Lorenz David R, Cantor Charles R, Collins James J
The Howard Hughes Medical Institute, Bioinformatics Program, Center for Advanced Biotechnology and Department of Biomedical Engineering. Boston University, 44 Cummington Street, Boston, MA 02215, USA.
Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1145-50. doi: 10.1073/pnas.0812551106. Epub 2009 Jan 21.
In this study, a reverse-engineering strategy was used to infer and analyze the structure and function of an aging and glucose repressed gene regulatory network in the budding yeast Saccharomyces cerevisiae. The method uses transcriptional perturbations to model the functional interactions between genes as a system of first-order ordinary differential equations. The resulting network model correctly identified the known interactions of key regulators in a 10-gene network from the Snf1 signaling pathway, which is required for expression of glucose-repressed genes upon calorie restriction. The majority of interactions predicted by the network model were confirmed using promoter-reporter gene fusions in gene-deletion mutants and chromatin immunoprecipitation experiments, revealing a more complex network architecture than previously appreciated. The reverse-engineered network model also predicted an unexpected role for transcriptional regulation of the SNF1 gene by hexose kinase enzyme/transcriptional repressor Hxk2, Mediator subunit Med8, and transcriptional repressor Mig1. These interactions were validated experimentally and used to design new experiments demonstrating Snf1 and its transcriptional regulators Hxk2 and Mig1 as modulators of chronological lifespan. This work demonstrates the value of using network inference methods to identify and characterize the regulators of complex phenotypes, such as aging.
在本研究中，采用了一种逆向工程策略来推断和分析出芽酵母酿酒酵母中衰老和葡萄糖抑制的基因调控网络的结构与功能。该方法利用转录扰动，将基因之间的功能相互作用建模为一阶常微分方程组。所得的网络模型正确识别了来自Snf1信号通路的一个10基因网络中关键调节因子的已知相互作用，而Snf1信号通路是热量限制时葡萄糖抑制基因表达所必需的。网络模型预测的大多数相互作用通过基因缺失突变体中的启动子 - 报告基因融合以及染色质免疫沉淀实验得到了证实，揭示了一个比之前所认识到的更为复杂的网络结构。逆向工程的网络模型还预测了己糖激酶/转录阻遏物Hxk2、中介亚基Med8和转录阻遏物Mig1对SNF1基因转录调控的意外作用。这些相互作用通过实验得到了验证，并用于设计新的实验，证明Snf1及其转录调节因子Hxk2和Mig1作为时序寿命的调节因子。这项工作证明了使用网络推断方法来识别和表征复杂表型（如衰老）的调节因子的价值。
