uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Measuring cis-regulatory energetics in living cells using allelic manifolds
Cold Spring Harbor Lab, Simons Ctr Quantitat Biol, POB 100, Cold Spring Harbor, NY 11724 USA.
Cold Spring Harbor Lab, Simons Ctr Quantitat Biol, POB 100, Cold Spring Harbor, NY 11724 USA.
Cold Spring Harbor Lab, Simons Ctr Quantitat Biol, POB 100, Cold Spring Harbor, NY 11724 USA;MIT, Dept Biol, Cambridge, MA 02139 USA.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Cold Spring Harbor Lab, Simons Ctr Quantitat Biol, POB 100, Cold Spring Harbor, NY 11724 USA;CALTECH, Dept Appl Phys, Pasadena, CA 91125 USA.
Show others and affiliations
2018 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 7, article id e40618Article in journal (Refereed) Published
Abstract [en]

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 coli TFs, CRP and sigma(70) RNA polymerase. Doing so, we consistently obtained energetic measurements precise to similar 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.

Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that minor issues remain unresolved (see decision letter).

Place, publisher, year, edition, pages
ELIFE SCIENCES PUBLICATIONS LTD , 2018. Vol. 7, article id e40618
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-372885DOI: 10.7554/eLife.40618ISI: 000453818300001PubMedID: 30570483OAI: oai:DiVA.org:uu-372885DiVA, id: diva2:1277104
Available from: 2019-01-09 Created: 2019-01-09 Last updated: 2019-01-09Bibliographically approved

Open Access in DiVA

fulltext(2540 kB)65 downloads
File information
File name FULLTEXT01.pdfFile size 2540 kBChecksum SHA-512
736d058eb2f61978eb84582580809406e7743a91d21acf2543a406612659852b203e6d755465740047a763a6cd5a48b6aa3f1f632ba9228181ed12a127f91d60
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records BETA

Jones, Daniel

Search in DiVA

By author/editor
Jones, Daniel
By organisation
Molecular Systems Biology
In the same journal
eLIFE
Genetics

Search outside of DiVA

GoogleGoogle Scholar
Total: 65 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 140 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf