Lascaris R F, Mager W H, Planta R J
Department of Biochemistry and Molecular Biology, IMBW, Biocentrum Amsterdam, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
Bioinformatics. 1999 Apr;15(4):267-77. doi: 10.1093/bioinformatics/15.4.267.
High-level transcriptional activation of most ribosomal protein (rp) genes in Saccharomyces cerevisiae is promoted by the global DNA-binding factor Rap1p. The creation of the complete database of yeast rp gene promoter sequences enabled us to develop a computational selection strategy aimed at acquiring detailed information concerning the DNA-binding specificity of Rap1p.
Rap1p sites in rp gene promoters are often found in duplicate, exhibiting strong preferences in both spacing and orientation. Using these preferences, a weight matrix was selected that represents the in vivo binding requirements of Rap1p. The resulting matrix renders the identification of functional Rap1p binding sites more accurate and allowed us to re-evaluate previous in vitro data. Tandemly arranged Rap1p binding sites appear to be typical for rp gene promoters and differ in preferred spacing from sites occurring in (sub)telomeric repeats. The preferred spacing that is found in duplicate Rap1p binding sites of rp gene promoters is restricted to a small window between 15 and 26 bp. This is proposed to reflect the borders within which binding co-operativity operates. The data presented clearly illustrate that computational selection strategies provide information that reaches beyond experimental data.
The rp database is available at the url: http://www. chem.vu.nl/BMB/Database.html.
酿酒酵母中大多数核糖体蛋白（rp）基因的高水平转录激活由全局DNA结合因子Rap1p促进。酵母rp基因启动子序列完整数据库的建立使我们能够开发一种计算选择策略，旨在获取有关Rap1p DNA结合特异性的详细信息。
rp基因启动子中的Rap1p位点通常成对出现，在间距和方向上都表现出强烈的偏好。利用这些偏好，选择了一个权重矩阵来代表Rap1p的体内结合要求。所得矩阵使功能性Rap1p结合位点的识别更加准确，并使我们能够重新评估以前的体外数据。串联排列的Rap1p结合位点似乎是rp基因启动子的典型特征，并且在优选间距上与（亚）端粒重复序列中出现的位点不同。在rp基因启动子的重复Rap1p结合位点中发现的优选间距限制在15至26 bp之间的小窗口内。这被认为反映了结合协同作用发生的边界。所呈现的数据清楚地表明，计算选择策略提供了超出实验数据的信息。
rp数据库可在以下网址获得：http://www.chem.vu.nl/BMB/Database.html。
