DNA Methylation: A Promising Biomarker and Potential Therapeutic Target

DNA methylation is a widely studied epigenetic modification with crucial roles in gene regulation, development, and disease, particularly in cancer. It has immense potential as a biomarker for early detection, monitoring, and treatment response. Noninvasive approaches, such as liquid biopsies, are increasingly being used to analyze DNA methylation, identify cancer signatures, and aid in diagnosis, treatment decisions, and personalized care. Given its pivotal role in disease, DNA methylation has emerged as a promising therapeutic target, with several DNA methyltransferase inhibitors already approved by the US Food and Drug Administration. However, more research is needed to fully unlock the clinical potential of DNA methylation.

Balancing Cost versus Coverage

Researchers face a difficult choice when selecting an assay for profiling DNA methylation (Table 1). Whole-genome bisulfite sequencing (WGBS), the gold standard for genome-wide DNA methylation analysis, offers full coverage of the genome at base-pair resolution but comes at a high cost due to the need for deep sequencing (>800 million reads per sample). Enzymatic Methyl-seq (EM-seq^™) uses a series of enzymatic reactions to generate single-base resolution DNA methylation profiles, and offers improved sensitivity at slightly lower sequencing depths.¹ However, regardless of method, whole-genome sequencing assays are impractical for many labs, due to their high sequencing costs, intensive computational processing, and need for bioinformatics expertise.²

Targeted approaches such as reduced representation bisulfite sequencing (RRBS), microarrays, and hybridization panels provide a more affordable and accessible alternative. Microarrays have been particularly useful in clinical research, where their high reproducibility and throughput have enabled innovative cancer biomarker research.^3,4 However, these methods only capture 3-15 percent of CpG sites and are typically biased towards CpG islands, limiting their utility for true genome-wide insights.^5,6

Another option is methylated DNA immunoprecipitation sequencing (MeDIP-seq), an affinity-based method that uses 5-methylcytosine antibodies to enrich methylated DNA before sequencing. This approach requires less sequencing than WGBS but comes with tradeoffs, including high variability due to chromatin fragmentation and poor antibody quality, as well as the need for large cell numbers. MeDIP-seq is also biased towards highly methylated and low-CG-content regions and often produces high background and false positives.^5,7

A Flexible and Cost-Effective Approach to Studying DNA Methylation

To address the limitations of existing DNA methylation profiling techniques, researchers are turning to EpiCypher’s CUTANA^™ meCUT&RUN. This novel platform captures 80 percent of methylated CpGs with only 20-50 million reads, offering a low-cost and highly sensitive strategy that bridges the gap between whole-genome and targeted enrichment approaches.

meCUT&RUN works by selectively enriching methylated DNA regions, avoiding harsh bisulfite-based conversion protocols that can degrade DNA. This approach maximizes yields while reducing cell input and sequencing requirements, making it especially useful for limited or precious samples. Compared to other enrichment-based approaches such as RRBS, meCUT&RUN detects >10-fold more DNA methylation at enhancers, gene bodies, transcription start sites, and repetitive elements, highlighting its potential for innovative studies of 5-methylcytosine in chromatin regulation. A key advantage of this assay is its modular design, allowing researchers to choose between direct sequencing of enriched fragments for efficient genome-wide mapping or adding an enzymatic conversion step (EM-seq^™) to achieve base-pair resolution.

Breaking Down Barriers in DNA Methylation Research

The trade-offs between sequencing cost, depth, and coverage have long hindered DNA methylation studies. Newer approaches like meCUT&RUN offer a more flexible and scalable solution, without sacrificing coverage or breaking the budget. As the field continues to evolve, this technology may help unlock the full potential of DNA methylation, from basic biology to clinical translation.

Learn more about CUTANA^™ meCUT&RUN here.