Discovery Of Ribozyme And New Structured NcRNA By Bioinformatics

HDV ribozyme and hammerhead ribozyme have been reported in plants.In this project,we attempted to detect ribozyme in unreported plants using Infernal,which is a RNA secondary structure prediction software,in the genomic database of 74 plant species we established.In addition to ribozymes,we have also discovered new structured ncRNA in the human genome and gymnosperm genomes using different bioinformatics pipelines.The main idea of the pipelines is the same.First download tens of animal or plant genomes to establish a database.Then extract the noncoding regions of the genomes,and remove the known ncRNAs which already have been uploaded to Rfam database.At the same time,because of the high proportion of repeat region in both animal and plant genomes,we had to remove the repeat sequences by different methods to avoid its adverse effects on predicting RNA secondary structure.After doing this,BLAST was used for homologous sequence alignment and CMfinder was used to predict RNA secondary structure.In order to increase the reliability of the predicted secondary structure,we selected secondary structures with more covariation and better conservation.Finally,more sequences that conformed to the inputted structural characteristics were discovered by Infernal to refine the secondary structures in a larger genome database.Through the above methods,we found the existence of active HDV ribozymes and type III hammerhead ribozymes in the previously unreported plant genomes predicting 123 and 319 ribozyme sequences,respectively.78 type I hammerhead ribozyme sequences were found in Selaginella moellendorffii genome.These revealed the extensive distribution of ribozymes.Second,an optimized bioinformatics pipeline was applied to predict 256 new structured ncRNAs with their related gene information in gymnosperms.Motif 22895 has proved to be expressed in Ginkgo genome.Last but not least,we researched the expressed new structural ncRNAs found in the MAP2K5 gene and LUC-7 gene of the human genome.Beyond that,we also found an expressed ultraconserved element in TEAD1 gene.These studies lay the foundation for the discovery of structured ncRNAs with biological functions.