Robison K, McGuire A M, Church G M
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
J Mol Biol. 1998 Nov 27;284(2):241-54. doi: 10.1006/jmbi.1998.2160.
A major mode of gene regulation occurs via the binding of specific proteins to specific DNA sequences. The availability of complete bacterial genome sequences offers an unprecedented opportunity to describe networks of such interactions by correlating existing experimental data with computational predictions. Of the 240 candidate Escherichia coli DNA-binding proteins, about 55 have DNA-binding sites identified by DNA footprinting. We used these sites to construct recognition matrices, which we used to search for additional binding sites in the E. coli genomic sequence. Many of these matrices show a strong preference for non-coding DNA. Discrepancies are identified between matrices derived from natural sites and those derived from SELEX (Systematic Evolution of Ligands by Exponential enrichment) experiments. We have constructed a database of these proteins and binding sites, called DPInteract (available at http://arep.med.harvard.edu/dpinteract).
基因调控的一种主要方式是通过特定蛋白质与特定DNA序列的结合来实现的。完整细菌基因组序列的可得性为通过将现有实验数据与计算预测相关联来描述此类相互作用网络提供了前所未有的机会。在240种候选大肠杆菌DNA结合蛋白中，约55种具有通过DNA足迹法鉴定的DNA结合位点。我们利用这些位点构建识别矩阵，并用其在大肠杆菌基因组序列中搜索其他结合位点。这些矩阵中的许多对非编码DNA表现出强烈偏好。我们还发现了源自天然位点的矩阵与源自SELEX（指数富集配体系统进化）实验的矩阵之间存在差异。我们构建了一个关于这些蛋白质和结合位点的数据库，称为DPInteract（可在http://arep.med.harvard.edu/dpinteract获取）。
