Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.
Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.
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DOI：
10.1371/journal.pone.0024279
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
van Nimwegen E
中科院分区：
文献类型：
--
作者：
Erb I;van Nimwegen E
大部分酵母转录因子的序列特异性和用于结合位点预测的比较基因组算法的可用性使得有可能在全基因组范围内全面注释转录因子结合位点。在这里，我们使用这样一个全基因组的注释，全面研究启动子结构在酵母中，专注于转录因子结合位点相对于转录起始位点的分布，和架构的TATA和TATA少启动子。对于大多数转录因子，结合位点位于更上游，并且在TATA启动子中比在TATA较少的启动子中在更宽的范围内变化。相比之下，一组“近端启动子基序”（GAT 1/GLN 3/DAL 80、FKH 1/2、PBF 1/2、RPN 4、NDT 80和ROX 1）优先出现在TATA较少的启动子中，并显示出在这些启动子中靠近转录起始位点结合的强烈偏好。我们提供的证据表明，前起始复合物在TATA启动子的TATA位点和TATA-少启动子的其他近端启动子基序的位点被募集。TATA-少启动子通常可以通过它们含有的近端启动子基序来分类，不同类别的TATA-少启动子显示不同的转录因子结合位点定位和核小体覆盖模式。这些观察结果表明，不同的转录起始调控模式可能在不同的启动子类别中起作用。此外，我们表明，在所有的启动子类，有一个密切的匹配之间的核小体自由区和区域的最高转录因子结合位点密度。转录因子结合位点密度和核小体消耗之间的这种密切的一致性表明转录因子和核小体之间直接和普遍的竞争结合启动子。
The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of ‘proximal promoter motifs’ (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1) occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters.
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