Conserved and divergent patterns of DNA methylation in higher vertebrates.
Bottom Line: DNA methylation in the genome plays a fundamental role in the regulation of gene expression and is widespread in the genome of eukaryotic species.For example, in higher vertebrates, there is a "global" methylation pattern involving complete methylation of CpG sites genome-wide, except in promoter regions that are typically enriched for CpG dinucleotides, or so called "CpG islands." Here, we comprehensively examined and compared the distribution of CpG sites within ten model eukaryotic species and linked the observed patterns to the role of DNA methylation in controlling gene transcription.Comparative analysis with four other higher vertebrates revealed that the primary regulatory role of the DNA methylation system is highly conserved in higher vertebrates.
Affiliation: Department of Biostatistics & Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China School of Biosciences, The University of Birmingham, Birmingham B15 2TT United Kingdom.Show MeSH
Mentions: Next, we calculated the expected proportions of CpG sites based on the random union of C and G nucleotides and compared the expectations with the observed proportions. We found that CpG dinucleotides were consistently and significantly enriched (observed > expected) in promoter regions in the six higher vertebrate genomes (P = 0.013, Mann–Whitney U test) (fig. 1 and table 1), consistent with the higher level of promoter GC content in these species. Meanwhile, the genome-wide CpG content was significantly lower than that expected in the higher vertebrate genomes (P < 0.005, Mann–Whitney U test). However, the lower vertebrate, invertebrate, and plant species showed a different pattern, in which the observed proportion of CpGs consistently but not significantly exceeded the expected in both the promoter regions and the entire genome (P = 0.061, Mann–Whitney U test) (fig. 1).Fig. 1.—
Affiliation: Department of Biostatistics & Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China School of Biosciences, The University of Birmingham, Birmingham B15 2TT United Kingdom.