Limits...
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.

Show MeSH

Related in: MedlinePlus

Distribution of MluI sites in repeat sequences and summary of sequence tag information. The distribution of MluI recognition sites in different classes of repeat sequences is presented in the top pie chart, and the bottom table summarizes the counting result of the tags collected for different classes of repeat sequences of the MCF-7 and MDA-MB-231 cell lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2696471&req=5

Figure 2: Distribution of MluI sites in repeat sequences and summary of sequence tag information. The distribution of MluI recognition sites in different classes of repeat sequences is presented in the top pie chart, and the bottom table summarizes the counting result of the tags collected for different classes of repeat sequences of the MCF-7 and MDA-MB-231 cell lines.

Mentions: Our MMSDK method also allows investigation of the DNA methylation status for repeat sequences. As described above, a T-test was performed for the comparison of the distribution of unmethylated sites in different repeat sequence categories in the two cancer cell lines. The summary of the collected tags information in repeat sequences for the cell lines is presented in Fig 2. Notably, a significant difference between two cell lines in the methylation level of long interspersed nuclear elements (LINE/L1) was observed (Fig 2).


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)

Distribution of MluI sites in repeat sequences and summary of sequence tag information. The distribution of MluI recognition sites in different classes of repeat sequences is presented in the top pie chart, and the bottom table summarizes the counting result of the tags collected for different classes of repeat sequences of the MCF-7 and MDA-MB-231 cell lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Distribution of MluI sites in repeat sequences and summary of sequence tag information. The distribution of MluI recognition sites in different classes of repeat sequences is presented in the top pie chart, and the bottom table summarizes the counting result of the tags collected for different classes of repeat sequences of the MCF-7 and MDA-MB-231 cell lines.
Mentions: Our MMSDK method also allows investigation of the DNA methylation status for repeat sequences. As described above, a T-test was performed for the comparison of the distribution of unmethylated sites in different repeat sequence categories in the two cancer cell lines. The summary of the collected tags information in repeat sequences for the cell lines is presented in Fig 2. Notably, a significant difference between two cell lines in the methylation level of long interspersed nuclear elements (LINE/L1) was observed (Fig 2).

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