Features and mechanisms of canonical and noncanonical genomic imprinting

Abstract

Genomic imprinting is the monoallelic expression of a gene based on parent of origin and is a consequence of differential epigenetic marking between the male and female germlines. Canonically, genomic imprinting is mediated by allelic DNA methylation. However, recently it has been shown that maternal H3K27me3 can result in DNA methylation-independent imprinting, termed "noncanonical imprinting." In this review, we compare and contrast what is currently known about the underlying mechanisms, the role of endogenous retroviral elements, and the conservation of canonical and noncanonical genomic imprinting.

Keywords: DNA methylation; chromatin; endogenous retroviruses; epigenetics; genomic imprinting.

Figure 1.

Mechanisms of establishment and maintenance of maternal canonical and noncanonical imprinting. (Left) Canonical imprinting: DNA methylation is targeted to transcribed gene bodies, including canonical imprinted gDMRs, in oogenesis by tetramers of DNMT3A and DNMT3L. There is widespread usage of long terminal repeats (LTRs) as alternative upstream promoters in the oocyte. In the preimplantation and postimplantation embryo, a complex of ZFP57 (or ZNF445), TRIM28 (KAP1), and H3K9 methyltransferase SETDB1 localizes to gDMRs recruiting DNMT1 to maintain DNA methylation on the maternal allele. In the postimplantation embryo, the gDMR is present in the fetus and placenta, enabling imprinted gene expression of a single gene or cluster of genes. (Right) Noncanonical imprinting: H3K27me3 is established by PRC2, which is in part dependent on PRC1 ubiquitination of H2AK119, across untranscribed regions in oogenesis, including noncanonically imprinted LTRs. In the preimplantation embryo, maternal H3K27me3 is progressively lost genome-wide, and whether an unknown factor is required to mark the maternal allele of noncanonically imprinted LTRs remains unclear. In the postimplantation embryo, noncanonical imprints become placental specific, acquiring DNA methylation on the maternal allele, creating secondary DMRs (sDMRs), in placental and extraembryonic cell types. In the fetus (not shown), the noncanonically imprinted LTRs become biallelically methylated. The acquisition of DNA methylation in postimplantation development at these domains is dependent on EHMT2 activity, through either the deposition of H3K9me2 or post-translational modification of proteins integral for de novo DNMT activity.

Figure 2.

Role for LTRs in genomic imprinting. Endogenous retroviral LTRs have been demonstrated to be essential in both the setting of imprinted differentially methylated regions (DMRs) in the germline (A,B) and in driving imprinting gene expression at a number of loci (C,D). (A) In spermatogenesis, expression of LTR-derived small RNAs upstream of Rasgrf1 is targeted by the piRNA-PIWI silencing pathway, which in turn recruits de novo methyltransferase DNMT3B to methylate the locus. (B) In oogenesis, the widespread occurrence of LTR-derived transcripts traversing canonical promoters results in their methylation via the recruitment of DNMT3A to sites of elongating transcription. (C) Within the intron of imprinted gene H13, an LTR-derived gene (Mcts2) harbors a maternal gDMR, resulting in imprinted expression of Mcts2 from the paternal allele. The allelic transcriptional activity of Mcts2 disrupts the transcriptional elongation of H13, causing its premature polyadenylation. (D) The allelic expression of several noncanonically imprinted genes is a consequence of LTRs acting as alternative promoters, forming chimeric transcripts with nearby genes.

Figure 3.

Identification of putative noncanonical imprinted DMRs in the human placenta. Using the epigenetic patterning characteristic of noncanonical DMRs in mice, we investigated publicly available data to identify putative maternal “noncanonical” DMRs in humans. (A) Previously reported candidate maternal DMRs from placenta were evaluated for oocyte DNA methylation and H3K27me3, selecting those domains that were unmethylated and enriched for H3K27me3 in oocytes (N = 65). (B) Screenshot of putative noncanonically imprinted DMR upstream of the MSX1 gene. Enrichment for H3K27me3 in human oocytes is shown using running 500-bp windows, with a 100-bp step, quantitated as RPKM. DNA methylation in human oocytes, sperm, blastocyst, and first trimester placental trophoblast is shown using 1-kb running windows, with a 500-bp step. (C) The box plot shows the allelic difference in DNA methylation at informative putative noncanonical imprinted genes (N = 26). Informative DMRs were defined as those with at least three CpGs covered by at least two reads on each allele. (D) Overlapping genomic features were compared between putative noncanonical DMRs (N = 65) and CpGs on the Illumina 450K array (N = 485,512) using the χ² statistic. P-value significance was adjusted for multiple comparisons using Bonferroni correction. (**) P < 0.001, (***) P < 0.0001. A random subset of genomic CpGs is shown in gray for context (N = 485,512).