---
_id: '3751'
abstract:
- lang: eng
  text: '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 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 ab initio from the known properties of the
    individual genetic components. Synthetic promoter shuffling may provide a useful
    experimental tool for studying naturally occurring promoter shuffling.'
article_number: e2030
author:
- first_name: Ali
  full_name: Kinkhabwala, Ali
  last_name: Kinkhabwala
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
citation:
  ama: Kinkhabwala A, Guet CC. Uncovering cis regulatory codes using synthetic promoter
    shuffling. <i>PLoS One</i>. 2008;3(4). doi:<a href="https://doi.org/10.1371/journal.pone.0002030">10.1371/journal.pone.0002030</a>
  apa: Kinkhabwala, A., &#38; Guet, C. C. (2008). Uncovering cis regulatory codes
    using synthetic promoter shuffling. <i>PLoS One</i>. Public Library of Science.
    <a href="https://doi.org/10.1371/journal.pone.0002030">https://doi.org/10.1371/journal.pone.0002030</a>
  chicago: Kinkhabwala, Ali, and Calin C Guet. “Uncovering Cis Regulatory Codes Using
    Synthetic Promoter Shuffling.” <i>PLoS One</i>. Public Library of Science, 2008.
    <a href="https://doi.org/10.1371/journal.pone.0002030">https://doi.org/10.1371/journal.pone.0002030</a>.
  ieee: A. Kinkhabwala and C. C. Guet, “Uncovering cis regulatory codes using synthetic
    promoter shuffling,” <i>PLoS One</i>, vol. 3, no. 4. Public Library of Science,
    2008.
  ista: Kinkhabwala A, Guet CC. 2008. Uncovering cis regulatory codes using synthetic
    promoter shuffling. PLoS One. 3(4), e2030.
  mla: Kinkhabwala, Ali, and Calin C. Guet. “Uncovering Cis Regulatory Codes Using
    Synthetic Promoter Shuffling.” <i>PLoS One</i>, vol. 3, no. 4, e2030, Public Library
    of Science, 2008, doi:<a href="https://doi.org/10.1371/journal.pone.0002030">10.1371/journal.pone.0002030</a>.
  short: A. Kinkhabwala, C.C. Guet, PLoS One 3 (2008).
date_created: 2018-12-11T12:04:58Z
date_published: 2008-04-30T00:00:00Z
date_updated: 2021-01-12T07:51:56Z
day: '30'
ddc:
- '570'
doi: 10.1371/journal.pone.0002030
extern: '1'
external_id:
  pmid:
  - '18446205'
file:
- access_level: open_access
  checksum: 42c26f8337298a9ecadbe34a16139466
  content_type: application/pdf
  creator: dernst
  date_created: 2019-05-10T11:00:36Z
  date_updated: 2020-07-14T12:46:15Z
  file_id: '6400'
  file_name: 2008_PLOS1_Kinkhabwala.PDF
  file_size: 679786
  relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
fulldoi: https://doi.org/10.1371/journal.pone.0002030
has_accepted_license: '1'
intvolume: '         3'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2477'
quality_controlled: '1'
status: public
title: Uncovering cis regulatory codes using synthetic promoter shuffling
tmp:
  image: /images/cc_0.png
  legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
  name: Creative Commons Public Domain Dedication (CC0 1.0)
  short: CC0 (1.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2008'
...