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
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TLDR
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.Abstract:
Noncoding RNAs (ncRNAs) have numerous roles in development and disease, and one of the prominent roles is to regulate gene expression A vast number of circular RNAs (circRNAs) have been identified, and some have been shown to function as microRNA sponges in animal cells Here, we report a class of circRNAs associated with RNA polymerase II in human cells In these circRNAs, exons are circularized with introns 'retained' between exons; we term them exon-intron circRNAs or EIciRNAs EIciRNAs predominantly localize in the nucleus, interact with U1 snRNP and promote transcription of their parental genes Our findings reveal a new role for circRNAs in regulating gene expression in the nucleus, in which EIciRNAs enhance the expression of their parental genes in cis, and highlight a regulatory strategy for transcriptional control via specific RNA-RNA interaction between U1 snRNA and EIciRNAsread more
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Unique features of long non-coding RNA biogenesis and function
Jeffrey J. Quinn,Howard Y. Chang +1 more
TL;DR: This Review describes special events in the lifetimes of lncRNAs — before, during and after transcription — and discusses how these events ultimately shape the unique characteristics and functional roles of lNCRNAs.
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
Regulation of circRNA biogenesis
Ling-Ling Chen,Li Yang +1 more
TL;DR: Current understanding of the regulation of circRNA biogenesis is highlighted, including both the competition between splicing and back-splicing and the previously under-appreciated alternative circularization.
Journal ArticleDOI
Circular RNA: A new star of noncoding RNAs
Shibin Qu,Xisheng Yang,Xiaolei Li,Jianlin Wang,Yuan Gao,Runze Shang,Wei Sun,Kefeng Dou,Haimin Li +8 more
TL;DR: Similar to miRNAs and long noncoding RNAs (lncRNAs), circRNAs are becoming a new research hotspot in the field of RNA and could be widely involved in the processes of life.
Journal ArticleDOI
The Biogenesis, Functions, and Challenges of Circular RNAs.
TL;DR: The recent progress on circRNA biogenesis and function is surveyed and technical obstacles in circRNA studies are discussed.
References
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Journal ArticleDOI
The Human Genome Browser at UCSC
W. James Kent,Charles W. Sugnet,Terrence S. Furey,Krishna M. Roskin,Tom H. Pringle,Alan M. Zahler,and David Haussler +6 more
TL;DR: A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu.
Journal ArticleDOI
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
Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
John L. Rinn,Michael Kertesz,Jordon K. Wang,Sharon L. Squazzo,Xiao Xu,Samantha A. Brugmann,L. Henry Goodnough,Jill A. Helms,Peggy J. Farnham,Eran Segal,Howard Y. Chang +10 more
TL;DR: The transcriptional landscape of the four human HOX loci is characterized at five base pair resolution in 11 anatomic sites and 231 HOX ncRNAs are identified that extend known transcribed regions by more than 30 kilobases, suggesting transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance.
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.