Project description:RNA structures are of crucial importance for biological function and gene regulation. Guanine (G)-rich sequences in RNA can assemble to form RNA G-quadruplex (rG4) structures; specific rG4s have been shown to regulate gene expression, and are associated with human diseases. However, no transcriptome-wide method has been reported to map rG4s, limiting our understanding of the rG4 structure and its relationship with function and regulation. Here we introduce a transcriptome-wide rG4 profiling method, rG4-Seq, in which the rG4-mediated reverse transcriptase stalling is read out by next-generation sequencing at nucleotide resolution. We apply this method to human RNA and report the first global map of rG4 structures for any organism. Our analysis identifies over 3,000 rG4s, and increases to over 11,000 upon addition of a rG4 stabilizing ligand Pyridostatin (PDS). Notably, we discover that besides canonical rG4s, many rG4s are non-canonical with novel structural features such as long-loops, bulges, and 2-quartet. We also find that rG4 formation is associated with its stability, Cytosine (C)-content, and the stability of alternative RNA structures. Our data reveals that rG4s can be found in messenger RNAs (mRNAs) and long intergenic noncoding RNAs (lincRNAs). In mRNAs, rG4s are enriched in untranslated regions, and are significantly correlated with microRNA target sites and polyadenylation signals. Remarkably, we found that majority of our in vitro identified rG4s can change the in silico predicted RNA structure to uncover alternative RNA conformation.. Futhermore, the rG4s that have analogues in many ortholog genes across different species show a preferential association with RNA processing and stability. rG4-seq is a broadly applicable method that enables the RNA G4 structurome and its biological roles to be interrogated and can be readily applied in other organisms on a transcriptome-wide scale. 12 samples, 150 bp single-ended RNA-Seq libraries from cell extracts after performing RTS reaction in different buffers (Li, K and K+PDS rich buffer). Each of the 3 conditions has 4 libraries from independent biological replicates.

Project description:Following meiosis resumption, the transcription was silencing; and large number of maternal mRNA was actively translated and degraded during oocyte maturation. However, due to the limitation of sample number and technology, the dynamic distribution of RNA structure and its correlation with RNA dynamic change have never been revealed. RNA G-quadruplex (rG4) was a four-stranded RNA secondary structure related to translation regulation and RNA stability. In this study, we developed a low-input technique of rG4 detection (G4-lace-seq), and found that rG4s were highly abundant in fully grown oocytes and reduced during oocyte maturation. We ingeniously applied rG4 stable ligand BYBX in aim to eliminate the DNA G-quadruplex obstruction, and phenotypic analysis showed that rG4 accumulation severely impaired oocytes maturation. Above all, RBPs proteomic spectra revealed RNA structure change caused by G4 accumulation directly weakened the binding of RBPs to RNA, especially the enrichment of G4s affect the RBP binding associated with RNA metabolism, and G4s on the 5′-UTR hindered 40s ribosome movement and binding of 60s ribosome eukaryotic translation initiation factors to RNA. Combined analysis of G4-Lace-seq with Ribo-lite and RNA-seq, further proved that rG4s accumulation on UTRs disrupted translational efficiency and maternal mRNA degradation during oocyte maturation. Overexpression of DHX36, a G4s helicase, rescued the defects caused by BYBX to oocytes and restored the development rates. Jointly analyzing the function and distribution of rG4s and the metabolic signature of maternal mRNA, we hypothesized that a large amount of rG4s present before meiosis resumption is necessary to protect long-term mRNA stability from degradation in a state of poor efficiency translation. Following meiosis resumption, rG4s were cleaned up, translation efficiency increased, and the mRNA became unstable and was rapidly degraded. Collectively, our results announced for the first time that G4, as a secondary structure, had a hand in in the special dynamic rule of RNA content and translation. rG4s clearance determined the fate of cytoplasmic maturation during oocyte maturation.

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RNA G-quadruplex dynamics control gene expression and genome stability through DHX36-mediated regulation

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