Abstract
BackgroundGuanine-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.ResultsUsing rG4-seq, we profile the landscape of those guanine-rich regions with the in vitro folding potential in the Arabidopsis 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 Arabidopsis 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.ConclusionsOur 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.
Highlights
Guanine-rich sequences are able to form complex RNA structures termed RNA G-quadruplexes in vitro
Profiling of G-rich regions with potential to fold into RG4s in Arabidopsis transcriptome To systematically search for G-rich regions with the potential to fold into RG4s in Arabidopsis, we used rG4-seq, an in vitro approach for detecting RG4 formation at a transcriptome-wide scale [25]
G-rich regions which folded into RG4s in vitro can cause reverse transcriptional stalling (RTS) [21, 25]
Summary
Guanine-rich sequences are able to form complex RNA structures termed RNA G-quadruplexes in vitro. Because of their high stability, RNA Gquadruplexes are proposed to exist in vivo and are suggested to be associated with important biological relevance. There is a lack of direct evidence for RNA Gquadruplex formation in living eukaryotic cells It is unclear whether any purported functions are associated with the specific sequence content or the formation of an RNA G-quadruplex structure. RNA structures, their folding in vitro has been widely studied, the folding in vivo is poorly understood One of such complex structures is RNA G-quadruplex (RG4), which is folded with guanine-rich (G-rich) sequences in vitro and consists of two or more layers of G-quartets involving both Hoogsteen and Watson-Crick base. It is crucial to determine whether RG4 truly exists in vivo, such that one can investigate and establish the relationship between RG4 and associated biological functions
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