Transcription closed and open complex formation coordinate expression of genes with a shared promoter region

Antti Häkkinen, Samuel M.D. Oliveira, Ramakanth Neeli-Venkata, Andre S. Ribeiro

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Many genes are spaced closely, allowing coordination without explicit control through shared regulatory elements and molecular interactions. We study the dynamics of a stochastic model of a gene-pair in a head-to-head configuration, sharing promoter elements, which accounts for the rate-limiting steps in transcription initiation. We find that only in specific regions of the parameter space of the rate-limiting steps is orderly coexpression exhibited, suggesting that successful cooperation between closely spaced genes requires the coevolution of compatible rate-limiting step configuration. The model predictions are validated using in vivo single-cell, single-RNA measurements of the dynamics of pairs of genes sharing promoter elements. Our results suggest that, in E. coli, the kinetics of the rate-limiting steps in active transcription can play a central role in shaping the dynamics of gene-pairs sharing promoter elements.

Original languageEnglish
Article number20190507
Number of pages11
JournalJournal of the Royal Society Interface
Issue number161
Publication statusPublished - 1 Dec 2019
Publication typeA1 Journal article-refereed


  • Bidirectional promoter
  • Gene expression noise
  • Transcription

Publication forum classification

  • Publication forum level 1

ASJC Scopus subject areas

  • Biotechnology
  • Biophysics
  • Bioengineering
  • Biomaterials
  • Biochemistry
  • Biomedical Engineering


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