Cell-type specific features of circular RNA expression.
TLDR
Using an improved computational approach for circular RNA identification, widespread circular RNA expression is found in Drosophila melanogaster and it is estimated that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA.Abstract:
Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program.read more
Citations
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Journal ArticleDOI
The biogenesis, biology and characterization of circular RNAs.
Lasse Sommer Kristensen,Maria S. Andersen,Lotte V. W. Stagsted,Karoline K. Ebbesen,Thomas B. Hansen,Jørgen Kjems +5 more
TL;DR: Advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of state-of-the-art approaches for their identification, and novel approaches to functional characterization are emerging.
Journal ArticleDOI
circRNA Biogenesis Competes with Pre-mRNA Splicing
Reut Ashwal-Fluss,Markus Meyer,Nagarjuna Reddy Pamudurti,Andranik Ivanov,Osnat Bartok,Mor Hanan,Naveh Evantal,Sebastian Memczak,Nikolaus Rajewsky,Sebastian Kadener +9 more
TL;DR: Evidence that animal circRNAs are generated cotranscriptionally and that their production rate is mainly determined by intronic sequences is provided and it is demonstrated that circularization and splicing compete against each other.
Journal ArticleDOI
Exon-intron circular RNAs regulate transcription in the nucleus
Zhaoyong Li,Chuan Huang,Chun Bao,Liang Chen,Mei Lin,Xiaolin Wang,Guolin Zhong,Bin Yu,Wanchen Hu,Limin Dai,Pengfei Zhu,Zhaoxia Chang,Qingfa Wu,Yi Zhao,Ya Jia,Ping Xu,Huijie Liu,Ge Shan +17 more
TL;DR: A new role for circRNAs in regulating gene expression in the nucleus is revealed, in which EIciRNAs enhance the expression of their parental genes in cis, and a regulatory strategy for transcriptional control via specific RNA-RNA interaction between U1 snRNA and EICIRNAs is highlighted.
Journal ArticleDOI
Detecting and characterizing circular RNAs
TL;DR: Evidence is emerging that some circRNAs might regulate microRNA (miRNA) function, and roles in transcriptional control have also been suggested.
Journal ArticleDOI
Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed
Agnieszka Rybak-Wolf,Christin Stottmeister,Petar Glažar,Marvin Jens,Natalia S. Pino,Sebastian A. Giusti,Mor Hanan,Mikaela Behm,Osnat Bartok,Reut Ashwal-Fluss,Margareta Herzog,Luisa Schreyer,Panagiotis Papavasileiou,Andranik Ivanov,Marie Öhman,Damian Refojo,Sebastian Kadener,Nikolaus Rajewsky +17 more
TL;DR: A circRNA brain expression atlas and evidence for important circRNA functions and values as biomarkers are provided and discovered and analyzed thousands of neuronal human and mouse circRNAs.
References
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Circular RNAs are a large class of animal RNAs with regulatory potency
Sebastian Memczak,Marvin Jens,Antigoni Elefsinioti,Francesca Torti,Janna Krueger,Agnieszka Rybak,Luisa Maier,Sebastian D. Mackowiak,Lea H. Gregersen,Mathias Munschauer,Alexander Loewer,Ulrike Ziebold,Markus Landthaler,Christine Kocks,Ferdinand le Noble,Nikolaus Rajewsky +15 more
TL;DR: It is found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7.
Journal ArticleDOI
Natural RNA circles function as efficient microRNA sponges
Thomas B. Hansen,Trine I. Jensen,Bettina Hjelm Clausen,Jesper B. Bramsen,Bente Finsen,Christian Kroun Damgaard,Jørgen Kjems +6 more
TL;DR: This study serves as the first functional analysis of a naturally expressed circular RNA, ciRS-7, which contains more than 70 selectively conserved miRNA target sites, and is highly and widely associated with Argonaute proteins in a miR-7-dependent manner.
Journal ArticleDOI
Circular RNAs are abundant, conserved, and associated with ALU repeats
William R. Jeck,Jessica A. Sorrentino,Kai Wang,Michael K. Slevin,Christin E. Burd,Jinze Liu,William F. Marzluff,Norman E. Sharpless +7 more
TL;DR: High-throughput sequencing of libraries prepared from ribosome-depleted RNA with or without digestion with the RNA exonuclease showed that ecircRNAs are abundant, stable, conserved and nonrandom products of RNA splicing that could be involved in control of gene expression.