Prediction And Analysis Of Alternative Promoters In Multiple Cell Lineages

Alternative promoters were found in a variety of cell lines and tissue types, which has increased the transcriptional regulation complexity of the task in the research of mammalian genome. Identify alternative promoters, and to annotate them in different organizations activities is major challenges to understand human genes and transcription regulation. In order to identify alternative promoter in different cell lines, we studied 7 cell line(A549, Gm12878, H1 hesc, Helas3, Hepg2, Huvec, K562) RNA polymerase II Ch IP- seq experimental data, and training the promoter transcription start site of upstream and downstream, a total of 10000 base pairs distribution pattern of RNA polymerase II, using particle swarm optimization(PSO) algorithm for the model parameters of maximum likelihood estimate. For each cell line expression gene scanning promoter, found that 38% to 46% of expression genes have alternative promoters in the 7 cell lines. Alternative promoters play an important regulatory role in the gene expression level, to make genome characteristics analysis found that 80% to 90% of the alternative promoters localized in Cp G- rich regions. We analyze transcription factor binding sites in more than one cell line, and 55 kinds of transcription factors combination of cell line Heles3, found that the transcription factor have prefer to binding in the upstream of transcription start site rather than downstream of transcription start site. Latest sequencing of transcription factors Ch IP- seq uniform Peaks data, can help to further research the relationship between transcription factors and promoter, and further analysis of the characterizing genes regulatory regions in mammalian genomes.