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      Circular RNAs: Biogenesis, Function and Role in Human Diseases

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          Abstract

          Circular RNAs (circRNAs) are currently classed as non-coding RNA (ncRNA) that, unlike linear RNAs, form covalently closed continuous loops and act as gene regulators in mammals. They were originally thought to represent errors in splicing and considered to be of low abundance, however, there is now an increased appreciation of their important function in gene regulation. circRNAs are differentially generated by backsplicing of exons or from lariat introns. Unlike linear RNA, the 3′ and 5′ ends normally present in an RNA molecule have been joined together by covalent bonds leading to circularization. Interestingly, they have been found to be abundant, evolutionally conserved and relatively stable in the cytoplasm. These features confer numerous potential functions to circRNAs, such as acting as miRNA sponges, or binding to RNA-associated proteins to form RNA-protein complexes that regulate gene transcription. It has been proposed that circRNA regulate gene expression at the transcriptional or post-transcriptional level by interacting with miRNAs and that circRNAs may have a role in regulating miRNA function in cancer initiation and progression. circRNAs appear to be more often downregulated in tumor tissue compared to normal tissue and this may be due to (i) errors in the back-splice machinery in malignant tissues, (ii) degradation of circRNAs by deregulated miRNAs in tumor tissue, or (iii) increasing cell proliferation leading to a reduction of circRNAs. circRNAs have been identified in exosomes and more recently, chromosomal translocations in cancer have been shown to generate aberrant fusion-circRNAs associated with resistance to drug treatments. In addition, though originally thought to be non-coding, there is now increasing evidence to suggest that select circRNAs can be translated into functional proteins. Although much remains to be elucidated about circRNA biology and mechanisms of gene regulation, these ncRNAs are quickly emerging as potential disease biomarkers and therapeutic targets in cancer.

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          Most cited references41

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          Aging, Cellular Senescence, and Cancer

          For most species, aging promotes a host of degenerative pathologies that are characterized by debilitating losses of tissue or cellular function. However, especially among vertebrates, aging also promotes hyperplastic pathologies, the most deadly of which is cancer. In contrast to the loss of function that characterizes degenerating cells and tissues, malignant (cancerous) cells must acquire new (albeit aberrant) functions that allow them to develop into a lethal tumor. This review discusses the idea that, despite seemingly opposite characteristics, the degenerative and hyperplastic pathologies of aging are at least partly linked by a common biological phenomenon: a cellular stress response known as cellular senescence. The senescence response is widely recognized as a potent tumor suppressive mechanism. However, recent evidence strengthens the idea that it also drives both degenerative and hyperplastic pathologies, most likely by promoting chronic inflammation. Thus, the senescence response may be the result of antagonistically pleiotropic gene action.
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            Circular intronic long noncoding RNAs.

            We describe the identification and characterization of circular intronic long noncoding RNAs in human cells, which accumulate owing to a failure in debranching. The formation of such circular intronic RNAs (ciRNAs) can be recapitulated using expression vectors, and their processing depends on a consensus motif containing a 7 nt GU-rich element near the 5' splice site and an 11 nt C-rich element close to the branchpoint site. In addition, we show that ciRNAs are abundant in the nucleus and have little enrichment for microRNA target sites. Importantly, knockdown of ciRNAs led to the reduced expression of their parent genes. One abundant such RNA, ci-ankrd52, largely accumulates to its sites of transcription, associates with elongation Pol II machinery, and acts as a positive regulator of Pol II transcription. This study thus suggests a cis-regulatory role of noncoding intronic transcripts on their parent coding genes. Copyright © 2013 Elsevier Inc. All rights reserved.
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              CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

              Recent studies reveal that circular RNAs (circRNAs) are a novel class of abundant, stable and ubiquitous noncoding RNA molecules in animals. Comprehensive detection of circRNAs from high-throughput transcriptome data is an initial and crucial step to study their biogenesis and function. Here, we present a novel chiastic clipping signal-based algorithm, CIRI, to unbiasedly and accurately detect circRNAs from transcriptome data by employing multiple filtration strategies. By applying CIRI to ENCODE RNA-seq data, we for the first time identify and experimentally validate the prevalence of intronic/intergenic circRNAs as well as fragments specific to them in the human transcriptome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0571-3) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Journal
                Front Mol Biosci
                Front Mol Biosci
                Front. Mol. Biosci.
                Frontiers in Molecular Biosciences
                Frontiers Media S.A.
                2296-889X
                06 June 2017
                2017
                : 4
                : 38
                Affiliations
                [1] 1Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin Dublin, Ireland
                [2] 2Department of Medical Oncology, Tallaght Hospital Dublin, Ireland
                [3] 3Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital Dublin, Ireland
                [4] 4Department of Clinical Medicine, Trinity College Dublin Dublin, Ireland
                [5] 5Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology Brisbane, QLD, Australia
                [6] 6Department of Medical Oncology, St. Vincent's University Hospital Dublin, Ireland
                [7] 7HOPE Directorate, St. James's Hospital Dublin, Ireland
                [8] 8Labmed Directorate, St. James's Hospital Dublin, Ireland
                [9] 9Department of Histopathology, St. James's Hospital Dublin, Ireland
                Author notes

                Edited by: Florent Hubé, UMR7216 Epigenetics and Cell Fate, France

                Reviewed by: Jeroen Pasterkamp, Utrecht University, Netherlands; Walter J. Lukiw, LSU Health Sciences Center New Orleans, United States

                *Correspondence: John Greene greenejo@ 123456tcd.ie

                This article was submitted to RNA, a section of the journal Frontiers in Molecular Biosciences

                Article
                10.3389/fmolb.2017.00038
                5459888
                28634583
                9847f15d-564f-438a-96e8-22abeb47fd45
                Copyright © 2017 Greene, Baird, Brady, Lim, Gray, McDermott and Finn.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 09 March 2017
                : 22 May 2017
                Page count
                Figures: 2, Tables: 3, Equations: 0, References: 112, Pages: 11, Words: 9775
                Funding
                Funded by: Prostate Cancer Foundation 10.13039/100000892
                Funded by: Irish Cancer Society 10.13039/501100001593
                Categories
                Molecular Biosciences
                Review

                circrnas,non-coding rna,mirna,diseases,cancer
                circrnas, non-coding rna, mirna, diseases, cancer

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