Identification and detection of RNA-RNA interactions using the yeast RNA hybrid system

Nicolas Piganeau; Renée Schroeder

doi:10.1038/nprot.2006.111

Identification and detection of RNA-RNA interactions using the yeast RNA hybrid system

Nat Protoc. 2006;1(2):689-94. doi: 10.1038/nprot.2006.111.

Authors

Nicolas Piganeau¹, Renée Schroeder

Affiliation

¹ Institute of Biochemistry, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany.

PMID: 17406297
DOI: 10.1038/nprot.2006.111

Abstract

To test RNA-RNA interactions in cells, we developed a yeast RNA hybrid system derived from the yeast three-hybrid system. In this setup, the activation of a reporter gene (HIS3 or lacZ) is dependent on the interaction of two RNAs. One ('RNA X') is fused to MS2 RNA, forming the bait, which binds to a fusion protein composed of the MS2 coat and the LexA proteins. The second ('RNA Y') is fused to an RNA-based transcriptional activator (m26-11), forming the prey. If prey (RNA Y) binds to bait (RNA X), the m26-11 transcriptional activator is tethered to the promoter of the reporter genes. This protocol describes how to use this RNA hybrid system. In addition to testing RNA-RNA interactions, it can also be used to screen RNA libraries to identify new interaction partners or for mutational analysis of two known interaction partners.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Pairing*
Base Sequence
Mutation
RNA / chemistry*
RNA / genetics
RNA / metabolism*
Saccharomyces cerevisiae / genetics*
Two-Hybrid System Techniques*

Substances

RNA