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Measuring cis-regulatory energetics in living cells using allelic manifolds

Forcier, Talitha L. and Ayaz, Andalus and Gill, Manraj S. and Jones, Daniel and Phillips, Rob and Kinney, Justin B. (2018) Measuring cis-regulatory energetics in living cells using allelic manifolds. eLife, 7 . Art. No. e40618. ISSN 2050-084X. https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526476

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Abstract

Gene expression in all organisms is controlled by cooperative interactions between DNA-bound transcription factors (TFs), but quantitatively measuring TF-DNA and TF-TF interactions remains difficult. Here we introduce a strategy for precisely measuring the Gibbs free energy of such interactions in living cells. This strategy centers on the measurement and modeling of ‘allelic manifolds’, a multidimensional generalization of the classical genetics concept of allelic series. Allelic manifolds are measured using reporter assays performed on strategically designed cis-regulatory sequences. Quantitative biophysical models are then fit to the resulting data. We used this strategy to study regulation by two Escherichia coliTFs, CRP and σ^(70) RNA polymerase. Doing so, we consistently obtained energetic measurements precise to ∼0.1 kcal/mol. We also obtained multiple results that deviate from the prior literature. Our strategy is compatible with massively parallel reporter assays in both prokaryotes and eukaryotes, and should therefore be highly scalable and broadly applicable.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.7554/eLife.40618DOIArticle
https://doi.org/10.1101/380972DOIDiscussion Paper
ORCID:
AuthorORCID
Jones, Daniel0000-0002-7902-996X
Phillips, Rob0000-0003-3082-2809
Kinney, Justin B.0000-0003-1897-3778
Additional Information:© 2018 Forcier et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. Received: 31 July 2018; Accepted: 27 November 2018; Published: 20 December 2018. We thank Stirling Churchman, Barak Cohen, David McCandlish, Bryce Nickels, and Saurabh Sinha for helpful discussions. We also thank Naama Barkai, Ulrich Gerland, Richard Neher, and one anonymous referee for reviewing this manuscript and providing helpful feedback. This work was supported by a CSHL/Northwell Health Alliance grant to JBK and by NIH Cancer Center Support Grant 5P30CA045508. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Author contributions: Talitha L Forcier, Data curation, Software, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing-review and editing; Andalus Ayaz, Data curation, Validation, Investigation, Methodology, Writing-review and editing; Manraj S Gill, Data curation, Validation, Investigation, Methodology; Daniel Jones, Conceptualization, Investigation, Methodology; Rob Phillips, Supervision, Funding acquisition, Writing—review and editing; Justin B Kinney, Conceptualization, Resources, Data curation, Software, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing—original draft, Project administration, Writing—review and editing. Data availability: All data used to make the Figures is available in Supplementary file 1. The PSAM for RNAP, previously published by Kinney et al. (2010), is also provided in Supplementary file 1 (with permission). Raw data, processed data, and analysis scripts are also available at https://github.com/jbkinney/17_inducibility (copy archived at https://github.com/elifesciences-publications/17_inducibility). No datasets have been deposited in public databases as part of this work.
Funders:
Funding AgencyGrant Number
Cold Spring Harbor Laboratory/Northwell Health AllianceUNSPECIFIED
NIH5P30CA045508
Record Number:CaltechAUTHORS:20181128-093526476
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526476
Official Citation:Measuring cis-regulatory energetics in living cells using allelic manifolds. Talitha Forcier, Andalus Ayaz, Manraj S. Gill, Daniel Jones, Rob Phillips, Justin B. Kinney. eLife 2018;7:e40618. doi: 10.7554/eLife.40618
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91275
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:28 Nov 2018 18:04
Last Modified:03 Oct 2019 20:33

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