From DNA Methylation and Histone Modifications to Non-Coding RNAs: Evaluating Tools for Epigenetic Research

Epigenetic biomarkers, such as DNA methylation, histone alterations, and non-coding RNAs, are increasingly recognized as essential instruments in disease diagnoses, prognostics, and customized therapy. As their clinical significance increases, so does the necessity for robust, interpretable, and scalable techniques that can accurately detect these molecular alterations. This review provides a critical and organized overview of contemporary technologies employed to characterize the principal categories of epigenetic modifications, encompassing PCR- and sequencing-based methods, high-resolution immunoprecipitation techniques, and CRISPR-enhanced detection systems. Although numerous procedures are technically well-established, their implementation outside research laboratories frequently faces substantial challenges: elevated prices, data intricacy, absence of standardization, and restricted translational frameworks. Furthermore, the interpretation of epigenetic data continues to pose a significant difficulty, especially for heterogeneous clinical samples and the swiftly advancing computational techniques. We examine the advantages and drawbacks of existing approaches, focusing on their incorporation into biomedical engineering platforms, including biosensors, lab-on-a-chip devices, and AI-assisted diagnostics. This review seeks to assist researchers, physicians, and engineers in choosing suitable technologies, comprehending their limitations, and pinpointing areas requiring urgent innovation by merging analytical rigor with a pragmatic viewpoint.