Complementary roles of genes regulated by two paternally methylated imprinted regions on chromosomes 7 and 12 in mouse placentation

Maternal RNA transcription in Dlk1-Dio3 domain is critical for proper development of the mouse placental vasculature

The placenta is a unique organ for ensuring normal embryonic growth in the uterine. Here, we found that maternal RNA transcription in Dlk1-Dio3 imprinted domain is essential for placentation. PolyA signals were inserted into Gtl2 to establish a mouse model to prevent the expression of maternal RNAs in the domain. The maternal allele knock-in (MKI) and homozygous (HOMO) placentas showed an expanded junctional zone, reduced labyrinth and poor vasculature impacting both fetal and maternal blood spaces. The MKI and HOMO models displayed dysregulated gene expression in the Dlk1-Dio3 domain. In situ hybridization detected Dlk1, Gtl2, Rtl1, miR-127 and Rian dysregulated in the labyrinth vasculature. MKI and HOMO induced Dlk1 to lose imprinting, and DNA methylation changes of IG-DMR and Gtl2-DMR, leading to abnormal gene expression, while the above changes didn't occur in paternal allele knock-in placentas. These findings demonstrate that maternal RNAs in the Dlk1-Dio3 domain are involved in placental vasculature, regulating gene expression, imprinting status and DNA methylation.

Placenta-specific epimutation at H19-DMR among common pregnancy complications: its frequency and effect on the expression patterns of H19 and IGF2

Background

H19 and IGF2 genes are imprinted and involved in regulating fetal and placental growth. The H19 differentially methylated region (DMR) is paternally methylated and maternally unmethylated and regulates the imprinted expression of H19 and IGF2. Epimutation at the H19-DMR in humans results in congenital growth disorders, Beckwith-Wiedemann and Silver-Russell syndromes, when erroneously its maternal allele becomes methylated and its paternal allele becomes unmethylated, respectively. Although H19 and IGF2 have been assessed for their involvement in pregnancy complications including fetal growth restriction (FGR) and pregnancy-induced hypertension (PIH)/hypertensive disorder of pregnancy (HDP) intensively in the last decade, it is still not established whether epimutation at the H19-DMR in the placenta results in pathogenic conditions in pregnancy. We aimed to assess the frequency of H19-DMR epimutation and its effects on the allelic expression patterns of H19 and IGF2 genes among normal and abnormal pregnancy cases.

Results

We enrolled two independently collected sets of placenta samples from normal pregnancies as controls and common pregnancy complications, FGR and PIH (HDP). The first set consisted of 39 controls and 140 FGR and/or PIH cases, and the second set consisted of 29 controls and 62 cases. For these samples, we initially screened for DNA methylation changes at H19-DMR and IGF2-DMRs by combined bisulfite restriction analysis, and further analyzed cases with methylation changes for their allelic methylation and expression patterns. We identified one case each of FGR and PIH showing hypomethylation of H19-DMR and IGF2-DMRs only in the placenta, but not in cord blood, from the first case/control set. For the PIH case, we were able to determine the allelic expression pattern of H19 to be biallelically expressed and the H19/IGF2 expression ratio to be highly elevated compared to controls. We also identified a PIH case with hypomethylation at H19-DMR and IGF2-DMRs in the placenta from the second case/control set.

Conclusions

Placental epimutation at H19-DMR was observed among common pregnancy complication cases at the frequency of 1.5% (3 out of 202 cases examined), but not in 68 normal pregnancy cases examined. Alteration of H19/IGF2 expression patterns due to hypomethylation of H19-DMR may have been involved in the pathogenesis of pregnancy complications in these cases.

Electronic supplementary material

The online version of this article (10.1186/s13148-019-0712-3) contains supplementary material, which is available to authorized users.

Overexpression of microRNAs from the Gtl2-Rian locus contributes to postnatal death in mice

The Dlk1-Dio3 imprinted domain functions in embryonic development but the roles of noncoding RNAs expressed from this domain remain unclear. We addressed this question by generating transgenic (TG) mice harbouring a BAC carrying IG-DMR (intergenic-differentially methylated region), Gtl2-DMR, Gtl2, Rtl1/Rtl1as, and part of Rian. High postnatal lethality (>85%) of the BAC-TG pups was observed in the maternally transmitted individuals (MAT-TG), but not following paternal transmission (PAT-TG). The DNA methylation status of IG-DMR and Gtl2-DMR in the BAC-allele was paternally imprinted similar to the genomic allele. The mRNA-Seq and miRNA-Seq analysis revealed marked expression changes in the MAT-TG, with 1,500 upregulated and 2,131 downregulated genes. The long noncoding RNAs and 12 miRNAs containing the BAC locus were markedly enhanced in the MAT-TG. We identified the 24 target genes of the overexpressed miRNAs and confirmed the downregulation in the MAT-TG. Notably, overexpression of mir770, mir493, and mir665 from Gtl2 in the MAT-TG embryos led to decreased expression of the 3 target genes, Col5a1, Pcgf2, and Clip2. Our results suggest that decreased expression of the 3 target genes concomitant with overexpression of the miRNAs within Gtl2 may be involved in the postnatal death in the MAT-TG. Because this imprinted domain is well conserved between mice and humans, the results of genetic and molecular analysis in mice hold important implications for related human disorders such as Temple syndrome.

Intrauterine hyperglycemia induces intergenerational Dlk1-Gtl2 methylation changes in mouse placenta

An intrauterine hyperglycemic environment has long-lasting effects on the offspring. Recent studies focused on fetal tissues, whereas we studied the development and molecular alteration of the placenta. By intercrossing male and female adult control (C) and first-generation offspring mice with gestational diabetes mellitus (F1-GDM), we obtained four groups of second generation (F2) offspring: 1) C♂-C♀, 2) C♂-GDM♀, 3) GDM♂-C♀, 4) GDM♂- GDM♀. Placental weights in F1-GDM offspring were lower than in the control group. Placental weights in F2-offspring decreased through the paternal line. Placental RNA was extracted and analyzed using microarrays on day18.5 of pregnancy. This revealed 35 upregulated imprinted genes and 10 down-regulated imprinted genes. Dlk1and Gtl2 were especially down-regulated and up-regulated, respectively, due to their abnormal methylation status. These findings suggest that intrauterine hyperglycemia decreased placental weight in the first generation, and this was transmitted paternally to the second generation in mice. They also suggest intrauterine hyperglycemia leads to abnormal placental Dlk1-Gtl2 expression due to DNA methylation in first and second generation mice.

Epigenetic disruptions of histone signatures for the trophectoderm and inner cell mass in mouse parthenogenetic embryos

Epigenetic asymmetry has been shown to be associated with the first lineage allocation event in preimplantation development, that is, the formation of the trophectoderm (TE) and inner cell mass (ICM) lineages in the blastocyst. Since parthenogenesis causes aberrant segregation between the TE and ICM lineages, we examined several development-associated histone modifications in parthenotes, including those involved in (i) transcriptional activation [acetylated histone H3 lysine 9 (H3K9Ac) and lysine 14 (H3K14Ac), trimethylated histone H3 lysine 4 (H3K4Me3), and dimethylated histone H3 arginine 26 (H3R26Me2)] and (ii) transcriptional repression [trimethylated histone H3 lysine 9 (H3K9Me3) and lysine 27 (H3K27Me3), and mono-ubiquitinated histone H2A lysine 119 (H2AK119u1)]. Here, we report that in parthenotes, H3R26Me2 expression decreased from the morula stage, while expression patterns and levels of H3K9Ac, H3K27Me3, and H2AK119u1 were unchanged until the blastocyst stage; whereas H3K14Ac, H3K4Me3, and H3K9Me3 showed normal patterns and levels of expressions. Relative to the decrease of H3K9Ac in the ICM and increase in the TE of parthenotes, we detected reduced expression of TAT-interactive protein 60 acetyltransferase and histone deacetylase 1 deacetylase in the ICM and TE of parthenotes, respectively. Relative to the decrease of H3R26Me2, we also observed decreased expression of coactivator-associated arginine methyltransferase 1 methyltransferase and increased expression of the Wnt effector transcription factor 7L2 and miR-181c microRNA in parthenotes. Furthermore, relative to the decrease in H3K27Me3 and H2AK119u1, we found increased phosphorylation of Akt1 and enhancer of zeste homolog 2 in parthenogenetic TE. Therefore, our findings that histone signatures are impaired in parthenotes provide a mechanistic explanation for aberrant lineage segregation and TE defects.

Roles of genes regulated by two paternally methylated imprinted regions on chromosomes 7 and 12 in mouse ontogeny

We studied the longevity of mice produced without sperm using the genomes of oocytes that are already committed to a germline cell lineage. The first sperm-free mouse "KAGUYA", which we term 'bi-maternal mouse', was born on 3 February, 2003. Bi-maternal embryos were generated using 2 sets of female genomes--one derived from fully grown oocytes from normal adults and the other from non-growing oocytes from newborn pups. These genomes were combined by nuclear transfer. We refined the technique for generating bi-maternal mice and found that genetic manipulations in only 2 regions--the imprinting centres of Igf2-H19 and Dlk1-Gtl2--on chromosomes 7 and 12 of the newborn pups allowed us to generate bi-maternal mice at a high rate. Studying bi-maternal conceptuses and mice provides further insight into the mechanisms by which paternally methylated imprinted genes regulate mammalian ontogenesis.

Involvement of insulin-like growth factor 2 in angiogenic factor transcription in Bi-maternal mouse conceptuses

Imprinted genes in which only one of the two parental chromosome copies is expressed have a substantial effect on mammalian ontogenesis. On mouse distal chromosome 7, the paternally expressed gene insulin-like growth factor 2 (Igf2) is separated by approximate 100 kb from the maternally expressed non-coding gene H19. However, there is limited knowledge of the manner in which Igf2 transcription affects the other genes involved in embryonic development. To clarify this, we performed quantitative gene expression analysis for representative angiogenic factors-Vegf, Flt1, Flt4, Flk1, Ang1, Ang2, Tie1, and Tie2-for 3 types of bi-maternal conceptuses containing genomes with non-growing (ng) and fully grown (fg) oocytes. The genetic backgrounds of the ng oocytes were 1) the wild type (ng(wt)), 2) mutant mice carrying a 3-kb deletion of the H19 transcription unit (ng(H19Delta3-KO)/fg) and 3) mutant mice carrying a 13-kb deletion in the H19 transcription unit, including the germline-derived differentially methylated region on chromosome 7 (ng(H19Delta13-KO)/fg). In the ng(wt)/fg and ng(H19Delta3-KO)/fg placentae, Vegf and Flt1 were upregulated compared with the mean value for the wt placenta, whereas in the ng(H19Delta13-KO)/fg placenta, these transcriptional levels were restored. In the fetus, however, only 2 genes among the 8 genes analyzed were significantly changed in the bi-maternal fetuses, indicating that the effects of the Igf2 mRNA level on angiogenic factor transcription in the fetus differed from those in the placenta. Our results indicated that the Igf2 mRNA level affects transcription of angiogenic factors in both bi-maternal placentae and fetuses.

Defining contributions of paternally methylated imprinted genes at the Igf2-H19 and Dlk1-Gtl2 domains to mouse placentation by transcriptomic analysis

Parental genome functions in ontogeny are determined by interactions among transcripts from the maternal and paternal genomes, which contain many genes whose expression is strictly dependent on their parental origin as a result of genomic imprinting. Comprehensive recognition of the interactions between parental genomes is important for understanding genomic imprinting in mammalian development. The placenta is a key organ for exploring the biological significance of genomic imprinting. To decipher the unknown roles of paternally methylated imprinted genes on chromosomes 7 and 12 in mouse placentation, we performed a transcriptomic analysis on placentae in three types of bimaternal conceptuses that contained genomes derived from both non-growing and fully grown oocytes. Furthermore, we used the Ingenuity pathway analysis software to predict key networks and identify functions specific to paternally methylated imprinted genes regulated by the Igf2-H19 imprinting control region and Dlk1-Dio3 imprinting control region. The data suggested that dynamic conversion of the gene expression profile by restoring the expression of paternally methylated imprinted genes resulted in phenotypic improvements in bimaternal placentae. These results provide a framework to further explore the role of epigenetic modifications in paternal genome during mouse placentation.

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.

Developmental ability of trophoblast stem cells in uniparental mouse embryos

Neither parthenogenetic (PG) nor androgenetic (AG) mouse embryos survive after day 9.5 of pregnancy, owing to the inadequate growth of extraembryonic tissues, including the placenta. At day 9.5 of pregnancy, the placental structures are poorly developed in PG embryos, while trophoblast giant cells are abundant at the implantation site in AG embryos. These findings suggest that both parental genomes are required for placental development. To gain further insight into the trophoblast lineage in PG and AG embryos, we attempted to derive trophoblast stem (TS)-like cell lines from uniparental embryos. Furthermore, we sought to assess their ability to differentiate into cells of the trophoblast lineage by using gene expression analysis. Three cell lines that expressed marker genes for undifferentiated TS cells (Cdx2 and Errbeta) were derived from AG embryos. Under differentiation conditions, these cells expressed the trophoblast giant cell-specific genes, but did not express the spongiotrophoblast-specific genes. In contrast, none of the four cell lines from PG embryos expressed marker genes for undifferentiated TS cells, but they expressed Oct3/4, a marker gene for embryonic stem cells. Immunohistochemical analysis indicated that PG blastocysts expressed Oct3/4 and Cdx2 specifically in inner cell mass and the trophectoderm respectively. These results suggest that PG embryos do not possess TS cells, because of the lack of the developmental ability of trophoblast cells.

Protocol for the production of viable bimaternal mouse embryos

A reliable nuclear transfer method was first reported in 1983; it provided definite evidence that parthenogenetic embryos are lethal at early postimplantation in mammals. Subsequently, nuclear transfer has been extensively used as an important and versatile tool for investigating embryo and somatic-cell cloning and nucleo-cytoplasmic interactions. Further development of this technique has enabled the generation of bimaternal embryos containing two haploid sets of maternal genomes from female germ cells of different origins. By using a 2-d nuclear transfer system for oocyte reconstruction, viable mice can be produced solely from maternal genomes, without the participation of the paternal genome. This oocyte reconstruction system, as described in this protocol, could provide valuable guidelines for exploring the potential endowments of gametes and for conferring novel properties to them.

Synergistic role of Igf2 and Dlk1 in fetal liver development and hematopoiesis in bi-maternal mice

Mouse bi-maternal embryos (BMEs) that contain two haploid sets of genomes from non-growing (ng) and fully-grown (fg) oocytes develop to embryonic day (E) 13.5. However, the ng/fg BMEs never develop beyond E13.5 because of repression of the paternally expressed imprinted genes, Igf2 and Dlk1. The present study was conducted to address the issue of whether fetal hematopoietic disorder is involved in the restricted development of BMEs. FACS analysis revealed that the livers of ng(wt)/fg BMEs contained increased numbers of immature c-kit(+)/ter119(-) hematopoietic cells, were while the numbers of mature c-kit(-)/ter119(+) hematopoietic cells were decreased. This finding was supported by histological observations. Quantitative gene expression analysis revealed that Igf2 and Dlk1 expression was repressed in the liver. To understand the role of paternally-methylated imprinted genes on chromosomes 7 and 12, particularly Igf2 and Dlk1, in fetal liver hematopoiesis, we constructed ng(Deltach7)/fg, ng(Deltach12)/fg and ng(DeltaDouble)/fg BMEs using ng oocytes harboring deletion of differentially methylated regions at distal chromosomes 7 and/or 12. The ng(Deltach7)/fg, ng(Deltach12)/fg and ng(DeltaDouble)/fg BMEs, respectively, express Igf2, Dlk1 and both, and these embryos developed to term with specific phenotypes; the ng(Deltach7)/fg and ng(Deltach12)/fg BMEs develop to term with severe growth retardation, and the ng(DeltaDouble)/fg BMEs can survive to become normal female adults. By inducing Igf2 and Dlk1 expression, the proportions of mature and immature hematopoietic cells in the livers of the ng(Deltach7)/fg, ng(Deltach12)/fg and ng(DeltaDouble)/fg BMEs were considerably restored, and particularly in the ng(DeltaDouble)/fg BMEs, hematopoiesis occurred normally with appropriate expressions of the related genes. These data suggest that inappropriate expression of Igf2 and Dlk1 is involved in impaired fetal hematopoiesis.

Appropriate expression of imprinted genes on mouse chromosome 12 extends development of bi-maternal embryos to term

Recently, we reported that the restored regulation of imprinted gene expression from two regions -H19 differentially methylated region (H19-DMR) and intergenic germline-derived DMR (IG-DMR) - is sufficient for accomplishing full-term development in mice. In the present study, we determined the developmental ability of the bi-maternal embryos (BMEs) containing the non-growing oocyte genome with the IG-DMR deletion (ng(Deltach12)) and fully-grown (fg) oocyte genome. Foetuses derived from ng(Deltach12)/fg BMEs were alive at E19.5 but could not survive further. Comparison with BMEs derived from Igf2+/- ng/fg genomes suggests that bi-allelic H19 expression might be involved in foetal development.

High-frequency generation of viable mice from engineered bi-maternal embryos

Mammalian development to adulthood typically requires both maternal and paternal genomes, because genomic imprinting places stringent limitations on mammalian development, strictly precluding parthenogenesis. Here we report the generation of bi-maternal embryos that develop at a high success rate equivalent to the rate obtained with in vitro fertilization of normal embryos. These bi-maternal mice developed into viable and fertile female adults. The bi-maternal embryos, distinct from parthenogenetic or gynogenetic conceptuses, were produced by the construction of oocytes from fully grown oocytes and nongrowing oocytes that contain double deletions in the H19 differentially methylated region (DMR) and the Dlk1-Dio3 intergenic germline-derived DMR. The results provide conclusive evidence that imprinted genes regulated by these two paternally methylated imprinting-control regions are the only paternal barrier that prevents the normal development of bi-maternal mouse fetuses to term.

Mechanisms regulating imprinted genes in clusters

Clustered imprinted genes are regulated by differentially methylated imprinting control regions (ICRs) that affect gene activity and repression in cis over a large region. Although a primary imprint signal for each of these clusters is DNA methylation, different mechanisms are used to establish and maintain these marks. The majority of ICRs are methylated in the maternal germline and are usually promoters for antisense transcripts whose elongation is associated with imprinting control in the domain. In contrast, ICRs methylated in the paternal germline do not appear to act as promoters and are located between genes. At least one, at the Igf2/H19 locus, is known to function as an insulator. Analysis of ICRs suggests that maternal and paternal methylation imprints function in distinct ways.