Chemical-assisted analysis of epigenetic modifications

Epigenetic modifications, particularly those occurring on nucleic acid bases, play a pivotal role in regulating gene expression and cellular function without altering the underlying nucleic acid sequences. These subtle chemical alterations, such as methylation, hydroxymethylation, and acylation, are intricately linked to various biological processes. The analysis of base modifications poses significant challenges because of their minimal structural differences from unmodified bases, which traditional methods relying on double-stranded complementarity often fail to distinguish effectively. Nevertheless, the distinct chemical properties conferred by these modifications provide an opportunity for the development of novel approaches for their specific recognition. In this review, we elucidate the biological significance of nucleic acid modifications, including their diverse types, genomic distribution, abundance, and functions. We then delve into the principles and applications of chemical-assisted analysis methods, which leverage the unique chemical properties of modified bases to transform them into detectable derivatives. We comprehensively discuss various base conversion strategies, encompassing oxidation, reduction, deamination, addition, substitution, and coupling reactions. Moreover, we address the limitations of current chemical-assisted methods, such as insufficient sensitivity for low-abundance modifications, stringent reaction conditions, variable conversion efficiencies, challenges in single-cell analysis, and the loss of spatial information. Finally, we emphasize the significance of nucleic acid modifications in unraveling biological processes and disease mechanisms, and highlight the potential of chemical-assisted methods in advancing epigenetic research and precision medicine.