Functional Analysis And Sequence Pattern Recognition Of G-quadruplex In Nucleic Acid

Besides the canonical double helix,DNA and RNA can fold into a special secondary strcture G –quadruplex.G–quadruplexes are found to play crucial roles in telomeres protection,DNA replication,transcription and RNA translation.However,existing studies have little research on G-quadruplexes in RNA.G-quadruplexes were sequenced and analyzed their regulatory function and sequence features,which might provide certain information on the in-depth study.Firstly,DMS-seq was applied to detect the secondary structure of m RNA and G-quadruplexes were predicted from the secondary structure.Therefore,G-quadruplexes could be sequenced through the method.The sequencing results showed that the G-quadruplex were not randomly distributed in the m RNA.They werethe least in the CDS region and their density was the highest in the 5'UTR,their number was the highest in the 3'UTR.And the G-quadruplexes were highly aggregated near the start codon and the stop codon.Functional analysis of the G-quadruplexes revealed that they have different functions at different positions in the m RNA.They may have a function of reducing gene expression on the 5'UTR,while the G-quadruplexes in the 3'UTR could indirectly increase gene expression through blocking the mi RNA binding to m RNA.Finally,the sequence analysis of G-quadruplexes showed that the sequenced G-quadruplexes had a significant correlation with their sequence,and then the GLAM2 tool was used to summarize the motif of the G-quadruplex,then the most important triplet codon features on the G-quadruplex sequences were obtained by decision tree: GGG,GGC,CCT,GCA,GGA,AGG,GAG.Finally,the convolutional neural network with excellent classification performance is visualized,and the features extracted by the convolution kernel are analyzed.The G-quadruplexes in m RNA were systematically studied,calculated the position distribution,explored the regulation function,and analyzed the sequence characteristics.The results may provide some reference for the elaboration and in-depth study of G-quadruplex in RNA.