Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 115, Issue 21, Pages E4796-E4805Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1722055115
Keywords
gene regulation; massively parallel reporter assay; quantitative models; DNA affinity chromatography; mass spectrometry
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Funding
- La Fondation Pierre-Gilles de Gennes
- Rosen Center at Caltech
- NIH [DP1 OD000217, R01 GM085286, 1R35 GM118043-01]
- Maximizing Investigators' Research Award [1S10RR029594-01A1]
- Gordon and Betty Moore Foundation [GBMF227]
- Beckman Institute
- HHMI International Student Research Fellowship
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Gene regulation is one of the most ubiquitous processes in biology. However, while the catalog of bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in these genomes are regulated. At present, characterizing the molecular mechanisms by which individual regulatory sequences operate requires focused efforts using low-throughput methods. Here, we take a first step toward multipromoter dissection and show how a combination of massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used to dissect multiple bacterial promoters in a systematic way. We show this approach on both well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all cases, we recover nucleotide-resolution models of promoter mechanism. For some promoters, including previously unannotated ones, the approach allowed us to further extract quantitative biophysical models describing input-output relationships. Given the generality of the approach presented here, it opens up the possibility of quantitatively dissecting the mechanisms of promoter function in E. coli and a wide range of other bacteria.
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