title: Expanded identification and characterization of mammalian circular RNAs.
abstract: BACKGROUND
  The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, the global properties of circRNAs are not well understood.
  
  
  RESULTS
  We developed a computational pipeline to identify circRNAs and quantify their relative abundance from RNA-seq data. Applying this pipeline to a large set of non-poly(A)-selected RNA-seq data from the ENCODE project, we annotated 7,112 human circRNAs that were estimated to comprise at least 10% of the transcripts accumulating from their loci. Most circRNAs are expressed in only a few cell types and at low abundance, but they are no more cell-type-specific than are mRNAs with similar overall expression levels. Although most circRNAs overlap protein-coding sequences, ribosome profiling provides no evidence for their translation. We also annotated 635 mouse circRNAs, and although 20% of them are orthologous to human circRNAs, the sequence conservation of these circRNA orthologs is no higher than that of their neighboring linear exons. The previously proposed miR-7 sponge, CDR1as, is one of only two circRNAs with more miRNA sites than expected by chance, with the next best miRNA-sponge candidate deriving from a gene encoding a primate-specific zinc-finger protein, ZNF91.
  
  
  CONCLUSIONS
  Our results provide a new framework for future investigation of this intriguing topological isoform while raising doubts regarding a biological function of most circRNAs.
authors: Junjie U
authors: JU
authors: Guo
authors: Vikram
authors: V
authors: Agarwal
authors: Huili
authors: H
authors: Guo
authors: David P
authors: DP
authors: Bartel
mesh_terms: D000818:Animals; D001483:Base Sequence; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D015870:Gene Expression; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D011161:Porifera / Q000235:genetics; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D000079962:RNA, Circular; D017423:Sequence Analysis, RNA; D020040:Trans-Splicing
chemical_list: D035683:MicroRNAs; D000079962:RNA, Circular; D012313:RNA