uncovering cis regulatory codes using synthetic promoter shuffling发现cis监管码使用合成启动子洗牌.pdfVIP

Uncovering cis Regulatory Codes Using Synthetic Promoter Shuffling Ali Kinkhabwala1,2*, Ca˘lin C. Guet1,3* 1 Laboratory of Living Matter and Center for Studies in Physics and Biology, Rockefeller University, New York, New York, United States of America, 2 Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany, 3 Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, United States of America Abstract Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture — operator sequences binding activators and repressors — of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three- input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the