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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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Distribution of CpGs with respect to the TSS. The horizontal axis represents the distance from the TSS, whereas the vertical axis represents the CpG fraction.
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evu238-F3: Distribution of CpGs with respect to the TSS. The horizontal axis represents the distance from the TSS, whereas the vertical axis represents the CpG fraction.

Mentions: A striking difference was apparent between HCP and LCP, both for the GC content fraction and the occurrence of CpG sites in relation to the transcription start site (TSS) (fig. 3 and supplementary fig. S3, Supplementary Material online). For the HCP in the higher vertebrates, both the proportion of CpG sites and the GC content fraction peaked consistently in the vicinity of the TSS and declined with increasing distance from the TSS. On the other hand, the proportions of CpG sites in LCP were approximately zero, despite a mild peak for the GC content fraction occurring immediately downstream of the TSS. These results indicate a high level of conservation of CpG site distribution among higher vertebrate species, suggestive of an important biological function. For zebrafish, the patterns of GC content fraction and CpG site density at all promoters were similar to those of the HCP of the higher vertebrates. The pattern was noticeably different for the invertebrate species, with the GC content fraction and CpG density exhibiting a sharp peak immediately downstream of the TSS, but either a flat curve (Arabidopsis and C. elegans), or surprisingly a valley (D. melanogaster), upstream of the TSS (fig. 3).Fig. 3.—


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)

Distribution of CpGs with respect to the TSS. The horizontal axis represents the distance from the TSS, whereas the vertical axis represents the CpG fraction.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu238-F3: Distribution of CpGs with respect to the TSS. The horizontal axis represents the distance from the TSS, whereas the vertical axis represents the CpG fraction.
Mentions: A striking difference was apparent between HCP and LCP, both for the GC content fraction and the occurrence of CpG sites in relation to the transcription start site (TSS) (fig. 3 and supplementary fig. S3, Supplementary Material online). For the HCP in the higher vertebrates, both the proportion of CpG sites and the GC content fraction peaked consistently in the vicinity of the TSS and declined with increasing distance from the TSS. On the other hand, the proportions of CpG sites in LCP were approximately zero, despite a mild peak for the GC content fraction occurring immediately downstream of the TSS. These results indicate a high level of conservation of CpG site distribution among higher vertebrate species, suggestive of an important biological function. For zebrafish, the patterns of GC content fraction and CpG site density at all promoters were similar to those of the HCP of the higher vertebrates. The pattern was noticeably different for the invertebrate species, with the GC content fraction and CpG density exhibiting a sharp peak immediately downstream of the TSS, but either a flat curve (Arabidopsis and C. elegans), or surprisingly a valley (D. melanogaster), upstream of the TSS (fig. 3).Fig. 3.—

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