Recognition Of Splice Sites And Studies On Mechanism Of Alternative Splicing

Alternative splicing of RNA appears to be widespread in eukaryotic genes, playing an important role in gene expression and regulation. It is one of the hottest topics in the post-genomic era. This thesis can be divided into three parts, focusing on the important phenomenon of alternative splicing.Firstly, in order to facilitate the study of alternative splicing of mammals, we developed database AsMamDB, which contains information about alternatively spliced genes of human, mouse and rat. It provides an excellent data set for researchers.Secondly, we focus on the recognition of splice sites. Due to the correlation of the different bases in the conservative sequences around splicing sites, hidden Markov model (HMM) is applied to the recognition of splicing sites. Experimental results showed that HMM well corresponds to the reality of the sequences at splicing sites. The method is good at the extraction of the statistical features of conservative sequences around splicing sites and has a quite high success rate in the recognition of both true and false splicing sites. Further more, we used this method to recognize alternatively spliced sites. Experimental results showed that they are similar to non-alternatively spliced sites in statistical characters of sequences. This result provides a methodology for further research on the splicing mechanism, especially for alternative splicing of eukaryotic genes.Finally, this thesis presents an initial study on the splicing and alternative splicing mechanism of eukaryotic genes. As the mechanism of alternative splicing is still unknown, several methods were tried for a better understanding. Purine / pyrimidine density was thought to be an important biochemical feature and was used to cluster sequences near splicing sites as well as alternatively spliced sites. Conserved motifs found in each cluster were searched against factor database and most of them were functional. The results showed that approximate and exact orientations, based on purine / pyrimidine density and motif factors, could be identified for the splicing of eukaryotic genes. The approximate orientation process located approximate splice site positions based on pyrimidine (or purine) concentration of nucleic acid sequences. The exact sites were then located based on information for several conservative purines or pyrimidines using information from the first step.