Genomic imprinting in development, growth, behavior and stem cells

Abstract

Genes that are subject to genomic imprinting in mammals are preferentially expressed from a single parental allele. This imprinted expression of a small number of genes is crucial for normal development, as these genes often directly regulate fetal growth. Recent work has also demonstrated intricate roles for imprinted genes in the brain, with important consequences on behavior and neuronal function. Finally, new studies have revealed the importance of proper expression of specific imprinted genes in induced pluripotent stem cells and in adult stem cells. As we review here, these findings highlight the complex nature and developmental importance of imprinted genes.

Keywords: Behavior; DNA methylation; Fetal growth; Imprinted genes; Induced pluripotency; Neuronal development.

Fig. 1.

Establishment, maintenance and erasure of genomic imprints during mouse development. Imprints are acquired in a sex-specific manner in the mature germline (light green circles) during development, with paternal imprints (blue chromosomes) being established prenatally and maternal imprints (pink chromosomes) established postnatally. These imprints are retained despite the global changes in DNA methylation that occur after fertilization, which include active demethylation of the paternal genome and passive demethylation of the maternal genome. These imprints are maintained in somatic tissues throughout adulthood. In primordial germ cells (PGCs, dark green circles), imprints are erased (gray chromosomes) and reset for the next generation.

Fig. 2.

Imprinting mechanisms. (A) The insulator model is best represented by the H19/Igf2 locus. The ICR on the paternal allele of this locus is DNA methylated. By contrast, the ICR on the maternal allele is unmethylated, which allows binding of the insulator protein CTCF and prevents enhancers from interacting with the insulin-like growth factor 2 (Igf2) promoter. Instead, the enhancers activate H19 expression. On the paternal allele, DNA methylation prevents CTCF from binding to the ICR, allowing the enhancers to activate Igf2 expression. (B) The ncRNA model is best illustrated by the Kcnq1 locus. Here, the ICR contains the promoter of the Kcnq1ot1 long ncRNA. On the paternal allele, the ICR is unmethylated, allowing the expression of Kcnq1ot1, which in turn silences the paternal alleles of the adjacent genes. On the maternal allele, Kcnq1ot1 is not expressed owing to DNA methylation of the ICR, and the adjacent imprinted genes are expressed. All imprinted domains are depicted for the mouse, although the human regions are largely conserved. T refers to the telomeric end of the cluster and C the proximal end of the chromosome. Not drawn to scale.

Fig. 3.

A summary of imprinted gene functions during embryogenesis. Examples of imprinted genes and their functions in the brain (top box), in the placenta (lower box) and in general growth (left-hand boxes) during embryonic development are listed.

Fig. 4.

Dlk1-Dio3 expression during iPSC induction. (A) Gtl2, a non-coding RNA in the Dlk1-Dio3 imprinted cluster, is expressed from the maternal allele in most somatic tissues. Within these tissues, the ICR (IG-ICR) within the cluster exhibits activating histone marks (H3K4me2 and H3Kac). Induction of pluripotency in somatic cells via exogenous expression of Oct4 (Pou5f1), Klf4, Sox2 and Myc frequently results in the aberrant silencing of maternal transcripts within the Dlk1-Dio3 cluster and DNA methylation of the ICR by DNMT3A (not pictured). The subsequent misexpression of Gtl2 and other Dlk1-Dio3 transcripts results in poor incorporation of these iPSCs into chimeric mice made using the tetraploid (4N) complementation method. No ‘all iPSC’ mice have been made from iPSCs with silenced Dlk1-Dio3. (B) The addition of ascorbic acid (vitamin C) during the iPSC reprogramming process results in activating histone marks at the IG-ICR, including H3K4me3, and the expression of Gtl2. The addition of ascorbic acid prevents the recruitment of DNMT3A (D3a) by an unknown mechanism. These iPSCs can give rise to ‘all iPSC’ mice.