Parameters of clustered suboptimal miRNA biogenesis

Abstract

The nuclear cleavage of a suboptimal primary miRNA hairpin by the Drosha/DGCR8 complex (“Microprocessor”) can be enhanced by an optimal miRNA neighbor, a phenomenon termed cluster assistance. Several features and biological impacts of this new layer of miRNA regulation are not fully known. Here, we elucidate the parameters of cluster assistance of a suboptimal miRNA and also reveal competitive interactions amongst optimal miRNAs within a cluster. We exploit cluster assistance as a functional assay for suboptimal processing and use this to invalidate putative suboptimal substrates, as well as identify a "solo" suboptimal miRNA. Finally, we report complexity in how specific mutations might affect the biogenesis of clustered miRNAs in disease contexts. This includes how an operon context can buffer the effect of a deleterious processing variant, but reciprocally how a point mutation can have a nonautonomous effect to impair the biogenesis of a clustered, suboptimal, neighbor. These data expand our knowledge regarding regulated miRNA biogenesis in humans and represent a functional assay for empirical definition of suboptimal Microprocessor substrates.

Recent progress in miRNA biogenesis and decay

“…The cleavage of suboptimal pri-miRNAs can be enhanced by a phenomenon called cluster assistance, where neighbouring miRNAs can compete or assist in biogenesis of miRNAs within the same cluster [ 25 ]. Examples of this include the Enhancer of Rudimentary Homolog (ERH), a protein identified to act as a co-factor of the Microprocessor complex for processing suboptimal hairpins [ 26 ], that can bind to helper hairpins and facilitate processing of otherwise defective hairpins, as, e.g., miR-451 where miR-141 binding helps processing by Microprocessor [ 27 , 28 ].…”