Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

Alexandra Westbrook, Xun Tang, Ryan Marshall, Colin S. Maxwell, James Chappell, Deepak K. Agrawal, Mary J. Dunlop, Vincent Noireaux, Chase L. Beisel, Julius Lucks, Elisa Franco*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

To build complex genetic networks with predictable behaviors, synthetic biologists use libraries of modular parts that can be characterized in isolation and assembled together to create programmable higher-order functions. Characterization experiments and computational models for gene regulatory parts operating in isolation are routinely used to predict the dynamics of interconnected parts and guide the construction of new synthetic devices. Here, we individually characterize two modes of RNA-based transcriptional regulation, using small transcription activating RNAs (STARs) and clustered regularly interspaced short palindromic repeats interference (CRISPRi), and show how their distinct regulatory timescales can be used to engineer a composed feedforward loop that creates a pulse of gene expression. We use a cell-free transcription-translation system (TXTL) to rapidly characterize the system, and we apply Bayesian inference to extract kinetic parameters for an ordinary differential equation-based mechanistic model. We then demonstrate in simulation and verify with TXTL experiments that the simultaneous regulation of a single gene target with STARs and CRISPRi leads to a pulse of gene expression. Our results suggest the modularity of the two regulators in an integrated genetic circuit, and we anticipate that construction and modeling frameworks that can leverage this modularity will become increasingly important as synthetic circuits increase in complexity.

Original languageEnglish (US)
Pages (from-to)1139-1151
Number of pages13
JournalBiotechnology and Bioengineering
Volume116
Issue number5
DOIs
StatePublished - May 2019

Keywords

  • Bayesian methods
  • CRISPRi
  • RNA-based circuits
  • model-guided design
  • sRNA

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology

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