Limits...
Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale.

Barrera V, Peinado MA - Nucleic Acids Res. (2012)

Bottom Line: Methylation of a CpG island is a faithful marker of silencing of its associated gene.This strategy is frequently applied in both locus-specific and genome-wide studies, but often without a validation of the representativeness of the interrogated CpG site compared with the whole element.This analysis provides a global validation framework for strategies based on the use of the methylation-sensitive HpaII restriction enzyme.

View Article: PubMed Central - PubMed

Affiliation: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.

ABSTRACT
Methylation of a CpG island is a faithful marker of silencing of its associated gene. Different approaches report the methylation status of a CpG island based on the determination of one or a few CpG sites by assuming the homogeneity of methylation along the element. This strategy is frequently applied in both locus-specific and genome-wide studies, but often without a validation of the representativeness of the interrogated CpG site compared with the whole element. We have evaluated the predictive informativeness of the HpaII sites located in CpG islands using data from high-resolution methylome maps, which offer the possibility to assess the methylation homogeneity of each CpG island and to determine the reporter accuracy of single sites as surrogate markers. An excellent correlation was observed between the HpaII and CpG island methylation levels (r > 0.93). At the qualitative level, the predictive sensitivity of HpaII was >95% with >92% specificity for methylated CpG islands and >90% sensitivity with >95% specificity for unmethylated CpG islands. This analysis provides a global validation framework for strategies based on the use of the methylation-sensitive HpaII restriction enzyme.

Show MeSH

Related in: MedlinePlus

Homogeneity of CpG methylation in CpG islands. The mean of all informative CpG sites located inside each CpG island (CpG island methylation coefficient, ßC) is plotted against the SD for four of the cell lines analysed in this study. Vertical dash lines delimit graph areas containing unmethylated (ßC mean <0.25) and methylated (ßC mean >0.75) CpG islands. The numbers of points represented in each area of the graph and the distribution histograms of both axes are shown. Illustrative DNA methylation profiles of CpG islands represented in each area are displayed using lollipop diagrams, in which empty dots represent unmethylated CpG sites, whereas gray-filled dots represent partially methylated sites and black-filled dots fully methylated sites. Only CpG islands with high coverage are displayed.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC3526261&req=5

gks928-F1: Homogeneity of CpG methylation in CpG islands. The mean of all informative CpG sites located inside each CpG island (CpG island methylation coefficient, ßC) is plotted against the SD for four of the cell lines analysed in this study. Vertical dash lines delimit graph areas containing unmethylated (ßC mean <0.25) and methylated (ßC mean >0.75) CpG islands. The numbers of points represented in each area of the graph and the distribution histograms of both axes are shown. Illustrative DNA methylation profiles of CpG islands represented in each area are displayed using lollipop diagrams, in which empty dots represent unmethylated CpG sites, whereas gray-filled dots represent partially methylated sites and black-filled dots fully methylated sites. Only CpG islands with high coverage are displayed.

Mentions: CpG island methylation heterogeneity was represented as the SD of the methylation coefficient among the CpG dinucleotides contained in a CpG island (Figure 1). As a whole, the greatest variability was observed for a small population of CpG islands with intermediate methylation values indicating alternative methylation status of individual CpG positions rather than a homogeneous intermediate methylation level of the CpG sites. Next, we explored the distribution of variability according to the methylation levels. As expected, methylated CpG islands exhibited the lowest levels of internal variability (Supplementary Figure S3). Surprisingly, unmethylated CpG islands exhibited high homogeneity in H1 cells but a broader distribution in the rest of samples, indicating a more relaxed methylation profile. Intermediately methylated CpG islands exhibited higher levels of internal variability, but once again, H1 cells showed less variability (Supplementary Figure S3). Together, these results indicate a high homogeneity in the methylation profiles of methylated CpG islands. Highly unmethylated and, especially, intermediately methylated CpG islands exhibit different levels of heterogeneity, which might suggest that, for a small number of CpG islands, individual CpG sites may not be representative of the global profile.Figure 1.


Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale.

Barrera V, Peinado MA - Nucleic Acids Res. (2012)

Homogeneity of CpG methylation in CpG islands. The mean of all informative CpG sites located inside each CpG island (CpG island methylation coefficient, ßC) is plotted against the SD for four of the cell lines analysed in this study. Vertical dash lines delimit graph areas containing unmethylated (ßC mean <0.25) and methylated (ßC mean >0.75) CpG islands. The numbers of points represented in each area of the graph and the distribution histograms of both axes are shown. Illustrative DNA methylation profiles of CpG islands represented in each area are displayed using lollipop diagrams, in which empty dots represent unmethylated CpG sites, whereas gray-filled dots represent partially methylated sites and black-filled dots fully methylated sites. Only CpG islands with high coverage are displayed.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3526261&req=5

gks928-F1: Homogeneity of CpG methylation in CpG islands. The mean of all informative CpG sites located inside each CpG island (CpG island methylation coefficient, ßC) is plotted against the SD for four of the cell lines analysed in this study. Vertical dash lines delimit graph areas containing unmethylated (ßC mean <0.25) and methylated (ßC mean >0.75) CpG islands. The numbers of points represented in each area of the graph and the distribution histograms of both axes are shown. Illustrative DNA methylation profiles of CpG islands represented in each area are displayed using lollipop diagrams, in which empty dots represent unmethylated CpG sites, whereas gray-filled dots represent partially methylated sites and black-filled dots fully methylated sites. Only CpG islands with high coverage are displayed.
Mentions: CpG island methylation heterogeneity was represented as the SD of the methylation coefficient among the CpG dinucleotides contained in a CpG island (Figure 1). As a whole, the greatest variability was observed for a small population of CpG islands with intermediate methylation values indicating alternative methylation status of individual CpG positions rather than a homogeneous intermediate methylation level of the CpG sites. Next, we explored the distribution of variability according to the methylation levels. As expected, methylated CpG islands exhibited the lowest levels of internal variability (Supplementary Figure S3). Surprisingly, unmethylated CpG islands exhibited high homogeneity in H1 cells but a broader distribution in the rest of samples, indicating a more relaxed methylation profile. Intermediately methylated CpG islands exhibited higher levels of internal variability, but once again, H1 cells showed less variability (Supplementary Figure S3). Together, these results indicate a high homogeneity in the methylation profiles of methylated CpG islands. Highly unmethylated and, especially, intermediately methylated CpG islands exhibit different levels of heterogeneity, which might suggest that, for a small number of CpG islands, individual CpG sites may not be representative of the global profile.Figure 1.

Bottom Line: Methylation of a CpG island is a faithful marker of silencing of its associated gene.This strategy is frequently applied in both locus-specific and genome-wide studies, but often without a validation of the representativeness of the interrogated CpG site compared with the whole element.This analysis provides a global validation framework for strategies based on the use of the methylation-sensitive HpaII restriction enzyme.

View Article: PubMed Central - PubMed

Affiliation: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.

ABSTRACT
Methylation of a CpG island is a faithful marker of silencing of its associated gene. Different approaches report the methylation status of a CpG island based on the determination of one or a few CpG sites by assuming the homogeneity of methylation along the element. This strategy is frequently applied in both locus-specific and genome-wide studies, but often without a validation of the representativeness of the interrogated CpG site compared with the whole element. We have evaluated the predictive informativeness of the HpaII sites located in CpG islands using data from high-resolution methylome maps, which offer the possibility to assess the methylation homogeneity of each CpG island and to determine the reporter accuracy of single sites as surrogate markers. An excellent correlation was observed between the HpaII and CpG island methylation levels (r > 0.93). At the qualitative level, the predictive sensitivity of HpaII was >95% with >92% specificity for methylated CpG islands and >90% sensitivity with >95% specificity for unmethylated CpG islands. This analysis provides a global validation framework for strategies based on the use of the methylation-sensitive HpaII restriction enzyme.

Show MeSH
Related in: MedlinePlus