The RNA stem–loop to G-quadruplex equilibrium controls mature microrna production inside the cell

Pandey, Satyaprakash ; Agarwala, Prachi ; Jayaraj, Gopal G. ; Gargallo, Raimundo ; Maiti, Souvik (2015) The RNA stem–loop to G-quadruplex equilibrium controls mature microrna production inside the cell Biochemistry, 54 (48). pp. 7067-7078. ISSN 0006-2960

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The biological role of the existence of overlapping structures in RNA is possible yet remains very unexplored. G-Rich tracts of RNA form G-quadruplexes, while GC-rich sequences prefer stem–loop structures. The equilibrium between alternate structures within RNA may occur and influence its functionality. We tested the equilibrium between G-quadruplex and stem–loop structure in RNA and its effect on biological processes using pre-miRNA as a model system. Dicer enzyme recognizes canonical stem–loop structures in pre-miRNA to produce mature miRNAs. Deviation from stem–loop leads to deregulated mature miRNA levels, providing readout of the existence of an alternate structure per se G-quadruplex-mediated structural interference in miRNA maturation. In vitro analysis using beacon and Dicer cleavage assays indicated that mature miRNA levels depend on relative amounts of K+ and Mg2+ ions, suggesting an ion-dependent structural shift. Further in cellulo studies with and without TmPyP4 (RNA G-quadruplex destabilizer) demonstrated that miRNA biogenesis is modulated by G-quadruplex to stem–loop equilibrium in a subset of pre-miRNAs. Our combined analysis thus provides evidence of the formation of noncanonical G-quadruplexes in competition with canonical stem–loop structure inside the cell and its effect on miRNA maturation in a comprehensive manner.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society.
ID Code:103378
Deposited On:02 Feb 2018 03:46
Last Modified:02 Feb 2018 03:46

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