The Hidden Layer of MicroRNA Regulation in Gynecologic Cancers: IsomiRs, Arm Switching, and RNA Epitranscriptomic Modifications

MicroRNAs (miRNAs) are key regulators of gene expression that act primarily by binding to target messenger RNAs (mRNAs). However, the biology of miRNAs is more complex than initially thought, with functional complexity extending beyond canonical sequences. A multilayered miRNA regulatory landscape involving isomiR generation, altered 5p/3p strand usage, arm switching, A-to-I RNA editing, and epitranscriptomic RNA modifications operates in eukaryotic cells to regulate miRNA function. Collectively, these mechanisms expand the functional diversity of miRNAs by regulating their biogenesis, stability, strand selection, and target specificity, increasing their functional plasticity and contributing to regulatory heterogeneity found in cells. IsomiRs arise from alternative Drosha/Dicer processing, terminal nucleotide additions, RNA editing, and genetic variation, producing functionally distinct isoforms. Arm switching alters gene regulatory outputs through context-dependent changes in predominant 5p/3p strand usage. In addition, epitranscriptomic RNA modifications, such as m6A and m5C, together with A-to-I RNA editing, represent an additional layer of miRNA regulation. These mechanisms can act directly on miRNAs or their precursors, or indirectly by modifying circRNAs and lncRNAs, thereby altering miRNA availability and function. Together, these processes form a dynamic regulatory network that influences key cancer hallmarks, including cell proliferation, apoptosis, epithelial–mesenchymal transition, metastasis, immune evasion, and therapy resistance. However, the contribution of these non-canonical regulatory layers to tumor-specific miRNA function remains poorly understood. In this review, we explore how isomiR generation, miRNA strand selection, arm switching, and epitranscriptomic regulation expand the functional diversity of miRNAs in gynecologic cancers.