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

The methylation profile, gene expression profile and DNA copy number variation of loci on Chromosome 1. Chromosome 1 was selected as a representative of the chromosome set. Similar information for the other chromosomes is presented in Additional file 8. A diagram of chromosome 1 is located in the middle. The common fragile sites are symmetrically indicated with thin solid black lines (the rare fragile sites marked with blue). The corresponding data for MCF-7 and MDA-MB-231 are presented to the left and the right sides of the chromosome, respectively. The DNA copy number variation, gene expression and methylation status are shown consecutively. For DNA copy number variation, green, red and mild yellow mean amplification, deletion and no change, respectively. The length of the red bars that are vertical to the chromosome indicates the expression level for the corresponding genes. The length of bars located the most outside of the figure represents the methylation extent for the corresponding MluI sites on the chromosome. Blue indicates tags mapped with high confidence (mapping quality more than 20) and yellow represents all mapped tags.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The methylation profile, gene expression profile and DNA copy number variation of loci on Chromosome 1. Chromosome 1 was selected as a representative of the chromosome set. Similar information for the other chromosomes is presented in Additional file 8. A diagram of chromosome 1 is located in the middle. The common fragile sites are symmetrically indicated with thin solid black lines (the rare fragile sites marked with blue). The corresponding data for MCF-7 and MDA-MB-231 are presented to the left and the right sides of the chromosome, respectively. The DNA copy number variation, gene expression and methylation status are shown consecutively. For DNA copy number variation, green, red and mild yellow mean amplification, deletion and no change, respectively. The length of the red bars that are vertical to the chromosome indicates the expression level for the corresponding genes. The length of bars located the most outside of the figure represents the methylation extent for the corresponding MluI sites on the chromosome. Blue indicates tags mapped with high confidence (mapping quality more than 20) and yellow represents all mapped tags.

Mentions: The profiles of genomic CNV for the MCF-7 and MDA-MB-231 cell lines are shown in Fig 3 and in Additional file 8. The dye-swap method robustly confirmed aberrations. MCF-7 and MDA-MB-231 cells both have overt genomic instability. The main genomic aberrations in MCF-7 are deletions on 1p, 6q, 8p, 11q, 13q, 16q, 18q and chrX, and amplifications on 1q, 8q, 9p, 17q and 20q. In contrast, amplifications on 6p, 8q, 11q, 12q and 19p, and deletions on 2q, 3q, 6q, 7q, 8p, 12p, 13p 15p, 18q and chrX were presented in MDA-MB-231. The deletion and amplification regions accounted for 33.78% and 8.34% in the whole genome in MDA-MB-231, respectively. For MCF-7 cells, the percentages of the deletion and amplification regions in the genome were 19.58% and 14.58%, respectively. The breakpoints in the genome for two cell lines were revealed by means of identification of the color-change points (points flanked by two adjacent DNA fragments indicating different CNV) in Fig 3. Fragile sites (cytogenetically defined) are also indicated on the chromosomes (Fig 3). In our study, 20% and 22% of the genome breakpoints were located in the neighborhood of common fragile sites in MCF-7 and MDA-MB-231, respectively.


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)

The methylation profile, gene expression profile and DNA copy number variation of loci on Chromosome 1. Chromosome 1 was selected as a representative of the chromosome set. Similar information for the other chromosomes is presented in Additional file 8. A diagram of chromosome 1 is located in the middle. The common fragile sites are symmetrically indicated with thin solid black lines (the rare fragile sites marked with blue). The corresponding data for MCF-7 and MDA-MB-231 are presented to the left and the right sides of the chromosome, respectively. The DNA copy number variation, gene expression and methylation status are shown consecutively. For DNA copy number variation, green, red and mild yellow mean amplification, deletion and no change, respectively. The length of the red bars that are vertical to the chromosome indicates the expression level for the corresponding genes. The length of bars located the most outside of the figure represents the methylation extent for the corresponding MluI sites on the chromosome. Blue indicates tags mapped with high confidence (mapping quality more than 20) and yellow represents all mapped tags.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The methylation profile, gene expression profile and DNA copy number variation of loci on Chromosome 1. Chromosome 1 was selected as a representative of the chromosome set. Similar information for the other chromosomes is presented in Additional file 8. A diagram of chromosome 1 is located in the middle. The common fragile sites are symmetrically indicated with thin solid black lines (the rare fragile sites marked with blue). The corresponding data for MCF-7 and MDA-MB-231 are presented to the left and the right sides of the chromosome, respectively. The DNA copy number variation, gene expression and methylation status are shown consecutively. For DNA copy number variation, green, red and mild yellow mean amplification, deletion and no change, respectively. The length of the red bars that are vertical to the chromosome indicates the expression level for the corresponding genes. The length of bars located the most outside of the figure represents the methylation extent for the corresponding MluI sites on the chromosome. Blue indicates tags mapped with high confidence (mapping quality more than 20) and yellow represents all mapped tags.
Mentions: The profiles of genomic CNV for the MCF-7 and MDA-MB-231 cell lines are shown in Fig 3 and in Additional file 8. The dye-swap method robustly confirmed aberrations. MCF-7 and MDA-MB-231 cells both have overt genomic instability. The main genomic aberrations in MCF-7 are deletions on 1p, 6q, 8p, 11q, 13q, 16q, 18q and chrX, and amplifications on 1q, 8q, 9p, 17q and 20q. In contrast, amplifications on 6p, 8q, 11q, 12q and 19p, and deletions on 2q, 3q, 6q, 7q, 8p, 12p, 13p 15p, 18q and chrX were presented in MDA-MB-231. The deletion and amplification regions accounted for 33.78% and 8.34% in the whole genome in MDA-MB-231, respectively. For MCF-7 cells, the percentages of the deletion and amplification regions in the genome were 19.58% and 14.58%, respectively. The breakpoints in the genome for two cell lines were revealed by means of identification of the color-change points (points flanked by two adjacent DNA fragments indicating different CNV) in Fig 3. Fragile sites (cytogenetically defined) are also indicated on the chromosomes (Fig 3). In our study, 20% and 22% of the genome breakpoints were located in the neighborhood of common fragile sites in MCF-7 and MDA-MB-231, respectively.

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