Abstract
BackgroundRNA secondary structures in the 5′-untranslated regions (5′-UTR) of mRNAs are key to the post-transcriptional regulation of gene expression. While it is evident that non-canonical Hoogsteen-paired G-quadruplex (rG4) structures somehow contribute to the regulation of translation initiation, the nature and extent of human mRNAs that are regulated by rG4s is not known. Here, we provide new insights into a mechanism by which rG4 formation modulates translation.ResultsUsing transcriptome-wide ribosome profiling, we identify rG4-driven mRNAs in HeLa cells and reveal that rG4s in the 5′-UTRs of inefficiently translated mRNAs associate with high ribosome density and the translation of repressive upstream open reading frames (uORF). We demonstrate that depletion of the rG4-unwinding helicases DHX36 and DHX9 promotes translation of rG4-associated uORFs while reducing the translation of coding regions for transcripts that comprise proto-oncogenes, transcription factors and epigenetic regulators. Transcriptome-wide identification of DHX9 binding sites shows that reduced translation is mediated through direct physical interaction between the helicase and its rG4 substrate.ConclusionThis study identifies human mRNAs whose translation efficiency is modulated by the DHX36- and DHX9-dependent folding/unfolding of rG4s within their 5′-UTRs. We reveal a previously unknown mechanism for translation regulation in which unresolved rG4s within 5′-UTRs promote 80S ribosome formation on upstream start codons, causing inhibition of translation of the downstream main open reading frames. Our findings suggest that the interaction of helicases with rG4s could be targeted for future therapeutic intervention.
Highlights
RNA secondary structures in the 5′-untranslated regions (5′-UTR) of mRNAs are key to the posttranscriptional regulation of gene expression
Translation efficiency of mRNAs marked by G-quadruplexes within their 5′-UTRs To identify transcripts regulated by rG4s in their 5′-UTR, we conducted transcriptome-wide ribosomal profiling [35, 36] of cycloheximide-treated HeLa cells
DHX9 and DHX36 are associated with polysomes and bind RNA G-quadruplexes To demonstrate a functional role for rG4 folding within 5′-UTR in translation regulation, we explored the contribution of helicases that bind and unwind rG4 structures towards controlling the translation efficiency of mRNAs with 5′-UTR rG4s
Summary
RNA secondary structures in the 5′-untranslated regions (5′-UTR) of mRNAs are key to the posttranscriptional regulation of gene expression. RNA secondary structures can modulate post-transcriptional regulation of gene expression. This can be achieved through controlling mRNA splicing, export, stability, localization and translation by either recruiting protein factors or by impeding scanning processes [1,2,3,4]. Stem-loop structures have been shown to improve the recognition of upstream initiator codons, in a suboptimal context, in vitro [17] and activate the translation of bacterial mRNAs [18]. RNA secondary structure folding can, in some contexts, increase the efficiency of initiation codon recognition and trigger the translation of alternative open reading frames
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
