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Updated: Mar 15, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

DREAM: A Simple Method for DNA Methylation Profiling by High-throughput Sequencing.

Jaroslav Jelinek¹, Jozef Madzo²

¹Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 North Broad Street, Rm 339 F, PAHB, Philadelphia, PA, 19140, USA. jjelinek@temple.edu.

Methods in Molecular Biology (Clifton, N.J.)

|September 2, 2016

Summary

This summary is machine-generated.

Digital Restriction Enzyme analysis of Methylation (DREAM) offers a simple, cost-effective method for genome-wide DNA methylation analysis. This robust technique accurately identifies methylation levels at thousands of CpG sites without bisulfite conversion.

Keywords:

CpG sites DNA methylation DREAM High-throughput sequencing Restriction endonuclease SmaI XmaI

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Published on: July 12, 2012

Area of Science:

Epigenetics
Genomics
Molecular Biology

Background:

DNA methylation is a crucial epigenetic modification regulating gene expression.
Accurate and scalable methods for genome-wide DNA methylation analysis are essential for biological research.
Existing methods may involve complex procedures or lack comprehensive coverage.

Purpose of the Study:

To introduce and validate the Digital Restriction Enzyme analysis of Methylation (DREAM) method.
To demonstrate DREAM's capability for high-throughput, genome-wide CpG site methylation analysis.
To highlight the simplicity, robustness, and cost-effectiveness of the DREAM technique.

Main Methods:

Utilizes sequential digestion of genomic DNA with SmaI and XmaI restriction enzymes, which have differential sensitivity to CpG methylation.
Generates unique sequence signatures at methylated and unmethylated CpG sites.
Involves ligation of restriction fragments to Illumina sequencing adaptors, followed by high-throughput sequencing and data analysis.

Main Results:

DREAM enables analysis of tens of thousands of CpG sites per genome.
The method achieves high accuracy with a background noise of less than 1%, suitable for detecting low methylation levels.
Sequencing 25 million reads per human DNA library yields over 50,000 unique CpG sites with high coverage.

Conclusions:

DREAM is a simple, robust, highly reproducible, and cost-effective method for DNA methylation analysis.
The method's ability to map reads directly to the reference genome without bisulfite conversion simplifies analysis across species.
DREAM provides accurate determination of DNA methylation levels at a large scale.