哺乳類基因啟動區的調控因子整合性分析系統

Abstract

座落在基因5’端的啟動區在基因轉錄的調控上扮演重要的角色，基因啟動區的序列跟結構上的特性影響著基因的轉錄初始化，雖然目前已有不少的基因啟動區相關的註解系統，但是並沒有ㄧ個是可以提供最完整的調控資訊，包含轉錄起始位置、轉錄子和轉錄子辨識位置、CpG island、重複序列、ATA box、CCAAT box、 GC box、統計上過度表現的寡核甘酸序列、單核甘酸多態性、DNA穩定性、GC含量、微小核醣核酸靶位點。為了方便基因啟動區的分析，此研究發展了一個整合性的系統，可以為哺乳類物種間（人類、大鼠、小鼠、狗、黑猩猩）的同源基因提供詳盡的調控資訊，此系統不但可以為已知基因的啟動區註解調控特性，也可以為使用者輸入的序列註解上可能的轉錄起始位置跟調控特性。並且這些基因啟動區所註解後的調控性質會以圖形化的方式呈現，這個整合性系統現在 http://RegProM.mbc.nctu.edu.tw/。

Promoters located at the 5’ ends of genes play an important role in gene transcriptional regulation. The sequence and structural features located in the gene promoter region are involved in regulating gene transcriptional initiation. Although numerous systems have been proposed for annotating promoter regions, none of them provided the comprehensive regulatory features such as Transcription Start Site, Transcription Factor Binding Site (TFBS), CpG island, repeats (SINE, LINE, tandem repeats, and so on), TATA box, CCAAT box, GC box, statistical over-represented (OR) oligonucleotide, single nucleotide polymorphism (SNP), DNA stability, GC-content and microRNA target sites. To facilitate the investigation of the gene promoters, this work presents an integrated system for annotating the regulatory features in homologous gene promoter regions of mammalian genomes, including human, mouse, rat, chimpanzee, and dog. The proposed system not only provides the regulatory features for the known gene promoter region, but also annotates the putative TSSs and regulatory features for the user inputted sequence. Furthermore, regulatory features are graphically visualized to facilitate the observation of gene promoters. The proposed integrated system is now available at http://regprom.mbc.nctu.edu.tw/.