Molecular mechanisms regulating differential expression of individual miRNAs within polycistronic clusters

MicroRNA (miRNA) genes are frequently located in close proximity within the genome, forming so-called clusters. These clusters are transcribed as polycistronic units, suggesting coordinated transcriptional regulation of the miRNAs they contain. However, individual mature miRNAs from the same cluster often accumulate at varying levels and exhibit distinct tissue-specific expression patterns, indicating the presence of regulatory mechanisms that modulate the differential expression of individual cluster members. This review summarizes the molecular mechanisms underlying the differential regulation of individual miRNAs encoded within polycistronic transcripts. These mechanisms range from strict genomic and transcriptional controls to dynamic post-transcriptional events. At the genomic and transcriptional levels, the use of alternative promoters enables independent transcription of specific cluster members, while alternative splicing can either facilitate or disrupt the processing of precursor hairpins. At the post-transcriptional level, epitranscriptomic modifications (including A-to-I editing, m⁶A methylation, m⁵C, m⁷G, and others) selectively modulate Drosha- and Dicer-mediated cleavage, target binding, and miRNA stability. Furthermore, precursor processing is governed by the structural characteristics of neighboring hairpins through a process termed "cluster assistance" and by RNA-binding proteins (RBPs) that recognize specific hairpin motifs to regulate biogenesis in a context-dependent manner. Understanding these diverse regulatory layers provides critical insight into how cells fine-tune the coordinated versus differential expression of miRNA clusters to achieve distinct physiological and pathological outcomes.