Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells.

[1]  Robert J. Marinelli,et al.  ESRRA-C11orf20 Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma , 2011, PLoS biology.

[2]  G. Danieli,et al.  A 3' consensus splice mutation in the human dystrophin gene detected by a screening for intra-exonic deletions. , 1992, Human molecular genetics.

[3]  P. Goodfellow,et al.  Expression of Sry, the mouse sex determining gene. , 1995, Development.

[4]  AC Tose.  Cell , 1993, Cell.

[5]  Xiang Shao,et al.  Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans , 2006, Bioinform..

[6]  B. Bailleul.  During in vivo maturation of eukaryotic nuclear mRNA, splicing yields excised exon circles. , 1996, Nucleic acids research.

[7]  P. Sarnow,et al.  Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. , 1995, Science.

[8]  H. Domdey,et al.  In vitro generation of a circular exon from a linear pre-mRNA transcript. , 1996, Nucleic acids research.

[9]  Jørgen Kjems,et al.  miRNA‐dependent gene silencing involving Ago2‐mediated cleavage of a circular antisense RNA , 2011, The EMBO journal.

[10]  P. Zaphiropoulos,et al.  Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[11]  P. Zaphiropoulos,et al.  Exon skipping and circular RNA formation in transcripts of the human cytochrome P-450 2C18 gene in epidermis and of the rat androgen binding protein gene in testis , 1997, Molecular and cellular biology.

[12]  C. Caldas,et al.  Exon scrambling of MLL transcripts occur commonly and mimic partial genomic duplication of the gene. , 1998, Gene.

[13]  P. Pandolfi,et al.  A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.

[14]  Peter Goodfellow,et al.  Circular transcripts of the testis-determining gene Sry in adult mouse testis , 1993, Cell.

[15]  J. Bowles,et al.  Expression of a linear Sry transcript in the mouse genital ridge , 1995, Nature Genetics.

[16]  William R. Jeck,et al.  Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk , 2010, PLoS genetics.

[17]  I. Nonaka,et al.  Circular dystrophin RNAs consisting of exons that were skipped by alternative splicing. , 1999, Human molecular genetics.

[18]  J. Houseley,et al.  Noncanonical RNAs from transcripts of the Drosophila muscleblind gene. , 2006, The Journal of heredity.

[19]  C. Cocquerelle,et al.  Splicing with inverted order of exons occurs proximal to large introns. , 1992, The EMBO journal.

[20]  Michael Q. Zhang,et al.  Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing , 2006, Nucleic acids research.

[21]  D. H. Robinson,et al.  Expression of the mouse testis‐determining gene Sry in male preimplantation embryos , 1995, Molecular reproduction and development.

[22]  J. Lytton,et al.  A Circularized Sodium-Calcium Exchanger Exon 2 Transcript* , 1999, The Journal of Biological Chemistry.

[23]  Mark Wade,et al.  Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. , 2011, Genome research.

[24]  A. Kornblihtt,et al.  First come, first served revisited: factors affecting the same alternative splicing event have different effects on the relative rates of intron removal. , 2010, RNA.

[25]  M. Coca-Prados,et al.  Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells , 1979, Nature.

[26]  N. Samani,et al.  A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species , 2005, Nucleic acids research.

[27]  Kathleen R. Cho,et al.  Scrambled exons , 1991, Cell.

[28]  Li Yang,et al.  Genomewide characterization of non-polyadenylated RNAs , 2011, Genome Biology.

[29]  C. Cocquerelle,et al.  Mis‐splicing yields circular RNA molecules , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.