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This study investigates the structural roles of RNA motifs within microRNA (miRNA) target sites across the human genome. By utilizing tools like miRanda and TargetScan, we identified key motifs, including splicing regulatory and transcriptional motifs, prevalent in the 3’ UTR regions of mRNAs. Our findings highlight the significance of RNA secondary structures in miRNA interactions, providing insights into post-transcriptional regulation. This research not only uncovers novel RNA motifs but also enhances existing web resources for RNA motif analysis.
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Whole Human Genome Survey of Motif and Domain in RNA Secondary Structural Regions of microRNA Target SitesPavithra .S, Aswathy Mary Paul, Reshmi G and M. Radhakrishna PillaiCancer Research Program-9Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India Introduction mRNA Motifs Search-Work Flow • MicroRNAs(miRNAs) are endogenous, non-protein-coding, 20-23 nucleotides long, single-stranded RNA molecules which regulates the human transcriptome through binding to its targets are critically depends on its structure. • RNA motifs are the structural elements which are recurrently occurred by non-Watson-Crick base pair found in secondary structural regions of RNA. • The RNA motifs occurs prevalently in the miRNAs target site may shows significance of the structural organization to interact with targets. • In this study we explored novel motifs and it will provide a valuable support for our web resource. Human mRNA sequences (NCBI) miRNAs target sites (miRanda, TargetScan) (c) (a) (b) RNA motifs (RegRNA) RNA Secondary Structure (RNAfold) (d) Objectives Secondary structures of miRNA and RNA motifs sequences. (a) hsa-miR-18a-3p (b)cftr, exon 12 motif, (c) ighg2 cgamma2 motif, (d) Musashi binding element (MBE) motif. • To predict the miRNAs target site for complete human RNA sequence. • To identify novel RNA motifs in the miRNAs binding target sites of 3’UTR in all transcripts including splice variants. • To determine the types of RNA secondary structure in corresponding regions. • To construct a workflow based on RNA motifs pattern occur in the RNA secondary structure of the miRNAs target site. Prevalently found RNA motifs Results Discussion and Conclusion • Splicing regulatory motifs, Transcriptional motifs, UTR motifs were found to be occur within the miRNAs target binding regions. • RNA motifs were found in the stable RNA secondary structural regions, it is playing an essential role in the RNA-RNA binding interactions. • This analysis highlights the different types of RNA motifs found in the miRNAs target sites and shows their interactions leads to post transcriptional regulation. Methodology • Retrieval of mRNA sequences from GenBank, NCBI. • To determine miRNAs target site to the corresponding mRNA sequence with available software's (miRanda, TargetScan). • To identify the potential RNA motifs (Splicing regulatory motifs, Transcriptional motifs, UTR motifs) with RegRNA. (http://regrna2.mbc.nctu.edu.tw/) Acknowledgement • This study is supported by Department of Biotechnology, Government of India (No-BT/PR14209/BID/07/328/2010). Table shows the RNA motifs and miRNAs target sites of mRNA sequences.
