title: PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.
abstract: During post-transcriptional gene regulation (PTGR), RNA binding proteins (RBPs) interact with all classes of RNA to control RNA maturation, stability, transport, and translation. Here, we describe Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), a transcriptome-scale method for identifying RBP binding sites on target RNAs with nucleotide-level resolution. This method is readily applicable to any protein directly contacting RNA, including RBPs that are predicted to bind in a sequence- or structure-dependent manner at discrete RNA recognition elements (RREs), and those that are thought to bind transiently, such as RNA polymerases or helicases.
authors.affiliation: Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS / NIH, 50 South Drive, 20892, Bethesda, MD, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Danan
authors.affiliation: Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS / NIH, 50 South Drive, 20892, Bethesda, MD, USA.
authors.forename: Sudhir
authors.initials: S
authors.lastname: Manickavel
authors.affiliation: Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS / NIH, 50 South Drive, 20892, Bethesda, MD, USA. markus.hafner@nih.gov.
authors.forename: Markus
authors.initials: M
authors.lastname: Hafner
mesh_terms: D001665:Binding Sites; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods*; D016601:RNA-Binding Proteins / Q000096:biosynthesis / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D016601:RNA-Binding Proteins
keywords: Binding site; Cross-linking and immunoprecipitation (CLIP); Noncoding RNA; Photoactivatable ribonucleoside enhanced cross-linking and immunoprecipitation (PAR-CLIP); Posttranscriptional gene regulation (PTGR); RNA; RNA recognition element (RRE); RNA-binding protein (RBP); mRNA