title: nRIP-seq: a technique to identify RNA targets of an RNA binding protein on a genome-wide scale.
abstract: Native RNA immunoprecipitation (nRIP) coupled with high-throughput sequencing (nRIP-seq) is a powerful technique that allows transcriptome-wide identification of the entire subset of coding and noncoding RNAs associated with a particular protein. Since this technology is carried out in a native condition without cross-linking, nRIP-seq detects RNAs that bind a protein directly or indirectly through a larger RNA-protein complex. Here, we use the interaction between RNA and chromatin modifiers, Polycomb proteins, as an example to describe this method. Using nRIP-seq, we provide a snapshot of Ezh2, a Polycomb component, and RNA interaction in mouse embryonic stem cells.
authors.affiliation: RNA Biology Program, Sanford Children's Health Research Center, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd., La Jolla, CA, 92037, USA, czhao@sanfordburnham.org.
authors.forename: Jing Crystal
authors.initials: JC
authors.lastname: Zhao
mesh_terms: D000818:Animals; D053595:Embryonic Stem Cells / Q000378:metabolism; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D047468:Immunoprecipitation / Q000379:methods*; D051379:Mice; D063146:Polycomb-Group Proteins / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D012313:RNA / Q000032:analysis / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*
chemical_list: D063146:Polycomb-Group Proteins; D016601:RNA-Binding Proteins; D012313:RNA