Genome-wide DNA methylation profiling using Infinium® assay.

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• DNA methylation analysis is crucial for understanding gene regulation and disease.
• Traditional bisulfite sequencing methods face limitations in parallelization.
• Array-based and next-generation sequencing technologies offer solutions for high-throughput analysis.

Purpose of the Study:

• To adapt Infinium genotyping technology for analyzing bisulfite-converted DNA.
• To simultaneously query the methylation status of over 27,000 CpG sites in gene promoter regions.
• To establish a scalable and reproducible platform for genome-wide methylation analysis.

Main Methods:

• Adapted Infinium genotyping assay to detect methylation at CpG sites using specific query probes.
• Designed pairs of 'methylated' and 'unmethylated' probes for each CpG site.
• Utilized bisulfite conversion with a modified Zymo EZ DNA Methylation™ kit.

Main Results:

• Applied the platform to 14 human tissues, 4 Coriell cell lines, and 6 cancer cell lines.
• Observed largely unmethylated CpG sites within CpG islands (CGIs) across tissues (~80%).
• Found moderate to high methylation in non-CpG islands (~12% unmethylated), with higher prevalence of tissue-specific methylation outside CGIs.

Conclusions:

• Demonstrated a scalable, array-based platform for quantitative and reproducible methylation readout.
• The platform successfully analyzed methylation patterns across diverse human samples.
• This technology is poised to enable analysis of millions of CpG sites per sample in the future.