Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
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DOI：
10.1093/nar/29.3.774
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发表时间：
2001-02-01
影响因子：
14.9
通讯作者：
Lawrence, CE
中科院分区：
文献类型：
--
作者：
McCue, LA;Thompson, W;Lawrence, CE
为了确定几种γ变形菌基因组中完整的转录因子（TF）结合位点，从而描述它们的转录调控网络，我们提出了一种识别这些位点的系统发育足迹方法。利用扩展的Gibbs采样算法，通过跨物种比较确定了大肠杆菌基因上游可能的转录调控位点。对184个记录转录调控位点的基因的仔细研究表明，当至少有两个其他γ变形菌物种的同源数据可用时，我们的预测与记录的位点相对应的比例为81%，而只有一个其他物种的数据可用时，这一比例为67%。剩余的预测包括真正的tf结合位点，这是通过对一个推定的转录因子（YijC）的亲和纯化来证明的，该转录因子与fabA基因上游的这样一个位点结合。2097个大肠杆菌基因的预测调控位点可在http://www.wadsworth.org/resnres/bioinfo/上找到。
Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using an extended Gibbs sampling algorithm. Close examination of a study set of 184 genes with documented transcription regulatory sites revealed that when orthologous data were available from at least two other gamma proteobacterial species, 81% of our predictions corresponded with the documented sites, and 67% corresponded when data from only one other species were available, That the remaining predictions included bona fide TF-binding sites was proven by affinity purification of a putative transcription factor (YijC) bound to such a site upstream of the fabA gene. Predicted regulatory sites for 2097 E.coli genes are available at http://www.wadsworth.org/resnres/bioinfo/.