Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution

Abstract

Background: DNA methylation by the Dnmt family occurs in vertebrates and invertebrates, including ascidians, and is thought to play important roles in gene regulation and genome stability, especially in vertebrates. However, the global methylation patterns of vertebrates and invertebrates are distinctive. Whereas almost all CpG sites are methylated in vertebrates, with the exception of those in CpG islands, the ascidian genome contains approximately equal amounts of methylated and unmethylated regions. Curiously, methylation status can be reliably estimated from the local frequency of CpG dinucleotides in the ascidian genome. Methylated and unmethylated regions tend to have few and many CpG sites, respectively, consistent with our knowledge of the methylation status of CpG islands and other regions in mammals. However, DNA methylation patterns and levels in vertebrates and invertebrates have not been analyzed in the same way.

Results: Using a new computational methodology based on the decomposition of the bimodal distributions of methylated and unmethylated regions, we estimated the extent of the global methylation patterns in a wide range of animals. We then examined the epigenetic changes in silico along the phylogenetic tree. We observed a gradual transition from fractional to global patterns of methylation in deuterostomes, rather than a clear demarcation between vertebrates and invertebrates. When we applied this methodology to six piscine genomes, some of which showed features similar to those of invertebrates.

Conclusions: The mammalian global DNA methylation pattern was probably not acquired at an early stage of vertebrate evolution, but gradually expanded from that of a more ancient organism.

Figure 1

CpG-score changes along the genomic coordinates. Genomic regions of 2-Mb were arbitrarily selected from the (A) ascidian (sea squirt) chr02q 3,857,310-5,857,309, (B) zebrafish chr1 21,198,157-23,198,156, (C) frog scaffold_1 4,936,533-6,936,532, and (D) human chr18 42,391,708-44,391,707. The horizontal lines crossing the graph are the barycenters of the two normal distributions (see Figure 3). Unmethylated regions are indicated by shaded tracts above the graph. Typical mosaic and global patterns are seen in the ascidian and human genomes, respectively.

Figure 2

Schematic representation of the phylogenetic relationships among deuterostomes. In total, 26 deuterostome genomes were examined in the present study. Out of them, 18 species are schematically represented here [26,31]. Human is placed at the bottom. The upper species are placed, the further they are diverged from human. As for teleosts, they are ordered in accordance with the two ratio (Tables 1 and 2).

Figure 3

Histograms showing the CpG-score frequencies in 2-kb genomic fragments. Each histogram covers the whole genome of the (A) sea urchin, (B) lancelet (amphioxus), (C) ascidian, (D) zebrafish, (E) frog, (F) anole (a kind of lizard), (G) chicken, (H) platypus, (I) opossum, (J) dog, (K) mouse, or (L) human. Apparent bimodal distributions are seen in the invertebrate deuterostomes. All distributions were compulsorily separated into two normal distributions. The two decomposed Gaussian curves and a merged curve are also drawn on each histogram.

Figure 4

Histograms showing the CpG-score frequencies in 2-kb genomic fragments obtained from experimental data for the DNA methylation levels of the human (A and B) and ascidian (C and D) genomes. The distributions of hypermethylated (A and C) and hypomethylated (B and D) fragments (gray) are shown with the whole data (white). In the human data, the right peaks are increased because of the preferential selection of CpG islands in the Human Epigenome Project.

Figure 5

Lengths of methylated (A) and unmethylated (B) regions and the two ratios (C) that can be used as indices of the global methylation pattern. The lengths are shown on a log scale. The consistent tendencies in the lengths and scatter of the lengths can be seen to parallel the course of deuterostome evolution. The ratios of the lengths are indicated by squares and the ratios of the standard deviations of the lengths are by triangles. Laurasiatherians include cow, horse, dog, and cat. Exceptionally high ratios were observed in the cat genome.