大鼠Pten和Runx3基因5'端非编码区序列的生物信息学分析

Bioinformatics analysis of 5' untranslated region of Runx3 and Pten in rats

目的分析大鼠Pten和Runx3基因5'端非编码区(5'-UTR)序列的CpG岛、启动子及其转录因子结合位点。方法通过NCBI获得大鼠Pten和Runx3基因全长序列及转录本,采用Blast中的可读框比对外显子、内显子及上游5'-UTR信息,所获得ATG上游2 kb、下游1 kb序列分别应用CpG island searcher软件、CpGPlot工具、Methprimer2.0工具预测CpG岛,NNPP工具、Promoter scan工具、FirstEF工具预测启动子,Matlspector、Match、Consite预测启动子区域转录结合位点。结果大鼠Pten基因和Runx3基因属于CpG岛关联基因,启动子可能分别位于-1 253^-684 bp和-690^-121 bp,Pten和Runx3基因在109和94种转录因子结合位点中,被≥2种软件共同预测有结合位点的转录因子分别有6和9种。结论初步获得大鼠Pten和Runx3基因5'-UTR序列的生物学信息,为进一步基因调控甲基化实验验证奠定了基础。

Objective To analyze the potential GpG island, promoter and transcriptional factor binding sites of 5＇ un- translatered region of Runx3 and Pten in rats. Methods By NCBI, the total full-length sequences and transcripts of Runx3 and Pten were obtained, and analyzed by open reading frame （ORF） in Blast. The sequences of the first exon, the intron and 5＇ untranslated region of Runx3 and Pten was taken from ATG between 2 000 bp upstream and 1 000 bp downstream and applied into CpG island searcher, CpGPlot, Methprimer 2. O, NNPP, Promoter scan, FirstEF, Matlspector, Match, Consite to predict the potential GpG island, promoter and transcriptional factor binding sites. Results The 5＇ untranslated region of Runx3 and Pten was both highly associated with CpG island. The potential promoter of Runx3 and Pten may be lo- cated - 1 253- -684 bp and -690- - 121 bp respectively. Totally 109 and 94 promoters and transcriptional factor binding sites of Runx3 and Pten were predicted by all the above online tools/software, of which 6 and 9 were overlapped by two and more software. Conclusion We primarily completes the bioinformatics analysis of 5＇ untranslated region of Runx3 and Pten in rats, which lays foundation for further gene regulating methylation experiments.