751
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Kramer MC, Liang D, Tatomer DC, Gold B, March ZM, Cherry S, Wilusz JE. Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes Dev 2015; 29:2168-82. [PMID: 26450910 PMCID: PMC4617980 DOI: 10.1101/gad.270421.115] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 09/18/2015] [Indexed: 01/08/2023]
Abstract
Kramer et al. discovered that circularization of the Drosophila laccase2 gene is regulated by both intronic repeats and trans-acting splicing factors. Unlike the previously characterized Muscleblind (Mbl) circular RNA, which requires the Mbl protein for its biogenesis, Laccase2 circular RNA levels are not controlled by Mbl or the Laccase2 gene product but rather by multiple hnRNP and SR proteins acting in a combinatorial manner. Thousands of eukaryotic protein-coding genes are noncanonically spliced to produce circular RNAs. Bioinformatics has indicated that long introns generally flank exons that circularize in Drosophila, but the underlying mechanisms by which these circular RNAs are generated are largely unknown. Here, using extensive mutagenesis of expression plasmids and RNAi screening, we reveal that circularization of the Drosophila laccase2 gene is regulated by both intronic repeats and trans-acting splicing factors. Analogous to what has been observed in humans and mice, base-pairing between highly complementary transposable elements facilitates backsplicing. Long flanking repeats (∼400 nucleotides [nt]) promote circularization cotranscriptionally, whereas pre-mRNAs containing minimal repeats (<40 nt) generate circular RNAs predominately after 3′ end processing. Unlike the previously characterized Muscleblind (Mbl) circular RNA, which requires the Mbl protein for its biogenesis, we found that Laccase2 circular RNA levels are not controlled by Mbl or the Laccase2 gene product but rather by multiple hnRNP (heterogeneous nuclear ribonucleoprotein) and SR (serine–arginine) proteins acting in a combinatorial manner. hnRNP and SR proteins also regulate the expression of other Drosophila circular RNAs, including Plexin A (PlexA), suggesting a common strategy for regulating backsplicing. Furthermore, the laccase2 flanking introns support efficient circularization of diverse exons in Drosophila and human cells, providing a new tool for exploring the functional consequences of circular RNA expression across eukaryotes.
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Affiliation(s)
- Marianne C Kramer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Dongming Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Beth Gold
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Zachary M March
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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752
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Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, Liu CC, Huang HD. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res 2015; 44:D209-15. [PMID: 26450965 PMCID: PMC4702939 DOI: 10.1093/nar/gkv940] [Citation(s) in RCA: 270] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/08/2015] [Indexed: 01/26/2023] Open
Abstract
Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA–miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.
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Affiliation(s)
- Yu-Chen Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Jian-Rong Li
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Chuan-Hu Sun
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Erik Andrews
- Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
| | - Rou-Fang Chao
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan Mackay Medicine, Nursing and Management College, Taipei, Taiwan Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chao Cheng
- Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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753
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Chuang TJ, Wu CS, Chen CY, Hung LY, Chiang TW, Yang MY. NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. Nucleic Acids Res 2015; 44:e29. [PMID: 26442529 PMCID: PMC4756807 DOI: 10.1093/nar/gkv1013] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022] Open
Abstract
Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts (trans-spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (>98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans-spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans-spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
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Affiliation(s)
- Trees-Juen Chuang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chan-Shuo Wu
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ying Chen
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Li-Yuan Hung
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Tai-Wei Chiang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Min-Yu Yang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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754
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Yang L. Splicing noncoding RNAs from the inside out. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:651-60. [PMID: 26424453 PMCID: PMC5054931 DOI: 10.1002/wrna.1307] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/12/2015] [Accepted: 08/21/2015] [Indexed: 12/21/2022]
Abstract
Eukaryotic precursor-messenger RNAs (pre-mRNAs) undergo splicing to remove intragenic regions (introns) and ligate expressed regions (exons) together. Unlike exons in the mature messenger RNAs (mRNAs) that are used for translation, introns that are spliced out of pre-mRNAs were generally believed to lack function and to be degraded. However, recent studies have revealed that a large group of spliced introns can escape complete degradation and are processed to generate noncoding RNAs (ncRNAs), including different types of small RNAs, long-noncoding RNAs, and circular RNAs. Strikingly, exonic sequences can be also back-spliced from pre-mRNAs to form stable circular RNAs. Together, the findings that ncRNAs can be spliced out of mRNA precursors not only expand the ever-growing repertoire of ncRNAs that originate from different genomic regions, but also reveal the unexpected transcriptomic complexity and functional capacity of eukaryotic genomes.
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Affiliation(s)
- Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology; CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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755
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Paz-Yaacov N, Bazak L, Buchumenski I, Porath HT, Danan-Gotthold M, Knisbacher BA, Eisenberg E, Levanon EY. Elevated RNA Editing Activity Is a Major Contributor to Transcriptomic Diversity in Tumors. Cell Rep 2015; 13:267-76. [PMID: 26440895 DOI: 10.1016/j.celrep.2015.08.080] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/02/2015] [Accepted: 08/28/2015] [Indexed: 01/08/2023] Open
Abstract
Genomic mutations in key genes are known to drive tumorigenesis and have been the focus of much attention in recent years. However, genetic content also may change farther downstream. RNA editing alters the mRNA sequence from its genomic blueprint in a dynamic and flexible way. A few isolated cases of editing alterations in cancer have been reported previously. Here, we provide a transcriptome-wide characterization of RNA editing across hundreds of cancer samples from multiple cancer tissues, and we show that A-to-I editing and the enzymes mediating this modification are significantly altered, usually elevated, in most cancer types. Increased editing activity is found to be associated with patient survival. As is the case with somatic mutations in DNA, most of these newly introduced RNA mutations are likely passengers, but a few may serve as drivers that may be novel candidates for therapeutic and diagnostic purposes.
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Affiliation(s)
- Nurit Paz-Yaacov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Lily Bazak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Eisenberg
- School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
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756
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Ye CY, Chen L, Liu C, Zhu QH, Fan L. Widespread noncoding circular RNAs in plants. THE NEW PHYTOLOGIST 2015; 208:88-95. [PMID: 26204923 DOI: 10.1111/nph.13585] [Citation(s) in RCA: 270] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/01/2015] [Indexed: 05/19/2023]
Abstract
A large number of noncoding circular RNAs (circRNAs) with regulatory potency have been identified in animals, but little attention has been given to plant circRNAs. We performed genome-wide identification of circRNAs in Oryza sativa and Arabidopsis thaliana using publically available RNA-Seq data, analyzed and compared features of plant and animal circRNAs. circRNAs (12037 and 6012) were identified in Oryza sativa and Arabidopsis thaliana, respectively, with 56% (10/18) of the sampled rice exonic circRNAs validated experimentally. Parent genes of over 700 exonic circRNAs were orthologues between rice and Arabidopsis, suggesting conservation of circRNAs in plants. The introns flanking plant circRNAs were much longer than introns from linear genes, and possessed less repetitive elements and reverse complementary sequences than the flanking introns of animal circRNAs. Plant circRNAs showed diverse expression patterns, and 27 rice exonic circRNAs were found to be differentially expressed under phosphate-sufficient and -starvation conditions. A significantly positive correlation was observed for the expression profiles of some circRNAs and their parent genes. Our results demonstrated that circRNAs are widespread in plants, revealed the common and distinct features of circRNAs between plants and animals, and suggested that circRNAs could be a critical class of noncoding regulators in plants.
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Affiliation(s)
- Chu-Yu Ye
- Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Li Chen
- Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Chen Liu
- Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, ACT, 2601, Australia
| | - Longjiang Fan
- Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
- Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
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757
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Pek JW, Okamura K. Regulatory RNAs discovered in unexpected places. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:671-86. [DOI: 10.1002/wrna.1309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/14/2015] [Accepted: 08/21/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Jun Wei Pek
- Temasek Life Sciences Laboratory; 1 Research Link, National University of Singapore; Singapore Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory; 1 Research Link, National University of Singapore; Singapore Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
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758
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Abstract
Non-coding RNAs have gained increasing attention, as their physiological and pathological functions are being gradually uncovered. MicroRNAs are the most well-studied ncRNAs, which play essential roles in translational repression and mRNA degradation. In contrast, long non-coding RNAs are distinguished from other small/short non-coding RNAs by length and regulate chromatin remodeling, gene transcription and posttranscriptional modifications. Recently, circular RNAs have emerged as endogenous, abundant, conserved and stable in mammalian cells. It has been demonstrated that circular RNAs can function as miRNA sponges. Other possible biological functions of circular RNAs are still under investigation. In this review, the biogenesis and biological functions of the three major types of ncRNAs, including miRNAs, lncRNAs and circRNAs, are overviewed. In addition, the role of ncRNAs in human diseases and potential clinical applications of ncRNAs are discussed.
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Affiliation(s)
- Nan Wu
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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759
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Abdelmohsen K, Gorospe M. Noncoding RNA control of cellular senescence. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:615-29. [PMID: 26331977 DOI: 10.1002/wrna.1297] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022]
Abstract
Senescent cells accumulate in normal tissues with advancing age and arise by long-term culture of primary cells. Senescence develops following exposure to a range of stress-causing agents and broadly influences the physiology and pathology of tissues, organs, and systems in the body. While many proteins are known to control senescence, numerous noncoding (nc)RNAs are also found to promote or repress the senescent phenotype. Here, we review the regulatory ncRNAs (primarily microRNAs and lncRNAs) identified to-date as key modulators of senescence. We highlight the major senescent pathways (p53/p21 and pRB/p16), as well as the senescence-associated secretory phenotype (SASP) and other senescence-associated events governed by ncRNAs, and discuss the importance of understanding comprehensively the ncRNAs implicated in cell senescence.
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Affiliation(s)
- Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
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760
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Abstract
Two studies published in this issue of Molecular Cell (Rybak-Wolf et al., 2015) and in the April issue of Nature Neuroscience (You et al., 2015) independently report the upregulated expression of back-spliced circular RNAs (circRNAs) in brains and suggest that they have a potential to regulate synaptic function.
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Affiliation(s)
- Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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761
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Chen I, Chen CY, Chuang TJ. Biogenesis, identification, and function of exonic circular RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:563-79. [PMID: 26230526 PMCID: PMC5042038 DOI: 10.1002/wrna.1294] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/11/2015] [Accepted: 06/16/2015] [Indexed: 01/20/2023]
Abstract
Circular RNAs (circRNAs) arise during post-transcriptional processes, in which a single-stranded RNA molecule forms a circle through covalent binding. Previously, circRNA products were often regarded to be splicing intermediates, by-products, or products of aberrant splicing. But recently, rapid advances in high-throughput RNA sequencing (RNA-seq) for global investigation of nonco-linear (NCL) RNAs, which comprised sequence segments that are topologically inconsistent with the reference genome, leads to renewed interest in this type of NCL RNA (i.e., circRNA), especially exonic circRNAs (ecircRNAs). Although the biogenesis and function of ecircRNAs are mostly unknown, some ecircRNAs are abundant, highly expressed, or evolutionarily conserved. Some ecircRNAs have been shown to affect microRNA regulation, and probably play roles in regulating parental gene transcription, cell proliferation, and RNA-binding proteins, indicating their functional potential for development as diagnostic tools. To date, thousands of ecircRNAs have been identified in multiple tissues/cell types from diverse species, through analyses of RNA-seq data. However, the detection of ecircRNA candidates involves several major challenges, including discrimination between ecircRNAs and other types of NCL RNAs (e.g., trans-spliced RNAs and genetic rearrangements); removal of sequencing errors, alignment errors, and in vitro artifacts; and the reconciliation of heterogeneous results arising from the use of different bioinformatics methods or sequencing data generated under different treatments. Such challenges may severely hamper the understanding of ecircRNAs. Herein, we review the biogenesis, identification, properties, and function of ecircRNAs, and discuss some unanswered questions regarding ecircRNAs. We also evaluate the accuracy (in terms of sensitivity and precision) of some well-known circRNA-detecting methods.
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Affiliation(s)
- Iju Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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762
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Huang C, Shan G. What happens at or after transcription: Insights into circRNA biogenesis and function. Transcription 2015; 6:61-4. [PMID: 26177684 DOI: 10.1080/21541264.2015.1071301] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Circular RNAs (circRNAs) are a large family of noncoding RNAs (ncRNAs) found in metazoans. Systematic studies of circRNAs have just begun. Here, we discuss circRNA biogenesis and functions with a focus on studies indicating great diversification of circRNAs. We highlight the recent identification of a special subtype of circRNAs, called EIciRNAs, and their role in transcriptional regulation. New insights on RNA-RNA interaction and other features associated with circRNA biology are also discussed.
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Affiliation(s)
- Chuan Huang
- a School of Life Sciences & CAS Key Laboratory of Brain Function and Disease; University of Science and Technology of China ; Hefei , Anhui Province , China
| | - Ge Shan
- a School of Life Sciences & CAS Key Laboratory of Brain Function and Disease; University of Science and Technology of China ; Hefei , Anhui Province , China
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763
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Ebbesen KK, Kjems J, Hansen TB. Circular RNAs: Identification, biogenesis and function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:163-8. [PMID: 26171810 DOI: 10.1016/j.bbagrm.2015.07.007] [Citation(s) in RCA: 380] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 12/21/2022]
Abstract
Circular RNAs are a novel class of non-coding RNA characterized by the presence of a covalent bond linking the 3' and 5' ends generated by backsplicing. Circular RNAs are widely expressed in a tissue and developmental-stage specific pattern and a subset displays conservation across species. Functional circRNAs have been shown to act as cytoplasmic microRNA sponges and RNA-binding protein sequestering agents as well as nuclear transcriptional regulators, illustrating the relevance of circular RNAs as participants in the regulatory networks governing gene expression. Here, we review the features that characterize circular RNAs, discuss putative circular RNA biogenesis pathways as well as review the uncovered functions of circular RNAs. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Karoline K Ebbesen
- Department of Molecular Biology and Genetics (MBG), Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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764
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Okada S, Sakurai M, Ueda H, Suzuki T. Biochemical and Transcriptome-Wide Identification of A-to-I RNA Editing Sites by ICE-Seq. Methods Enzymol 2015; 560:331-53. [PMID: 26253977 DOI: 10.1016/bs.mie.2015.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inosine (I) is a modified adenosine (A) in RNA. In Metazoa, I is generated by hydrolytic deamination of A, catalyzed by adenosine deaminase acting RNA (ADAR) in a process called A-to-I RNA editing. A-to-I RNA editing affects various biological processes by modulating gene expression. In addition, dysregulation of A-to-I RNA editing results in pathological consequences. I on RNA strands is converted to guanosine (G) during cDNA synthesis by reverse transcription. Thus, the conventional method used to identify A-to-I RNA editing sites compares cDNA sequences with their corresponding genomic sequences. Combined with deep sequencing, this method has been applied to transcriptome-wide screening of A-to-I RNA editing sites. This approach, however, produces a large number of false positives mainly owing to mapping errors. To address this issue, we developed a biochemical method called inosine chemical erasing (ICE) to reliably identify genuine A-to-I RNA editing sites. In addition, we applied the ICE method combined with RNA-seq, referred to as ICE-seq, to identify transcriptome-wide A-to-I RNA editing sites. In this chapter, we describe the detailed protocol for ICE-seq, which can be applied to various sources and taxa.
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Affiliation(s)
- Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masayuki Sakurai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroki Ueda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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765
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Tajaddod M, Jantsch MF, Licht K. The dynamic epitranscriptome: A to I editing modulates genetic information. Chromosoma 2015; 125:51-63. [PMID: 26148686 PMCID: PMC4761006 DOI: 10.1007/s00412-015-0526-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 02/03/2023]
Abstract
Adenosine to inosine editing (A to I editing) is a cotranscriptional process that contributes to transcriptome complexity by deamination of adenosines to inosines. Initially, the impact of A to I editing has been described for coding targets in the nervous system. Here, A to I editing leads to recoding and changes of single amino acids since inosine is normally interpreted as guanosine by cellular machines. However, more recently, new roles for A to I editing have emerged: Editing was shown to influence splicing and is found massively in Alu elements. Moreover, A to I editing is required to modulate innate immunity. We summarize the multiple ways in which A to I editing generates transcriptome variability and highlight recent findings in the field.
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Affiliation(s)
- Mansoureh Tajaddod
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria
| | - Michael F Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria. .,Department of Cell Biology, Center of Cell Biology and Anatomy, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090, Vienna, Austria.
| | - Konstantin Licht
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, A-1030, Vienna, Austria.
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766
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767
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Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J. Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biol 2015; 16:126. [PMID: 26076956 PMCID: PMC4506483 DOI: 10.1186/s13059-015-0690-5] [Citation(s) in RCA: 423] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 06/08/2015] [Indexed: 02/06/2023] Open
Abstract
Background The pervasive expression of circular RNA is a recently discovered feature of gene expression in highly diverged eukaryotes, but the functions of most circular RNAs are still unknown. Computational methods to discover and quantify circular RNA are essential. Moreover, discovering biological contexts where circular RNAs are regulated will shed light on potential functional roles they may play. Results We present a new algorithm that increases the sensitivity and specificity of circular RNA detection by discovering and quantifying circular and linear RNA splicing events at both annotated and un-annotated exon boundaries, including intergenic regions of the genome, with high statistical confidence. Unlike approaches that rely on read count and exon homology to determine confidence in prediction of circular RNA expression, our algorithm uses a statistical approach. Using our algorithm, we unveiled striking induction of general and tissue-specific circular RNAs, including in the heart and lung, during human fetal development. We discover regions of the human fetal brain, such as the frontal cortex, with marked enrichment for genes where circular RNA isoforms are dominant. Conclusions The vast majority of circular RNA production occurs at major spliceosome splice sites; however, we find the first examples of developmentally induced circular RNAs processed by the minor spliceosome, and an enriched propensity of minor spliceosome donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, these results suggest a potentially significant role for circular RNA in human development. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0690-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Linda Szabo
- Stanford Department of Biochemistry and Stanford Cancer Institute, Stanford, CA, USA.
| | - Robert Morey
- UC San Diego Department of Reproductive Medicine, San Diego, CA, USA.
| | - Nathan J Palpant
- Center for Cardiovascular Biology, Institute for Stem Cell and Regenerative Medicine, Departments of Pathology, Bioengineering and Medicine/Cardiology, University of Washington, Seattle, WA, 98109, USA.
| | - Peter L Wang
- Stanford Department of Biochemistry and Stanford Cancer Institute, Stanford, CA, USA.
| | - Nastaran Afari
- UC San Diego Department of Reproductive Medicine, San Diego, CA, USA.
| | - Chuan Jiang
- UC San Diego Department of Reproductive Medicine, San Diego, CA, USA.
| | - Mana M Parast
- UC San Diego Department of Pathology, San Diego, CA, USA.
| | - Charles E Murry
- Center for Cardiovascular Biology, Institute for Stem Cell and Regenerative Medicine, Departments of Pathology, Bioengineering and Medicine/Cardiology, University of Washington, Seattle, WA, 98109, USA.
| | - Louise C Laurent
- UC San Diego Department of Reproductive Medicine, San Diego, CA, USA.
| | - Julia Salzman
- Stanford Department of Biochemistry and Stanford Cancer Institute, Stanford, CA, USA.
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768
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Barrett SP, Wang PL, Salzman J. Circular RNA biogenesis can proceed through an exon-containing lariat precursor. eLife 2015; 4:e07540. [PMID: 26057830 PMCID: PMC4479058 DOI: 10.7554/elife.07540] [Citation(s) in RCA: 330] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/08/2015] [Indexed: 12/22/2022] Open
Abstract
Pervasive expression of circular RNA is a recently discovered feature of eukaryotic gene expression programs, yet its function remains largely unknown. The presumed biogenesis of these RNAs involves a non-canonical 'backsplicing' event. Recent studies in mammalian cell culture posit that backsplicing is facilitated by inverted repeats flanking the circularized exon(s). Although such sequence elements are common in mammals, they are rare in lower eukaryotes, making current models insufficient to describe circularization. Through systematic splice site mutagenesis and the identification of splicing intermediates, we show that circular RNA in Schizosaccharomyces pombe is generated through an exon-containing lariat precursor. Furthermore, we have performed high-throughput and comprehensive mutagenesis of a circle-forming exon, which enabled us to discover a systematic effect of exon length on RNA circularization. Our results uncover a mechanism for circular RNA biogenesis that may account for circularization in genes that lack noticeable flanking intronic secondary structure.
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Affiliation(s)
- Steven P Barrett
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Peter L Wang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
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769
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Qu S, Yang X, Li X, Wang J, Gao Y, Shang R, Sun W, Dou K, Li H. Circular RNA: A new star of noncoding RNAs. Cancer Lett 2015; 365:141-8. [PMID: 26052092 DOI: 10.1016/j.canlet.2015.06.003] [Citation(s) in RCA: 1264] [Impact Index Per Article: 140.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/01/2015] [Accepted: 06/01/2015] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are a novel type of RNA that, unlike linear RNAs, form a covalently closed continuous loop and are highly represented in the eukaryotic transcriptome. Recent studies have discovered thousands of endogenous circRNAs in mammalian cells. CircRNAs are largely generated from exonic or intronic sequences, and reverse complementary sequences or RNA-binding proteins (RBPs) are necessary for circRNA biogenesis. The majority of circRNAs are conserved across species, are stable and resistant to RNase R, and often exhibit tissue/developmental-stage-specific expression. Recent research has revealed that circRNAs can function as microRNA (miRNA) sponges, regulators of splicing and transcription, and modifiers of parental gene expression. Emerging evidence indicates that circRNAs might play important roles in atherosclerotic vascular disease risk, neurological disorders, prion diseases and cancer; exhibit aberrant expression in colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC); and serve as diagnostic or predictive biomarkers of some diseases. 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. Herein, we review the formation and properties of circRNAs, their functions, and their potential significance in disease.
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Affiliation(s)
- Shibin Qu
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Xisheng Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Xiaolei Li
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Jianlin Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Yuan Gao
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Runze Shang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Wei Sun
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Kefeng Dou
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Haimin Li
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China.
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770
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Daniel C, Lagergren J, Öhman M. RNA editing of non-coding RNA and its role in gene regulation. Biochimie 2015; 117:22-7. [PMID: 26051678 DOI: 10.1016/j.biochi.2015.05.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/27/2015] [Indexed: 12/28/2022]
Abstract
It has for a long time been known that repetitive elements, particularly Alu sequences in human, are edited by the adenosine deaminases acting on RNA, ADAR, family. The functional interpretation of these events has been even more difficult than that of editing events in coding sequences, but today there is an emerging understanding of their downstream effects. A surprisingly large fraction of the human transcriptome contains inverted Alu repeats, often forming long double stranded structures in RNA transcripts, typically occurring in introns and UTRs of protein coding genes. Alu repeats are also common in other primates, and similar inverted repeats can frequently be found in non-primates, although the latter are less prone to duplex formation. In human, as many as 700,000 Alu elements have been identified as substrates for RNA editing, of which many are edited at several sites. In fact, recent advancements in transcriptome sequencing techniques and bioinformatics have revealed that the human editome comprises at least a hundred million adenosine to inosine (A-to-I) editing sites in Alu sequences. Although substantial additional efforts are required in order to map the editome, already present knowledge provides an excellent starting point for studying cis-regulation of editing. In this review, we will focus on editing of long stem loop structures in the human transcriptome and how it can effect gene expression.
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Affiliation(s)
- Chammiran Daniel
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 106 91 Stockholm, Sweden
| | - Jens Lagergren
- School of Computer Science and Communication, Science for Life Laboratory (SciLifeLab), Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 106 91 Stockholm, Sweden.
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771
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Rybak-Wolf A, Stottmeister C, Glažar P, Jens M, Pino N, Giusti S, Hanan M, Behm M, Bartok O, Ashwal-Fluss R, Herzog M, Schreyer L, Papavasileiou P, Ivanov A, Öhman M, Refojo D, Kadener S, Rajewsky N. Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed. Mol Cell 2015; 58:870-85. [DOI: 10.1016/j.molcel.2015.03.027] [Citation(s) in RCA: 1467] [Impact Index Per Article: 163.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/03/2015] [Accepted: 03/20/2015] [Indexed: 12/13/2022]
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772
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Wilusz JE. Repetitive elements regulate circular RNA biogenesis. Mob Genet Elements 2015; 5:1-7. [PMID: 26442181 DOI: 10.1080/2159256x.2015.1045682] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 01/17/2023] Open
Abstract
It was long assumed that eukaryotic precursor mRNAs (pre-mRNAs) are almost always spliced to generate a linear mRNA that is subsequently translated to produce a protein. However, it is now clear that thousands of protein-coding genes can be non-canonically spliced to produce circular noncoding RNAs, some of which are expressed at much higher levels than their associated linear mRNAs. How then does the splicing machinery decide whether to generate a linear mRNA or a circular RNA? Recent work has revealed that intronic repetitive elements, including sequences derived from transposons, are critical regulators of this decision. In most cases, circular RNA biogenesis appears to be initiated when complementary sequences from 2 different introns base pair to one another. This brings the splice sites from the intervening exon(s) into close proximity and facilitates the backsplicing event that generates the circular RNA. As many pre-mRNAs contain multiple intronic repeats, distinct circular transcripts can be produced depending on which repeats base pair to one another. Intronic repeats are thus critical regulatory sequences that control the functional output of their host genes, and potentially cause the functions of protein-coding genes to be highly divergent across species.
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Affiliation(s)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics; Perelman School of Medicine; University of Pennsylvania ; Philadelphia, PA USA
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773
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Bitton DA, Atkinson SR, Rallis C, Smith GC, Ellis DA, Chen YYC, Malecki M, Codlin S, Lemay JF, Cotobal C, Bachand F, Marguerat S, Mata J, Bähler J. Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast. Genome Res 2015; 25:884-96. [PMID: 25883323 PMCID: PMC4448684 DOI: 10.1101/gr.185371.114] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 03/31/2015] [Indexed: 12/31/2022]
Abstract
Exon skipping is considered a principal mechanism by which eukaryotic cells expand their transcriptome and proteome repertoires, creating different splice variants with distinct cellular functions. Here we analyze RNA-seq data from 116 transcriptomes in fission yeast (Schizosaccharomyces pombe), covering multiple physiological conditions as well as transcriptional and RNA processing mutants. We applied brute-force algorithms to detect all possible exon-skipping events, which were widespread but rare compared to normal splicing events. Exon-skipping events increased in cells deficient for the nuclear exosome or the 5′-3′ exonuclease Dhp1, and also at late stages of meiotic differentiation when nuclear-exosome transcripts decreased. The pervasive exon-skipping transcripts were stochastic, did not increase in specific physiological conditions, and were mostly present at less than one copy per cell, even in the absence of nuclear RNA surveillance and during late meiosis. These exon-skipping transcripts are therefore unlikely to be functional and may reflect splicing errors that are actively removed by nuclear RNA surveillance. The average splicing rate by exon skipping was ∼0.24% in wild type and ∼1.75% in nuclear exonuclease mutants. We also detected approximately 250 circular RNAs derived from single or multiple exons. These circular RNAs were rare and stochastic, although a few became stabilized during quiescence and in splicing mutants. Using an exhaustive search algorithm, we also uncovered thousands of previously unknown splice sites, indicating pervasive splicing; yet most of these splicing variants were cryptic and increased in nuclear degradation mutants. This study highlights widespread but low frequency alternative or aberrant splicing events that are targeted by nuclear RNA surveillance.
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Affiliation(s)
- Danny A Bitton
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Sophie R Atkinson
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Charalampos Rallis
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Graeme C Smith
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - David A Ellis
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Yuan Y C Chen
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Michal Malecki
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Sandra Codlin
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Jean-François Lemay
- Université de Sherbrooke, Department of Biochemistry, Sherbrooke, Quebec J1H 5N4, Canada
| | - Cristina Cotobal
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - François Bachand
- Université de Sherbrooke, Department of Biochemistry, Sherbrooke, Quebec J1H 5N4, Canada
| | - Samuel Marguerat
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Jürg Bähler
- University College London, Research Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, United Kingdom
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774
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Petkovic S, Müller S. RNA circularization strategies in vivo and in vitro. Nucleic Acids Res 2015; 43:2454-65. [PMID: 25662225 PMCID: PMC4344496 DOI: 10.1093/nar/gkv045] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
In the plenitude of naturally occurring RNAs, circular RNAs (circRNAs) and their biological role were underestimated for years. However, circRNAs are ubiquitous in all domains of life, including eukaryotes, archaea, bacteria and viruses, where they can fulfill diverse biological functions. Some of those functions, as for example playing a role in the life cycle of viral and viroid genomes or in the maturation of tRNA genes, have been elucidated; other putative functions still remain elusive. Due to the resistance to exonucleases, circRNAs are promising tools for in vivo application as aptamers, trans-cleaving ribozymes or siRNAs. How are circRNAs generated in vivo and what approaches do exist to produce ring-shaped RNAs in vitro? In this review we illustrate the occurrence and mechanisms of RNA circularization in vivo, survey methods for the generation of circRNA in vitro and provide appropriate protocols.
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Affiliation(s)
- Sonja Petkovic
- Institut für Biochemie, Ernst Moritz Arndt Universität Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst Moritz Arndt Universität Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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775
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Masaki S, Yoshimoto R, Kaida D, Hata A, Satoh T, Ohno M, Kataoka N. Identification of the specific interactors of the human lariat RNA debranching enzyme 1 protein. Int J Mol Sci 2015; 16:3705-21. [PMID: 25671812 PMCID: PMC4346921 DOI: 10.3390/ijms16023705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/04/2015] [Indexed: 01/30/2023] Open
Abstract
In eukaryotes, pre-mRNA splicing is an essential step for gene expression. We have been analyzing post-splicing intron turnover steps in higher eukaryotes. Here, we report protein interaction between human Debranching enzyme 1 (hDbr1) and several factors found in the Intron Large (IL) complex, which is an intermediate complex of the intron degradation pathway. The hDbr1 protein specifically interacts with xeroderma pigmentosum, complementeation group A (XPA)-binding protein 2 (Xab2). We also attempted to identify specific interactors of hDbr1. Co-immunoprecipitation experiments followed by mass spectrometry analysis identified a novel protein as one of the specific interactors of hDbr1. This protein is well conserved among many species and shows the highest similarity to yeast Drn1, so it is designated as human Dbr1 associated ribonuclease 1 (hDrn1). hDrn1 directly interacts with hDbr1 through protein–protein interaction. Furthermore, hDrn1 shuttles between the nucleus and the cytoplasm, as hDbr1 protein does. These findings suggest that hDrn1 has roles in both the nucleus and the cytoplasm, which are highly likely to involve hDbr1.
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Affiliation(s)
- So Masaki
- Medical Innovation Center, Laboratory for Malignancy Control Research, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Rei Yoshimoto
- Chemical Genetics Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan.
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan.
| | - Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, 2630 Sugitani, Toyama-shi, Toyama 930-0194, Japan.
| | - Asuka Hata
- Medical Innovation Center, Laboratory for Malignancy Control Research, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Takayuki Satoh
- Frontier Research Core for Life Sciences, University of Toyama, 2630 Sugitani, Toyama-shi, Toyama 930-0194, Japan.
| | - Mutsuhito Ohno
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Naoyuki Kataoka
- Medical Innovation Center, Laboratory for Malignancy Control Research, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8507, Japan.
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan.
- Medical Top Track Program, Medical Research Institute, Tokyo Dental and Medical University, Tokyo 113-8510, Japan.
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776
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