title: The RNA Stem-Loop to G-Quadruplex Equilibrium Controls Mature MicroRNA Production inside the Cell.
abstract: 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 Mg(2+) 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.
authors.affiliation: Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.|CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India.
authors.forename: Satyaprakash
authors.initials: S
authors.lastname: Pandey
authors.affiliation: Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.|CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India.
authors.forename: Prachi
authors.initials: P
authors.lastname: Agarwala
authors.affiliation: Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.|CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India.
authors.forename: Gopal G
authors.initials: GG
authors.lastname: Jayaraj
authors.affiliation: Solution Equilibria and Chemometrics Group, Department of Analytical Chemistry, University of Barcelona , Diagonal 645, E-08028 Barcelona, Spain.
authors.forename: Raimundo
authors.initials: R
authors.lastname: Gargallo
authors.affiliation: Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.|CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India.|Academy of Scientific and Innovative Research (AcSIR) , Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India.
authors.forename: Souvik
authors.initials: S
authors.lastname: Maiti
mesh_terms: D001483:Base Sequence; D054856:G-Quadruplexes; D005786:Gene Expression Regulation; D006801:Humans; D061986:MCF-7 Cells; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D043244:Ribonuclease III / Q000378:metabolism*; D006163:Ribonuclease T1 / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: C531388:MIRN27 microRNA, human; D035683:MicroRNAs; C487931:mirnlet7 microRNA, human; D043244:Ribonuclease III; D006163:Ribonuclease T1