title: Capture and Identification of miRNA Targets by Biotin Pulldown and RNA-seq.
abstract: MicroRNAs (miRNAs) are small noncoding RNAs that regulate the stability and expression of target RNAs in a sequence-dependent manner. Identifying miRNA-regulated genes is key to understanding miRNA function. Here, we describe an unbiased biochemical pulldown method to identify with high-specificity miRNA targets. Regulated transcripts are enriched in streptavidin-captured mRNAs that bind to a transfected biotinylated miRNA mimic. The method is relatively simple, does not involve cross-linking and can be performed with only a million cells. Addition of an on-bead RNase digestion step also identifies miRNA recognition elements (MRE).
authors.affiliation: Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, 02115, USA.|Department of Pediatrics, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA.
authors.forename: Shen Mynn
authors.initials: SM
authors.lastname: Tan
authors.affiliation: Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, 02115, USA. Judy.Lieberman@childrens.harvard.edu.|Department of Pediatrics, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA. Judy.Lieberman@childrens.harvard.edu.
authors.forename: Judy
authors.initials: J
authors.lastname: Lieberman
mesh_terms: D001710:Biotin / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics* / Q000302:isolation & purification; D012333:RNA, Messenger / Q000235:genetics* / Q000302:isolation & purification; D012260:Ribonucleases / Q000235:genetics; D019809:Streptavidin / Q000737:chemistry
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D001710:Biotin; D019809:Streptavidin; D012260:Ribonucleases
keywords: MicroRNA; Noncoding RNA; Target identification; miRNA recognition element