title: Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP.
abstract: The identification of endogenous targets remains an important challenge in understanding microRNA (miRNA) function. Past approaches using in silico methods and reporter constructs lack biological context that may enhance or inhibit target recognition. To address these limitations, several labs have utilized crosslinking and immunoprecipitation (CLIP) of Argonaute (Ago) proteins to identify miRNA targets. Recently, the Ule Lab introduced individual-nucleotide resolution CLIP (iCLIP) to increase the sensitivity of identifying protein-RNA interaction sites. Here we adapt the iCLIP protocol for use in Caenorhabditis elegans to identify endogenous sites targeted by the worm Argonaute (ALG-1) primarily responsible for miRNA function.
authors.affiliation: Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Broughton
authors.forename: Amy E
authors.initials: AE
authors.lastname: Pasquinelli
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000302:isolation & purification* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000302:isolation & purification* / Q000378:metabolism; D017931:DNA Primers / Q000235:genetics; D047468:Immunoprecipitation / Q000379:methods; D035683:MicroRNAs / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D008969:Molecular Sequence Data; D034622:RNA Interference; D016601:RNA-Binding Proteins / Q000302:isolation & purification* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: C558782:ALG-1 protein, C elegans; D060565:Argonaute Proteins; D029742:Caenorhabditis elegans Proteins; D017931:DNA Primers; D035683:MicroRNAs; D016601:RNA-Binding Proteins
keywords: Argonaute; C. elegans; iCLIP; miRNA