/H19 locus through binding to a shared enhancer. Accordingly, these data identify a network of imprinted genes, including Zac1, which controls embryonic growth and which may be the basis for the implementation of a common mechanism of gene regulation during mammalian evolution.

Epigenetics in development

It has become increasingly evident in recent years that development is under epigenetic control. Epigenetics is the study of heritable changes in gene function that occur independently of alterations to primary DNA sequence. The best-studied epigenetic modifications are DNA methylation, and changes in chromatin structure by histone modifications, and histone exchange. An exciting, new chapter in the field is the finding that long-distance chromosomal interactions also modify gene expression. Epigenetic modifications are key regulators of important developmental events, including X-inactivation, genomic imprinting, patterning by Hox genes and neuronal development. This primer covers these aspects of epigenetics in brief, and features an interview with two epigenetic scientists.

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.

Recent assembly of an imprinted domain from non-imprinted components

Genomic imprinting, representing parent-specific expression of alleles at a locus, raises many questions about how—and especially why—epigenetic silencing of mammalian genes evolved. We present the first in-depth study of how a human imprinted domain evolved, analyzing a domain containing several imprinted genes that are involved in human disease. Using comparisons of orthologous genes in humans, marsupials, and the platypus, we discovered that the Prader-Willi/Angelman syndrome region on human Chromosome 15q was assembled only recently (105–180 million years ago). This imprinted domain arose after a region bearing UBE3A (Angelman syndrome) fused with an unlinked region bearing SNRPN (Prader-Willi syndrome), which had duplicated from the non-imprinted SNRPB/B′. This region independently acquired several retroposed gene copies and arrays of small nucleolar RNAs from different parts of the genome. In their original configurations, SNRPN and UBE3A are expressed from both alleles, implying that acquisition of imprinting occurred after their rearrangement and required the evolution of a control locus. Thus, the evolution of imprinting in viviparous mammals is ongoing.

Humans and other mammals have two copies of the genome. For most genes, both copies are active. However, some genes are active only when they are inherited from the father, others only when inherited from the mother. These “imprinted” genes are clustered in domains that are controlled coordinately. Only mammals show genomic imprinting. It is not understood how or why genes became imprinted during mammalian evolution. The authors used comparisons between humans and the most distantly related mammals, marsupials and monotremes, to discover how one of these imprinted domains evolved. The authors studied an imprinted domain on human Chromosome 15, mutations which cause Prader-Willi and Angelman syndromes (PWS-AS). They discovered that the PWS and AS genes lie on different chromosomes in kangaroos and platypus and are not imprinted. Other imprinted genes in the domain, including the putative control region, are absent from the genome and derived from copies of genes from yet other chromosomes. The arrangement in kangaroos and platypus is present also in the chicken genome, so it must be ancestral. This study concludes that the PWS-AS imprinted region was assembled relatively recently from non-imprinted components that were moved together or copied from all over the genome.

Maximum likelihood inference of imprinting and allele-specific expression from EST data

MOTIVATION

In a diploid organism the proportion of transcripts that are produced from the two parental alleles can differ substantially due, for example to epigenetic modification that causes complete or partial silencing of one parental allele or to cis acting polymorphisms that affect transcriptional regulation. Counts of SNP alleles derived from EST sequences have been used to identify both novel candidates for genomic imprinting as well as examples of genes with allelic differences in expression.

RESULTS

We have developed a set of statistical models in a maximum likelihood framework that can make highly efficient use of public transcript data to identify genes with unequal representation of alternative alleles in cDNA libraries. We modelled both imprinting and allele-specific expression and applied the models to a large dataset of SNPs mapped to EST sequences. Using simulations, matched closely to real data, we demonstrate significantly improved performance over existing methods that have been applied to the same data. We further validated the power of this approach to detect imprinting using a set of known imprinted genes and inferred a set of candidate imprinted genes, several of which are in close proximity to known imprinted genes. We report evidence that there are undiscovered imprinted genes in known imprinted regions. Overall, more than half of the genes for which the most data are available show some evidence of allele-specific expression.

AVAILABILITY

Software is available from the authors on request.

Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo

The mouse Kcnq1 imprinted domain is located on distal chromosome 7 and contains several imprinted genes that are paternally repressed. Repression of these genes is regulated by a non-coding antisense transcript, Kcnq1ot1, which is paternally expressed. Maternal repression of Kcnq1ot1 is controlled by DNA methylation originating in the oocyte. Some genes in the region are imprinted only in the placenta, whereas others are imprinted in both extra-embryonic and embryonic lineages. Here, we show that Kcnq1ot1 is paternally expressed in preimplantation embryos from the two-cell stage, and that ubiquitously imprinted genes proximal to Kcnq1ot1 are already repressed in blastocysts, ES cells and TS cells. Repressive histone marks such as H3K27me3 are present on the paternal allele of these genes in both ES and TS cells. Placentally imprinted genes that are distal to Kcnq1ot1, by contrast, are not imprinted in blastocysts, ES or TS cells. In these genes, paternal silencing and differential histone marks arise during differentiation of the trophoblast lineage between E4.5 and E7.5. Our findings show that the dynamics during preimplantation development of gene inactivation and acquisition of repressive histone marks in ubiquitously imprinted genes of the Kcnq1 domain are very similar to those of imprinted X inactivation. By contrast, genes that are only imprinted in the placenta, while regulated by the same non-coding RNA transcript Kcnq1ot1, undergo epigenetic inactivation during differentiation of the trophoblast lineage. Our findings establish a model for how epigenetic gene silencing by non-coding RNA may depend on distance from the non-coding RNA and on lineage and differentiation specific factors.

Dosage compensation in mammals: fine-tuning the expression of the X chromosome

Mammalian females have two X chromosomes and males have only one. This has led to the evolution of special mechanisms of dosage compensation. The inactivation of one X chromosome in females equalizes gene expression between the sexes. This process of X-chromosome inactivation (XCI) is a remarkable example of long-range, monoallelic gene silencing and facultative heterochromatin formation, and the questions surrounding it have fascinated biologists for decades. How does the inactivation of more than a thousand genes on one X chromosome take place while the other X chromosome, present in the same nucleus, remains genetically active? What are the underlying mechanisms that trigger the initial differential treatment of the two X chromosomes? How is this differential treatment maintained once it has been established, and how are some genes able to escape the process? Does the mechanism of X inactivation vary between species and even between lineages? In this review, X inactivation is considered in evolutionary terms, and we discuss recent insights into the epigenetic changes and developmental timing of this process. We also review the discovery and possible implications of a second form of dosage compensation in mammals that deals with the unique, potentially haploinsufficient, status of the X chromosome with respect to autosomal gene expression.

Differences between human embryonic stem cell lines

The promise of human embryonic stem cell (hESC) lines for treating injuries and degenerative diseases, for understanding early human development, for disease modelling and for drug discovery, has brought much excitement to scientific communities as well as to the public. Although all of the lines derived worldwide share the expression of characteristic pluripotency markers, many differences are emerging between lines that may be more associated with the wide range of culture conditions in current use than the inherent genetic variation of the embryos from which embryonic stem cells were derived. Thus, the validity of many comparisons between lines published thus far is difficult to interpret. This article reviews the evidence for differences between lines, focusing on studies of pluripotency marker molecules, transcriptional profiling, genetic stability and epigenetic stability, for which there is most evidence. Recognition and assessment of environmentally induced differences will be important to facilitate the development of culture systems that maximize stability in culture and provide lines with maximal potential for safety and success in the range of possible applications.

Genomic organization and allelic expression of UBE3A in chicken

UBE3A, the gene associated with Angelman syndrome, is part of a cluster of genes in the human chromosome 15q11-q13/mouse chromosome 7C region, that is subject to genomic imprinting. In human and mouse brain, UBE3A is expressed predominantly from the maternal allele, and the paternal allele is silenced. A current model concerning the evolution of genomic imprinting, the parental conflict hypothesis, posits that this epigenetic phenomenon is restricted to eutherian mammals. It has been recently reported, however, that several chicken orthologues of mammalian imprinted loci display DNA replication asynchrony, a property of imprinted genes. A separate group also reported monoallelic expression of chicken IGF2 in developing chicken embryos. These observations could suggest that genomic imprinting may occur in chicken. We have assembled the predicted mRNA consensus sequence for the chicken UBE3A gene using published ESTs. We report a high degree of homology with the human UBE3A at the nucleotide and protein levels, as well as a highly conserved genomic organization. Biallelic expression of UBE3A is observed in embryonic chicken brain and limb, indicating that UBE3A is not subject to genomic imprinting in chicken.

RPS6KA2, a putative tumour suppressor gene at 6q27 in sporadic epithelial ovarian cancer

We had previously defined by allele loss studies a minimal region at 6q27 (between D6S264 and D6S297) to contain a putative tumour suppressor gene. The p90 ribosomal S6 kinase-3 gene (p90 Rsk-3, RPS6KA2) maps in this interval. It is a serine-threonine kinase that signals downstream of the mitogen-activated protein kinase pathway. It is expressed in normal ovarian epithelium, whereas reduced or absent in tumours or cell lines. We show that RPS6KA2 is monoallelically expressed in the ovary suggesting that loss of a single expressed allele is sufficient to cause complete loss of expression in cancer cells. Further, we have identified two new isoforms of RPS6KA2 with an alternative start codon. Homozygous deletions were identified within the RPS6KA2 gene in two cell lines. Re-expression of RPS6KA2 in ovarian cancer cell lines suppressed colony formation. In UCI101 cells, the expression of RPS6KA2 reduced proliferation, caused G1 arrest, increased apoptosis, reduced levels of phosphorylated extracellular signal-regulated kinase and altered other cell cycle proteins. In contrast, small interfering RNA against RPS6KA2 showed the opposite effect in 41M cells. The above results suggest that RPS6KA2 is a putative tumour suppressor gene to explain allele loss at 6q27.

The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export

Expression of the Air ncRNA is necessary to silence multiple genes in cis in the imprinted Igf2r cluster. However, its mode of action is unknown. Here, we characterize co- and post-transcriptional features of Air that identify it as a new member of the class of nuclear regulatory RNAs. We show that Air is transcribed from a DNA methylation-sensitive promoter by RNA polymerase II (RNAPII). However, although it is capped and polyadenylated similar to other RNAPII transcripts, the majority of Air transcripts evade cotranscriptional splicing resulting in a mature 108 kb ncRNA. As a consequence, the mature unspliced Air is nuclear localized and highly unstable. These features show that Air is an atypical RNAPII transcript whose properties indicate that its mode of action in gene silencing may not depend on the RNA per se but instead is related to its actual transcription.

Evidence of influence of genomic DNA sequence on human X chromosome inactivation

A significant number of human X-linked genes escape X chromosome inactivation and are thus expressed from both the active and inactive X chromosomes. The basis for escape from inactivation and the potential role of the X chromosome primary DNA sequence in determining a gene's X inactivation status is unclear. Using a combination of the X chromosome sequence and a comprehensive X inactivation profile of more than 600 genes, two independent yet complementary approaches were used to systematically investigate the relationship between X inactivation and DNA sequence features. First, statistical analyses revealed that a number of repeat features, including long interspersed nuclear element (LINE) and mammalian-wide interspersed repeat repetitive elements, are significantly enriched in regions surrounding transcription start sites of genes that are subject to inactivation, while Alu repetitive elements and short motifs containing ACG/CGT are significantly enriched in those that escape inactivation. Second, linear support vector machine classifiers constructed using primary DNA sequence features were used to correctly predict the X inactivation status for >80% of all X-linked genes. We further identified a small set of features that are important for accurate classification, among which LINE-1 and LINE-2 content show the greatest individual discriminatory power. Finally, as few as 12 features can be used for accurate support vector machine classification. Taken together, these results suggest that features of the underlying primary DNA sequence of the human X chromosome may influence the spreading and/or maintenance of X inactivation.

Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L

The DNMT3-like protein, DNMT3L, is required for germ line DNA methylation, although it is inactive as a DNA methyltransferase per se. Previous studies have shown that DNMT3L physically associates with the active de novo DNA methyltransferases, DNMT3A and DNMT3B, and stimulates their catalytic activities in a cell culture system. However, the mechanism by which DNMT3L stimulates de novo methylation remains unclear. Here, we have purified the full-length human DNMT3A2 and DNMT3L proteins and determined unique conditions that allow for the proper reconstitution of the stimulation of DNMT3A2 de novo methyltransferase activity by DNMT3L. These conditions include the use of buffers resembling physiological conditions and the preincubation of the two proteins. Under these conditions, maximal stimulation is reached at equimolar amounts of DNMT3L and DNMT3A2 proteins, and the catalytic efficiency of DNMT3A2 is increased up to 20-fold. Biochemical analysis revealed that whereas DNMT3L on its own does not significantly bind to the methyl group donor, S-adenosyl-L-methionine (SAM), it strongly increases the binding of SAM to DNMT3A2. DNA binding, on the contrary, was not appreciably improved. Analysis of DNA methyltransferase complexes in solution using size exclusion chromatography revealed that DNMT3A2 forms large structures of heterogeneous sizes, whereas DNMT3L appears as a monomer. Binding of DNMT3L to DNMT3A2 promotes a dramatic reorganization of DNMT3A2 subunits and leads to the formation of specific complexes with enhanced DNA methyltransferase activity and increased SAM binding.

Chromatin and epigenetics in development: blending cellular memory with cell fate plasticity

The epigenetic regulation of chromatin structure and composition has often been studied molecularly in the context of specific DNA-dependent processes. However, epigenetics also play important global roles in shaping and maintaining cell identity, and in patterning the body plan during normal development. Moreover, alterations in epigenetic regulation are involved in many diseases, including cancer. The advances in our understanding of the impact of epigenetics in development and disease were discussed at a recent Keystone symposium.

Tissue-specific reactivation of gene expression at an imprinted locus

Genomic imprinting is the phenomenon where the expression pattern of an allele at a locus differs depending on the allele's parent of origin. In most cases, one of the two alleles is transcriptionally silent. Recent empirical work has shown some genes to be imprinted in a tissue-specific manner, where the silenced allele becomes reactivated in particular cell lineages during development. Here I describe an evolutionary model of tissue-specific transcriptional reactivation. The model describes the relationships among various inclusive fitness functions and phenotypic effects necessary for natural selection to favor the epigenetic reprogramming required for this sort of reactivation, and makes predictions regarding the nature and magnitude of phenotypic and fitness consequences of mutations in particular somatic tissues. In particular, if an imprinted gene is reactivated in one of two tissues that interact in producing a particular phenotype, expression of the gene in those two tissues is expected to have opposite phenotypic effects. The model predicts that in some cases, mutations affecting the silenced allele at an imprinted locus may be phenotypically more severe than those affecting the expressed allele. These predictions are contrasted with those of an alternative explanation for reactivation: protection against deleterious recessive somatic mutations. The inclusive-fitness model of reactivation indicates that the intragenomic conflicts present in the parental germ lines and developing embryo persist though adult life, and can have complex effects on phenotypes and patterns of gene expression in somatic tissues.

Lessons from comparative analysis of species-specific imprinted genes

Genomic imprinting is generally believed to be conserved in all mammals except for egg-laying monotremes, suggesting that it is closely related to placental and fetal growth. As expected, the imprinting status of most imprinted genes is conserved between mouse and human, and some are imprinted even in marsupials. On the other hand, a small number of genes were reported to exhibit species-specific imprinting that is not necessarily accounted for by either the placenta or conflict hypotheses. Since mouse and human represent a single, phylogenetically restricted clade in the mammalian class, a much broader comparison including mammals diverged earlier than rodents is necessary to fully understand the species-specificity and variation in evolution of genomic imprinting. Indeed, comparative analysis of a species-specific imprinted gene Impact using a broader range of mammals led us to propose an alternative dosage control hypothesis for the evolution of genomic imprinting.

How imprinting centres work

Imprinted genes tend to be clustered in the genome. Most of these clusters have been found to be under the control of discrete DNA elements called imprinting centres (ICs) which are normally differentially methylated in the germline. ICs can regulate imprinted expression and epigenetic marks at many genes in the region, even those which lie several megabases away. Some of the molecular and cellular mechanisms by which ICs control other genes and regulatory regions in the cluster are becoming clear. One involves the insulation of genes on one side of the IC from enhancers on the other, mediated by the insulator protein CTCF and higher-order chromatin interactions. Another mechanism may involve non-coding RNAs that originate from the IC, targeting histone modifications to the surrounding genes. Given that several imprinting clusters contain CTCF dependent insulators and/or non-coding RNAs, it is likely that one or both of these two mechanisms regulate imprinting at many loci. Both mechanisms involve a variety of epigenetic marks including DNA methylation and histone modifications but the hierarchy of and interactions between these modifications are not yet understood. The challenge now is to establish a chain of developmental events beginning with differential methylation of an IC in the germline and ending with imprinting of many genes, often in a lineage dependent manner.

Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila

Dosage compensation in Drosophila is dependent on MSL proteins and involves hypertranscription of the male X chromosome, which ensures equal X-linked gene expression in both sexes. Here, we report the purification of enzymatically active MSL complexes from Drosophila embryos, Schneider cells, and human HeLa cells. We find a stable association of the histone H4 lysine 16-specific acetyltransferase MOF with the RNA/protein containing MSL complex as well as with an evolutionary conserved complex. We show that the MSL complex interacts with several components of the nuclear pore, in particular Mtor/TPR and Nup153. Strikingly, knockdown of Mtor or Nup153 results in loss of the typical MSL X-chromosomal staining and dosage compensation in Drosophila male cells but not in female cells. These results reveal an unexpected physical and functional connection between nuclear pore components and chromatin regulation through MSL proteins, highlighting the role of nucleoporins in gene regulation in higher eukaryotes.

Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis

Fertilization in flowering plants initiates the development of the embryo and endosperm, which nurtures the embryo. A few genes subjected to imprinting are expressed in endosperm from their maternal allele, while their paternal allele remains silenced. Imprinting of the FWA gene involves DNA methylation. Mechanisms controlling imprinting of the Polycomb group (Pc-G) gene MEDEA (MEA) are not yet fully understood. Here we report that MEA imprinting is regulated by histone methylation. This epigenetic chromatin modification is mediated by several Pc-G activities during the entire plant life cycle. We show that Pc-G complexes maintain MEA transcription silenced throughout vegetative life and male gametogenesis. In endosperm, the maternal allele of MEA encodes an essential component of a Pc-G complex, which maintains silencing of the paternal MEA allele. Hence, we conclude that a feedback loop controls MEA imprinting. This feedback loop ensures a complete maternal control of MEA expression from both parental alleles and might have provided a template for evolution of imprinting in plants.

Limited evolutionary conservation of imprinting in the human placenta

The epigenetic phenomenon of genomic imprinting provides an additional level of gene regulation that is confined to a limited number of genes, frequently, but not exclusively, important for embryonic development. The evolution and maintenance of imprinting has been linked to the balance between the allocation of maternal resources to the developing fetus and the mother's well being. Genes that are imprinted in both the embryo and extraembryonic tissues show extensive conservation between a mouse and a human. Here we examine the human orthologues of mouse genes imprinted only in the placenta, assaying allele-specific expression and epigenetic modifications. The genes from the KCNQ1 domain and the isolated human orthologues of the imprinted genes Gatm and Dcn all are expressed biallelically in the human, from first-trimester trophoblast through to term. This lack of imprinting is independent of promoter CpG methylation and correlates with the absence of the allelic histone modifications dimethylation of lysine-9 residue of H3 (H3K9me2) and trimethylation of lysine-27 residue of H3 (H3K27me3). These specific histone modifications are thought to contribute toward regulation of imprinting in the mouse. Genes from the IGF2R domain show polymorphic concordant expression in the placenta, with imprinting demonstrated in only a minority of samples. Together these findings have important implications for understanding the evolution of mammalian genomic imprinting. Because most human pregnancies are singletons, this absence of competition might explain the comparatively relaxed need in the human for placental-specific imprinting.

Histone modifications: signalling receptors and potential elements of a heritable epigenetic code

The genetic code epitomises simplicity, near universality and absolute predictive power. By contrast, epigenetic information, in the form of histone modifications, is characterised by complexity, diversity and an overall tendency to respond to changes in genomic function rather than to predict them. Perhaps the transient changes in histone modifications involved in intranuclear signalling and ongoing chromatin functions mask stable, predictive modifications that lie beneath. The current rapid progress in unravelling the diversity and complexity of epigenetic information might eventually reveal an underlying histone or epigenetic code. But whether it does or not, it will certainly provide unprecedented opportunities, both for understanding how the genome responds to environmental and metabolic change and for manipulating its activities for experimental and therapeutic benefit.

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.

Genomic imprinting in plants and mammals: how life history constrains convergence

In both flowering plants and mammals, DNA methylation is involved in silencing alleles of imprinted genes, but surprising differences in imprinting control are emerging between the two taxa which may be traced to differences in their life cycles. Imprinted gene expression in plants occurs in the endosperm, a separate fertilisation product which transmits nutrients to the embryo and does not contribute a genome to the next generation. Regulation of expression of the known imprinted genes in Arabidopsis involves a cascade of gene expression beginning in the gametophyte, a haploid life phase interposed between the meiotic products and the gametes, which evolved from free-living organisms that constitute the dominant life phase of lower plants. Although the gametophytes of flowering plants are highly reduced they still express large numbers of genes, perhaps reflecting their evolutionary legacy, and which may now be recruited for control of imprinting. Strikingly, the genes at the top of the expression cascade appear to be specifically activated by demethylation, rather than targeted for silencing. Unlike in mammals, there is no evidence for global resetting of methylation in plants, and although imprinting involves the activity of a maintenance methyltransferase, de novo methyltransferases do not appear to be required. Plants do not set aside a germline; instead the cells that undergo meiosis to produce gametophytes differentiate in the adult plant during flower development. Both the late differentiation of the lineage producing germ cells, and the extent of gene expression during the haploid phase, may be incompatible with global resetting of methylation. Resetting may be unnecessary in any case because the adult plant expresses imprinted loci either biallelically or not at all, suggesting there is no chromosomal memory of parent-of-origin in the lineage that produces the gametophytes. Thus several features of the plant life cycle may account for the different strategies used by plants and animals to regulate parent-specific gene expression.

Accuracy of DNA methylation pattern preservation by the Dnmt1 methyltransferase

DNA methyltransferase 1 (Dnmt1) has a central role in copying the pattern of DNA methylation after replication which is one manifestation of epigenetic inheritance. With oligonculeotide substrates we show that mouse Dnmt1 has a 30- to 40-fold preference for hemimethylated DNA that is almost lost after addition of fully methylated oligonucleotides. Using long hemimethylated DNA substrates that carry defined methylation patterns and bisulfite analysis of the methylation reaction products, we show a 15-fold preference for hemimethylated CG sites. Dnmt1 moves along the DNA in a random walk methylating hemimethylated substrates with high processivity (>50 sites are visited on average which corresponds to linear diffusion over 6000 bp). The frequency of skipping sites is very low (<0.3%) and there is no detectable flanking sequence preference. CGCTC sites tend to terminate the processive methylation of DNA by Dnmt1. Unmethylated DNA is modified non-processively with a preference for methylation at CCGG sites. We simulate the propagation of methylation patterns using a stochastic model with the specificity of Dnmt1 observed here and conclude that either methylation of several sites is required to propagate the methylation information over several cellular generations or additional epigenetic information must be used.

Chromatin modifications in the germinal vesicle (GV) of mammalian oocytes

The nucleus of eukaryotic cells is organized into functionally specialized compartments that are essential for the control of gene expression, chromosome architecture and cellular differentiation. The mouse oocyte nucleus or germinal vesicle (GV) exhibits a unique chromatin configuration that is subject to dynamic modifications during oogenesis. This process of 'epigenetic maturation' is critical to confer the female gamete with meiotic as well as developmental competence. In spite of its biological significance, little is known concerning the cellular and molecular mechanisms regulating large-scale chromatin structure in mammalian oocytes. Here, recent findings that provide mechanistic insight into the complex relationship between large-scale chromatin structure and global transcriptional repression in pre-ovulatory oocytes will be discussed. Post-translational modifications of histone proteins such as acetylation and methylation are crucial for heterochromatin formation and thus play a key role in remodeling the oocyte genome. This strategy involves multiple and hierarchical chromatin modifications that regulate nuclear dynamics in response to a developmentally programmed signal(s), presumably of paracrine origin, before the resumption of meiosis. Models for the experimental manipulation of large-scale chromatin structure in vivo and in vitro will be instrumental to determine the key cellular pathways and oocyte-derived factors involved in genome-wide chromatin modifications. Importantly, analysis of the functional differentiation of chromatin structure in the oocyte genome with high resolution and in real time will have wide-ranging implications to understand the role of nuclear organization in meiosis, the events of nuclear reprogramming and the spatio-temporal regulation of gene expression during development and differentiation.

Allele-specific deposition of macroH2A1 in imprinting control regions

In the current study, we analyzed the deposition patterns of macroH2A1 at a number of different genomic loci located in X chromosome and autosomes. MacroH2A1 is preferentially deposited at methylated CpG-rich regions located close to promoters. The macroH2A1 deposition patterns at the methylated CpG islands of several imprinted domains, including the imprinting control regions (ICRs) of Xist, Peg3, H19/Igf2, Gtl2/Dlk1 and Gnas domains, show consistent allele-specificity towards inactive, methylated alleles. The macroH2A1 deposition levels at the ICRs and other differentially methylated regions of these domains are also either higher or comparable to those observed at the inactive X chromosome of female mammals. Overall, our results indicate that besides DNA methylation macroH2A1 is another epigenetic component in the chromatin of ICRs displaying differential association with two parental alleles.

ATRX syndrome in a girl with a heterozygous mutation in theATRX Zn finger domain and a totally skewed X-inactivation pattern

Mutations in the X-encoded gene ATRX are known to give rise to syndromic mental retardation in male patients whereas female carriers show preferential inactivation of the mutated X chromosome and appear healthy. Here, we describe a 4-year-old girl with typical features of ATRX syndrome, carrying the recurrent R246C mutation of ATRX. We show that her pattern of X-inactivation is totally skewed and that her active X chromosome which harbors the ATRX mutation, was maternally inherited. To our knowledge, this is the first report of ATRX syndrome in a female patient. Since she was born after in vitro fertilization (IVF), we propose a possible link between assisted reproduction technologies (ART) and the unexpected X chromosome methylation pattern that we observed.

Phenotype of triploid embryos

The phenotypes of triploid fetuses and placentae are now well established and known to correlate with parental origin of the extra haploid set of chromosomes. In fetuses, it is not clear whether there is a direct parent of origin effect on the fetus itself or if the phenotypes are the result of growth differences influenced by abnormalities in growth and function of the placenta. Examining the phenotype of triploid embryos at an earlier stage in gestation, when the placenta effects may be less pronounced, could help clarify this question. A phenotype characteristic of triploidy in the embryonic period has been described; however, parental origin was not determined in these embryonic cases. In the present study, a population of triploid embryos is assessed to determine if there is a correlation between parental origin and phenotype. Parental origin was determined in 27 first trimester miscarriages. Digyny accounted for 19 cases and diandry for eight cases. Assessment of embryonic phenotype with parental origin showed no correlation between the phenotype of the embryo and parental origin of the extra haploid set. While there may be subtle effects of imprinting on embryonic development, they are not as obvious as they are in the mouse, consistent with the general trend of fewer imprinted genes in human beings compared with the mouse.