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Building Enhancers from the Ground Up: A Synthetic Biology Approach

Amit, Roee and Garcia, Hernan G. and Phillips, Rob and Fraser, Scott E. (2011) Building Enhancers from the Ground Up: A Synthetic Biology Approach. Cell, 146 (1). pp. 105-118. ISSN 0092-8674. PMCID PMC3155781.

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A challenge of the synthetic biology approach is to use our understanding of a system to recreate a biological function with specific properties. We have applied this framework to bacterial enhancers, combining a driver, transcription factor binding sites, and a poised polymerase to create synthetic modular enhancers. Our findings suggest that enhancer-based transcriptional control depends critically and quantitatively on DNA looping, leading to complex regulatory effects when the enhancer cassettes contain additional transcription factor binding sites for TetR, a bacterial transcription factor. We show through a systematic interplay of experiment and thermodynamic modeling that the level of gene expression can be modulated to convert a variable inducer concentration input into discrete or step-like output expression levels. Finally, using a different DNA-binding protein (TraR), we show that the regulatory output is not a particular feature of the specific DNA-binding protein used for the enhancer but a general property of synthetic bacterial enhancers.

Item Type:Article
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URLURL TypeDescription CentralArticle
Fraser, Scott E.0000-0002-5377-0223
Additional Information:© 2011 Elsevier Inc. Received 24 August 2010; revised 25 January 2011; accepted 14 June 2011. Published: July 7, 2011. Available online 7 July 2011. We would especially like to thank Prof. Frances H. Arnold for providing lab space and the forum to conduct thorough discussions as this project was evolving. We would also like to thank Eric H. Davidson for important early discussions and Alex J. Ninfa for plasmids and strains. R.A. was supported by a NIH Ruth L. Kirschstein fellowship, a Caltech CBCD grant, and the NIH through award NIH ARRA R01 GM085286-01S. R.P. and H.G.G. gratefully acknowledge awards NIH ARRA R01 GM085286-01S, R01 GM085286, and the NIH Director’s PIONEER Award DP1 OD000217.
Funding AgencyGrant Number
NIH Ruth L. Kirschstein FellowshipUNSPECIFIED
NIHARRA R01 GM085286-01S
NIHR01 GM085286
NIH Directors Pioneer AwardDP1 OD000217A
Issue or Number:1
PubMed Central ID:PMC3155781
Record Number:CaltechAUTHORS:20110725-075342594
Persistent URL:
Official Citation:Roee Amit, Hernan G. Garcia, Rob Phillips, Scott E. Fraser, Building Enhancers from the Ground Up: A Synthetic Biology Approach, Cell, Volume 146, Issue 1, 8 July 2011, Pages 105-118, ISSN 0092-8674, DOI: 10.1016/j.cell.2011.06.024. (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:24515
Deposited By: Ruth Sustaita
Deposited On:25 Jul 2011 15:41
Last Modified:03 Oct 2019 02:57

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