Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

Simon Alamos; Armando Reimer; Clay Westrum; Meghan A Turner; Paul Talledo; Jiaxi Zhao; Emma Luu; Hernan G Garcia

doi:10.1016/j.cels.2022.12.008

Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

Cell Syst. 2023 Mar 15;14(3):220-236.e3. doi: 10.1016/j.cels.2022.12.008. Epub 2023 Jan 24.

Authors

Simon Alamos¹, Armando Reimer², Clay Westrum³, Meghan A Turner¹, Paul Talledo⁴, Jiaxi Zhao³, Emma Luu³, Hernan G Garcia⁵

Affiliations

¹ Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA.
² Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA.
³ Department of Physics, University of California at Berkeley, Berkeley, CA, USA.
⁴ Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
⁵ Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA; Department of Physics, University of California at Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA. Electronic address: hggarcia@berkeley.edu.

Abstract

How enhancers interpret morphogen gradients to generate gene expression patterns is a central question in developmental biology. Recent studies have proposed that enhancers can dictate whether, when, and at what rate promoters engage in transcription, but the complexity of endogenous enhancers calls for theoretical models with too many free parameters to quantitatively dissect these regulatory strategies. To overcome this limitation, we established a minimal promoter-proximal synthetic enhancer in embryos of Drosophila melanogaster. Here, a gradient of the Dorsal activator is read by a single Dorsal DNA binding site. Using live imaging to quantify transcriptional activity, we found that a single binding site can regulate whether promoters engage in transcription in a concentration-dependent manner. By modulating the binding-site affinity, we determined that a gene's decision to transcribe and its transcriptional onset time can be explained by a simple model where the promoter traverses multiple kinetic barriers before transcription can ensue.

Keywords: Drosophila melanogaster; biophysics; developmental biology; quantitative biology; transcriptional dynamic; transcriptional modeling; transcriptional regulation.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Drosophila Proteins* / genetics
Drosophila Proteins* / metabolism
Drosophila melanogaster* / genetics
Drosophila melanogaster* / metabolism
Enhancer Elements, Genetic / genetics
Gene Expression Regulation, Developmental / genetics
Probability

Substances

Drosophila Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding