Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation
Jakub Orzechowski Westholm,Pedro Miura,Pedro Miura,Sara Olson,Sol Shenker,Sol Shenker,Brian Joseph,Piero Sanfilippo,Susan E. Celniker,Brenton R. Graveley,Eric C. Lai +10 more
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TLDR
This work exploits massive Drosophila total RNA-sequencing data, >5 billion paired-end reads from >100 libraries covering diverse developmental stages, tissues, and cultured cells, to rigorously annotate >2,500 fruit fly circular RNAs, which exhibit commonalities and distinctions from mammalian circles.About:
This article is published in Cell Reports.The article was published on 2014-12-11 and is currently open access. It has received 791 citations till now. The article focuses on the topics: Sequence analysis & Drosophila melanogaster.read more
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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
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.
Journal ArticleDOI
Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs
Qiupeng Zheng,Chunyang Bao,Weijie Guo,Weijie Guo,Shuyi Li,Shuyi Li,Jie Chen,Bing Chen,Yanting Luo,Dongbin Lyu,Yan Li,Guohai Shi,Linhui Liang,Jianren Gu,Xianghuo He,Shenglin Huang +15 more
TL;DR: The results provide evidence that circular RNA produced from precursor mRNA may have a regulatory role in human cells and characterize one abundant circRNA derived from Exon2 of the HIPK3 gene, termed circHIPK3.
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.
References
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M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
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Circular RNAs are a large class of animal RNAs with regulatory potency
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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.
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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.
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MicroRNA targeting specificity in mammals: determinants beyond seed pairing.
Andrew Grimson,Kyle Kai-How Farh,Wendy K. Johnston,Philip W. Garrett-engele,Lee P. Lim,David P. Bartel +5 more
TL;DR: Five general features of site context that boost site efficacy are uncovered: AU-rich nucleotide composition near the site, proximity to sites for coexpressed miRNAs (which leads to cooperative action), proximity to residues pairing to miRNA nucleotides 13-16, positioning within the 3'UTR at least 15 nt from the stop codon, and positioning away from the center of long UTRs.
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