Imprinted genes show unique patterns of sequence conservation

Abstract

Background: Genomic imprinting is an evolutionary conserved mechanism of epigenetic gene regulation in placental mammals that results in silencing of one of the parental alleles. In order to decipher interactions between allele-specific DNA methylation of imprinted genes and evolutionary conservation, we performed a genome-wide comparative investigation of genomic sequences and highly conserved elements of imprinted genes in human and mouse.

Results: Evolutionarily conserved elements in imprinted regions differ from those associated with autosomal genes in various ways. Whereas for maternally expressed genes strong divergence of protein-encoding sequences is most prominent, paternally expressed genes exhibit substantial conservation of coding and noncoding sequences. Conserved elements in imprinted regions are marked by enrichment of CpG dinucleotides and low (TpG+CpA)/(2·CpG) ratios indicate reduced CpG deamination. Interestingly, paternally and maternally expressed genes can be distinguished by differences in G+C and CpG contents that might be associated with unusual epigenetic features. Especially noncoding conserved elements of paternally expressed genes are exceptionally G+C and CpG rich. In addition, we confirmed a frequent occurrence of intronic CpG islands and observed a decelerated degeneration of ancient LINE-1 repeats. We also found a moderate enrichment of YY1 and CTCF binding sites in imprinted regions and identified several short sequence motifs in highly conserved elements that might act as additional regulatory elements.

Conclusions: We discovered several novel conserved DNA features that might be related to allele-specific DNA methylation. Our results hint at reduced CpG deamination rates in imprinted regions, which affects mostly noncoding conserved elements of paternally expressed genes. Pronounced differences between maternally and paternally expressed genes imply specific modes of evolution as a result of differences in epigenetic features and a special response to selective pressure. In addition, our data support the potential role of intronic CpG islands as epigenetic key regulatory elements and suggest that evolutionary conserved LINE-1 elements fulfill regulatory functions in imprinted regions.

Figure 1

Distribution of repetitive elements in phastCons sequences. PCSs that contain at least 1 bp of a repetitive element were summed up in categories according to the first overlapping repeat. The most prominent enrichment is that of PCSs overlapping with LINE-1 repeats (L1, red) in the intergenic regions of imprinted genes relative to the autosomal genome. MER: medium reiteration frequency repeats; MIR: mammalian-wide interspersed repeats; LTR: long terminal repeats; low compl./simple: low complexity regions and simple repeats; L2: LINE-2 repeats.

Figure 2

Conservation score and length of exonic phastCons sequences. Using the human genome as a reference, conservation scores (A) and lengths (B) of PCSs that overlap with coding exons were determined. Compared to autosomal data (black bars), the PCSs of maternally expressed genes (red bars) are shorter and have lower conservation scores whereas PCSs of paternally expressed ones (blue bars) are similar to PCSs of autosomal genes.

Figure 3

Distribution of phastCons sequences at exon boundaries. Shown are the frequencies of PCSs in introns and exons as a function of their distance from the closest exon boundary in a semi-logarithmic representation. The y-axis shows the normalized PCS density calculated as the number of PCSs per 100 bp bin divided by the number of introns in the respective group (imprinted, autosomal). On the x-axis, the position of the exon boundary is marked as zero. PCSs with negative distances are either partially or completely located in exons (thick black bar). Most of these are concentrated within a distance of 2000 bp from the exon boundary. Likewise, the number of PCSs that are completely located in introns (thin black line; positive distances) decreases rapidly within increasing distance. Beyond a distance of 10 kb (not shown here), only a few PCSs are found. Imprinted genes (red stars) possess more PCSs within about ± 2000 bp of the exon boundary than autosomal genes (blue diamonds).