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. 2012:2012:598987.
doi: 10.1155/2012/598987. Epub 2012 Mar 4.

Features of methylation and gene expression in the promoter-associated CpG islands using human methylome data

Xin Du  1 , Leng Han, An-Yuan Guo, Zhongming Zhao
Affiliations

Features of methylation and gene expression in the promoter-associated CpG islands using human methylome data

Xin Du et al. Comp Funct Genomics. 2012.

Abstract

CpG islands are typically located in the 5' end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones' algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.'s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level.

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Figures

Figure 1
Figure 1
Distribution of features of CpG islands identified by different algorithms. (a) Length. (b) GC content (%). (c) CpG O/E.
Figure 2
Figure 2
Methylation level of the CpG islands or clusters in the whole genomic regions or associated with the promoter regions. (a) Methylation data was based on human methylome from H1 cell line. (b) Methylation data was based on human methylome from IMR90 cell line.
Figure 3
Figure 3
Relationship between methylation level of promoter-associated CpG islands and the number of expressed tissues. (a) H1 cell line. (b) IMR90 cell line.
Figure 4
Figure 4
Relationship between methylation level of promoter-associated CpG islands and expression strength. (a) Methylation data was based on human methylome from H1 cell line. (b) Methylation data was based on human methylome from IMR90 cell line.
Figure 5
Figure 5
Correlation between the number of expressed tissues and expression strength.
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