RPAD (RNase R treatment, polyadenylation, and poly(A)+ RNA depletion) method to isolate highly pure circular RNA.
Reads0
Chats0
TLDR
RPAD enables the elucidation of circRNA biogenesis, sequence, and function by facilitating the isolation of highly pure circRNAs from total RNA pools.About:
This article is published in Methods.The article was published on 2019-02-15 and is currently open access. It has received 47 citations till now. The article focuses on the topics: Circular RNA & RNA.read more
Citations
More filters
Journal ArticleDOI
Integration of bioinformatic predictions and experimental data to identify circRNA-miRNA associations
Martina Dori,Silvio Bicciato +1 more
TL;DR: The potential to define miRNA “sponging” as a more general function of circRNAs is explored, the different approaches to predict miRNA response elements (MREs) in known or novel circRNA sequences are described and experiments based on Ago2-IP and experimentally validated miRNA:target duplexes are discussed.
Journal ArticleDOI
circSamd4 represses myogenic transcriptional activity of PUR proteins
Poonam R. Pandey,Jen-Hao Yang,Dimitrios Tsitsipatis,Amaresh C. Panda,Ji Heon Noh,Ji Heon Noh,Kyoung Mi Kim,Kyoung Mi Kim,Rachel Munk,Thomas Nicholson,Douglas Hanniford,Diana Argibay,Xiaoling Yang,Jennifer L. Martindale,Ming-Wen Chang,Simon W. Jones,Eva Hernando,Payel Sen,Supriyo De,Kotb Abdelmohsen,Myriam Gorospe +20 more
TL;DR: RNA sequencing analysis of circRNAs differentially expressed during myogenesis revealed that circSamd4 expression increased robustly in mouse C2C12 myoblasts differentiating into myotubes, and the association of PUR proteins with circSamD4 enhances myogenesis by contributing to the derepression of MHC transcription.
Journal ArticleDOI
Noncoding RNAs in Cardiovascular Disease: Current Knowledge, Tools and Technologies for Investigation, and Future Directions: A Scientific Statement From the American Heart Association.
Saumya Das,Ravi V. Shah,Stefanie Dimmeler,Jane E. Freedman,Christopher L. Holley,Jin-Moo Lee,Kathryn J. Moore,Kiran Musunuru,Da-Zhi Wang,Junjie Xiao,Ke-Jie Yin,Vascular Biology +11 more
TL;DR: The use of network approaches and advanced computational tools to understand the interaction of different noncoding RNA species to mediate a particular phenotype may be required to fully comprehend the function of nonc coding RNAs in mediating disease phenotypes.
Journal ArticleDOI
Circular RNAs-The Road Less Traveled.
TL;DR: The possible mechanism of circular RNA biogenesis, its structure, properties, degradation, and the growing amount of evidence regarding the detection methods and its role in animal and plant systems are discussed.
Journal ArticleDOI
Computational approaches for circular RNA analysis.
TL;DR: An overview on different computational analysis tools and pipelines that became available throughout the last years of circRNAs research is provided and a set of valuable validation strategies, in silico as well as in vitro‐based approaches are provided.
References
More filters
Journal ArticleDOI
Primer3—new capabilities and interfaces
Andreas Untergasser,Ioana Cutcutache,Triinu Koressaar,Jian Ye,Brant C. Faircloth,Maido Remm,Steven G. Rozen +6 more
TL;DR: Primer3’s current capabilities are described, including more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers.
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
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Thomas Derrien,Rory Johnson,Giovanni Bussotti,Andrea Tanzer,Sarah Djebali,Hagen Tilgner,Gregory Guernec,David C. Martin,Angelika Merkel,David G. Knowles,Julien Lagarde,Lavanya Veeravalli,Xiaoan Ruan,Yijun Ruan,Timo Lassmann,Piero Carninci,James B. Brown,Leonard Lipovich,José M. González,Mark G. Thomas,Carrie A. Davis,Ramin Shiekhattar,Thomas R. Gingeras,Tim Hubbard,Cedric Notredame,Jennifer Harrow,Roderic Guigó +26 more
TL;DR: The most complete human lncRNA annotation to date is presented, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts, and expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes.
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.