Epigenetic methylation events are heritable modifications that regulate gene expression without altering the DNA sequence itself. They serve as regulatory mechanisms for a wide range of biological processes and genetic diseases, and irregular methylation patterns have been correlated with certain cancers. Methylation microarrays facilitate global investigation of regulatory events,
in vivo, without the limitations of gene-specific analyses or the hands-on time required by chromatography-based methods. Agilent's CpG and promoter microarrays enable genome-wide scanning of methylation events, while our custom arrays allow you to target specific regions for finer resolution evaluation. Through SurePrint inkjet technology, unique probe design algorithms, and validated protocols, Agilent's DNA Methylation Solution empowers you with the flexibility, sensitivity, and specificity to identify the methylation events that matter most to you.
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Additional Information
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| Applications Enabled by the Agilent DNA Methylation System |
DNA methylation technology enables researchers to successfully focus on critical areas previously hampered by the lack of useful tools. It allows researchers to:
- Uncover and validate gene regulation and regulatory networks by comprehensive determination of methylation profiles.
- Identify and characterize molecular events associated with DNA methylation.
- Elucidate modes of action and potential therapeutic activities of compounds and target genes by understanding the relation of DNA methylation to transcriptional control.
Featured Publication
Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG Island recovery assay.
Rausch T. et al., (2007) PNAS 104(13):5527-32
De novo methylation of CpG islands is a common phenomenon in human cancer, but the mechanisms of cancer-associated DNA methylation are not known. We have used tiling arrays in combination with the methylated CpG island recovery assay to investigate methylation of CpG islands genome-wide and at high resolution. We find that all four HOX gene clusters on chromosomes 2, 7, 12, and 17 are preferential targets for DNA methylation in cancer cell lines and in early-stage lung cancer. CpG islands associated with many other homeobox genes, such as SIX, LHX, PAX, DLX, and Engrailed, were highly methylated as well. Altogether, more than half (104 of 192) of all CpG island-associated homeobox genes in the lung cancer cell line A549 were methylated. Analysis of paralogous HOX genes showed that not all paralogues undergo cancer-associated methylation simultaneously. The HOXA cluster was analyzed in greater detail. Comparison with ENCODE-derived data shows that lack of methylation at CpG-rich sequences correlates with presence of the active chromatin mark, histone H3 lysine-4 methylation in the HOXA region. Methylation analysis of HOXA genes in primary squamous cell carcinomas of the lung led to the identification of the HOXA7- and HOXA9-associated CpG islands as frequent methylation targets in stage 1 tumors. Homeobox genes are potentially useful as DNA methylation markers for early diagnosis of the disease. The finding of widespread methylation of homeobox genes lends support to the hypothesis that a substantial fraction of genes methylated in human cancer are targets of the Polycomb complex.
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| Key Features and Benefits of the Agilent's DNA Methylation System |
Comprehensive genome-wide and focused coverage
Each Agilent DNA methylation microarray (CpG Island design) features a total of ~244,000 oligonucleotide probes in human and ~105,000 probes in mouse. Probes are spaced every ~100bp across the known CpG Islands Other available formats in addition to CpG designs include whole genome tiling sets and focused promoter sets.
Superior microarray performance and capability
Proprietary microarray technology using optimized 60-mer oligonucleotide probes and a convenient two-color labeling system delivers higher sensitivity, accuracy, and greater reproducibility than one-color systems. These unique features allow sensitive measurements of weak- and infrequent-binding events, as well as direct comparisons of samples on the same microarray.
Flexible and versatile user-defined microarray formats
The inherent flexibility of our microarrays allows users to define content - up to 244K customizable features per microarray - for any tiling density, genomic region, and organism of interest.
Quick turnaround
Agilent's SurePrint technology features a flexible, industrial-scale inkjet printing process that synthesizes oligonucleotide probes in situ onto 1" x 3" slides. The maskless process allows quick iteration of microarray designs in response to fast-paced content changes in the continuously evolving genomics environment. This allows researchers easy access to high-quality arrays loaded with relevant and rich content.
Access to probe sequence and annotation information
Agilent gives you complete access to probe sequences and annotation files to facilitate searching of public databases and extraction of biological information.
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| Describing the DNA Methylation Workflow |
The DNA methylation workflow includes a variety of assay preparation methods, followed by hybridizing of the sample to the microarray for subsequent analysis. Agilent CpG Island microarrays are compatible with both affinity-based and restriction enzyme-based methods of enriching methylated DNA.
Figure 1. Affinity-based isolation of methylated DNA. The methyl DNA immunoprecipitation (mDIP) method uses a monoclonal antibody against 5-methylcytosine to isolate methylated DNA from the genome. mDIP is one example of enriching methylated DNA. The resulting fraction of methylated DNA is purified, Cyanine 5 (Cy5)-labeled, and competitively hybridized against similarly Cyanine 3 (Cy3)-labeled "input" genomic DNA onto a single microarray. The microarray is washed, scanned, and analyzed with Agilent Feature Extraction software. Relative DNA methylation levels for each probe/CpG island are reflected in changes in Cyanine 5/Cyanine 3 ratios.
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| Agilent DNA Methylation Microarrays |
Agilent DNA Methylation Product Platform