真核细胞中记忆的合理设计。
Rational design of memory in eukaryotic cells.
作者信息
Ajo-Franklin Caroline M, Drubin David A, Eskin Julian A, Gee Elaine P S, Landgraf Dirk, Phillips Ira, Silver Pamela A
机构信息
Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
出版信息
Genes Dev. 2007 Sep 15;21(18):2271-6. doi: 10.1101/gad.1586107.
Abstract
The ability to logically engineer novel cellular functions promises a deeper understanding of biological systems. Here we demonstrate the rational design of cellular memory in yeast that employs autoregulatory transcriptional positive feedback. We built a set of transcriptional activators and quantitatively characterized their effects on gene expression in living cells. Modeling in conjunction with the quantitative characterization of the activator-promoter pairs accurately predicts the behavior of the memory network. This study demonstrates the power of taking advantage of components with measured quantitative parameters to specify eukaryotic regulatory networks with desired properties.
摘要
从逻辑上设计新型细胞功能的能力有望让我们更深入地理解生物系统。在此，我们展示了在酵母中对细胞记忆的合理设计，该设计采用了自动调节转录正反馈。我们构建了一组转录激活因子，并定量表征了它们对活细胞中基因表达的影响。结合激活因子 - 启动子对的定量表征进行建模，能够准确预测记忆网络的行为。这项研究证明了利用具有测量定量参数的组件来指定具有所需特性的真核调节网络的强大力量。
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本文引用的文献
1
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Curr Biol. 2007 Apr 17;17(8):668-77. doi: 10.1016/j.cub.2007.03.016. Epub 2007 Mar 29.
2
Designing biological systems.设计生物系统。
Genes Dev. 2007 Feb 1;21(3):242-54. doi: 10.1101/gad.1507207.
3
Single-cell quantification of molecules and rates using open-source microscope-based cytometry.使用基于开源显微镜的细胞计数法对分子和速率进行单细胞定量分析。
Nat Methods. 2007 Feb;4(2):175-81. doi: 10.1038/nmeth1008. Epub 2007 Jan 21.
4
Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans.白色念珠菌中白色-不透明转换的主要调节因子WOR1的双稳态表达
Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12813-8. doi: 10.1073/pnas.0605270103. Epub 2006 Aug 11.
5
Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop.白色念珠菌中白色-不透明转换的表观遗传特性基于一个自我维持的转录反馈环。
Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12807-12. doi: 10.1073/pnas.0605138103. Epub 2006 Aug 9.
6
Synthetic biology: new engineering rules for an emerging discipline.合成生物学：一门新兴学科的新工程规则。
Mol Syst Biol. 2006;2:2006.0028. doi: 10.1038/msb4100073. Epub 2006 May 16.
7
A bottom-up approach to gene regulation.一种自下而上的基因调控方法。
Nature. 2006 Feb 16;439(7078):856-60. doi: 10.1038/nature04473.
8
Counting cytokinesis proteins globally and locally in fission yeast.在裂殖酵母中对胞质分裂蛋白进行整体和局部计数。
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9
Hysteresis in a synthetic mammalian gene network.合成哺乳动物基因网络中的滞后现象。
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Novel gene switches for targeted and timed expression of proteins of interest.用于靶向和定时表达感兴趣蛋白质的新型基因开关。
Mol Ther. 2005 Aug;12(2):290-8. doi: 10.1016/j.ymthe.2005.03.029.
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