Genomic imprinting mechanisms in mammals

Abstract

Genomic imprinting is a form of epigenetic gene regulation that results in expression from a single allele in a parent-of-origin-dependent manner. This form of monoallelic expression affects a small but growing number of genes and is essential to normal mammalian development. Despite extensive studies and some major breakthroughs regarding this intriguing phenomenon, we have not yet fully characterized the underlying molecular mechanisms of genomic imprinting. This is in part due to the complexity of the system in that the epigenetic markings required for proper imprinting must be established in the germline, maintained throughout development, and then erased before being re-established in the next generation's germline. Furthermore, imprinted gene expression is often tissue or stage-specific. It has also become clear that while imprinted loci across the genome seem to rely consistently on epigenetic markings of DNA methylation and/or histone modifications to discern parental alleles, the regulatory activities underlying these markings vary among loci. Here, we discuss different modes of imprinting regulation in mammals and how perturbations of these systems result in human disease. We focus on the mechanism of genomic imprinting mediated by insulators as is present at the H19/Igf2 locus, and by non-coding RNA present at the Igf2r and Kcnq1 loci. In addition to imprinting mechanisms at autosomal loci, what is known about imprinted X-chromosome inactivation and how it compares to autosomal imprinting is also discussed. Overall, this review summarizes many years of imprinting research, while pointing out exciting new discoveries that further elucidate the mechanism of genomic imprinting, and speculating on areas that require further investigation.

Fig. 1

Regulation of imprinted expression at the human and mouse H19/Igf2 loci. Shown is the organization of the mouse (top) and human (bottom) locus (not drawn to scale). Genomic positions in base pairs based on NCBI build 36 (humans) and 37 (mouse). CTCF target sites (designated as CTSs in human and shown with black bars) are indicated within the ICR/DMD/IC1 (yellow bar). (A) Methylation status and gene expression are shown for the mouse H19/Igf2 locus. Arrows at genes denote active status while arrows pointing right to left denote interactions between enhancers and gene promoters. (B) Microdeletions at IC1 in BWS patients are denoted by hatched-marked bars (modified from [133]). See text for references. The CTSs that are deleted in each case are represented in parenthesis beside each deletion. The corresponding methylation status of the maternally inherited allele for each deletion is depicted to the right as unmethylated (open lollipops), methylated (filled lollipops) or partially methylated (half-filled lollipops).

Fig. 2

Regulation of imprinting clusters through long ncRNAs. (A) Imprinting on proximal mouse chromosome 17. Igf2r, Slc22a2 and Slc22a3 are expressed from the maternal chromosome (pink boxes) and Air is expressed from the paternal chromosome (blue arrow). Non-imprinted genes at this domain include Mas1, Plg and Slc22a1 (grey boxes). The ICR, which serves as the promoter to Air, is shown with a yellow box. The ICR is hypermethylated on the maternal strand, preventing transcription of Air and allowing Igf2r, Slc22a2 and Slc22a3 to be transcribed. On the paternal chromosome the ICR is unmethylated, Air is expressed and surrounding genes (Igf2r, Slc22a2 and Slc22a3) are repressed (indicated with a dotted arrow). (B) Imprinting of the mouse Kcnq1 domain. Maternally-expressed genes are indicated by pink boxes and the paternally-expressed long ncRNA Kcnq1ot1 is shown with a blue arrow. KvDMR1, which is the ICR for this region and harbors the promoter for Kcnq1ot1, is designated by a yellow box and is methylated on the maternal allele. The promoter for Cdkn1c is methylated on the paternal allele after fertilization. The two CTCF binding sites within KvDMR1 are designated with vertical arrows. See text for additional details. Transcriptional activity of a given gene is indicated by arrows. Not drawn to scale.

Fig. 3

Kinetics of X-chromosome inactivation during development in mice. Stages after zygotic genome activation are represented together with a schematic view of the XCI pattern. Xist domain is depicted by a green oval. Xist, Tsix and X-linked genes expression are depicted by green, yellow and red dots, respectively. (A) Acquisition of a maternal imprint during oocyte growth and of a paternal imprint either during spermatogenesis or early after fertilization. (B) Establishment of imprinted X-chromosome inactivation (XCI). The marks on the paternal Xp are indicated along the arrow to reflect when they start to be acquired. Cot-1 exclusion refers to the absence of labelling of essentially intergenic transcripts by RNA fluorescence in situ hybridization using a Cot-1 probe. Whether the X-chromosome is preinactivated at the 2-cell stage is unresolved [75,77]. Tsix RNA is present in a fraction of cells in E3.5 blastocysts but it is not known if the expression is equivalent in the trophectoderm and the ICM. (C) Reactivation and random XCI in the embryonic lineage (blue). In the ICM of E4.5 blastocysts and in ES cells, which are derived from the ICM, the Xist domain and the heterochromatin marks on the Xp are lost and Xist and Tsix are expressed biallelically. However, Xist expression is very low and hence not represented here (Sun et al., 2006). In the epiblast after E5.5 and in differentiated ES cells, either the paternal or the maternal X-chromosome is inactivated due to random XCI. Known heterochromatin marks associated with the inactive X-chromosome are indicated. (D) Maintenance of imprinted XCI in the trophoblast (light red) and primitive endoderm (yellow) lineages. In the trophoblast lineage, the imprinted pattern of XCI is maintained without interruption. Tsix expression in the trophoblast lineage at E6.5 is inferred from its expression pattern at earlier and later stages and from its requirement on Xm early after implantation. In the primitive endoderm lineage, XCI is imprinted, but it is not known if the Xp is continuously inactive or if it is transiently reactivated when the primitive endoderm differentiates from the ICM (green question mark). Also, Tsix pattern of expression has not been reported in the primitive endoderm lineage (yellow question mark). Known marks on the Xp are indicated for TS cells [81,91,134,135] and XEN cells [91,136], which are cell models of the trophectoderm and the visceral endoderm, respectively. See text for additional references. Xp, paternal X-chromosome; Xm, maternal X-chromosome; ICM, inner cell mass; TE, trophectoderm; EPI, epiblast; EC, ectoplacental cone; EE, extraembryonic ectoderm; ES cells, embryonic stem cells; TS cells, trophoblast stem cells; XEN cells, extraembryonicextraembryonic stem cells; PRC1, Polycomb-Repressive Complex 1; PRC2, Polycomb-Repressive Complex 2.