Creating small transcription activating RNAs

Nat Chem Biol. 2015 Mar;11(3):214-20. doi: 10.1038/nchembio.1737. Epub 2015 Feb 2.

Abstract

We expanded the mechanistic capability of small RNAs by creating an entirely synthetic mode of regulation: small transcription activating RNAs (STARs). Using two strategies, we engineered synthetic STAR regulators to disrupt the formation of an intrinsic transcription terminator placed upstream of a gene in Escherichia coli. This resulted in a group of four highly orthogonal STARs that had up to 94-fold activation. By systematically modifying sequence features of this group, we derived design principles for STAR function, which we then used to forward engineer a STAR that targets a terminator found in the Escherichia coli genome. Finally, we showed that STARs could be combined in tandem to create previously unattainable RNA-only transcriptional logic gates. STARs provide a new mechanism of regulation that will expand our ability to use small RNAs to construct synthetic gene networks that precisely control gene expression.

Publication types

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

MeSH terms

  • Escherichia coli / genetics
  • Gene Expression Regulation, Bacterial / genetics*
  • Gene Regulatory Networks
  • Genome, Bacterial
  • Kinetics
  • Models, Genetic
  • Plasmids / genetics
  • RNA / chemical synthesis*
  • RNA / genetics*
  • RNA, Bacterial / chemical synthesis
  • RNA, Bacterial / genetics
  • Terminator Regions, Genetic / genetics
  • Transcription Termination, Genetic
  • Transcription, Genetic*

Substances

  • RNA, Bacterial
  • RNA