Genomic imprinting in mammals

Abstract

Genomic imprinting affects a subset of genes in mammals and results in a monoallelic, parental-specific expression pattern. Most of these genes are located in clusters that are regulated through the use of insulators or long noncoding RNAs (lncRNAs). To distinguish the parental alleles, imprinted genes are epigenetically marked in gametes at imprinting control elements through the use of DNA methylation at the very least. Imprinted gene expression is subsequently conferred through lncRNAs, histone modifications, insulators, and higher-order chromatin structure. Such imprints are maintained after fertilization through these mechanisms despite extensive reprogramming of the mammalian genome. Genomic imprinting is an excellent model for understanding mammalian epigenetic regulation.

Figure 1.

Mouse models to study genomic imprinting that allow the maternal and paternal chromosome to be distinguished. Mammals are diploid and inherit a complete chromosome set from the maternal and paternal parent. However, mice can be generated that (1) inherit two copies of a chromosome pair from one parent and no copy from the other parent (known as UPD), (2) inherit a partial chromosomal deletion from one parent and a wild-type chromosome from the other parent, and (3) inherit chromosomes carrying single-nucleotide polymorphisms (known as SNPs) from one parent and a wild-type chromosome from the other parent. Offspring with UPDs or deletions are likely to display lethal phenotypes, whereas SNPs will allow the production of viable offspring.

Figure 2.

A maternal and paternal genome are needed for mammalian reproduction. The nuclear transfer technique used micropipettes and high-powered microscopes to remove the male or female nuclei from a newly fertilized egg and place them in various combinations into a second “host” fertilized egg that had already been enucleated, thereby generating anew diploid embryos with two maternal (gynogenetic) or two paternal (androgenetic) genomes or a biparental genome (wild-type). Gynogenetic and androgenetic embryos were lethal at early embryonic stages. Only reconstituted embryos that received both a maternal and paternal nucleus (wild-type) survived to produce living young. These experiments show the necessity for both the maternal and paternal genome in mammalian reproduction, and indicate the two parental genomes express different sets of genes needed for complete embryonic development.

Figure 3.

Imprint acquisition and erasure in mammalian development. Imprints are acquired by the gametes; thus, oocytes and sperm already carry imprinted chromosomes (first-generation imprints). After fertilization when the embryo is diploid, the imprint is maintained on the same parental chromosome after each cell division in cells of the embryo, yolk sac, placenta, and also in the adult. The germ cells are formed in the embryonic gonad and the imprints are erased only in these cells before sex determination. As the embryo develops into a male, the gonads differentiate to testes that produce haploid sperm that acquire a paternal imprint on their chromosomes. Similarly, in developing females, chromosomes in the ovaries acquire maternal imprints (second-generation imprints).

Figure 4.

Imprinted genes play a role in mammalian reproduction. Mammals are diploid and reproduction requires fertilization of a haploid female egg by a haploid male sperm to recreate a diploid embryo. Only females are anatomically equipped for reproduction, but they cannot use parthenogenesis to reproduce (the possibility of which is represented by a pink dashed line) because essential imprinted genes needed for fetal growth are imprinted and silenced on maternal chromosomes. These genes are expressed only from paternal chromosomes; thus, both parental genomes are needed for reproduction in mammals. Parthenogenesis is the production of diploid offspring from two copies of the same maternal genome.

Figure 5.

Imprinted genes are expressed from one parental allele and often clustered. Most imprinted genes (yellow) are found in clusters that include multiple protein-coding mRNAs (IG) and at least one noncoding RNA (IG-NC). Nonimprinted genes can also be present (NI in gray). The imprinting mechanism is cis acting and imprinted expression is controlled by an imprint control element (ICE) that carries an epigenetic imprint inherited from one parental gamete. One pair of diploid chromosomes is shown: the pink is of maternal origin and the blue of paternal origin. Arrow, expressed gene; slashed circle, repressed gene.

Figure 6.

Imprinted expression is regulated by gametic DMRs (G-DMR). (Left) The effect of deleting the gametic DMR from the imprinted chromosome (green). (Right) The effect of deleting the G-DMR from the nonimprinted chromosome (yellow). In many imprinted clusters (e.g., Igf2r, Kcnq1, and Dlk1), experimental deletion of the G-DMR only affects the chromosome carrying the nonimprinted G-DMR. This results in a loss of repression of the imprinted protein-coding mRNA genes (IG) and a gain of repression of the imprinted lncRNA gene (IG-NC). Note that in some imprinted clusters (Igf2 and Pws) that are not illustrated here, the methylated G-DMR appears also to be required for expression of some of the imprinted mRNAs in cis. del, deleted DNA; G-DMR, gametic differentially DNA-methylated region; NG, nonimprinted gene; arrow, expressed allele; slashed circle, repressed allele; imprint, epigenetic modification leading to a change in gene expression in cis.

Figure 7.

Establishment, maintenance, and erasure of genomic imprints in mouse development. In the germline, primordial germ cells (PGCs) undergo multiple changes in chromatin structure and DNA demethylation during migration into the genital ridge (gonad). Imprints are then acquired in a sex-specific manner in the germline (green shading). DNA methylation is targeted specifically to paternally and maternally DNA-methylated ICEs—prenatally in prospermatogonia and postnatally during oocyte maturation. These imprints are maintained despite global changes in DNA methylation after fertilization (orange shading): active demethylation of the paternal genome in the zygote and passive maternal demethylation in the preimplantation embryo. Candidates for protection of methylation regions include ZFP57 and PGC7/STELLA. De novo DNA methylation of the genome begins at the morula stage, during which time unmethylated alleles of imprinted genes must be protected. These imprints are maintained in somatic cells throughout the lifetime of the organism, whereas imprinting in extraembryonic tissues is thought to be less dependent on maintenance of DNA methylation. In the germline, imprints are erased and reset for the next generation (red shading). PTM, post-translational modification; MAT, maternal genome; PAT, paternal genome.

Figure 8.

Two cis-acting silencing mechanisms at imprinted gene clusters. (A) Insulator model for the Igf2 cluster. The expression pattern for endoderm is shown. On the maternal chromosome, the unmethylated ICE binds the CTCF protein and forms an insulator that prevents the common endoderm enhancers (E) from activating Igf2 and Ins2. Instead the enhancers activate the nearby H19 lncRNA promoter. On the paternal chromosome, the methylated ICE cannot bind CTCF and an insulator does not form; hence the Igf2 and Ins2 mRNA genes are expressed only on this chromosome. The H19 lncRNA is methylated, most likely because of spreading from the 2-kb distant methylated ICE, and silenced. (B) lncRNA model for the Igf2r cluster. The expression pattern for placenta is shown. On the maternal chromosome, the methylated ICE contains the Airn lncRNA promoter that is directly silenced by the DNA methylation imprint. The Igf2r, Slc22a2, and Slc22a3 mRNA genes are expressed only on this chromosome. Mas1 and Slc22a1 are not expressed in placenta (filled diamond). On the paternal chromosome, the Airn lncRNA promoter lying in the unmethylated ICE is expressed and silences Igf2r (in part by kicking off RNA polymerase II), Slc22a2, and Slc22a3 in cis. Note that in both models, the DNA methylation imprint silences the lncRNA and permits mRNA expression. ICE, imprint control element; gray arrow, expressed allele of an imprinted gene; slashed circle, repressed allele of an imprinted gene; thick gray arrows, long distance effect in cis.