Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq

Methods. 2014 May 1;67(1):13-9. doi: 10.1016/j.ymeth.2013.11.001. Epub 2013 Nov 17.


Post-transcriptional regulation of messenger RNA contributes to numerous aspects of gene expression. The key component to this level of regulation is the interaction of RNA-binding proteins (RBPs) and their associated target mRNA. Splicing, stability, localization, translational efficiency, and alternate codon use are just some of the post-transcriptional processes regulated by RBPs. Central to our understanding of these processes is the need to characterize the network of RBP-mRNA associations and create a map of this functional post-transcriptional regulatory system. Here we provide a detailed methodology for mRNA isolation using RBP immunoprecipitation (RIP) as a primary partitioning approach followed by microarray (Chip) or next generation sequencing (NGS) analysis. We do this by using specific antibodies to target RBPs for the capture of associated RNA cargo. RIP-Chip/Seq has proven to be is a versatile, genomic technique that has been widely used to study endogenous RBP-RNA associations.

Keywords: Microarray expression profiling; Post-Transcription; RIP-Chip; RIP-Seq; RNA-binding proteins (RBPs); Ribonomics; mRNA localization.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antibodies, Immobilized / chemistry
  • Binding Sites
  • Chromatin Immunoprecipitation
  • Chromosome Mapping
  • Gene Expression Profiling*
  • Gene Library
  • Gene Regulatory Networks
  • HeLa Cells
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • Principal Component Analysis
  • Protein Binding
  • RNA Interference*
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / physiology
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, RNA


  • Antibodies, Immobilized
  • RNA, Messenger
  • RNA-Binding Proteins