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Investigation of the epigenetic stability of human embryonic stem cells (hESCs) is a crucial step for their use in cell-replacement therapies, as well as for assessing whether hESCs model epigenetic regulation in human pre-implantation cell types. To address these issues, we have examined the expression of imprinted genes in a previous study and more recently in 46 individual hESC lines as part of the International Stem Cell Initiative. Our results show that nearly all hESC lines examined possessed a substantial degree of epigenetic stability, despite differences in genetic background and in their derivation and initial propagation conditions. However, some hESCs did show loss of allele-specific expression, which could have implications for hESC differentiation and epigenetic stability (both in vitro and after clinical transplantation). A benefit of our and other recent studies of genomic imprinting in hESCs was the identification of imprinted genes that provide a useful indication of epigenetic stability. SNRPN, IPW and KCNQ1OT1 were highly stable and thus appeared insensitive to perturbation; in contrast, H19, IGF2 and MEG3 were more variable and thus could potentially provide a sensitive indication of epigenetic status. In this review, we examine the differences between imprinted genes in their susceptibility to perturbation and discuss the potential molecular basis for these differences. This examination provides insight into the regulation of genomic imprinting in hESCs and the corresponding peri-implantation stages of human development.

Imprinted genes have prominent effects on placentation; however, there is limited knowledge about the manner in which the genes controlled by two paternally methylated regions on chromosomes 7 and 12 contribute to placentation. In order to clarify the functions of these genes in mouse placentation, we examined transcription levels of the paternally methylated genes, tissue differentiation and development and the circulatory system in placentae derived from three types of bi-maternal conceptuses that contained genomes of non-growing (ng) and fully grown (fg) oocytes. The genetic backgrounds of the ng oocytes were as follows: one was derived from the wild-type (ngWT) and another from mutant mice carrying a 13 kb deletion in the H19 transcription unit including the germline-derived differentially methylated region (H19-DMR) on chromosome 7 (ngDeltach7). Another set of oocytes was derived from mutant mice carrying a 4.15 kb deletion in the intergenic germline-derived DMR (IG-DMR) on chromosome 12 (ngDeltach12). Although placental mass was lower in the ngWT/fg placentae compared with that in the WT placentae, it was recovered in the ngDeltach7/fg placentae, but not in the ngDeltach12/fg placentae. The ngDeltach7/fg placental growth improvement was associated with severe dysplasia such as an expanded spongiotrophoblast layer and a malformed labyrinthine zone. In contrast, the ngDeltach12/fg placentae retained the layer structures with expanded giant cells, but their total masses were smaller with a normal circulatory system in order. Our findings demonstrate that the genes controlled by the two paternally methylated regions, H19-DMR and IG-DMR, complementarily organize placentation.

X chromosome inactivation is a developmentally regulated process that causes one of the two X chromosomes in normal female mammals to become transcriptionally silenced, thus equalizing the expression of X-linked genes between the sexes. Such dosage compensation depends upon dynamic genetic and epigenetic events occurring very early in development. X inactivation is controlled by an X inactivation centre that is associated with the expression of non-coding RNAs required for the silencing. Also associated with the inactive X are repressive histone modifications and polycomb protein-mediated states, which are progressively acquired during the inactivation process. In mouse, two forms of X inactivation have been described. Random X inactivation happens in the derivatives of the inner cell mass (ICM) giving rise to embryos where the maternally inherited X(Xm) is inactive in some cells and the paternally derived X (Xp) is inactive in others. Random X inactivation occurs around the time of implantation. Imprinted X inactivation, the preferential inactivation of the Xp chromosome, occurs earlier and, although there has been some debate as to the precise timing of initiation of this event, is apparent in all cells early in preimplantation development, then is subsequently confined to the cells of the extraembryonic lineages. A picture is emerging whereby initial epigenetic asymmetry between the two parental X chromosomes is reprogrammed in a lineage specific manner resulting in a switch from imprinted to random inactivation in embryonic derivatives. Neither the underlying reason nor the full extent of these early lineage specific epigenetic changes is known, but they may be correlated with more genome-wide reprogramming events essential for normal development.

A human imprinted domain at 14q32 contains two co-expressed and reciprocally imprinted genes, DLK1 and GTL2, which are expressed from the paternally and maternally inherited alleles, respectively. We have previously shown that another imprinted locus, on human 15q11-q13, contains a large number of tandemly repeated C/D small nucleolar RNA genes (or C/D snoRNAs) only expressed from the paternal allele. Here we show that the region downstream from the GTL2 gene is also characterized by a transcription unit spanning many repeated intron-encoded C/D snoRNA genes, most of them arranged into two tandem arrays of 31 and 9 copies. Intriguingly, these snoRNAs depart from previously reported rRNA or snRNA methylation guides by their tissue-specific expression and by their lack of complementarity to rRNA or snRNA within their sequences. Analysis of the orthologous region in the mouse shows that the previously reported maternally expressed Rian gene, located downstream of Gtl2 on the distal 12 chromosome, encodes at least nine C/D snoRNAs. Through a systematic search in rodents, we could identify other C/D snoRNA genes in this domain. All snoRNAs identified on mouse distal 12 are brain-specific and only expressed from the maternally inherited allele. The human imprinted 14q32 domain therefore shares common genomic features with the imprinted 15q11-q13 loci. This link between tandemly repeated C/D snoRNA genes and genomic imprinting suggests a role for these snoRNAs and/or their host non-coding RNA genes in the evolution and/or mechanism of the epigenetic imprinting process.

Dlk1 and Gtl2 are reciprocally imprinted genes located 80 kb apart on mouse chromosome 12. Similarities between this domain and that of the well characterized Igf2-H19 locus have been previously noted. Comparative genomic and epigenetic analysis of these two domains might help identify allele-specific epigenetic regulatory elements and common features involved in aspects of imprinting control. Here we describe a detailed methylation analysis of the Dlk1-Gtl2 domain on both parental alleles in the mouse. Like the Igf2-H19 domain, areas of differential methylation are hypermethylated on the paternal allele and hypomethylated on the maternal allele. Three differentially methylated regions (DMRs), each with different epigenetic characteristics, have been identified. One DMR is intergenic, contains tandem repeats and is the only region that inherits a paternal methylation mark from the germline. An intronic DMR contains a conserved putative CTCF-binding domain. All three DMRs have both unique and common features compared to those identified in the Igf2-H19 domain.