CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs

Sci Rep. 2016 Aug 11;6:31313. doi: 10.1038/srep31313.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • HeLa Cells
  • Humans
  • Immunoprecipitation
  • Protein Binding
  • RNA / genetics
  • RNA / metabolism*
  • RNA, Circular
  • RNA-Binding Proteins / metabolism*
  • Sequence Analysis, RNA / methods*

Substances

  • IGF2BP3 protein, human
  • RNA, Circular
  • RNA-Binding Proteins
  • RNA