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Conserved and divergent patterns of DNA methylation in higher vertebrates.

Jiang N, Wang L, Chen J, Wang L, Leach L, Luo Z - Genome Biol Evol (2014)

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.

View Article: PubMed Central - PubMed

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.

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Phylogenies of six higher vertebrate species reconstructed either from DNA and protein sequence data (A) or from conservation level of HCP or LCP status in gene promoters (B).
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evu238-F4: Phylogenies of six higher vertebrate species reconstructed either from DNA and protein sequence data (A) or from conservation level of HCP or LCP status in gene promoters (B).

Mentions: Divergence in the conservation level of promoter status reflected evolutionary divergence between the species. We therefore reconstructed the phylogeny among these species using the conservation level of promoter status and compared it with the phylogeny constructed from DNA/protein sequence data of each species (Hedges 2002). Figure 4 shows that the two phylogenetic trees are remarkably similar. The main discrepancy between the two trees occurs at the point where the dog links into the phylogenies. In our tree based on promoter status conservation level, the dog species diverged prior to all of the other mammals (fig. 4B), whereas in the tree based on DNA and protein sequence data (fig. 4A), the dog and cow diverged from the other three mammals around 92 Ma, before the two separated around 83 Ma (Hedges 2002). This discrepancy can most likely be attributed to the poor quality of sequence annotation for the dog genome. In fact, promoters have been identified for only 11% (1,481/13,410) of all dog genes.Fig. 4.—


Conserved and divergent patterns of DNA methylation in higher vertebrates.

Jiang N, Wang L, Chen J, Wang L, Leach L, Luo Z - Genome Biol Evol (2014)

Phylogenies of six higher vertebrate species reconstructed either from DNA and protein sequence data (A) or from conservation level of HCP or LCP status in gene promoters (B).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255770&req=5

evu238-F4: Phylogenies of six higher vertebrate species reconstructed either from DNA and protein sequence data (A) or from conservation level of HCP or LCP status in gene promoters (B).
Mentions: Divergence in the conservation level of promoter status reflected evolutionary divergence between the species. We therefore reconstructed the phylogeny among these species using the conservation level of promoter status and compared it with the phylogeny constructed from DNA/protein sequence data of each species (Hedges 2002). Figure 4 shows that the two phylogenetic trees are remarkably similar. The main discrepancy between the two trees occurs at the point where the dog links into the phylogenies. In our tree based on promoter status conservation level, the dog species diverged prior to all of the other mammals (fig. 4B), whereas in the tree based on DNA and protein sequence data (fig. 4A), the dog and cow diverged from the other three mammals around 92 Ma, before the two separated around 83 Ma (Hedges 2002). This discrepancy can most likely be attributed to the poor quality of sequence annotation for the dog genome. In fact, promoters have been identified for only 11% (1,481/13,410) of all dog genes.Fig. 4.—

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.

View Article: PubMed Central - PubMed

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