Computational Identification Of RNA Editing Sites And Alternative Splicing Events By RNA-Seq Data

RNA editing and alternative splicing are post-transcriptional events which playimportant role in RNA processing. The study of RNA editing and alternative splicing hasbecome one of the most challenging and exciting tasks for transcriptomics andbioinformatics in the post-genomic ear. Here, we analyze the recognition of RNA editingand alternative splicing events. The thesis includes two parts as follows:Firstly, RNA-Seq data were used to identify RNA editing sites in chimpanzee. Byaligning RNA-Seq data to chimpanzee genome sequences, all RNA-DNA mismatch siteswere observed and regarded as a candidate set. Low quality sites were filtered outaccording to genome sequencing quality scores. The other filters containing SNP sites andrandom sequencing errors were also applied on the candidate set. Finally，a total of8334RNA editing sites were identified in chimpanzee. RNA editing sites located in known genewere analyzed for biological function as well as the feature of the sequences surroundingthe RNA editing site.Secondly, RNA-Seq data were used for predicting alternative splicing events inDrosophila melanogaster. In this work,39718fruit fly splice sites were detected based onDrosophila melanogaster testis RNA-Seq data by using TopHat software, of which10584were new discoveries. By different donor/acceptor splice site combinations, acomputational identification method had been developed and was successfully applied tofour distinct classes of alternative splicing events: alternative donor site, alternativeacceptor site, intron retention and exon skipping. In this work,8477alternative splicingevents were predicted. RT-PCR successfully validated novel alternative splicing events andnew isoforms in two genes.In this work, plenty of RNA editing sites and novel alternative splicing events were identified by RNA-Seq data. Our results provide data support for further understanding themechanism of RNA editing and alternative splicing.