Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq

Methods Mol Biol. 2014:1126:399-410. doi: 10.1007/978-1-62703-980-2_27.

Abstract

Eukaryotic genomes encode a large number of RNA-binding proteins, which play critical roles in many aspects of gene regulation. To functionally characterize these proteins, a key step is to map their interactions with target RNAs. UV crosslinking and immunoprecipitation coupled with high-throughput sequencing has become the standard method for this purpose. Here we describe the detailed procedure that we have used to characterize the protein-RNA interactions of the mRNA 3' processing factors.

Publication types

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

MeSH terms

  • Binding Sites
  • Eukaryota
  • Genome
  • High-Throughput Nucleotide Sequencing / methods
  • Immunoprecipitation / methods*
  • Molecular Biology / methods*
  • RNA / genetics*
  • RNA / isolation & purification
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / isolation & purification

Substances

  • RNA-Binding Proteins
  • RNA