Data for: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly-interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc finger-based TFs. We show that circuits ‘wired’ using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-termcontinuous culture. Our naturally-inspired approach offers a simple, generalizable means for building high-fidelity, ..., These data were generated to support the characterization of a toolkit used to construct cooperatively binding synthetic transcription factors (synTFs) in yeast to both build stable genetic circuits and better understand eukaryotic transcriptional regulation. Our inducible synthetic zinc finger-derived transcription factors harbor an activation domain and bind to 9 bp cis regulatory elements that we integrate into the yeast genome. We use these transcriptional activators to build insulated genetic circuits, characterizing their performance, and the fitness of yeast cells expressing the activators, in our published work. We demonstrate circuit stability in competition experiments as well as long-term evolution experiments and describe a circuit with memory that functions via positive feedback following a short induction period.
Our datasets, comprised of data gathered using flow cytometry from which we calculate activation, as well as cellular fitness measurements and growth rate measure..., The .fcs raw datasets require FlowJo to open, and the .pzfx processed data files require GraphPad Prism.

真核生物转录调控的一个普遍特征是转录因子（transcription factors, TFs）与DNA顺式调控基序之间的协同自组装。学界普遍认为，该策略可使基因网络中原本相互作用微弱、特异性较低的分子组分之间建立特异性调控连接。本研究借助在酵母中构建的合成基因回路，发现基于人工锌指的转录因子之间的协同多价相互作用可产生高调控特异性。我们证实，采用协同转录因子组装策略“接线”的基因回路，可有效隔绝宿主细胞基因组的异常失调。正如我们在实验与数学模型中所展示的，该机制足以挽救回路驱动的适应性缺陷，使回路在长期连续培养中具备遗传与功能稳定性。这种受自然启发的方法为构建高保真……提供了一种简单且可推广的途径。

本数据集旨在支持一套工具包的表征工作，该工具包用于在酵母中构建可协同结合的合成转录因子（synthetic transcription factors, synTFs），既可用于构建稳定的遗传回路，也可用于加深对真核生物转录调控的理解。我们的可诱导合成锌指来源转录因子携带有激活结构域，可结合我们整合至酵母基因组的9bp顺式调控元件。我们利用这些转录激活因子构建了绝缘型遗传回路，并在已发表的研究中表征了其性能以及表达该激活因子的酵母细胞的适应性。我们在竞争实验与长期进化实验中证实了回路的稳定性，并描述了一种经短暂诱导后通过正反馈发挥功能的具有记忆功能的回路。

本数据集包含通过流式细胞术采集的数据（我们通过该数据计算激活程度）、细胞适应性测量结果以及生长速率测量……其中.fcs原始数据集需使用FlowJo软件打开，.pzfx处理后的数据文件需使用GraphPad Prism软件打开。