Bajic Vladimir B, Choudhary Vidhu, Hock Chuan Koh
Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore.
In Silico Biol. 2004;4(2):109-25.
We analyzed an extended core promoter regions covering [-70,+60] segment relative to the transcription start site of human promoters contained in the Eukaryotic Promoter Database. The analysis was made by using the Match program ver. 1.9 with an optimized setting and the TRANSFAC Professional database ver. 7.2. This analysis revealed that the most common transcription factor binding site in the examined collection of core promoters appears to be initiator (characterized by GEN_INI), which is expected. The other less obvious sites found were Spz1, E2F-1, ZF5, and C/EBP. The 'cap' site was also in this most common group. Over-representation of these sites relative to the non-promoter background data ranged from 0.3167 to 32.1645. These sites were characterized by being present in more than 60% of promoter sequences. Interestingly, the TATA-box has been found in only 11.63% of all examined promoters. The study is complemented by separate analyses of promoter groups having different GC content. These additional analyses revealed that the most common promoter elements found also include AP-2, CdxA, Pax-2, SRY, STAT1 and STAT5A. It was also observed that a number of promoter elements show strong preference either for the GC-rich or the GC-poor core promoters.
我们分析了真核生物启动子数据库中包含的人类启动子转录起始位点相对的[-70,+60]区段的扩展核心启动子区域。分析使用了优化设置的Match程序1.9版和TRANSFAC Professional数据库7.2版。该分析表明，在所检测的核心启动子集合中，最常见的转录因子结合位点似乎是起始子（由GEN_INI表征），这在意料之中。发现的其他不太明显的位点有Spz1、E2F-1、ZF5和C/EBP。“帽”位点也在这个最常见的组中。相对于非启动子背景数据，这些位点的过度代表性范围为0.3167至32.1645。这些位点的特征是存在于超过60%的启动子序列中。有趣的是，在所有检测的启动子中，仅11.63%发现了TATA框。该研究通过对具有不同GC含量的启动子组进行单独分析得到补充。这些额外的分析表明，发现的最常见的启动子元件还包括AP-2、CdxA、Pax-2、SRY、STAT1和STAT5A。还观察到，许多启动子元件对富含GC或GC含量低的核心启动子表现出强烈偏好。
