RNA G-quadruplexes regulate mammalian mirtron biogenesis

TL;DR

RNA G-quadruplexes in the 5′ arm of mammalian mirtrons help regulate their splicing and biogenesis.

Contribution

Discovery that RNA G-quadruplexes in the 5′ arm of mammalian mirtrons are key regulatory elements for their biogenesis.

Findings

Mammalian mirtrons are enriched for RNA G-quadruplexes in their 5′ arm, unlike plant and invertebrate mirtrons.

Disruption of RNA G-quadruplexes in the 5′ arm inhibits splicing and maturation of mirtrons.

RNA G-quadruplexes in the 5′ arm facilitate splicing-mediated biogenesis of mammalian mirtrons.

Abstract

Mirtrons are a predominant class of noncanonical microRNAs derived from introns through a Drosha-independent, splicing-dependent pathway. Unregulated splicing of introns containing hairpins may adversely impact Dicer/Ago-mediated canonical microRNA biogenesis. However, the mechanism regulating mirtron biogenesis remains poorly understood. We found that the 5′ arm of plant mirtrons and invertebrate mirtrons are enriched for uracils; in contrast, the 5′ arm of vertebrate mirtrons are enriched for guanines. Further analysis revealed that most of the mammalian mirtrons contain an RNA G-quadruplex (rG4); this was not observed among plant/invertebrate mirtrons. Interestingly, almost all the rG4s in mammalian mirtrons were present in the 5′ arm. Predicted rG4s in human mirtrons form a G-quadruplex structure in vitro and rG4 formation in the 5′ arm of mirtrons facilitates splicing-mediated biogenesis of mirtrons. Notably, the disruption of rG4s in the 5′ arm of mirtrons inhibits splicing and maturation; while mutations outside the rG4-motif do not impact mirtron biogenesis. Our findings support the notion that rG4s at the 5′ arm are key regulatory elements in the evolutionary landscape of mammalian mirtrons. This work advances our current understanding of mirtron biogenesis and highlights additional roles for rG4s in small RNA biology.

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