RNA G-quadruplex structures exist and function in vivo

Abstract

15Guanine-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 cells. Therefore, it is unclear whether any purported functions are associated with the specific sequence content or the formation of an RNA 20 G-quadruplex structure. Here, we profiled the landscape of those guanine-rich regions with the in vitro folding potential in the Arabidopsis transcriptome. We found 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 determined that hundreds of RNA G-quadruplex structures are strongly folded in both Arabidopsis and rice, 25 providing direct evidence of RNA G-quadruplex formation in living eukaryotic cells. Subsequent genetic and biochemical analysis showed that RNA G-quadruplex folding was sufficient to regulate translation and modulate plant growth. Our study reveals the existence of RNA Gquadruplex in vivo, and indicates that RNA G-quadruplex structures act as important regulators of plant development and growth. 30 We thank Prof.

Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice

“…G4s are considered to act as molecular switches to regulate gene expression in metazoan cells (Eddy and Maizels, 2006). In plants, a few studies have reported the role of G4 sequences, such as in transport and gene expression (Garg et al, 2016), growth and development (Yang et al, 2020b), hydrolase activity (Cagirici et al, 2021), stress response, energy status, and sugar availability (Yadav et al, 2017). Here, we report their role in N-response or NUE for the first time.…”

“…But together, they span diverse genotypes, N-forms and growth conditions yielding thousands of DEGs and enabling comprehensive meta-analyses. Identification of co-expressed genes/modules by methods such as WGCNA is one of the ways to distill the essence from all these datasets, but so far this was done only with individual N-responsive transcriptomic datasets in rice (Coneva et al, 2014;Zhang et al, 2019;Ueda et al, 2020;Yang et al, 2020b). Therefore, the present study utilized 16 microarray datasets for which the DEGs could be extracted from publicly available datasets and shortlisted 8 of them that shared the largest number of 3020 DEGs for WGCNA and other analyses.…”

Essential Roles and Risks of G-Quadruplex Regulation: Recognition Targets of ALS-Linked TDP-43 and FUS

“…Identification of non-canonical G4 motifs is different from that of canonical RNA sequences (Guo and Bartel, 2016;Yang et al, 2020). For example, cross-linking and immunoprecipitation (CLIP), one of the most used methods for identifying RNAs as protein binding targets from whole cellular RNA, often result in selective loss of most non-canonical G4 motifs.…”

Plant Small RNA World Growing Bigger: tRNA-Derived Fragments, Longstanding Players in Regulatory Processes

“…Although this might be true for mammalian cells, the same effect was not observed in Arabidopsis (Jackowiak et al, 2017). Recently, G-quadruplex structures were detected in Arabidopsis and rice, with different folding predictions in both species and developmental stages, suggesting that this structures could be spatio-temporal specific (Yang et al, 2020). The 4 Gs present in Arabidopsis tRNA-half (Ala) are not essential to affect protein synthesis.…”