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Sun X, Zhao X, Xu Y, Yan Y, Han L, Wei M, He M. Potential therapeutic strategy for cancer: Multi-dimensional cross-talk between circRNAs and parental genes. Cancer Lett 2024; 588:216794. [PMID: 38453043 DOI: 10.1016/j.canlet.2024.216794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
In many ways, circular RNAs (circRNAs) have been demonstrated to be crucial in the onset and advancement of cancer throughout the last ten years and have become a new focus of intense research in the field of RNAs. Accumulating studies have demonstrated that circRNAs can regulate parental gene expression via a variety of biological pathways. Furthermore, research into the complex interactions between circRNAs and their parental genes will shed light on their biological roles and open up new avenues for circRNAs' potential clinical translational uses. However, to date, multi-dimensional cross-talk between circRNAs and parental genes have not been systematically elucidated. Particularly intriguing is circRNA's exploration of tumor targeting, and potential therapeutic uses based on the parental gene regulation perspective. Here, we discuss their biogenesis, take a fresh look at the molecular mechanisms through which circRNAs control the expression of their parental genes in cancer. We further highlight We further highlight the latest circRNA clinical translational applications, including prognostic diagnostic markers, cancer vaccines, gDNA, and so on. Demonstrating the potential benefits and future applications of circRNA therapy.
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Affiliation(s)
- Xiaoyu Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Xinyi Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Yan Xu
- Department of Urology, The First Hospital of China Medical University, Shenyang, China.
| | - Yuanyuan Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Li Han
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China; Liaoning Medical Diagnosis and Treatment Center, Liaoning Province, China.
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
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2
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Zong W, Zhang T, Chen B, Lu Q, Cao X, Wang K, Yang Z, Chen Z, Yang Y. Emerging roles of noncoding micro RNAs and circular RNAs in bovine mastitis: Regulation, breeding, diagnosis, and therapy. Front Microbiol 2022; 13:1048142. [DOI: 10.3389/fmicb.2022.1048142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Bovine mastitis is one of the most troublesome and costly problems in the modern dairy industry, which is not only difficult to monitor, but can also cause economic losses while having significant implications on public health. However, efficacious preventative methods and therapy are still lacking. Moreover, new drugs and therapeutic targets are in increasing demand due to antibiotic restrictions. In recent years, noncoding RNAs have gained popularity as a topic in pathological and genetic studies. Meanwhile, there is growing evidence that they play a role in regulating various biological processes and developing novel treatment platforms. In light of this, this review focuses on two types of noncoding RNAs, micro RNAs and circular RNAs, and summarizes their characterizations, relationships, potential applications as selection markers, diagnostic or treatment targets and potential applications in RNA-based therapy, in order to shed new light on further research.
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3
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Sun X, Kang Y, Li M, Li Y, Song J. The emerging regulatory mechanisms and biological function of circular RNAs in skeletal muscle development. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194888. [DOI: 10.1016/j.bbagrm.2022.194888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/07/2022]
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4
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Mechanism and Function of Circular RNA in Regulating Solid Tumor Radiosensitivity. Int J Mol Sci 2022; 23:ijms231810444. [PMID: 36142355 PMCID: PMC9499630 DOI: 10.3390/ijms231810444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022] Open
Abstract
Radiotherapy is an important tool in the treatment of malignant tumors, and exploring how to make radiotherapy more effective is a new way to break through the current bottleneck in the development of radiation oncology. Circular RNAs (circRNAs) are a special class of endogenous non-coding RNAs. Numerous studies have shown that circRNAs have shown great potential in regulating the biological functions of tumors, including proliferation, migration, invasion, and treatment resistance, and that differences in their expression levels are closely related to the clinical prognosis of tumor patients. This review systematically compares the mechanisms of circRNAs in the process of tumor development and radiosensitivity and provides insight into the clinical translation of circRNAs in radiotherapy.
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5
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Plitta-Michalak B, Stricker N, Pavez Loriè E, Chen I, Pollet M, Krutmann J, Volkmer B, Greinert R, Boukamp P, Rapp A. Development and characterisation of an irradiation device for biomedical studies covering the solar spectrum with individual regulated spectral bands. Photochem Photobiol Sci 2022; 21:1701-1717. [PMID: 35749054 DOI: 10.1007/s43630-022-00252-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022]
Abstract
To understand the importance of terrestrial solar exposure on human skin, not only individual spectral components need to be considered in biomedical studies, but also the relevance of the combined action profile of the complete solar spectrum (cSS) must be established. We therefore developed a novel irradiation device that combines the emission of four individual lamps (UVB, UVA, VIS and nIR) to achieve exposure from 280 to 1400 nm with individual controllable lamps. The integrated irradiance of each spectral band is similar to the solar spectrum. The lamps can be utilised individually or in any desired combination. Here we present the design, realisation, and validation of this irradiation device as well as biological results on cellular metabolism (MTT assay), cell cycle alterations, and clonogenic growth in HaCaT cells after exposures to the individual spectral bands as well as their simultaneous combinations. Thereby, we demonstrate that UVB combined with UVA is the main determinant for the metabolic activity within cSS. Also, UVB-dependent effects dominate cell cycle regulation in cSS, whilst UVA and nIR have little influence. Lastly, also clonogenic growth is dominated by the UVB action profile in cSS, despite nIR showing modulatory activity when applied in combination with UVB. Together, this highlights the regulatory influence of the different spectral bands on the three biological endpoints and demonstrates their modulation when being part of the complete solar spectrum.
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Affiliation(s)
- B Plitta-Michalak
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany.,Department of Chemistry, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - N Stricker
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - E Pavez Loriè
- IUF-Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany.,Ludwig Boltzmann Institute for Traumatology, the Research Center in Cooperation with AUVA, Donaueschingenstraße 13, 1200, Vienna, Austria
| | - I Chen
- Centre of Dermatology, Elbe Clinics, Am Krankenhaus 1, 21614, Buxtehude, Germany
| | - M Pollet
- IUF-Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - J Krutmann
- IUF-Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - B Volkmer
- Centre of Dermatology, Elbe Clinics, Am Krankenhaus 1, 21614, Buxtehude, Germany
| | - R Greinert
- Centre of Dermatology, Elbe Clinics, Am Krankenhaus 1, 21614, Buxtehude, Germany
| | - P Boukamp
- IUF-Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - A Rapp
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany.
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6
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Akhlaghpour H. An RNA-Based Theory of Natural Universal Computation. J Theor Biol 2021; 537:110984. [PMID: 34979104 DOI: 10.1016/j.jtbi.2021.110984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of universal computation, i.e., Turing-equivalent in scope. Generic finite-dimensional dynamical systems (which encompass most models of neural networks, intracellular signaling cascades, and gene regulatory networks) fall short of universal computation, but are assumed to be capable of explaining cognition and development. I present a class of models that bridge two concepts from distant fields: combinatory logic (or, equivalently, lambda calculus) and RNA molecular biology. A set of basic RNA editing rules can make it possible to compute any computable function with identical algorithmic complexity to that of Turing machines. The models do not assume extraordinarily complex molecular machinery or any processes that radically differ from what we already know to occur in cells. Distinct independent enzymes can mediate each of the rules and RNA molecules solve the problem of parenthesis matching through their secondary structure. In the most plausible of these models all of the editing rules can be implemented with merely cleavage and ligation operations at fixed positions relative to predefined motifs. This demonstrates that universal computation is well within the reach of molecular biology. It is therefore reasonable to assume that life has evolved - or possibly began with - a universal computer that yet remains to be discovered. The variety of seemingly unrelated computational problems across many scales can potentially be solved using the same RNA-based computation system. Experimental validation of this theory may immensely impact our understanding of memory, cognition, development, disease, evolution, and the early stages of life.
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Affiliation(s)
- Hessameddin Akhlaghpour
- Laboratory of Integrative Brain Function, The Rockefeller University, New York, NY, 10065, USA
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7
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Zhang Z, Fan Y, Deng K, Liang Y, Zhang G, Gao X, El-Samahy MA, Zhang Y, Deng M, Wang F. Circular RNA circUSP13 sponges miR-29c to promote differentiation and inhibit apoptosis of goat myoblasts by targeting IGF1. FASEB J 2021; 36:e22097. [PMID: 34935184 DOI: 10.1096/fj.202101317r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/10/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022]
Abstract
Circular RNAs (circRNAs) are an indispensable element of post-transcriptional gene regulation, influencing a variety of biological processes including myogenic differentiation; however, little is known about the function of circRNA in goat myogenic differentiation. Using RNA-sequencing data from our laboratory, we explored the influences of circUSP13, as a candidate circRNA, on myoblast differentiation since its expression is higher in myoblasts of lamb (first day of age) than that of the fetus (75th day of pregnancy). In in vitro experiments, circUSP13 significantly promoted differentiation and inhibited apoptosis in goat primary myoblasts. Mechanistically, circUSP13 localized with miR-29c in the cytoplasm of goat myoblasts to regulate IGF1 expression. We further demonstrated that circUSP13 sponges miR-29c, promoting IGF1 expression that upregulated the expression of MyoG and MyHC. Thus, our results identified circUSP13 as a molecular marker for breeding programs of mutton production, as well as the circUSP13-miR-29c-IGF1 axis as a potential therapeutic target for combating muscle wasting.
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Affiliation(s)
- Zhen Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yixuan Fan
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Kaiping Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yaxu Liang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Guomin Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiao Gao
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - M A El-Samahy
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yanli Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Mingtian Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
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8
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Yang Q, Li F, He AT, Yang BB. Circular RNAs: Expression, localization, and therapeutic potentials. Mol Ther 2021; 29:1683-1702. [PMID: 33484969 PMCID: PMC8116570 DOI: 10.1016/j.ymthe.2021.01.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are RNAs with a unique circular structure that is generated from back-splicing processes. These circular molecules were discovered more than 40 years ago but failed to raise scientific interest until lately. Increasing studies have found that these circular RNAs might not just be byproducts of the splicing process but possess important regulatory functions through different cellular events. Most circular RNAs are currently being studied in the field of cancer, and many of them have been confirmed to be involved in the process of tumorigenesis. However, many circular RNAs are implicated in the developmental stages of diseases other than cancer. In this review, we focus on discussing the role of circular RNAs in non-cancer diseases, especially in cardiovascular diseases. Following the summary of the life cycle of circRNAs, we provide input on studying circRNA-protein interactions based on our experience, which modulate protein translocation. Furthermore, we outline the potential of circRNAs to be potent biomarkers, effective therapeutic targets, and potential treatments in cardiovascular diseases as well as other non-cancer fields.
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Affiliation(s)
- Qiwei Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Medical Research Center, Second Hospital of Jilin University, Changchun, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Feiya Li
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Alina T He
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada.
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9
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Exosomal circRNAs: A new star in cancer. Life Sci 2021; 269:119039. [PMID: 33454367 DOI: 10.1016/j.lfs.2021.119039] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/20/2020] [Accepted: 01/01/2021] [Indexed: 12/13/2022]
Abstract
As a disease that seriously endangers human health, cancer still lacks effective treatment because of its complicated mechanism of action. Currently, an emerging class of RNAs, named circular RNAs (circRNAs), has been found to be closely related to cancer. CircRNAs have a stable closed loop structure which would be hardly degraded in blood or body fluids. Exosomes are found naturally in a variety of cells, mediating cell-to-cell communication, or participating in multiple processes of tumor development. Researchers have found that abnormally expressed circRNAs may be associated with the occurrence and development of malignancies. As a kind of exosome-derived non-coding RNAs, exosomal circRNAs have also played important roles in cancer progression and acted as diagnostic and prognostic biomarkers for cancer, and thus arousing more and more attention. This article reviews the functions, mechanisms and values of the exosomal circRNAs in tumors in order to provide new ideas and novel biomarkers for the diagnosis and treatment of cancer.
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10
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Yang J, Chen J, Wu S, Fei X, Wang X, Wang K. <p>Microarray Expression Profiles and Bioinformatics Analyses Reveal Aberrant Circular RNAs Expression in Bladder Cancer</p>. Onco Targets Ther 2020; 13:10889-10899. [PMID: 33149606 PMCID: PMC7602908 DOI: 10.2147/ott.s270747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/24/2020] [Indexed: 11/23/2022] Open
Abstract
Background Increasing evidence shows that circular RNAs (circRNAs) are involved in many biological processes, functioning as microRNA (miRNA) sponges. The aim of this study is to identify differentially expressed circRNAs in bladder cancer (BCa). Methods The transcriptome of circRNAs in BCa was assayed by microarray. Quantitative real-time PCR was performed to verify the results. Then, potential miRNA response elements (MREs) between circRNAs and miRNAs were predicted. Pathway and ontology enrichment analyses were performed to identify mechanisms related to the gene regulation of differentially expressed circRNAs. Results Three hundred and eighty-six up-regulated and 394 down-regulated circRNAs were identified, and their potential MREs were predicted in BCa. Conclusion The differentially expressed circRNAs indicate that circRNAs could play important roles in the molecular pathogenesis of BCa.
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Affiliation(s)
- Jun Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang110004, People’s Republic of China
| | - Junwen Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang110004, People’s Republic of China
| | - Si Wu
- Department of Biobank, Shengjing Hospital of China Medical University, Shenyang110004, People’s Republic of China
| | - Xiang Fei
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang110004, People’s Republic of China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang110004, People’s Republic of China
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang110004, People’s Republic of China
- Correspondence: Kefeng WangDepartment of Urology, Shengjing Hospital of China Medical University, 36# Sanhao Street, Heping District, Shenyang, Liaoning, People’s Republic of ChinaTel +86 18940254849Fax +86 24 31939077 Email
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11
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Tian J, Fu Y, Li Q, Xu Y, Xi X, Zheng Y, Yu L, Wang Z, Yu B, Tian J. Differential Expression and Bioinformatics Analysis of CircRNA in PDGF-BB-Induced Vascular Smooth Muscle Cells. Front Genet 2020; 11:530. [PMID: 32547599 PMCID: PMC7272660 DOI: 10.3389/fgene.2020.00530] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022] Open
Abstract
Atherosclerosis is mediated by various factors and plays an important pathological foundation for cardiovascular and cerebrovascular diseases. Abnormal vascular smooth muscle cells (VSMCs) proliferation and migration have an essential role in atherosclerotic lesion formation. Circular RNAs (circRNA) have been widely detected in different species and are closely related to various diseases. However, the expression profiles and molecular regulatory mechanisms of circRNAs in VSMCs are still unknown. We used high-throughput RNA-seq as well as bioinformatics tools to systematically analyze circRNA expression profiles in samples from different VSMC phenotypes. Polymerase chain reaction (PCR), Sanger sequencing, and qRT-PCR were performed for circRNA validation. A total of 22191 circRNAs corresponding to 6273 genes (host genes) in the platelet-derived growth factor (PDGF-BB) treated group, the blank control group or both groups, were detected, and 112 differentially expressed circRNAs were identified between the PDGF-BB treated and control groups, of which 59 were upregulated, and 53 were downregulated. We selected 9 circRNAs for evaluation of specific head-to-tail splicing, and 10 differentially expressed circRNAs between the two groups for qRT-PCR validation. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses enrichment analyses revealed that the parental genes of the circRNAs mainly participated in cardiac myofibril assembly and positive regulation of DNA-templated transcription, indicating that they might be involved in cardiovascular diseases. Finally, we constructed a circRNA-miRNA network based on the dysregulated circRNAs and VSMC-related microRNAs. Our study is the first to show the differential expression of circRNAs in PDGF-BB-induced VSMCs and may provide new ideas and targets for the prevention and therapy of vascular diseases.
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Affiliation(s)
- Jiangtian Tian
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yahong Fu
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qi Li
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Pathology, Harbin Medical University, Harbin, China
| | - Ying Xu
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Basic Medical College of Mudanjiang Medical College, Mudanjiang, China
| | - Xiangwen Xi
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuqi Zheng
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Li Yu
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhuozhong Wang
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bo Yu
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jinwei Tian
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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12
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Patop IL, Wüst S, Kadener S. Past, present, and future of circRNAs. EMBO J 2019; 38:e100836. [PMID: 31343080 PMCID: PMC6694216 DOI: 10.15252/embj.2018100836] [Citation(s) in RCA: 741] [Impact Index Per Article: 148.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 05/15/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022] Open
Abstract
Exonic circular RNAs (circRNAs) are covalently closed RNA molecules generated by a process named back-splicing. circRNAs are highly abundant in eukaryotes, and many of them are evolutionary conserved. In metazoans, circular RNAs are expressed in a tissue-specific manner, are highly stable, and accumulate with age in neural tissues. circRNA biogenesis can regulate the production of the linear RNA counterpart in cis as back-splicing competes with linear splicing. Recent reports also demonstrate functions for some circRNAs in trans: Certain circRNAs interact with microRNAs, some are translated, and circRNAs have been shown to regulate immune responses and behavior. Here, we review current knowledge about animal circRNAs and summarize new insights into potential circRNA functions, concepts of their origin, and possible future directions in the field.
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Affiliation(s)
| | - Stas Wüst
- Department of BiologyBrandeis UniversityWalthamMAUSA
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13
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Pervouchine DD. Circular exonic RNAs: When RNA structure meets topology. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194384. [PMID: 31102674 DOI: 10.1016/j.bbagrm.2019.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022]
Abstract
Although RNA circularization was first documented in the 1990s, the extent to which it occurs was not known until recent advances in high-throughput sequencing enabled the widespread identification of circular RNAs (circRNAs). Despite this, many aspects of circRNA biogenesis, structure, and function yet remain obscure. This review focuses on circular exonic RNAs, a subclass of circRNAs that are generated through backsplicing. Here, I hypothesize that RNA secondary structure can be the common factor that promotes both exon skipping and spliceosomal RNA circularization, and that backsplicing of double-stranded regions could generate topologically linked circRNA molecules. CircRNAs manifest themselves by the presence of tail-to-head exon junctions, which were previously attributed to post-transcriptional exon permutation and repetition. I revisit these observations and argue that backsplicing does not automatically imply RNA circularization because tail-to-head exon junctions give only local information about transcript architecture and, therefore, they are in principle insufficient to determine globally circular topology. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Dmitri D Pervouchine
- Skolkovo Institute of Science and Technology, 3 Nobel St, Moscow 143026, Russia; Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, Moscow 119234, Russia.
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14
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Hall IF, Climent M, Quintavalle M, Farina FM, Schorn T, Zani S, Carullo P, Kunderfranco P, Civilini E, Condorelli G, Elia L. Circ_Lrp6, a Circular RNA Enriched in Vascular Smooth Muscle Cells, Acts as a Sponge Regulating miRNA-145 Function. Circ Res 2019; 124:498-510. [PMID: 30582454 DOI: 10.1161/circresaha.118.314240] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RATIONALE microRNAs (miRNAs) modulate gene expression by repressing translation of targeted genes. Previous work has established a role for miRNAs in regulating vascular smooth muscle cell (VSMC) activity. Whether circular RNAs are involved in the modulation of miRNA activity in VSMCs is unknown. OBJECTIVE We aimed to identify circular RNAs interacting with miRNAs enriched in VSMCs and modulating the cells' activity. METHODS AND RESULTS RNA sequencing and bioinformatics identified several circular RNAs enriched in VSMCs; however, only one, possessing multiple putative binding sites for miR-145, was highly conserved between mouse and man. This circular RNA gemmed from alternative splicing of Lrp6 (lipoprotein receptor 6), a gene highly expressed in vessels and implicated in vascular pathologies and was thus named circ_Lrp6. Its role as a miR-145 sponge was confirmed by determining reciprocal interaction through RNA immunoprecipitation, stimulated emission depletion microscopy, and competitive luciferase assays; functional inhibition of miR-145 was assessed by measuring expression of the target genes ITGβ8 (integrin-β8), FASCIN (fascin actin-bundling protein 1), KLF4 (Kruppel-like factor 4), Yes1 (YES proto-oncogene 1), and Lox (lysyl oxidase). The interaction was preferentially localized to P-bodies, sites of mRNA degradation. Using loss- and gain-of-function approaches, we found that circ_Lrp6 hindered miR-145-mediated regulation of VSMC migration, proliferation, and differentiation. Differential expression of miR-145 and circ_Lrp6 in murine and human vascular diseases suggests that the ratio of circ_Lrp6 bound to miR-145 versus unbound could play a role in vascular pathogenesis. Viral delivery of circ_Lrp6 shRNA prevented intimal hyperplasia in mouse carotids. CONCLUSIONS circ_Lrp6 is an intracellular modulator and a natural sponge for miR-145, counterbalancing the functions of the miRNA in VSMCs.
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Affiliation(s)
- Ignacio Fernando Hall
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
- Humanitas University, Rozzano, Milan, Italy (I.F.H., S.Z., P.C., E.C., G.C.)
| | - Montserrat Climent
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
| | - Manuela Quintavalle
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
| | - Floriana Maria Farina
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
| | - Tilo Schorn
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
| | - Stefania Zani
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
- Humanitas University, Rozzano, Milan, Italy (I.F.H., S.Z., P.C., E.C., G.C.)
| | - Pierluigi Carullo
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
- Humanitas University, Rozzano, Milan, Italy (I.F.H., S.Z., P.C., E.C., G.C.)
- Institute of Genetics and Biomedical Research, National Research Council, Rozzano, Milan, Italy (P.C., G.C., L.E.)
| | - Paolo Kunderfranco
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
| | - Efrem Civilini
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
- Humanitas University, Rozzano, Milan, Italy (I.F.H., S.Z., P.C., E.C., G.C.)
| | - Gianluigi Condorelli
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
- Humanitas University, Rozzano, Milan, Italy (I.F.H., S.Z., P.C., E.C., G.C.)
- Institute of Genetics and Biomedical Research, National Research Council, Rozzano, Milan, Italy (P.C., G.C., L.E.)
| | - Leonardo Elia
- From the Humanitas Research Hospital, Rozzano, Milan, Italy (I.F.H., M.C., M.Q., F.M.F., T.S., S.Z., P.C., P.K., E.C., G.C., L.E.)
- Institute of Genetics and Biomedical Research, National Research Council, Rozzano, Milan, Italy (P.C., G.C., L.E.)
- Department of Molecular and Translational Medicine, University of Brescia, Italy (L.E.)
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15
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Hu Q, Zhou T. EIciRNA-mediated gene expression: tunability and bimodality. FEBS Lett 2018; 592:3460-3471. [PMID: 30223292 DOI: 10.1002/1873-3468.13253] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/04/2018] [Accepted: 09/12/2018] [Indexed: 01/15/2023]
Abstract
Biological experiments have verified that EIciRNAs (a class of circRNA) produced from pre-mRNA can regulate gene expression, but the effect of regulation remains unexplored. Here, we refine a mechanistic gene model from experimental facts, in which we assume pre-mRNA synthesizes EIciRNAs and mRNAs in a probabilistic manner, with the probability called the pathway strength, and the resulting EIciRNAs positively regulate the pre-mRNA synthesis. We show that there is a critical pathway strength such that the mRNA mean and the mRNA noise reach the highest and lowest levels, respectively. The EIciRNA can induce the unimodal and bimodal mRNA expressions, as well as the transition between them. Our investigation hints that EIciRNA is a non-negligible factor affecting cell-to-cell variability in gene expression.
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Affiliation(s)
- Qi Hu
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, China
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16
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Abstract
Circular RNAs (circRNAs) are recognized as a special species of transcripts in metazoans with increasing studies, and northern blotting is a direct way to confirm the existence and to evaluate the size of individual circRNAs. Northern blotting probes can be radioactive isotope (32P) labeled, which is not environment-friendly and sometimes inconvenient to use. Here, we describe a nonradioactive northern blot protocol with digoxigenin-labeled probe to detect circRNA.
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Affiliation(s)
- Xiaolin Wang
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, China
| | - Ge Shan
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, China.
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17
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Chi JS, Li JZ, Jia JJ, Zhang T, Liu XM, Yi L. Long non-coding RNA ANRIL in gene regulation and its duality in atherosclerosis. Curr Med Sci 2017; 37:816-822. [PMID: 29270737 DOI: 10.1007/s11596-017-1812-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/16/2017] [Indexed: 02/05/2023]
Abstract
The antisense transcript long non-coding RNA (lncRNA) (antisense non-coding RNA in the INK4 locus, ANRIL) is an antisense of the cyclin-dependent kinase inhibitor 2B (CDKN2B) gene on chromosome 9p21 that contains an overlapping 299-bp region and shares a bidirectional promoter with alternate open reading frame (ARF). In the context of gene regulation, ANRIL is responsible for directly recruiting polycomb group (PcG) proteins, including polycomb repressive complex-1 (PRC-1) and polycomb repressive complex-2 (PRC-2), to modify the epigenetic chromatin state and subsequently inhibit gene expression in cis-regulation. On the other hand, previous reports have indicated that ANRIL is capable of binding to a specific site or sequence, including the Alu element, E2F transcription factor 1 (E2F1), and CCCTC-binding factor (CTCF), to achieve trans-regulation functions. In addition to its function in cell proliferation, adhesion and apoptosis, ANRIL is very closely associated with atherosclerosis- related diseases. The different transcripts and the SNPs that are related to atherosclerotic vascular diseases (ASVD-SNPs) are inextricably linked to the development and progression of atherosclerosis. Linear transcripts have been shown to be a risk factor for atherosclerosis, whereas circular transcripts are protective against atherosclerosis. Furthermore, ANRIL also acts as a component of the inflammatory pathway involved in the regulation of inflammation, which is considered to be one of the causes of atherosclerosis. Collectively, ANRIL plays an important role in the formation of atherosclerosis, and the artificial modification of ANRIL transcripts should be considered following the development of this disease.
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Affiliation(s)
- Jie-Shan Chi
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
- Shantou University Medical College, Shantou, 515041, China
| | - Jian-Zhou Li
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Jing-Jing Jia
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Ting Zhang
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Xiao-Ma Liu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Li Yi
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, 518000, China.
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18
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Zhong Z, Lv M, Chen J. Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma. Sci Rep 2016; 6:30919. [PMID: 27484176 PMCID: PMC4971518 DOI: 10.1038/srep30919] [Citation(s) in RCA: 329] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 07/11/2016] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs), a kind of non-coding RNAs, have shown large capabilities in gene regulation. However, the mechanisms underlying circRNAs remain largely unknown so far. Recent studies demonstrated that circRNAs play miRNA sponge effects and regulate gene expression by microRNA response elements. Here, we screened circRNA expression profiles of bladder carcinoma using microarray assay. A total of 469 dysregulated circular transcripts are found in bladder cancer compared with normal tissues, among which 285 were up-regulated and 184 were down-regulated. Six circRNAs were identified to have significant differences by qRT-PCR. We speculated that circRNAs might involve in cancer-related pathways via interactions with miRNA by multiple bioinformatical approaches. Therefore, we further predicted that circTCF25 could sequester miR-103a-3p/miR-107, which potentially lead to the up-regulation of thirteen targets related to cell proliferation, migration and invasion. Subsequently, we demonstrated that over-expression of circTCF25 could down-regulate miR-103a-3p and miR-107, increase CDK6 expression, and promote proliferation and migration in vitro and vivo. This is the first study to exploit circRNA profiling and circRNA/miRNA interactions in bladder cancer. Our work laid the foundation to investigate the functions of circRNAs in cancers. The data also suggest that circTCF25 might be a new promising marker for bladder cancer.
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Affiliation(s)
- Zhenyu Zhong
- The First Clinical College, Chongqing Medical University, Chongqing 400016, China
| | - Mengxin Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Junxia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
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19
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Izuogu OG, Alhasan AA, Alafghani HM, Santibanez-Koref M, Elliott DJ, Elliot DJ, Jackson MS. PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. BMC Bioinformatics 2016; 17:31. [PMID: 26758031 PMCID: PMC4711006 DOI: 10.1186/s12859-016-0881-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 01/06/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Transcripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues and cell types from many eukaryotes, and are now known to be mostly circular, cytoplasmic, and non-coding. Although there is no uniformly ascribed function, several have been shown to be involved in gene regulation. Accurate identification of these transcripts can, however, be difficult due to artefacts from a wide variety of sources. RESULTS Here, we present a computational method, PTESFinder, to identify these transcripts from high throughput RNAseq data. Uniquely, it systematically excludes potential artefacts emanating from pseudogenes, segmental duplications, and template switching, and outputs both PTES and canonical exon junction counts to facilitate comparative analyses. In comparison with four existing methods, PTESFinder achieves highest specificity and comparable sensitivity at a variety of read depths. PTESFinder also identifies between 13 % and 41.6 % more structures, compared to publicly available methods recently used to identify human circular RNAs. CONCLUSIONS With high sensitivity and specificity, user-adjustable filters that target known sources of false positives, and tailored output to facilitate comparison of transcript levels, PTESFinder will facilitate the discovery and analysis of these poorly understood transcripts.
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Affiliation(s)
- Osagie G Izuogu
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, UK.
| | - Abd A Alhasan
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, UK.
| | - Hani M Alafghani
- Security Forces Hostpital, P. O. Box 2748-24268-8541, Makkah, Kingdom of Saudi Arabia.
| | | | | | - David J Elliot
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, UK.
| | - Michael S Jackson
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, UK.
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20
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Circular RNA enrichment in platelets is a signature of transcriptome degradation. Blood 2015; 127:e1-e11. [PMID: 26660425 DOI: 10.1182/blood-2015-06-649434] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 12/01/2015] [Indexed: 02/07/2023] Open
Abstract
In platelets, splicing and translation occur in the absence of a nucleus. However, the integrity and stability of mRNAs derived from megakaryocyte progenitor cells remain poorly quantified on a transcriptome-wide level. As circular RNAs (circRNAs) are resistant to degradation by exonucleases, their abundance relative to linear RNAs can be used as a surrogate marker for mRNA stability in the absence of transcription. Here we show that circRNAs are enriched in human platelets 17- to 188-fold relative to nucleated tissues and 14- to 26-fold relative to samples digested with RNAse R to selectively remove linear RNA. We compare RNAseq read depths inside and outside circRNAs to provide in silico evidence of transcript circularity, show that exons within circRNAs are enriched on average 12.7 times in platelets relative to nucleated tissues and identify 3162 genes significantly enriched for circRNAs, including some where all RNAseq reads appear to be derived from circular molecules. We also confirm that this is a feature of other anucleate cells through transcriptome sequencing of mature erythrocytes, demonstrate that circRNAs are not enriched in cultured megakaryocytes, and demonstrate that linear RNAs decay more rapidly than circRNAs in platelet preparations. Collectively, these results suggest that circulating platelets have lost >90% of their progenitor mRNAs and that translation in platelets occurs against the backdrop of a highly degraded transcriptome. Finally, we find that transcripts previously classified as products of reverse transcriptase template switching are both enriched in platelets and resistant to decay, countering the recent suggestion that up to 50% of rearranged RNAs are artifacts.
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21
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Shen T, Han M, Wei G, Ni T. An intriguing RNA species--perspectives of circularized RNA. Protein Cell 2015; 6:871-80. [PMID: 26349458 PMCID: PMC4656206 DOI: 10.1007/s13238-015-0202-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 07/28/2015] [Indexed: 12/30/2022] Open
Abstract
Circular RNAs (circRNAs), a kind of covalently closed RNA molecule, were used to be considered a type of by-products of mis-splicing events and were discovered sporadically due to the technological limits in the early years. With the great technological progress such as high-throughput next-generation sequencing, numerous circRNAs have recently been detected in many species. CircRNAs were expressed in a spatio-temporally specific manner, suggesting their regulatory functional potentials were overlooked previously. Intriguingly, some circRNAs were indeed found with critical physiological functions in certain circumstances. CircRNAs have a more stable molecular structure that can resist to exoribonuclease comparing to those linear ones, and their molecular functions include microRNA sponge, regulatory roles in transcription, mRNA traps that compete with linear splicing, templates for translation and possibly other presently unknown roles. Here, we review the discovery and characterization of circRNAs, the origination and formation mechanism, the physiological functions and the molecular roles, along with the methods for detection of circRNAs. We further look into the future and propose key questions to be answered for these magical RNA molecules.
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Affiliation(s)
- Ting Shen
- MOE Key Laboratory of Contemporary Anthropology & State Key Laboratory of Genetics Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Miao Han
- MOE Key Laboratory of Contemporary Anthropology & State Key Laboratory of Genetics Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Gang Wei
- MOE Key Laboratory of Contemporary Anthropology & State Key Laboratory of Genetics Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Ting Ni
- MOE Key Laboratory of Contemporary Anthropology & State Key Laboratory of Genetics Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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22
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Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, Zhu P, Chang Z, Wu Q, Zhao Y, Jia Y, Xu P, Liu H, Shan G. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol 2015; 22:256-64. [PMID: 25664725 DOI: 10.1038/nsmb.2959] [Citation(s) in RCA: 2041] [Impact Index Per Article: 226.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/19/2014] [Indexed: 02/06/2023]
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 EIciRNAs.
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Affiliation(s)
- Zhaoyong Li
- 1] School of Life Sciences, University of Science and Technology of China, Hefei, China. [2] Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China
| | - Chuan Huang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chun Bao
- 1] School of Life Sciences, University of Science and Technology of China, Hefei, China. [2] Department of Physics, Central China Normal University, Wuhan, China. [3] Institute of Biophysics, Central China Normal University, Wuhan, China
| | - Liang Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Mei Lin
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaolin Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Guolin Zhong
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Bin Yu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wanchen Hu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Limin Dai
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Pengfei Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhaoxia Chang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Ya Jia
- 1] Department of Physics, Central China Normal University, Wuhan, China. [2] Institute of Biophysics, Central China Normal University, Wuhan, China
| | - Ping Xu
- National Center for Protein Sciences, Beijing, China
| | - Huijie Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ge Shan
- 1] School of Life Sciences, University of Science and Technology of China, Hefei, China. [2] Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China
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23
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Jividen K, Li H. Chimeric RNAs generated by intergenic splicing in normal and cancer cells. Genes Chromosomes Cancer 2014; 53:963-71. [PMID: 25131334 DOI: 10.1002/gcc.22207] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/16/2014] [Indexed: 12/30/2022] Open
Abstract
A hallmark of many neoplasias is chromosomal rearrangement, an event that commonly results in the fusion of two separate genes. The RNA and protein resulting from these gene fusions often play critical roles in cancer development, maintenance, and progression. Traditionally, these fusion products are thought to be produced solely due to DNA level changes and are therefore considered unique to cancer. Recent advances in microarray and deep-sequencing have revealed many more fusion transcripts. Surprisingly, some are without detectable rearrangement at the DNA level. Reports have demonstrated that at least some of these chimeric RNAs are generated via intergenic splicing. In this review, we highlight three examples of these noncanonical chimeric transcripts that are formed by trans-splicing or cis-splicing of adjacent genes and summarize the knowledge we have regarding these noncanonical fusions. We discuss the implications of the chimeric RNAs in both cancer and normal physiology, as some of these fusion transcripts are found in normal, noncancerous cells with sequences identical to those generated by canonical chromosomal translocation found in cancer cells. Finally, we present methods that are currently being used to discover additional chimeric RNAs.
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Affiliation(s)
- Kasey Jividen
- Department of Pathology, University of Virginia, Charlottesville, VA
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24
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Yu CY, Liu HJ, Hung LY, Kuo HC, Chuang TJ. Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro? Nucleic Acids Res 2014; 42:9410-23. [PMID: 25053845 PMCID: PMC4132752 DOI: 10.1093/nar/gku643] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Global transcriptome investigations often result in the detection of an enormous number of transcripts composed of non-co-linear sequence fragments. Such ‘aberrant’ transcript products may arise from post-transcriptional events or genetic rearrangements, or may otherwise be false positives (sequencing/alignment errors or in vitro artifacts). Moreover, post-transcriptionally non-co-linear (‘PtNcl’) transcripts can arise from trans-splicing or back-splicing in cis (to generate so-called ‘circular RNA’). Here, we collected previously-predicted human non-co-linear RNA candidates, and designed a validation procedure integrating in silico filters with multiple experimental validation steps to examine their authenticity. We showed that >50% of the tested candidates were in vitro artifacts, even though some had been previously validated by RT-PCR. After excluding the possibility of genetic rearrangements, we distinguished between trans-spliced and circular RNAs, and confirmed that these two splicing forms can share the same non-co-linear junction. Importantly, the experimentally-confirmed PtNcl RNA events and their corresponding PtNcl splicing types (i.e. trans-splicing, circular RNA, or both sharing the same junction) were all expressed in rhesus macaque, and some were even expressed in mouse. Our study thus describes an essential procedure for confirming PtNcl transcripts, and provides further insight into the evolutionary role of PtNcl RNA events, opening up this important, but understudied, class of post-transcriptional events for comprehensive characterization.
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Affiliation(s)
- Chun-Ying Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hsiao-Jung Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Li-Yuan Hung
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Trees-Juen Chuang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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25
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The miRNA-mediated cross-talk between transcripts provides a novel layer of posttranscriptional regulation. ADVANCES IN GENETICS 2014; 85:149-99. [PMID: 24880735 DOI: 10.1016/b978-0-12-800271-1.00003-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Endogenously expressed transcripts that are posttranscriptionally regulated by the same microRNAs (miRNAs) will, in principle, compete for the binding of their shared small noncoding RNA regulators and modulate each other's abundance. Recently, the levels of some coding as well as noncoding transcripts have indeed been found to be regulated in this way. Transcripts that engage in such regulatory interactions are referred to as competitive endogenous RNAs (ceRNAs). This novel layer of posttranscriptional regulation has been shown to contribute to diverse aspects of organismal and cellular biology, despite the number of functionally characterized ceRNAs being as yet relatively low. Importantly, increasing evidence suggests that the dysregulation of some ceRNA interactions is associated with disease etiology, most preeminently with cancer. Here we review how posttranscriptional regulation by miRNAs contributes to the cross-talk between transcripts and review examples of known ceRNAs by highlighting the features underlying their interactions and what might be their biological relevance.
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Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF. Atypical RNAs in the coelacanth transcriptome. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:342-51. [PMID: 24174405 DOI: 10.1002/jez.b.22542] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/22/2013] [Accepted: 08/16/2013] [Indexed: 01/15/2023]
Abstract
Circular and apparently trans-spliced RNAs have recently been reported as abundant types of transcripts in mammalian transcriptome data. Both types of non-colinear RNAs are also abundant in RNA-seq of different tissue from both the African and the Indonesian coelacanth. We observe more than 8,000 lincRNAs with normal gene structure and several thousands of circularized and trans-spliced products, showing that such atypical RNAs form a substantial contribution to the transcriptome. Surprisingly, the majority of the circularizing and trans-connecting splice junctions are unique to atypical forms, that is, are not used in normal isoforms.
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Affiliation(s)
- Anne Nitsche
- Department of Computer Science, Bioinformatics Group, University of Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
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Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene 2013; 514:1-30. [PMID: 22909801 PMCID: PMC5632952 DOI: 10.1016/j.gene.2012.07.083] [Citation(s) in RCA: 509] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.
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Affiliation(s)
- Olga Kelemen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuan Wen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
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Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 2012; 7:e30733. [PMID: 22319583 PMCID: PMC3270023 DOI: 10.1371/journal.pone.0030733] [Citation(s) in RCA: 1852] [Impact Index Per Article: 154.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/28/2011] [Indexed: 01/07/2023] Open
Abstract
Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells.
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Affiliation(s)
- Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Charles Gawad
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pediatric Hematology/Oncology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter Lincoln Wang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Norman Lacayo
- Department of Pediatric Hematology/Oncology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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Zaphiropoulos PG. Trans-splicing in Higher Eukaryotes: Implications for Cancer Development? Front Genet 2011; 2:92. [PMID: 22303386 PMCID: PMC3268641 DOI: 10.3389/fgene.2011.00092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 12/07/2011] [Indexed: 12/28/2022] Open
Abstract
Trans-splicing, the possibility of exons from distinct pre-mRNAs to join together, is still a concept in gene expression that is generally regarded of limited significance. However, recent work has provided evidence that in human tumors trans-splicing events may precede chromosomal rearrangements. In fact, it has been suggested that the trans-spliced molecules could act as “guides” that facilitate the genomic translocation. This perspective highlights the development of the ideas of trans-splicing in higher eukaryotes during the last 25 years, from a bizarre phenomenon to a biological event that is attaining stronger recognition.
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Al-Balool HH, Weber D, Liu Y, Wade M, Guleria K, Nam PLP, Clayton J, Rowe W, Coxhead J, Irving J, Elliott DJ, Hall AG, Santibanez-Koref M, Jackson MS. Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Res 2011; 21:1788-99. [PMID: 21948523 PMCID: PMC3205564 DOI: 10.1101/gr.116442.110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 07/28/2011] [Indexed: 12/31/2022]
Abstract
In silico analyses have established that transcripts from some genes can be processed into RNAs with rearranged exon order relative to genomic structure (post-transcriptional exon shuffling, or PTES). Although known to contribute to transcriptome diversity in some species, to date the structure, distribution, abundance, and functional significance of human PTES transcripts remains largely unknown. Here, using high-throughput transcriptome sequencing, we identify 205 putative human PTES products from 176 genes. We validate 72 out of 112 products analyzed using RT-PCR, and identify additional PTES products structurally related to 61% of validated targets. Sequencing of these additional products reveals GT-AG dinucleotides at >95% of the splice junctions, confirming that they are processed by the spliceosome. We show that most PTES transcripts are expressed in a wide variety of human tissues, that they can be polyadenylated, and that some are conserved in mouse. We also show that they can extend into 5' and 3' UTRs, consistent with formation via trans-splicing of independent pre-mRNA molecules. Finally, we use real-time PCR to compare the abundance of PTES exon junctions relative to canonical exon junctions within the transcripts from seven genes. PTES exon junctions are present at <0.01% to >90% of the levels of canonical junctions, with transcripts from MAN1A2, PHC3, TLE4, and CDK13 exhibiting the highest levels. This is the first systematic experimental analysis of PTES in human, and it suggests both that the phenomenon is much more widespread than previously thought and that some PTES transcripts could be functional.
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Affiliation(s)
- Haya H. Al-Balool
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - David Weber
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Yilei Liu
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Mark Wade
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Kamlesh Guleria
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Pitsien Lang Ping Nam
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Jake Clayton
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - William Rowe
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Jonathan Coxhead
- NewGene Limited, Bioscience Building, International Centre for Life, Newcastle upon Tyne NE1 4EP, United Kingdom
| | - Julie Irving
- NewGene Limited, Bioscience Building, International Centre for Life, Newcastle upon Tyne NE1 4EP, United Kingdom
| | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Andrew G. Hall
- Northern Institute for Cancer Research, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Michael S. Jackson
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
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Kowarz E, Merkens J, Karas M, Dingermann T, Marschalek R. Premature transcript termination, trans-splicing and DNA repair: a vicious path to cancer. AMERICAN JOURNAL OF BLOOD RESEARCH 2011; 1:1-12. [PMID: 22432062 PMCID: PMC3301421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 04/04/2011] [Indexed: 05/31/2023]
Abstract
So far, about 800 different chromosomal translocations have been characterized in hemato-malignant and solid tumors. Chromosomal translocations mostly result in the expression of chimeric fusion proteins associated with enhanced proliferation and/or malignant transformation. Here, we demonstrate that genes frequently involved in such genetic rearrangements exhibit a unique feature: premature transcriptional termination. These early-terminated RNA molecules have an abundance of 10-20% when compared to their cognate full-length transcripts. They exhibit an unsaturated splice donor site that gives rise to trans-splicing events, leading to RNAs displaying exon repetitions or chimeric fusion RNAs. These arbitrary fusion RNAs mimic the presence of a chromosomal translocation in genetically unaffected cells. Based on our and published data, we propose the hypothesis that these artificial "chimeric fusion transcripts" may influence DNA repair processes, resulting in the generation of de novo chromosomal translocations. This idea provides a rational explanation why different individuals suffer from nearly identical genetic rearrangements.
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Affiliation(s)
- Eric Kowarz
- Institute of Pharmaceutical Biology, DCAL, ZAFES, CEF, JWG-University of Frankfurt, BiocenterMax-von-Laue-Str.9, D-60438 Frankfurt, Main, Germany
| | - Jennifer Merkens
- Institute of Pharmaceutical Biology, DCAL, ZAFES, CEF, JWG-University of Frankfurt, BiocenterMax-von-Laue-Str.9, D-60438 Frankfurt, Main, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry, ZAFES, CEF, JWG-University of Frankfurt, BiocenterMax-von-Laue-Str. 9, D-60438 Frankfurt, Main, Germany
| | - Theo Dingermann
- Institute of Pharmaceutical Biology, DCAL, ZAFES, CEF, JWG-University of Frankfurt, BiocenterMax-von-Laue-Str.9, D-60438 Frankfurt, Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, DCAL, ZAFES, CEF, JWG-University of Frankfurt, BiocenterMax-von-Laue-Str.9, D-60438 Frankfurt, Main, Germany
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Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 2010; 6:e1001233. [PMID: 21151960 PMCID: PMC2996334 DOI: 10.1371/journal.pgen.1001233] [Citation(s) in RCA: 709] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 11/02/2010] [Indexed: 12/02/2022] Open
Abstract
Human genome-wide association studies have linked single nucleotide polymorphisms (SNPs) on chromosome 9p21.3 near the INK4/ARF (CDKN2a/b) locus with susceptibility to atherosclerotic vascular disease (ASVD). Although this locus encodes three well-characterized tumor suppressors, p16INK4a, p15INK4b, and ARF, the SNPs most strongly associated with ASVD are ∼120 kb from the nearest coding gene within a long non-coding RNA (ncRNA) known as ANRIL (CDKN2BAS). While individuals homozygous for the atherosclerotic risk allele show decreased expression of ANRIL and the coding INK4/ARF transcripts, the mechanism by which such distant genetic variants influence INK4/ARF expression is unknown. Here, using rapid amplification of cDNA ends (RACE) and analysis of next-generation RNA sequencing datasets, we determined the structure and abundance of multiple ANRIL species. Each of these species was present at very low copy numbers in primary and cultured cells; however, only the expression of ANRIL isoforms containing exons proximal to the INK4/ARF locus correlated with the ASVD risk alleles. Surprisingly, RACE also identified transcripts containing non-colinear ANRIL exonic sequences, whose expression also correlated with genotype and INK4/ARF expression. These non-polyadenylated RNAs resisted RNAse R digestion and could be PCR amplified using outward-facing primers, suggesting they represent circular RNA structures that could arise from by-products of mRNA splicing. Next-generation DNA sequencing and splice prediction algorithms identified polymorphisms within the ASVD risk interval that may regulate ANRIL splicing and circular ANRIL (cANRIL) production. These results identify novel circular RNA products emanating from the ANRIL locus and suggest causal variants at 9p21.3 regulate INK4/ARF expression and ASVD risk by modulating ANRIL expression and/or structure. Unbiased studies of the human genome have identified strong genetic determinants of atherosclerotic vascular disease (ASVD) on chromosome 9p21.3. This region of the genome does not encode genes previously linked to ASVD, but does contain the INK4/ARF tumor suppressor locus. Products of the INK4/ARF locus regulate cell division, a process thought to be important in ASVD pathology. We and others have suggested that genetic variants in 9p21.3 influence INK4/ARF gene expression; however, the mechanisms by which these distant polymorphisms (>100,000 bp away) influence transcription of the locus is unknown. The ASVD–associated genetic variants lie within the predicted structure of a non-coding RNA (ncRNA) called ANRIL. Based upon recent work suggesting that other ncRNAs can repress nearby coding genes, we considered the possibility that ANRIL structure may regulate INK4/ARF gene expression. Coupling molecular analysis with state-of-the-art sequencing technologies in a wide variety of cell types from normal human donors and cancer cells, we found that ANRIL encodes a heterogeneous species of rare RNA transcripts. Moreover, we identified novel, circular ANRIL isoforms (cANRIL) whose expression correlated with INK4/ARF transcription and ASVD risk. These studies suggest a new model wherein ANRIL structure influences INK4/ARF expression and susceptibility to atherosclerosis.
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Affiliation(s)
- Christin E. Burd
- The Curriculum in Toxicology, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - William R. Jeck
- Department of Genetics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Yan Liu
- Department of Genetics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Hanna K. Sanoff
- The Division of Hematology and Oncology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Zefeng Wang
- Department of Pharmacology, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Norman E. Sharpless
- The Curriculum in Toxicology, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Genetics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Medicine, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
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33
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Hui J. Regulation of mammalian pre-mRNA splicing. ACTA ACUST UNITED AC 2009; 52:253-60. [DOI: 10.1007/s11427-009-0037-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 12/01/2008] [Indexed: 12/22/2022]
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Abstract
Alternative splicing is a well-characterized mechanism by which multiple transcripts are generated from a single mRNA precursor. By allowing production of several protein isoforms from one pre-mRNA, alternative splicing contributes to proteomic diversity. But what do we know about the origin of this mechanism? Do the same evolutionary forces apply to alternatively and constitutively splice exons? Do similar forces act on all types of alternative splicing? Are the products generated by alternative splicing functional? Why is "improper" recognition of exons and introns allowed by the splicing machinery? In this review, we summarize the current knowledge regarding these issues from an evolutionary perspective.
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Affiliation(s)
- Eddo Kim
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, Israel
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35
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Recent papers on zebrafish and other aquarium fish models. Zebrafish 2008; 2:289-97. [PMID: 18248187 DOI: 10.1089/zeb.2005.2.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Crane CF. Patterned sequence in the transcriptome of vascular plants. BMC Genomics 2007; 8:173. [PMID: 17573970 PMCID: PMC1940011 DOI: 10.1186/1471-2164-8-173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 06/15/2007] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Microsatellites (repeated subsequences based on motifs of one to six nucleotides) are widely used as codominant genetic markers because of their frequent polymorphism and relative selective neutrality. Minisatellites are repeats of motifs having seven or more nucleotides. The large number of EST sequences now available in public databases offers an opportunity to compare microsatellite and minisatellite properties and evaluate their evolution over a broad range of plant taxa. RESULTS Repeated motifs from one to 250 nucleotides long were identified in 6793306 expressed sequence tags (ESTs) from 88 genera of vascular plants, using a custom data-processing pipeline that allowed limited variation among repeats. The pipeline processed trimmed but otherwise unfiltered sequence and output nonredundant loci of at least 15 nucleotides, with degree of polymorphism and PCR primers wherever possible. Motifs that were an integral multiple of three in length were more abundant and richer in G/C than other motifs. From 80 to 85% of minisatellite motifs represented repeats within proteins, up to the 228-nucleotide repeat of ubiquitin, but not all of these repeats preserved reading frame. The remaining 15 to 20% of minisatellite motifs were associated with transcribed repetitive elements, e.g., retrotransposons. Relative microsatellite motif frequencies did not correlate tightly to phylogenetic relationship. Evolution of increased microsatellite and EST GC content was evident within the grasses. Microsatellites were less frequent in the transcriptome of genera with large genomes, but there was no evidence for greater dilution of the transcriptome with transposable element transcripts in these genera. CONCLUSION The relatively low correlation of microsatellite spectrum to phylogeny suggests that repeat loci evolve more rapidly than the surrounding sequence, although tissue specificity of the different EST libraries is a complicating factor. In-frame motifs are more abundant and higher in GC than frame-shifting motifs, but most EST minisatellite loci appear to represent repeats in translated sequence, regardless of whether reading frame is preserved. Motifs of four to six nucleotides are as polymorphic in EST collections as the commonly used motifs of two and three nucleotides, and they can be exploited as genetic markers with little additional effort.
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Affiliation(s)
- Charles F Crane
- Agricultural Research Service, United States Department of Agriculture, and Department of Botany and Plant Pathology, Purdue University, 915 W. State St, West Lafayette, Indiana 47907-2054, USA.
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Unneberg P, Claverie JM. Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data. PLoS One 2007; 2:e254. [PMID: 17330142 PMCID: PMC1804257 DOI: 10.1371/journal.pone.0000254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 02/06/2007] [Indexed: 11/18/2022] Open
Abstract
Recent studies on chromosome conformation show that chromosomes colocalize in the nucleus, bringing together active genes in transcription factories. This spatial proximity of actively transcribing genes could provide a means for RNA interaction at the transcript level. We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal interactions. We suggest that chimeric transcripts may be the result of close encounters of active genes, either as functional products or "noise" in the transcription process, and that they could be used as probes for chromosome interactions. We have found a total of 5,614 chimeric ESTs and 587 chimeric mRNAs that meet our selection criteria. Due to their higher quality, the mRNA findings are of particular interest and we hope that they may serve as food for thought for specialists in diverse areas of molecular biology.
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Affiliation(s)
- Per Unneberg
- Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique (CNRS) UPR-2589, Institut de Biologie Structurale et Microbiologie, Marseille, France.
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Dixon RJ, Eperon IC, Samani NJ. Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression. ACTA ACUST UNITED AC 2006; 23:150-5. [PMID: 17105720 DOI: 10.1093/bioinformatics/btl575] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Exon repetition describes the presence of tandemly repeated exons in mRNA in the absence of duplications in the genome. The regulation of this process is not fully understood. We therefore investigated the entire flanking intronic sequences of exons involved in exon repetition for common sequence elements. RESULTS A computational analysis of 48 human single exon repetition events identified two common sequence motifs. One of these motifs is pyrimidine-rich and is more common in the upstream intron, whilst the other motif is highly enriched in purines and is more common in the downstream intron. As the two motifs are complementary to each other, they support a model by which exon repetition occurs as a result of trans-splicing between separate pre-mRNA transcripts from the same gene that are brought together during transcription by complementary intronic sequences. The majority of the motif instances overlap with the locations of mobile elements such as Alu elements. We explore the potential importance of complementary intron sequences in a rat gene that undertakes natural exon repetition in a strain specific manner. The possibility that distant complementary sequences can stimulate inter-transcript splicing during transcription suggests an unsuspected new role for potential secondary structures in endogenous genes.
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Affiliation(s)
- Richard J Dixon
- Department of Cardiovascular Sciences Leicester, LE3 9Q, UK.
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Houseley JM, Garcia-Casado Z, Pascual M, Paricio N, O'Dell KMC, Monckton DG, Artero RD. Noncanonical RNAs from transcripts of the Drosophila muscleblind gene. ACTA ACUST UNITED AC 2006; 97:253-60. [PMID: 16714427 DOI: 10.1093/jhered/esj037] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
It has become increasingly evident that eukaryotic cells produce RNA molecules from coding genes with constitutions other than those of typically spliced mRNA transcripts. Here we describe new cDNAs from the Drosophila melanogaster muscleblind (mbl) locus that identify two such atypical RNA molecules: RNAs containing an incomplete exon 2 tandem repetition (mblE2E2') or having exons with a different order compared to the corresponding genomic DNA (mblE2E3'E2'; exon scrambling). The existence of exon duplications and rearrangements in the genomic locus that might explain such cDNAs was ruled out by genomic Southern blotting and in silico analysis of the Drosophila genome sequence. The incomplete exon 2 tandem repetition was confirmed by sequencing reverse transcriptase-polymerase chain reaction (RT-PCR) products, rapid amplification of cDNA ends, and detection of a band consistent with cDNA sizes in total RNA northern blots. RT-PCRs with exon-specific primers downstream of exon 2 were unable to amplify products other than those expected from canonical mbl isoforms, thus indicating that no other exons were efficiently spliced downstream of exon 2. Moreover, mblE2E2' transcripts seem to be poorly polyadenylated, if at all, and behave aberrantly in a polyacrylamide gel electrophoresis (PAGE) mobility assay. Taken together, lack of polyadenylation, lack of downstream splicing events, small size of mblE2E2', and PAGE behavior all suggest that these noncanonical transcripts may be circular RNAs. The functional implications for these noncanonical transcripts are unclear. A developmental expression profile of mblE2E2' revealed an almost constant expression except during early embryogenesis and early adulthood. The protein putatively encoded is unlikely to be functional because an in-frame stop codon occurs almost immediately after the splice site. Such noncanonical transcripts have previously been observed in vertebrates, and these data provide the first experimental evidence for similar phenomena in invertebrates.
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Affiliation(s)
- Jonathan M Houseley
- Department of Genetics, University of Valencia, Doctor Moliner 50, 46100 Burjasot, Valencia, Spain
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Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res 2006; 34:e63. [PMID: 16682442 PMCID: PMC1458517 DOI: 10.1093/nar/gkl151] [Citation(s) in RCA: 482] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Besides linear RNAs, pre-mRNA splicing generates three forms of RNAs: lariat introns, Y-structure introns from trans-splicing, and circular exons through exon skipping. To study the persistence of excised introns in total cellular RNA, we used three Escherichia coli 3' to 5' exoribonucleases. Ribonuclease R (RNase R) thoroughly degrades the abundant linear RNAs and the Y-structure RNA, while preserving the loop portion of a lariat RNA. Ribonuclease II (RNase II) and polynucleotide phosphorylase (PNPase) also preserve the lariat loop, but are less efficient in degrading linear RNAs. RNase R digestion of the total RNA from human skeletal muscle generates an RNA pool consisting of lariat and circular RNAs. RT-PCR across the branch sites confirmed lariat RNAs and circular RNAs in the pool generated by constitutive and alternative splicing of the dystrophin pre-mRNA. Our results indicate that RNase R treatment can be used to construct an intronic cDNA library, in which majority of the intron lariats are represented. The highly specific activity of RNase R implies its ability to screen for rare intragenic trans-splicing in any target gene with a large background of cis-splicing. Further analysis of the intronic RNA pool from a specific tissue or cell will provide insights into the global profile of alternative splicing.
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Affiliation(s)
| | | | - Jinhua Wang
- Cold Spring Harbor Laboratory1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Michael Q. Zhang
- Cold Spring Harbor Laboratory1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | | | - Akila Mayeda
- To whom correspondence should be addressed. Tel: +1 305 243 4621; Fax: +1 305 243 3065;
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Roux M, Levéziel H, Amarger V. Cotranscription and intergenic splicing of the PPARG and TSEN2 genes in cattle. BMC Genomics 2006; 7:71. [PMID: 16595010 PMCID: PMC1450281 DOI: 10.1186/1471-2164-7-71] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Accepted: 04/04/2006] [Indexed: 11/30/2022] Open
Abstract
Background Intergenic splicing resulting in the combination of mRNAs sequences from distinct genes is a newly identified mechanism likely to contribute to protein diversity. Few cases have been described, most of them involving neighboring genes and thus suggesting a cotranscription event presumably due to transcriptional termination bypass. Results We identified bovine chimeric transcripts resulting from cotranscription and intergenic splicing of two neighboring genes, PPARG and TSEN2. These two genes encode the Peroxisome Proliferator Activated Receptors γ1 and γ2 and the tRNA Splicing Endonuclease 2 homolog and are situated in the same orientation about 50 kb apart on bovine chromosome 22q24. Their relative position is conserved in human and mouse. We identified two types of chimeric transcripts containing all but the last exon of the PPARG gene followed by all but the first exon of the TSEN2 gene. The two chimers differ by the presence/absence of an intermediate exon resulting from transcription of a LINE L2 sequence situated between the two genes. Both transcripts use canonical splice sites for all exons coming from both genes, as well as for the LINE L2 sequence. One of these transcripts harbors a premature STOP codon and the other encodes a putative chimeric protein combining most of the PPARγ protein and the entire TSEN2 protein, but we could not establish the existence of this protein. Conclusion By showing that both individual and chimeric transcripts are transcribed from PPARG and TSEN2, we demonstrated regulation of transcription termination. Further, the existence and functionality of a chimeric protein harboring active motifs that are a priori unrelated is hypothesized.
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Affiliation(s)
- Matthieu Roux
- Unité de Génétique Moléculaire Animale, UMR1061 INRA/Université de Limoges, Faculté des Sciences et Techniques, 123 av Albert Thomas, 87060 Limoges Cedex, France
| | - Hubert Levéziel
- Unité de Génétique Moléculaire Animale, UMR1061 INRA/Université de Limoges, Faculté des Sciences et Techniques, 123 av Albert Thomas, 87060 Limoges Cedex, France
| | - Valérie Amarger
- Unité de Génétique Moléculaire Animale, UMR1061 INRA/Université de Limoges, Faculté des Sciences et Techniques, 123 av Albert Thomas, 87060 Limoges Cedex, France
- UMR 1280 Physiologie des Adaptations Nutritionnelles, Centre INRA de Nantes, BP71627, 44316 Nantes cedex 3, France
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