Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock
Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock
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DOI：
10.1073/pnas.0802636105
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发表时间：
2008-09-30
影响因子：
11.1
通讯作者：
Ueda, Hiroki R.
中科院分区：
文献类型：
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作者：
Kumaki, Yuichi;Ukai-Tadenuma, Maki;Ueda, Hiroki R.
哺乳动物的生物钟由Clock/BMal1结合元件、DBP/E4BP4结合元件和RevErbA/ROR结合元件介导的调控环组成。作为在系统水平上理解振荡器动态转录调控的一步，我们构建并使用了一个哺乳动物启动子/增强子数据库(http://promoter.cdb.riken.jp/))，其中包含时钟/BMal1结合元件、DBP/E4BP4结合元件和RevErbA/RoR结合元件的计算模型，以预测时钟的新靶点，并随后在细胞和生物水平上验证这些靶点。我们通过产生和测试自然界中不存在的合成调控元件进一步证明了这些模型的预测性，并表明这些元件产生了高幅度的昼夜节律基因调控。对这些合成元件进行的生化实验揭示了反式激活因子和反式阻遏因子之间的亲和力平衡在产生高幅度昼夜转录输出中的重要性。这些结果突出了比较基因组学方法在系统水平识别和基于知识的动态调节电路设计方面的力量。
Mammalian circadian clocks consist of regulatory loops mediated by Clock/Bmal1-binding elements, DBP/E4BP4 binding elements, and RevErbA/ROR binding elements. As a step toward system-level understanding of the dynamic transcriptional regulation of the oscillator, we constructed and used a mammalian promoter/enhancer database (http://promoter.cdb.riken.jp/) with computational models of the Clock/Bmal1-binding elements, DBP/E4BP4 binding elements, and RevErbA/ROR binding elements to predict new targets of the clock and subsequently validated these targets at the level of the cell and organism. We further demonstrated the predictive nature of these models by generating and testing synthetic regulatory elements that do not occur in nature and showed that these elements produced high-amplitude circadian gene regulation. Biochemical experiments to characterize these synthetic elements revealed the importance of the affinity balance between transactivators and transrepressors in generating high-amplitude circadian transcriptional output. These results highlight the power of comparative genomics approaches for system-level identification and knowledge-based design of dynamic regulatory circuits.