Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters
Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters
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DOI：
10.1016/j.gene.2006.09.029
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发表时间：
2007-03-01
期刊：
影响因子：
3.5
通讯作者：
Martinez, Ernest
中科院分区：
文献类型：
--
作者：
Yang, Chuhu;Bolotin, Eugene;Martinez, Ernest
真核基因的核心启动子是最小的DNA区域，它招募基本的转录机制来指导高效和准确的转录启动。含有特定核心启动子元件如TATA盒和启动子(INR)的人和酵母基因的部分仍不清楚，针对TATA缺失基因的核心启动子基序仍有待鉴定。在这里，我们提供的基因组规模的计算分析表明，类似于76%的人类核心启动子缺乏TATA样元件，具有高GC含量，并富含Sp1结合位点。我们进一步确定了两个基序-M3(SCGGAAGY)和M22(TGCGCANK)-优先出现在人TATA缺失的核心启动子中。大约24%的人类基因具有TATA样元件，其启动子通常是富含AT的；然而，只有大约10%的含有TATA的启动子具有典型的TATA盒(TATAWR)。相比之下，约46%的人类核心启动子含有共识INR(YYANVNY)，约30%为含INR的TATA缺失基因。值得注意的是，大约46%的人类启动子同时缺乏TATA样元件和共识INR元件。令人惊讶的是，哺乳动物类型的INR序列存在于转录起始点(TSS)区域，并且倾向于聚集在类似于40%的酵母核心启动子的区域，并且特定核心启动子类型的频率在酵母和人类基因组中似乎是保守的。基因本体论分析表明，人类中没有TATA的基因，如酵母中的基因，经常参与基本的“家务”过程，而含有TATA的基因往往受到高度调控，例如受到生物或压力刺激的影响。这些结果揭示了特定的核心启动子类型在酵母和人类中的出现及其相关生物学过程中出人意料的相似之处，并指出了新的脊椎动物特有的DNA基序，这些基序可能在TATA非依赖转录中发挥选择性作用。(C)2006爱思唯尔B.V.保留所有权利。
The core promoter of eukaryotic genes is the minimal DNA region that recruits the basal transcription machinery to direct efficient and accurate transcription initiation. The fraction of human and yeast genes that contain specific core promoter elements such as the TATA box and the initiator (INR) remains unclear and core promoter motifs specific for TATA-less genes remain to be identified. Here, we present genome-scale computational analyses indicating that similar to 76% of human core promoters lack TATA-like elements, have a high GC content, and are enriched in Sp1-binding sites. We further identify two motifs-M3 (SCGGAAGY) and M22 (TGCGCANK)-that occur preferentially in human TATA-less core promoters. About 24% of human genes have a TATA-like element and their promoters are generally AT-rich; however, only similar to 10% of these TATA-containing promoters have the canonical TATA box (TATAWAWR). In contrast, similar to 46% of human core promoters contain the consensus INR (YYANVNY) and similar to 30% are INR-containing TATA-less genes. Significantly, similar to 46% of human promoters lack both TATA-like and consensus INR elements. Surprisingly, mammalian-type INR sequences are present-and tend to cluster-in the transcription start site (TSS) region of similar to 40% of yeast core promoters and the frequency of specific core promoter types appears to be conserved in yeast and human genomes. Gene Ontology analyses reveal that TATA-less genes in humans, as in yeast, are frequently involved in basic "housekeeping" processes, while TATA-containing genes are more often highly regulated, such as by biotic or stress stimuli. These results reveal unexpected similarities in the occurrence of specific core promoter types and in their associated biological processes in yeast and humans and point to novel vertebrate-specific DNA motifs that might play a selective role in TATA-independent transcription. (c) 2006 Elsevier B.V. All rights reserved.