Huisinga Kathryn L, Pugh B Franklin
Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Genome Biol. 2007;8(4):R46. doi: 10.1186/gb-2007-8-4-r46.
Eukaryotic genes are controlled by proteins that assemble stepwise into a transcription complex. How the individual biochemically defined assembly steps are coordinated and applied throughout a genome is largely unknown. Here, we model and experimentally test a portion of the assembly process involving the regulation of the TATA binding protein (TBP) throughout the yeast genome.
Biochemical knowledge was used to formulate a series of coupled TBP regulatory reactions involving TFIID, SAGA, NC2, Mot1, and promoter DNA. The reactions were then linked to basic segments of the transcription cycle and modeled computationally. A single framework was employed, allowing the contribution of specific steps to vary from gene to gene. Promoter binding and transcriptional output were measured genome-wide using ChIP-chip and expression microarray assays. Mutagenesis was used to test the framework by shutting down specific parts of the network.
The model accounts for the regulation of TBP at most transcriptionally active promoters and provides a conceptual tool for interpreting genome-wide data sets. The findings further demonstrate the interconnections of TBP regulation on a genome-wide scale.
真核基因由逐步组装成转录复合物的蛋白质控制。单个生化定义的组装步骤如何在整个基因组中协调并应用，目前很大程度上尚不清楚。在此，我们对酵母基因组中涉及TATA结合蛋白（TBP）调控的部分组装过程进行建模并进行实验测试。
利用生化知识构建了一系列涉及TFIID、SAGA、NC2、Mot1和启动子DNA的耦合TBP调控反应。然后将这些反应与转录周期的基本片段相联系并进行计算建模。采用了一个单一的框架，使得特定步骤的贡献因基因而异。使用染色质免疫沉淀芯片（ChIP-chip）和表达微阵列分析在全基因组范围内测量启动子结合和转录输出。通过关闭网络的特定部分，利用诱变来测试该框架。
该模型解释了大多数转录活性启动子处TBP的调控情况，并为解释全基因组数据集提供了一个概念工具。这些发现进一步证明了全基因组范围内TBP调控的相互联系。
