The evolution of mammalian genomic imprinting was accompanied by the acquisition of novel CpG islands

Abstract

Parent-of-origin-dependent expression of imprinted genes is mostly associated with allele-specific DNA methylation of the CpG islands (CGIs) called germ line differentially methylated regions (gDMRs). Although the essential role of gDMRs for genomic imprinting has been well established, little is known about how they evolved. In several imprinted loci, the CGIs forming gDMRs may have emerged with the insertion of a retrotransposon or retrogene. To examine the generality of the hypothesis that the CGIs forming gDMRs were novel CGIs recently acquired during mammalian evolution, we reviewed the time of novel CGI emergence for all the maternal gDMR loci using the novel data analyzed in this study combined with the data from previous reports. The comparative sequence analyses using mouse, human, dog, cow, elephant, tammar, opossum, platypus, and chicken genomic sequences were carried out for Peg13, Meg1/Grb10, Plagl1/Zac1, Gnas, and Slc38a4 imprinted loci to obtain comprehensive results. The combined data showed that emergence of novel CGIs occurred universally in the maternal gDMR loci at various time points during mammalian evolution. Furthermore, the analysis of Meg1/Grb10 locus provided evidence that gradual base pair-wise sequence change was involved in the accumulation of CpG sequence, suggesting the mechanism of novel CGI emergence is more complex than the suggestion that CpG sequences originated solely by insertion of CpG-rich transposable elements. We propose that acquisition of novel CGIs was a key genomic change for the evolution of imprinting and that it usually occurred in the maternal gDMR loci.

FIG. 1.—

Comparison of CpG contents and conservation among the orthologous genomic regions around the Peg13 gDMR. The upper green graphs show CpG contents in the genomic sequences. The lower pink graphs show conserved regions in the genomic sequences between one species and the other species located just below (e.g., The pink graph seen in the mouse row is the comparison of mouse [base] and human and the graph in the human row is the comparison of human [base] and dog). The broken lines indicate where some conservation peaks in the upper row correspond in the next lower row. The arrowhead indicates the transcription start site with the direction, and the gray box shows exon. Gaps in the sequences are represented by the light gray shadows in graph regions. The CGI forming gDMR in mouse and the corresponding CGI in other species are yellow highlighted.

FIG. 2.—

Comparison of CpG contents and conservation among the orthologous genomic regions around the Meg1/Grb10 gDMR. For this locus, each CpG site in the genomic sequences is represented by green bar because of the relatively shorter 20 kb genomic regions to compare. Explanations for other components are the same as the figure 1.

FIG. 3.—

Comparison of CpG contents and conservation among the orthologous genomic regions around the Plagl1/Zac1 gDMR. Explanations for the each component are the same as the figure 1.

FIG. 4.—

Comparison of CpG contents and conservation among the orthologous genomic regions around the Gnas gDMR. Explanations for the each component are the same as the figure 1. For the names of transcription start sites, “NE” represents Nesp, “NA” for Nespas, “XL” for Gnasxl, “1A” for Gnas1A, and “1” for Gnas exon 1.

FIG. 5.—

Comparison of CpG contents and conservation among the orthologous genomic regions around the Slc38a4 gDMR. (A) Explanations for the each component are the same as the figure 1. (B) White circles indicate unmethylated CpGs.

FIG. 6.—

The timing of the novel CGI emergence in each maternal gDMR locus during mammalian evolution. The arrowheads represent the acquisition of novel CGI to the each locus. The genes associated with novel CGI emergence are shown above the arrowheads.

FIG. 7.—

Genomic sequence alignment of the small conserved region from Meg1/Grb10 gDMR corresponding region among three mammalian subgroups. The aligned genomic sequences are from the small conserved region in each species indicated by the right broken line in the figure 2. The vertical bars represent conserved nucleotides. Each CpG site is red colored and yellow highlighted.