Tagmentation-based method to improve global DNA methylation assays

This technology is a tagmentation-based method for global DNA methylation and sequencing that uses a fusion protein without DNA-targeting antibodies, enabling efficient and convenient analysis of methylation patterns in normal and disease conditions, including early cancer detection.

Unmet Need: Method for improving the efficiency and convenience of MeDIP-seq

DNA methylation provides critical insight into the essential regulatory elements that influence genome expression and underlying disease pathology, particularly in cancer. Methylated DNA immunoprecipitation sequencing (MeDIP-seq) has been widely used to analyze DNA methylation in cells. However, key steps such as DNA sonication, primer ligation, and T/A tailing introduce inefficiencies in library preparation, cause DNA loss, and add technical complexity, creating bottlenecks that limit the scalability and sensitivity of the process.

The Technology: An efficient, simple, sensitive method to study DNA methylation

This technology uses DNA tagmentation to tagment genomic DNA into smaller fragments, improving upon traditional sonication-based methods that cause DNA loss and require a sonicator. The fusion protein adds sequence tags during tagmentation, eliminating the need for inefficient steps such as primer ligation and T/A tailing found in conventional MeDIP-seq protocols. The method does not require an antibody or other DNA-based targeting molecules and enables streamlined library preparation through a single PCR step. It improves efficiency by generating high-quality MeDIP-seq libraries from as little as 100 ng of input DNA, compared to the 1000 ng typically required, in less than two days.

This technology has been validated with liver tumor and normal tissue samples.

Applications:

• Research tool for studying DNA methylation in developmental biology
• Assay for evaluating the impact of therapeutics on DNA methylation and transcription
• Research tool for identifying disease-associated DNA methylation biomarkers
• Method for improving ongoing workflows for studies focused on DNA methylation
• Analysis tool for other DNA modifications, such as hydroxymethylation

Advantages:

• Reduces the cost of DNA methylation analysis
• Requires less input genomic DNA
• Streamlines and simplifies library preparation procedures
• Increases efficiency in generating high-quality MeDIP-seq libraries from minimal starting material

Lead Inventor:

Zhiguo Zhang, Ph.D.

Patent Information:

Patent Pending (WO/2024/137934)

Related Publications:

• Hua X, Zhou H, Wu HC, Furnari J, Kotidis CP, Rabadan R, Genkinger JM, Bruce JN, Canoll P, Santella RM, Zhang Z. Tumor detection by analysis of both symmetric-and hemi-methylation of plasma cell-free DNA. Nature Communications. 2024 Jul 20;15(1):6113.

Tech Ventures Reference:

• IR CU23112

• Licensing Contact: Joan Martinez