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Analysis of combinatorial cis-regulation in synthetic and genomic promoters

Author

Listed:
  • Jason Gertz

    (Center for Genome Sciences, Washington University in Saint Louis School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA)

  • Eric D. Siggia

    (Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA)

  • Barak A. Cohen

    (Center for Genome Sciences, Washington University in Saint Louis School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA)

Abstract

Gene promoters: expressing themselves Despite countless catalogues of genomic binding sites for transcription factors, predicting the expression of a gene purely based on its DNA sequence has remained very inaccurate. Gertz et al. present a general thermodynamic model that accurately captures the relationship between a gene promoter sequence, including weak, statistically undetectable regulatory sites, and its expression output. The work implies that chromatin plays a relatively minor role in directing gene expression and will facilitate rational genetic design in biotechnology and synthetic biology.

Suggested Citation

  • Jason Gertz & Eric D. Siggia & Barak A. Cohen, 2009. "Analysis of combinatorial cis-regulation in synthetic and genomic promoters," Nature, Nature, vol. 457(7226), pages 215-218, January.
    • Handle: RePEc:nat:nature:v:457:y:2009:i:7226:d:10.1038_nature07521
    DOI: 10.1038/nature07521
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    Cited by:

    1. Manuel Cambón & Óscar Sánchez, 2022. "Thermodynamic Modelling of Transcriptional Control: A Sensitivity Analysis," Mathematics, MDPI, vol. 10(13), pages 1-18, June.
    2. Haiqing Xu & Chuan Li & Chuan Xu & Jianzhi Zhang, 2023. "Chance promoter activities illuminate the origins of eukaryotic intergenic transcriptions," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Muir Morrison & Manuel Razo-Mejia & Rob Phillips, 2021. "Reconciling kinetic and thermodynamic models of bacterial transcription," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-30, January.
    4. Farzaneh Khajouei & Saurabh Sinha, 2018. "An information theoretic treatment of sequence-to-expression modeling," PLOS Computational Biology, Public Library of Science, vol. 14(9), pages 1-24, September.
    5. Kroll, K.M. & Ferrantini, A. & Domany, E., 2010. "Introduction to biology and chromosomal instabilities in cancer," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(20), pages 4374-4388.

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