RNA G-quadruplex structures exist and function in vivo in plants

<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>Guanine-rich sequences are able to form complex RNA structures termed RNA G-quadruplexes in vitro. Because of their high stability, RNA G-quadruplexes are proposed to exist in vivo and are suggested to be associated with important biological relevance. However, there is a lack of direct evidence for RNA G-quadruplex formation in living eukaryotic cells. Therefore, it is unclear whether any purported functions are associated with the specific sequence content or the formation of an RNA G-quadruplex structure.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>Using rG4-seq, we profile the landscape of those guanine-rich regions with the in vitro folding potential in the <jats:italic>Arabidopsis</jats:italic> transcriptome. We find a global enrichment of RNA G-quadruplexes with two G-quartets whereby the folding potential is strongly influenced by RNA secondary structures. Using in vitro and in vivo RNA chemical structure profiling, we determine that hundreds of RNA G-quadruplex structures are strongly folded in both <jats:italic>Arabidopsis</jats:italic> and rice, providing direct evidence of RNA G-quadruplex formation in living eukaryotic cells. Subsequent genetic and biochemical analyses show that RNA G-quadruplex folding is able to regulate translation and modulate plant growth.</jats:p> </jats:sec><jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Our study reveals the existence of RNA G-quadruplex in vivo and indicates that RNA G-quadruplex structures act as important regulators of plant development and growth.</jats:p> </jats:sec>