Identification and characterization of the potential promoter regions of 1031 kinds of human genes
Identification and characterization of the potential promoter regions of 1031 kinds of human genes
复制标题
DOI：
10.1101/gr.gr-1640r
复制
发表时间：
2001-05-01
期刊：
影响因子：
7
通讯作者：
Sugano, S
中科院分区：
文献类型：
--
作者：
Suzuki, Y;Tsunoda, T;Sugano, S
为了了解转录调控的机制，鉴定和鉴定位于mRNA起始点附近的启动子是至关重要的。为了从大量的基因组序列中鉴定启动子，我们使用了通过对用寡核苷酸封顶方法构建的cDNA文库进行大规模测序而确定的mRNA起始点。我们将mRNA起始点与基因组序列进行比对，并检索到相邻序列作为1031个基因的潜在启动子区域(PPR)。搜索PPR序列以确定主要启动子元件的频率。在1031个PPR中，329个(32%)含有TATA盒，872个(85%)含有引发剂，999个(97%)含有CC盒，663个(%)含有CAAT盒。此外，493例(48%)PPR位于CpG岛。这种CpG岛的频率在TATA(+)/LNR(+)PPR和普遍表达的基因的PPR中降低。在具有高度结肠特异性表达模式的CGM2基因、DRA基因和TM30pl基因的PPR中，普遍观察到E盒的共同序列。PPR也可用于研究启动子SNPs。
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the "oligo-capping" method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained CC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA(+)/lnr(+) PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful For exploring promoter SNPs.