G-quadruplexes formation in the 5'UTRs of mRNAs associated with colorectal cancer pathways.

Rachel Jodoin,Jean-Pierre Perreault

doi:10.1371/journal.pone.0208363

Abstract

RNA G-quadruplexes (rG4) are stable non-canonical secondary structures composed of G-rich sequences. Many rG4 structures located in the 5’UTRs of mRNAs act as translation repressors due to their high stability which is thought to impede ribosomal scanning. That said, it is not known if these are mRNA-specific examples, or if they are indicative of a global expression regulation mechanism of the mRNAs involved in a common pathway based on structure folding recognition. Gene-ontology analysis of mRNAs bearing a predicted rG4 motif in their 5’UTRs revealed an enrichment for mRNAs associated with the colorectal cancer pathway. Bioinformatic tools for rG4 prediction, and experimental in vitro validations were used to confirm and compare the folding of the predicted rG4s of the mRNAs associated with dysregulated pathways in colorectal cancer. The rG4 folding was confirmed for the first time for 9 mRNAs. A repressive effect of 3 rG4 candidates on the expression of a reporter gene was also measured in colorectal cancer cell lines. This work highlights the fact that rG4 prediction is not yet accurate, and that experimental characterization is still essential in order to identify the precise rG4 folding sequences and the possible common features shared between the rG4 overrepresented in important biological pathways.

Highlights

RNA G-quadruplexes are non-canonical secondary structures based on the stacking of multiple g-quartets
Numerous rG4 structures located in the 5’UTRs of individual mRNAs have been identified as translational repressors. It is not known if rG4 motifs are enriched in particular mRNA families or in certain cellular pathways
The final list of 2 004 potential rG4 structures (PG4) mRNAs was compared to the background of all homo sapiens GO-annotated mRNAs in search of possible enrichment in certain biological pathways

Summary

Introduction

RNA G-quadruplexes (rG4) are non-canonical secondary structures based on the stacking of multiple g-quartets. A G-quartet is a coplanar array of four guanines (G) linked by Hoogsteen base-pairs and stabilized in its center by a monovalent cation, usually K+. Many rG4 located in the 5’UTRs of mRNAs have been described [1,2,3]. Based on a search for canonical motifs only, more than 2 000 human 5’UTRs were predicted to possess potential rG4 structures (PG4) [5,6]. A recent study using a next-generation sequencing technique called rG4-seq showed an enrichment of rG4 in the UTRs of mRNAs [7].

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Conclusion