@article{TEXTUAL,
      recid = {8232},
      author = {Kinkhabwala, Ali and Guet, Călin C.},
      title = {Uncovering <i>cis</i> Regulatory Codes Using  Synthetic Promoter Shuffling},
      journal = {PLOS ONE},
      address = {2008-04-30},
      number = {TEXTUAL},
      abstract = {<p>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 <em>cis</em>  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  <em>cis</em> 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 spectrum of complex regulatory functions  that can be encoded by complex promoters. From an  engineering point of view, synthetic promoter shuffling  enables the experimental testing of the functional  properties of complex promoters that cannot necessarily be  inferred <em>ab initio</em> from the known properties of  the individual genetic components. Synthetic promoter  shuffling may provide a useful experimental tool for  studying naturally occurring promoter shuffling.</p>},
      url = {http://knowledge.uchicago.edu/record/8232},
}