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An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines.

Li J, Gao F, Li N, Li S, Yin G, Tian G, Jia S, Wang K, Zhang X, Yang H, Nielsen AL, Bolund L - BMC Genomics (2009)

Bottom Line: By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines.However a cohort of individual genomic loci with significantly different DNA methylation status between two cell lines was identified.Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Human Genetics, University of Aarhus, The Bartholin building, Aarhus C, Denmark. jianl@humgen.au.dk

ABSTRACT

Background: DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. Development of sensitive methods for global detection of DNA methylation events is of particular importance.

Results: We here describe a technique, called modified methylation-specific digital karyotyping (MMSDK) based on methylation-specific digital karyotyping (MSDK) with a novel sequencing approach. Briefly, after a tandem digestion of genomic DNA with a methylation-sensitive mapping enzyme and a fragmenting enzyme, short sequence tags are obtained. These tags are amplified, followed by direct, massively parallel sequencing (Solexa 1G Genome Analyzer). This method allows high-throughput and low-cost genome-wide DNA methylation mapping. We applied this method to investigate global DNA methylation profiles for widely used breast cancer cell lines, MCF-7 and MDA-MB-231, which are representatives for luminal-like and mesenchymal-like cancer types, respectively. By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines. However a cohort of individual genomic loci with significantly different DNA methylation status between two cell lines was identified. Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells.

Conclusion: The MMSDK method will be a valuable tool to increase the current knowledge of genome wide DNA methylation profiles.

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Related in: MedlinePlus

Correlations between gene expression and DNA methylation. Figure A and B present the plots of the relationships between the gene expression and the methylation of promoters with CGI, promoters without CGI, exons, and introns for MCF-7 and MDA-MB-231 cells, respectively. On the X-axis scale, the degree of methylation for each spot is calculated as the number of tags for a given site divided by the average number of tags for all MluI sites. Similarly, the degree of gene expression on the Y-axis scale is calculated as the expression value for a given gene divided by the average expression value for all genes. Both the methylation and expression values are log-transformed.
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Figure 4: Correlations between gene expression and DNA methylation. Figure A and B present the plots of the relationships between the gene expression and the methylation of promoters with CGI, promoters without CGI, exons, and introns for MCF-7 and MDA-MB-231 cells, respectively. On the X-axis scale, the degree of methylation for each spot is calculated as the number of tags for a given site divided by the average number of tags for all MluI sites. Similarly, the degree of gene expression on the Y-axis scale is calculated as the expression value for a given gene divided by the average expression value for all genes. Both the methylation and expression values are log-transformed.

Mentions: Furthermore, we explored the relationships between the methylation state of promoters, first exons and introns and the corresponding gene expression pattern. Significant correlations between the methylation state of promoters with CGIs and the corresponding gene expression were identified in MCF-7 (R2 = 0.1461032, P-value: 4.845e-06) as well as in MDA-MB-231 (R2 = 0.1238432, P-value: 0.0001093), respectively. Additionally, we found a similar significant correlation between the methylation state of the promoters lacking CGIs and gene expression in MCF-7 (R2 = 0.14512, P-value: 0.0007437). Interestingly, we did not find such a correlation in MDA-MB-231 cells (R2 = 0.06501603, P-value: 0.1324). No significant correlation was found between gene expression and the methylation of the first exon and intron for either of the cell lines in our study (data not shown). The plots of gene expressions and methylation profiles of the different sequence categories (CGIs promoters, first exons and introns) are presented in Fig 4.


An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines.

Li J, Gao F, Li N, Li S, Yin G, Tian G, Jia S, Wang K, Zhang X, Yang H, Nielsen AL, Bolund L - BMC Genomics (2009)

Correlations between gene expression and DNA methylation. Figure A and B present the plots of the relationships between the gene expression and the methylation of promoters with CGI, promoters without CGI, exons, and introns for MCF-7 and MDA-MB-231 cells, respectively. On the X-axis scale, the degree of methylation for each spot is calculated as the number of tags for a given site divided by the average number of tags for all MluI sites. Similarly, the degree of gene expression on the Y-axis scale is calculated as the expression value for a given gene divided by the average expression value for all genes. Both the methylation and expression values are log-transformed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2696471&req=5

Figure 4: Correlations between gene expression and DNA methylation. Figure A and B present the plots of the relationships between the gene expression and the methylation of promoters with CGI, promoters without CGI, exons, and introns for MCF-7 and MDA-MB-231 cells, respectively. On the X-axis scale, the degree of methylation for each spot is calculated as the number of tags for a given site divided by the average number of tags for all MluI sites. Similarly, the degree of gene expression on the Y-axis scale is calculated as the expression value for a given gene divided by the average expression value for all genes. Both the methylation and expression values are log-transformed.
Mentions: Furthermore, we explored the relationships between the methylation state of promoters, first exons and introns and the corresponding gene expression pattern. Significant correlations between the methylation state of promoters with CGIs and the corresponding gene expression were identified in MCF-7 (R2 = 0.1461032, P-value: 4.845e-06) as well as in MDA-MB-231 (R2 = 0.1238432, P-value: 0.0001093), respectively. Additionally, we found a similar significant correlation between the methylation state of the promoters lacking CGIs and gene expression in MCF-7 (R2 = 0.14512, P-value: 0.0007437). Interestingly, we did not find such a correlation in MDA-MB-231 cells (R2 = 0.06501603, P-value: 0.1324). No significant correlation was found between gene expression and the methylation of the first exon and intron for either of the cell lines in our study (data not shown). The plots of gene expressions and methylation profiles of the different sequence categories (CGIs promoters, first exons and introns) are presented in Fig 4.

Bottom Line: By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines.However a cohort of individual genomic loci with significantly different DNA methylation status between two cell lines was identified.Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Human Genetics, University of Aarhus, The Bartholin building, Aarhus C, Denmark. jianl@humgen.au.dk

ABSTRACT

Background: DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. Development of sensitive methods for global detection of DNA methylation events is of particular importance.

Results: We here describe a technique, called modified methylation-specific digital karyotyping (MMSDK) based on methylation-specific digital karyotyping (MSDK) with a novel sequencing approach. Briefly, after a tandem digestion of genomic DNA with a methylation-sensitive mapping enzyme and a fragmenting enzyme, short sequence tags are obtained. These tags are amplified, followed by direct, massively parallel sequencing (Solexa 1G Genome Analyzer). This method allows high-throughput and low-cost genome-wide DNA methylation mapping. We applied this method to investigate global DNA methylation profiles for widely used breast cancer cell lines, MCF-7 and MDA-MB-231, which are representatives for luminal-like and mesenchymal-like cancer types, respectively. By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines. However a cohort of individual genomic loci with significantly different DNA methylation status between two cell lines was identified. Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells.

Conclusion: The MMSDK method will be a valuable tool to increase the current knowledge of genome wide DNA methylation profiles.

Show MeSH
Related in: MedlinePlus