Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time
- California Institute of Technology, United States
- California Institute of Technology, United States
- Cold Spring Harbor Laboratory, United States
Abstract
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli, for ≈ 65% of promoters we remain ignorant of their regulation. Until we crack this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method, Reg-Seq, that links massively-parallel reporter assays with mass spectrometry to produce a base pair resolution dissection of more than 100 E. coli promoters in 12 growth conditions. We demonstrate that the method recapitulates known regulatory information. Then, we examine regulatory architectures for more than 80 promoters which previously had no known regulatory information. In many cases, we also identify which transcription factors mediate their regulation. This method clears a path for highly multiplexed investigations of the regulatory genome of model organisms, with the potential of moving to an array of microbes of ecological and medical relevance.
Data availability
Sequencing data has been deposited in the SRA under accession no.PRJNA599253 and PRJNA603368Mass spectrometry data is deposited in the CalTech data repository at doi:10.22002/d1.1336Model files and inferred information footprints are deposited in the CalTech data repository at doi:10.22002/D1.1331Processed sequencing data sets and analysis software are available in the GitHub repository available at https://doi.org/10.5281/zenodo.3953312
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RNAseq data for the Reg-Seq projectShort Read Archive, PRJNA599253.
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Mass Spectrometry data for the Reg-Seq projectCalTech Data, 10.22002/d1.1336.
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Sequencing Data for mapping mutated constructsShort Read Archive, PRJNA603368.
Article and author information
Author details
Nathan M Belliveau
Michael J Sweredoski
Funding
National Institutes of Health (Director's Pioneer Award)
- Rob Phillips
National Institutes of Health (National Research Service Award,5T32GM007616-38)
- Suzannah M Beeler
National Institutes of Health (Maximizing Investigators Research Award)
- Rob Phillips
Howard Hughes Medical Institute (International Student Research Fellowship)
- Nathan M Belliveau
National Institutes of Health (1S10OD02001301)
- Annie Moradian
National Institutes of Health (1S10OD02001301)
- Michael J Sweredoski
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Armita Nourmohammad, University of Washington, United States
Publication history
- Received: January 20, 2020
- Accepted: September 18, 2020
- Accepted Manuscript published: September 21, 2020 (version 1)
- Version of Record published: October 16, 2020 (version 2)
Copyright
© 2020, Ireland et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time
eLife 9:e55308.
https://doi.org/10.7554/eLife.55308
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