CRISPR technologies for detecting DNA and RNA methylation: Mechanisms, platforms, and translational opportunities
Abstract DNA and RNA methylation are key epigenetic and epitranscriptomic modifications involved in gene regulation, genome stability, RNA metabolism, and disease progression. Aberrant methylation patterns in cell‐free DNA and RNA have emerged as valuable biomarkers for cancer detection, disease monitoring, and therapeutic stratification. However, conventional methods such as bisulfite sequencing, methylation‐specific PCR, MeRIP‐seq, SCARLET, and LC–MS/MS often require harsh processing, high sample input, complex instrumentation, or lack site‐specific resolution, limiting their clinical and point‐of‐care applications. CRISPR‐based diagnostics provide a promising alternative by combining programmable nucleic acid recognition with collateral cleavage‐mediated signal amplification. This review summarizes recent CRISPR strategies for detecting DNA and RNA methylation, including chemical conversion‐assisted assays, restriction enzyme‐mediated detection, direct amplification‐free sensing based on methylation‐modulated Cas activity, detection of oxidized cytosine derivatives, reverse transcription‐mediated Cas12 detection of m6A, and structure‐sensitive Cas13 sensing. We highlight how methylation‐dependent sequence conversion, enzyme accessibility, polymerase behavior, and nucleic acid structure can be translated into CRISPR‐readable signals. Finally, we discuss current translational challenges and emerging opportunities in point‐of‐care methylation diagnostics, integrated DNA–RNA profiling, engineered Cas effectors, AI‐guided assay design, and CRISPR‐compatible methylome analysis.