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

Du X, Han L, Guo AY, Zhao Z - Comp. Funct. Genomics (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Central China Normal University, Wuhan 430079, China.

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.

No MeSH data available.


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.
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fig2: 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.

Mentions: At the genome level, our results showed that TJ-CGIs had a higher average methylation level (mC/C ratio = 0.403) than CGCs-15 (mC/C ratio = 0.266), CGCs-20 (mC/C ratio = 0.205), and UCSC-CGIs (mC/C ratio = 0.297) in the H1 cell line. Here, mC/C denotes the ratio of methylated over unmethylated nucleotides C at the CpG sites. A similar pattern could be observed in the IMR90 cell line, as shown in Figure 2.


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

Du X, Han L, Guo AY, Zhao Z - Comp. Funct. Genomics (2012)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3303704&req=5

fig2: 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.
Mentions: At the genome level, our results showed that TJ-CGIs had a higher average methylation level (mC/C ratio = 0.403) than CGCs-15 (mC/C ratio = 0.266), CGCs-20 (mC/C ratio = 0.205), and UCSC-CGIs (mC/C ratio = 0.297) in the H1 cell line. Here, mC/C denotes the ratio of methylated over unmethylated nucleotides C at the CpG sites. A similar pattern could be observed in the IMR90 cell line, as shown in Figure 2.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Central China Normal University, Wuhan 430079, China.

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.

No MeSH data available.