Mechanisms of genomic imprinting

Abstract

Imprinted genes represent a curious defiance of normal Mendelian genetics. Mammals inherit two complete sets of chromosomes, one from the mother and one from the father, and most autosomal genes will be expressed from both the maternal and the paternal alleles. Imprinted genes, however, are expressed from only one chromosome, in a parent-of-origin-dependent manner. Because silent and active promoters are present in a single nucleus, the differences in activity cannot be explained by transcription-factor abundance. Thus, transcription of imprinted genes represents a clear situation in which epigenetic mechanisms restrict gene expression and, therefore, offers a model for understanding the role of DNA modifications and chromatin structure in maintaining appropriate patterns of expression. Furthermore, because of their parent-of-origin-restricted expression, phenotypes determined by imprinted genes are susceptible not only to genetic alterations in the genes but also to disruptions in the epigenetic programs controlling regulation. Imprinted genes are often associated with human diseases, including disorders affecting cell growth, development, and behavior.

Figure 1

Clusters of imprinted genes on mouse distal 7 (syntenic with human 11p15.5) (a) and human 15q11-q13 (syntenic with mouse central 7) (b). Transcripts are depicted by arrows, with the direction indicated if known. Regions showing parent-of-origin–dependent DNA methylation are shown as CH₃. The thickened segments of the lines represent the AS-IC and PWS-IC elements, as indicated. These sites are required in cis for normal imprinting on human 15q11-13.

Figure 2

Effect that mutations in the H19DMR region have on expression of H19 and Igf2. a, Wild-type expression. Most wild-type cells express only the maternal H19 allele and only the paternal Igf2 allele. Expression of both genes is driven by shared enhancer elements. Endodermal enhancers (unblackened ovals) and skeletal muscle enhancers (blackened ovals) are ∼8 and ∼24 kb upstream of the H19 promoter, which is ∼90 kb upstream of the Igf2 promoter. Paternal chromosome–specific CpG methylation is noted in upstream sequences called “H19DMR” (thickened segments of lines). Differential methylation of this region is observed in sperm and is maintained during the global methylation changes observed during early embryogenesis. After implantation, the hypermethylation (CH₃) spreads to include the H19 promoter and gene body. The maternal chromosome shows hypersensitivity to nuclease digestion (vertical arrows) in the DMR region and at the H19 promoter, whereas the Igf2 promoter appears to be equally sensitive to digestion on both chromosomes. b, Mechanistically linked imprinting of H19 and Igf2. The H19D13 allele replaces the H19 gene, including its promoter and H19DMR, with the NeoR gene. The shared endodermal and mesodermal enhancers are unaffected by this mutation, which, on maternal inheritance, results in biallelic expression of Igf2. c, H19DMR, necessary to silence paternal expression of H19. H19DDMR removes sequences that are differentially methylated on the paternal chromosome. When inherited through the paternal germline or removed from the paternal chromosome early during embryogenesis, H19 expression becomes biallelic. d, Silencing of the paternal H19 allele, mediated by epigenetic changes driven by H19DMR but not directly dependent on DMR function. When DMR sequences are removed from the paternal chromosome only late during embryogenesis, H19 expression remains monoallelic. e, H19DMR, necessary to silence expression of Igf2 from the maternal allele. When inherited through the maternal germline or removed from the maternal chromosome early during embryogenesis, Igf2 expression becomes biallelic. f, Silencing of the maternal Igf2 allele, directly dependent on the action of H19DMR. Even when the DMR is removed from the maternal chromosome only late during embryogenesis, Igf2 expression becomes biallelic. g, H19DMR and transcriptional insulator function. In DMR^move, H19DMR was inserted between the H19/Igf2 endodermal and mesodermal enhancers. After maternal inheritance of the DMR^move chromosome, H19 expression in skeletal muscle, but not in the liver, was lost. h, Biallelic expression of Igf2, allowed by moving of the endodermal enhancer elements closer to Igf2, where they are no longer separated from the Igf2 promoter by the DMR. “Early embryo” (c and e) indicates that deletions were generated in preimplantation embryos. “Late embryo” (d and f) describes deletions generated in differentiated muscle cells.