Exploring mRNA 3′-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening

Abstract

Guanine-rich RNA sequences can fold into non-canonical, four stranded helical structures called G-quadruplexes that have been shown to be widely distributed within the mammalian transcriptome, as well as being key regulatory elements in various biological mechanisms. That said, their role within the 3′-untranslated region (UTR) of mRNA remains to be elucidated and appreciated. A bioinformatic analysis of the 3′-UTRs of mRNAs revealed enrichment in G-quadruplexes. To shed light on the role(s) of these structures, those found in the LRP5 and FXR1 genes were characterized both in vitro and in cellulo. The 3′-UTR G-quadruplexes were found to increase the efficiencies of alternative polyadenylation sites, leading to the expression of shorter transcripts and to possess the ability to interfere with the miRNA regulatory network of a specific mRNA. Clearly, G-quadruplexes located in the 3′-UTRs of mRNAs are cis-regulatory elements that have a significant impact on gene expression.

A Matter of Location: Influence of G-Quadruplexes on Escherichia coli Gene Expression

“…For eukaryotes, functions of 3 0 -UTR G-quadruplexes as cis-regulatory elements have been reported (Beaudoin and Perreault, 2013). In our study, we inserted the G-rich sequence 4 nt downstream of the eGFP stop codon in the pQE-eGFP reporter plasmid (Figures 1E and 1F).…”

“…Quadruplexes can be induced far away from a transcription start site (TSS), functioning as silencer or enhancer of transcription (Perrone et al, 2013;Zhang et al, 2013). In addition to 5 0 untranslated regions (UTRs), potential quadruplexes have also been identified in the 3 0 -UTRs near transcription termination, splicing, and polyadenylation sites Beaudoin and Perreault, 2013). Quadruplexes have also been described to interfere with translation.…”

MOV10 and FMRP Regulate AGO2 Association with MicroRNA Recognition Elements

“…To examine the MOV10 iCLIP sites for putative GQs, we used the GQ prediction program QGRS Mapper (Kikin et al, 2006; Menendez et al, 2012) and found that 27.2% of the MOV10 3’UTR CLIP sites contained predicted GQs--nearly twice that predicted in a large-scale screen of 3’UTRs (Beaudoin and Perreault, 2013). To ask directly whether MOV10 bound GQs, we tested its ability to bind the RNA sc1, a model GQ that binds FMRP with nanomolar affinity (Darnell et al, 2001).…”

RNA G-quadruplexes and their potential regulatory roles in translation

“…Subsequently, it was discovered that 1,453 human pG4 sequences possess 2 short distal loops of 1 nucleotide in length and a long central loop of up to 70 nucleotides long in the 5′-UTRs, which significantly expands the number of pG4s in the transcriptome 49 . A bioinformatic search for “regular” G-quadruplex in 3′-UTRs of the human transcriptome, detected 8,903 pG4 sequences showing that the enrichment for G-quadruplex is not limited to the 5′-UTRs 50 . Additionally, other bioinformatic analyses, in-line probing and luciferase reporter assays revealed the existence of pG4 sequences in both the 5′- and 3′-UTR of transcripts, indicating G4 structures function in the post-transcription regulation in cellulo , and neighboring C-rich sequences that affect G4 folding 14,49,51 .…”