title: Capturing microRNA targets using an RNA-induced silencing complex (RISC)-trap approach.
abstract: Identifying targets is critical for understanding the biological effects of microRNA (miRNA) expression. The challenge lies in characterizing the cohort of targets for a specific miRNA, especially when targets are being actively down-regulated in miRNA- RNA-induced silencing complex (RISC)-messengerRNA (mRNA) complexes. We have developed a robust and versatile strategy called RISCtrap to stabilize and purify targets from this transient interaction. Its utility was demonstrated by determining specific high-confidence target datasets for miR-124, miR-132, and miR-181 that contained known and previously unknown transcripts. Two previously unknown miR-132 targets identified with RISCtrap, adaptor protein CT10 regulator of kinase 1 (CRK1) and tight junction-associated protein 1 (TJAP1), were shown to be endogenously regulated by miR-132 in adult mouse forebrain. The datasets, moreover, differed in the number of targets and in the types and frequency of microRNA recognition element (MRE) motifs, thus revealing a previously underappreciated level of specificity in the target sets regulated by individual miRNAs.
authors.affiliation: Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA. ang@ohsu.edu
authors.forename: Xiaolu A
authors.initials: XA
authors.lastname: Cambronne
authors.forename: Rongkun
authors.initials: R
authors.lastname: Shen
authors.forename: Paul L
authors.initials: PL
authors.lastname: Auer
authors.forename: Richard H
authors.initials: RH
authors.lastname: Goodman
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D057809:HEK293 Cells; D006801:Humans; D046911:Macromolecular Substances; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D021122:Protein Subunits; D050737:Proto-Oncogene Proteins c-crk / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D034743:RNA-Induced Silencing Complex / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017384:Sequence Deletion; D062725:Tight Junction Proteins / Q000378:metabolism
chemical_list: C509207:MIRN124 microRNA, human; C547077:MIRN132 microRNA, human; C540193:MIrn181 microRNA, human; D046911:Macromolecular Substances; D035683:MicroRNAs; D021122:Protein Subunits; D050737:Proto-Oncogene Proteins c-crk; D012333:RNA, Messenger; D034743:RNA-Induced Silencing Complex; C445327:TJAP1 protein, human; D062725:Tight Junction Proteins