Unit

UNIT 27.4 RNA Immunoprecipitation for Determining RNA-Protein Associations In Vivo

  1. Chris Gilbert,
  2. Jesper Q. Svejstrup

Published Online: 1 AUG 2006

DOI: 10.1002/0471142727.mb2704s75

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Gilbert, C. and Svejstrup, J. Q. 2006. RNA Immunoprecipitation for Determining RNA-Protein Associations In Vivo. Current Protocols in Molecular Biology. 75:27.4:27.4.1–27.4.11.

Author Information

  1. Cancer Research UK, London Research Institute, Clare Hall Laboratories, Hertfordshire, U.K.

Publication History

  1. Published Online: 1 AUG 2006
  2. Published Print: JUL 2006

Abstract

Similar to chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP) can be used to detect the association of individual proteins with specific nucleic acid regions, in this case on RNA. Live cells are treated with formaldehyde to generate protein-RNA cross-links between molecules that are in close proximity in vivo. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the formaldehyde cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR. The basics of RIP are very similar to those of ChIP, but with some important caveats. This unit describes the RIP procedure for Saccharomyces cerevisiae. Although the corresponding steps for metazoan cells have not yet been worked out, it is likely that the yeast procedure can easily be adapted for use in other organisms.

Keywords:

  • RNA immunoprecipitation;
  • RIP;
  • chromatin immunoprecipitation;
  • ChIP;
  • Transcription;
  • RNA metabolism