Conserved R Structures Regulate Translation Processes And Construction Of A Comprehensive Of RNA Structure Database

RNA carries genetic information to proteins and functions as a regulator by folding into complex and diverse structures through base pairing.With the development of prediction methods and experimental techniques,the RNA structure has been delineated more and more clearly.However,many species’ evolutionarily conserved RNA structures have not been identified at the transcriptome-wide level,and the regulatory functions of these RNA structures during translation remain unclear.This study identified transcriptome-wide evolutionarily conserved RNA structures in eight species,analyzed conserved RNA structures’ regulatory role in the translation process in Saccharomyces cerevisiae,and constructed a comprehensive analysis database of RNA structures.This study predicted the conserved RNA structures(Conserved RNA structure,CRS)of eight species and identified the covariation of base pairing in these CRS.The study used a structural rather than sequence conservation method to predict CRS in these species.This method alleviates the low CRS discovery rate defect due to the lack of conservation of base pairing.The presence of covariant signals can provide evidence for the functional existence of RNA structures.Still,if the sequence lacks observable covariant signs,it is not easy to determine whether the conserved RNA structures are functional.Therefore,this paper examined covariation in these CRS and found that most species had higher levels of covariation power and observed base pairing with covariation.The study also analyzed the relationship between these CRS and ribosome translation efficiency and found that the occurrence of CRS in transcripts is positively correlated with ribosome translation efficiency.BDzscore,a metric of CRS maintenance level in vivo,was constructed to identify the conserved RNA structure in vivo(Conserved RNA structure in vivo,CRSv)with S.cerevisiae as the representative.By comparing the maintenance levels of CRSv and stable RNA structures in vivo,it was found that CRS was more likely to exist in vivo than stable RNA structures with lower free energy.Most of the genes in which CRSv is located are related to binding function,which also reflects that the conserved RNA structure of S.cerevisiae tends to play a regulatory role in the binding function-related genes.The study also found that rare codons occurred more frequently in the flanking sequence of CRSv than in other regions,which suggests that rare codons exist in coordination with CRSv to regulate the translation process.In particular,the frequency of rare codons was significantly higher upstream of CRSv than in other regions.These rare codons in front of CRSv may act as ribosomes’ speed bumps,preventing ribosomes from bumping into RNA structures at high local rates.Rare codons in CRS are lower than those in flanking sequences,suggesting that cells do not tend to form regions of slow translation locally.There is a high structural coverage between CRSv and RNA binding domain with known functions.These RNA structures are widely distributed in CDS and are remarkably conserved.Here,many CRSvs tend to interact with RNA binding proteins,which may have complex synergistic regulatory functions.Moreover,the study also analyzed the ribosomal translation rate of CRSv and its flanking sequences,and the ribosomal translation rate was lower in the front 9nt position of CRSv.These aggregations of ribosomes in front of CRSv suggest that one of the roles of RNA structures in translation is to block ribosomal movement.Through the collection,sorting,comparison,and analysis of in vivo RNA structure data and conserved RNA structure,this paper built a comprehensive in vivo RNA structure analysis database,RSVdb(https://taolab.nwsuaf.edu.cn/rsvdb/).RSVdb contains 626,225 transcripts of RNA structure data from 178 samples of 10 studies of 8 model organisms.The database analyzes and compares data from different studies and methods to provide users with RNA structure statistics and differences among these studies.RSVdb also predicts RNA structure with in vivo data constraints and intuitively shows the difference between the original structure and RNA structure with in vivo data constraints.All of the above structural statistics and predicted data are available for download.In the updated version,four functions were added:prediction of CRS,analysis of covariant within CRS,prediction of G-quadruplex,and analysis of RNA structural heterogeneity.These functions make up for the lack of RNA structure conserved analysis and in-depth utilization of in vivo sequencing data in the original database and expand the analysis function of RSVdb.In conclusion,starting from the conservation of RNA structures,this paper identified the conserved RNA structures of multiple species at the transcriptome-wide level and discussed the role of conserved RNA structures in the translation process.Finally,a comprehensive RNA structure database was constructed.With the continuous progress of prediction methods and experimental methods,researchers can observe the internal translation process with a clearer and clearer perspective.The original regulatory cognition of the translation process will be constantly updated and improved with the emergence of new technologies and methods.