The specification of imprints in mammals

Abstract

At the heart of genomic imprinting in mammals are imprinting control regions (ICRs), which are the discrete genetic elements that confer imprinted monoallelic expression to several genes in imprinted gene clusters. A characteristic of the known ICRs is that they acquire different epigenetic states, exemplified by differences in DNA methylation, in the sperm and egg, and these imprint marks remain on the sperm- and oocyte-derived alleles into the next generation as a lifelong memory of parental origin. Although there has been much focus on gametic marking of ICRs as the point of imprint specification, recent mechanistic studies and genome-wide DNA methylation profiling do not support the existence of a specific imprinting machinery in germ cells. Rather, ICRs are part of more widespread methylation events that occur during gametogenesis. Instead, a decisive component in the specification of imprints is the choice of which sites of gamete-derived methylation to maintain in the zygote and preimplantation embryo at a time when much of the remainder of the genome is being demethylated. Among the factors involved in this selection, the zinc-finger protein Zfp57 can be regarded as an imprint-specific, sequence-specific DNA binding factor responsible for maintaining methylation at most ICRs. The recent insights into the balance of gametic and zygotic contributions to imprint specification should help understand mechanistic opportunities and constraints on the evolution of imprinting in mammals.

Figure 1

Examples of directly and indirectly regulated imprinted regions. Schematic representation of the (a) Peg3 imprinted gene on chromosome 7 and (b) the Igf2r imprinted cluster on chromosome 17. The expression status of the genes on the maternal and paternal alleles is illustrated; active promoters are represented by horizontal arrows. (a) The differentially methylated ICR established during germ cell development is located at the promoter of the Peg3 gene and directly regulates the monoallelic transcription of this gene. (b) The maternally methylated ICR indirectly regulates the monoallelic expression of the adjacent genes at this locus, partially mediated by the monoallelic methylation acquired at the nearby secondary DMR at the Igf2r promoter.

Figure 2

Factors involved in the maintenance of DNA methylation at imprinting control regions (ICRs) during early embryonic development. In the preimplantation embryo, the parental alleles of ICRs are bound by specific complexes to maintain their differential methylation status during the genome-wide epigenetic reprogramming. (a) The unmethylated ICR has the properties typical of a CpG island. It coincides with an expressed promoter and is, therefore, associated with the RNA polymerase II (pol II) complex. Unmethylated CpG sites are bound by the Cfp1 protein, which recruits the Set1 complex to trimethylate H3K4 which, in turn, reinforces the DNA hypomethylated state, as methylated H3K4 is antagonistic to binding of Dnmt3a/Dnmt3L. Protection against de novo DNA methylation of the unmethylated ICR allele could, therefore, be accomplished by generic factors acting at CpG islands, rather than imprint-specific factors. (b) The methylated ICR is bound by the Zfp57:Kap1 complex and Uhrf1 to direct the action of Dnmt1; the complex also interacts with the Setdb1 methyltransferase, which deposits the repressive histone modification H3K9me3. In addition, recognition of H3K9me2 by the PGC7/Stella protein may protect against demethylation in the zygote. Maintenance of DNA methylation at an ICR, therefore, involves the interplay between the imprint-specific factor Zfp57 and generic factors, such as Dnmt1.