Methylation mapping is inherently more complex than genome sequencing, because the methylome exhibits much more variability than the genome. While each of us has only one genome, methylomes vary with age and between tissues, are altered by environmental factors, and show aberrations in diseases. Thus, mapping a person’s methylome at different ages, in different tissue types, and in various disease states is expected to yield valuable information about the mechanisms that lead to aging and disease.

Methods for DNA Methylation Analysis

A variety of methods to tackle the complex question of DNA methylation have evolved over time including bisulfite conversion, digestion with methylation-sensitive restriction enzymes, and antibody- or 5-methylcytosine binding protein–based purification of methylated DNA.

The 5500xl Genetic Analyzer enables accurate, ultra–high-throughput sequencing, mapping, and counting of short DNA reads and, in combination with any of the above methylation profiling strategies, can be used for comprehensive, genome-wide mapping of methylation sites.

Three genome-wide methylation profiling strategies are available for the 5500xl Genetic Analyzer. The size of the target genome and the level of resolution you require will determine which solution will best suit your needs.

Enzymatic Genome Partitioning

Methylation-sensitive and methylation-dependent restriction enzymes are used to compartmentalize the genome into methylated and unmethylated fractions. This method allows the methylation status of both unique and repetitive DNA sequences to be analyzed, which is not possible using microarrays. Deep sequencing with the 5500xl Genetic Analyzer then allows comprehensive, genome-wide methylation profiles to be constructed.

Learn more at genome.cshlp.org.

 

Enriching for Methylated DNA

MethylMiner™ Methylated DNA Enrichment Kit employs the methylCpG binding domain (MBD) of the human MBD2 protein to enrich double-stranded DNA based on CpG methylation density, with increased sensitivity over antibody-based methods. The MethylMiner™ Methylated DNA Enrichment Kit combined with ultra-deep sequencing on the 5500xl Genetic Analyzer provides a cost-effective and seamless method for profiling genome-wide methylation patterns.

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Bisulfite Conversion

All unmethylated cytosines in the genome are converted to uracil when treated with bisulfite (methylated cytosines are unaltered by this treatment). In this way, bisulfite conversion preserves the methylation status of every CpG prior to sequencing using the 5500xl Genetic Analyzer. The accuracy and throughput of the 5500xl Genetic Analyzer gives you the power to interrogate every CpG in the genome for whole-methylome analysis. Bisulfite conversion can also be coupled with the MethylMiner™ Methylated DNA Enrichment Kit for individual CpG analysis of the methylated fraction of the genome.

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Step-by-Step Guide to DNA Methylation Analysis

The three traditional methylation profiling strategies can be successfully adapted onto SOLiD® System for a much more complete epigenomic mapping. Depending upon your specific scientific question, you might consider the following approaches:

  • Enzymatic Genomic Partition
    Separate the genome into methylated and unmethylated compartments with methylation sensitive or dependent restriction enzymes.
  • Bisulfite Conversion
    Chemical modification of the unmethylated cytosines in the genome.
  • Enrichment of Methylated DNA
    Purification of methylated genomic fragments.

For help choosing the best strategy for your research, please contact your field application specialist.

Learn More:

User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community.  Access is through the 5500 Series User Hub.  Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub.

The tools you need for each step in the Methylation data analysis workflow:

 
Data Analysis Step Applied Biosystems Software 3rd-Party Software***
1. Align reads to reference in color space
  • ICS
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
2. Generate quality metrics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
3. Generate sequencing and alignment statistics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
4. Identify Polymorphisms
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
5. Translate color space to base space  
6. Visualize in context of annotation
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
7. Convert to SRF for publishing    
*** Need XSQ --> csfasta/qual converter

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Targeted Methylation Analysis using Capillary Electrophoresis

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.