Spatial promoter recognition signatures may enhance transcription factor specificity in yeast.
Spatial promoter recognition signatures may enhance transcription factor specificity in yeast.
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DOI：
10.1371/journal.pone.0053778
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Eisen MB
中科院分区：
文献类型：
--
作者：
Lusk RW;Eisen MB
由DNA结合转录因子识别的位点的短长度和高度简并性限制了它们可以携带的信息量，并且单个位点很少足以介导特定靶标的调节。微生物基因组的计算分析表明，许多因子在相对于其靶启动子处于特定方向和位置时发挥最佳功能。为了进一步研究这一点，我们开发并训练了结合位点定位的空间模型，并将其应用于酵母酿酒酵母的基因组。我们发现了38个转录因子的启动子内位点的非随机组织、结合位点密度的差异或两者兼而有之的证据。我们发现，这些签名允许转录因子的结合位点特异性有很大的差异，以共享类似的启动子特异性。我们说明了如何空间信息决定的定位和密度的结合位点原则上可以增加生物体的信息，用于区分转录因子的真正目标，我们表明如何利用这些信息可能在生物信息学分析的相同目的。
The short length and high degeneracy of sites recognized by DNA-binding transcription factors limit the amount of information they can carry, and individual sites are rarely sufficient to mediate the regulation of specific targets. Computational analysis of microbial genomes has suggested that many factors function optimally when in a particular orientation and position with respect to their target promoters. To investigate this further, we developed and trained spatial models of binding site positioning and applied them to the genome of the yeast Saccharomyces cerevisiae. We found evidence of non-random organization of sites within promoters, differences in binding site density, or both for thirty-eight transcription factors. We show that these signatures allow transcription factors with substantial differences in binding site specificity to share similar promoter specificities. We illustrate how spatial information dictating the positioning and density of binding sites can in principle increase the information available to the organism for differentiating a transcription factor’s true targets, and we indicate how this information could potentially be leveraged for the same purpose in bioinformatic analyses.
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