MicroRNA-based single-gene circuits buffer protein synthesis rates against perturbations

ACS Synth Biol. 2014 May 16;3(5):324-31. doi: 10.1021/sb4001867. Epub 2014 Jan 30.

Abstract

Achieving precise control of mammalian transgene expression has remained a long-standing, and increasingly urgent, challenge in biomedical science. Despite much work, single-cell methods have consistently revealed that mammalian gene expression levels remain susceptible to fluctuations (noise) and external perturbations. Here, we show that precise control of protein synthesis can be realized using a single-gene microRNA (miRNA)-based feed-forward loop (sgFFL). This minimal autoregulatory gene circuit consists of an intronic miRNA that targets its own transcript. In response to a step-like increase in transcription rate, the network generated a transient protein expression pulse before returning to a lower steady state level, thus exhibiting adaptation. Critically, the steady state protein levels were independent of the size of the stimulus, demonstrating that this simple network architecture effectively buffered protein production against changes in transcription. The single-gene network architecture was also effective in buffering against transcriptional noise, leading to reduced cell-to-cell variability in protein synthesis. Noise was up to 5-fold lower for a sgFFL than for an unregulated control gene with equal mean protein levels. The noise buffering capability varied predictably with the strength of the miRNA-target interaction. Together, these results suggest that the sgFFL single-gene motif provides a general and broadly applicable platform for robust gene expression in synthetic and natural gene circuits.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Cell Line
  • Feedback, Physiological
  • Gene Regulatory Networks / genetics*
  • Luminescent Proteins / genetics
  • Luminescent Proteins / metabolism
  • Mice
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Models, Genetic*
  • Protein Biosynthesis / genetics*
  • Red Fluorescent Protein
  • Signal Transduction / genetics
  • Signal Transduction / physiology
  • Synthetic Biology / methods*

Substances

  • Luminescent Proteins
  • MicroRNAs