title: CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs.
abstract: Circular RNAs (circRNAs) constitute a new class of noncoding RNAs in higher eukaryotes generated from pre-mRNAs by alternative splicing. Here we investigated in mammalian cells the association of circRNAs with proteins. Using glycerol gradient centrifugation, we characterized in cell lysates circRNA-protein complexes (circRNPs) of distinct sizes. By polysome-gradient fractionation we found no evidence for efficient translation of a set of abundant circRNAs in HeLa cells. To identify circRNPs with a specific protein component, we focused on IMP3 (IGF2BP3, insulin-like growth factor 2 binding protein 3), a known tumor marker and RNA-binding protein. Combining RNA-seq analysis of IMP3-co-immunoprecipitated RNA and filtering for circular-junction reads identified a set of IMP3-associated circRNAs, which were validated and characterized. In sum, our data suggest that specific circRNP families exist defined by a common protein component. In addition, this provides a general approach to identify circRNPs with a given protein component.
authors: Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
authors: Tim
authors: T
authors: Schneider
authors: Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
authors: Lee-Hsueh
authors: LH
authors: Hung
authors: Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
authors: Silke
authors: S
authors: Schreiner
authors: Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
authors: Stefan
authors: S
authors: Starke
authors: Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
authors: Heinrich
authors: H
authors: Eckhof
authors: Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
authors: Oliver
authors: O
authors: Rossbach
authors: Biochemistry I, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany.
authors: Stefan
authors: S
authors: Reich
authors: Biochemistry I, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany.
authors: Jan
authors: J
authors: Medenbach
authors: Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
authors: Albrecht
authors: A
authors: Bindereif
mesh_terms: D019295:Computational Biology; D006367:HeLa Cells; D006801:Humans; D047468:Immunoprecipitation; D011485:Protein Binding; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D000079962:RNA, Circular; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: C498780:IGF2BP3 protein, human; D000079962:RNA, Circular; D016601:RNA-Binding Proteins; D012313:RNA