Methylation Analysis by Sequencing

Enlarge Image
Figure 1. Qualitative Information for each CpG Loci across the Entire Amplicon. For a given CpG dinucleotide the result of the sample will be mixed, non-methylated, or methylated.

DNA methylation is involved in the regulation of many cellular processes, including X chromosome inactivation, chromosome stability, chromatin structure, embryonic development, and transcription. Bisulfite sequencing is the gold standard for validating methylation experiments, as only sequencing provides direct detection of methylation events as well as information across the entire region. One of the key steps in this process, bisulfite DNA conversion, allows precise analysis of methylation in the target region by converting all non-methylated cytosines into uracils (methylated cytosines remain unchanged).

Two sequencing workflows can be use to determine the methylation status:

  • Bisulfite-Specific, PCR-Based Sequencing:
    This application is used to identify which CpG dinucleotides are important for the biological process under investigation. The researcher performs direct PCR sequencing of a pool of fragments to determine (qualitatively) which CpG dinucleotide has changed.
  • Bisulfite-Specific, Cloning-Based Sequencing
    In this application, a population of fragments is segregated by cloning, providing quantitative results. Analysis is aimed at calculating the percentage of methylation observed for specific CpG dinucleotides in a candidate region.

Step-by-Step Guide to Methylation Analysis

DNA Purification kit

DNA extraction is a critical first step in the experimental workflow of DNA sequencing-based methylation analysis. The overall quality, accuracy and length of the DNA sequence read can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction.

Recommended Products: DNA Isolation

Highlighted Products for Methylation Analysis:

3500 Series Genetic Analyzers

BigDye® Terminator Purification Kit

BigDye XTerminator Purification Kit

Select Language