1
|
Ma XK, Zhai SN, Yang L. Approaches and challenges in genome-wide circular RNA identification and quantification. Trends Genet 2023; 39:897-907. [PMID: 37839990 DOI: 10.1016/j.tig.2023.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023]
Abstract
Numerous circular RNAs (circRNAs) produced from back-splicing of exon(s) have been recently revealed on a genome-wide scale across species. Although generally expressed at a low level, some relatively abundant circRNAs can play regulatory roles in various biological processes, prompting continuous profiling of circRNA in broader conditions. Over the past decade, distinct strategies have been applied in both transcriptome enrichment and bioinformatic tools for detecting and quantifying circRNAs. Understanding the scope and limitations of these strategies is crucial for the subsequent annotation and characterization of circRNAs, especially those with functional potential. Here, we provide an overview of different transcriptome enrichment, deep sequencing and computational approaches for genome-wide circRNA identification, and discuss strategies for accurate quantification and characterization of circRNA.
Collapse
Affiliation(s)
- Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Si-Nan Zhai
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| |
Collapse
|
2
|
Pisignano G, Michael DC, Visal TH, Pirlog R, Ladomery M, Calin GA. Going circular: history, present, and future of circRNAs in cancer. Oncogene 2023; 42:2783-2800. [PMID: 37587333 PMCID: PMC10504067 DOI: 10.1038/s41388-023-02780-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023]
Abstract
To date, thousands of highly abundant and conserved single-stranded RNA molecules shaped into ring structures (circRNAs) have been identified. CircRNAs are multifunctional molecules that have been shown to regulate gene expression transcriptionally and post-transcriptionally and exhibit distinct tissue- and development-specific expression patterns associated with a variety of normal and disease conditions, including cancer pathogenesis. Over the past years, due to their intrinsic stability and resistance to ribonucleases, particular attention has been drawn to their use as reliable diagnostic and prognostic biomarkers in cancer diagnosis, treatment, and prevention. However, there are some critical caveats to their utility in the clinic. Their circular shape limits their annotation and a complete functional elucidation is lacking. This makes their detection and biomedical application still challenging. Herein, we review the current knowledge of circRNA biogenesis and function, and of their involvement in tumorigenesis and potential utility in cancer-targeted therapy.
Collapse
Affiliation(s)
- Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - David C Michael
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tanvi H Visal
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Radu Pirlog
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol, BS16 1QY, UK
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
3
|
Circular RNA Fibroblast Growth Factor Receptor 1 Promotes Pancreatic Cancer Progression by Targeting MicroRNA-532-3p/PIK3CB Axis. Pancreas 2022; 51:930-942. [PMID: 36607937 DOI: 10.1097/mpa.0000000000002119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE The aim of the study is to explore the contribution and mechanism of circular RNA fibroblast growth factor receptor 1 (circFGFR1) in pancreatic ductal adenocarcinoma (PDAC) progression. METHODS Expressions of circFGFR1, microRNA (miR)-532-3p, and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta (PIK3CB) were assessed by quantitative real-time polymerase chain reaction or in situ hybridization. Fluorescence in situ hybridization determined the subcellular localization of circFGFR1. Immunohistochemistry was used to detect PIK3CB expression in PDAC tissues. Cell growth was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and colony formation assays. Wound healing, transwell, and flow cytometry assays examined the migration, invasion, and apoptosis. Dual-luciferase and RNA pull-down assay verified the interactions between circFGFR1/PIK3CB and miR-532-3p. In vivo xenograft tumor growth and lung metastasis were assessed in nude mice. RESULTS Functionally, knockdown of circFGFR1 restrained in vitro PDAC cell growth, migration, invasion, and in vivo xenograft tumor growth and lung metastasis. In addition, circFGFR1 could sponge miR-532-3p to upregulate PIK3CB level. Rescue experiments revealed that the tumor-suppressive effects caused by miR-532-3p mimics could be reversed by circFGFR1 or PIK3CB overexpression. CONCLUSIONS Our data revealed that circFGFR1 driven the malignant progression of PDAC by targeting miR-532-3p/PIK3CB axis, suggesting that inhibition of circFGFR1 might be considered as a therapeutic target for PDAC.
Collapse
|
4
|
Wang J, Wen Y, Xu J, Yue B, Zhong J, Zheng L, Lei C, Chen H, Huang Y. Circ RIMKLB promotes myoblast proliferation and inhibits differentiation by sponging miR-29c to release KCNJ12. Epigenetics 2022; 17:1686-1700. [PMID: 35348434 PMCID: PMC9621043 DOI: 10.1080/15592294.2022.2058211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Muscle development is a complex process that was regulated by many factors, among which non-coding RNAs (ncRNAs) play a vital role in regulating multiple life activities of muscle cells. Circular RNA (circRNA), a type of non-coding RNA with closed-loop structure, has been reported to affect multiple life processes. However, the roles of circRNAs on muscle development have not been fully elucidated. The present study aimed to determine whether and how circRIMKLB affects muscle development. Our study revealed that circRIMKLB promoted myoblast proliferation and inhibited differentiation. Besides, miR-29c was proved as a downstream target of circRIMKLB using dual-luciferase reporter assay and RNA-binding protein immunoprecipitation (RIP) assay. Also, potassium inwardly rectifying channel subfamily J member 12 (KCNJ12) was identified as a novel target of miR-29c via dual-luciferase reporter assay, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR), and western blot. CircRIMKLB and KCNJ12 were both proved to regulate cell cycle on muscle regeneration after injury in vivo. In conclusion, we demonstrated that circRIMKLB sponged miR-29c, releasing KCNJ12 to regulate myoblast proliferation and differentiation and regulating cell cycle during muscle regeneration after injury in vivo.
Collapse
Affiliation(s)
- Jian Wang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&f University, Yangling, Shaanxi, China
| | - Yifan Wen
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&f University, Yangling, Shaanxi, China
| | - Jiawei Xu
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&f University, Yangling, Shaanxi, China
| | - Binglin Yue
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&f University, Yangling, Shaanxi, China
| | - Jialin Zhong
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&f University, Yangling, Shaanxi, China
| | - Li Zheng
- College of Animal Science & Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&f University, Yangling, Shaanxi, China
| | - Hong Chen
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&f University, Yangling, Shaanxi, China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&f University, Yangling, Shaanxi, China
| |
Collapse
|
5
|
Radanova M, Mihaylova G, Nazifova-Tasinova N, Levkova M, Tasinov O, Ivanova D, Mihaylova Z, Donev I. Oncogenic Functions and Clinical Significance of Circular RNAs in Colorectal Cancer. Cancers (Basel) 2021; 13:3395. [PMID: 34298612 PMCID: PMC8303601 DOI: 10.3390/cancers13143395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/13/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is ranked as the second most commonly diagnosed disease in females and the third in males worldwide. Therefore, the finding of new more reliable biomarkers for early diagnosis, for prediction of metastasis, and resistance to conventional therapies is an important challenge in overcoming the disease. The current review presents circular RNAs (circRNAs) with their unique features as potential prognostic and diagnostic biomarkers in CRC. The review highlights the mechanism of action and the role of circRNAs with oncogenic functions in the CRC as well as the association between their expression and clinicopathological characteristics of CRC patients. The comprehension of the role of oncogenic circRNAs in CRC pathogenesis is growing rapidly and the next step is using them as suitable new drug targets in the personalized treatment of CRC patients.
Collapse
Affiliation(s)
- Maria Radanova
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Medical University of Varna, 9000 Varna, Bulgaria; (M.R.); (G.M.); (N.N.-T.); (O.T.); (D.I.)
- Laboratory of Molecular Pathology, University Hospital “St. Marina”, 9000 Varna, Bulgaria
| | - Galya Mihaylova
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Medical University of Varna, 9000 Varna, Bulgaria; (M.R.); (G.M.); (N.N.-T.); (O.T.); (D.I.)
| | - Neshe Nazifova-Tasinova
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Medical University of Varna, 9000 Varna, Bulgaria; (M.R.); (G.M.); (N.N.-T.); (O.T.); (D.I.)
| | - Mariya Levkova
- Department of Medical Genetics, Molecular Medicine and Nutrigenomics, Medical University of Varna, 9000 Varna, Bulgaria;
| | - Oskan Tasinov
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Medical University of Varna, 9000 Varna, Bulgaria; (M.R.); (G.M.); (N.N.-T.); (O.T.); (D.I.)
| | - Desislava Ivanova
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Medical University of Varna, 9000 Varna, Bulgaria; (M.R.); (G.M.); (N.N.-T.); (O.T.); (D.I.)
| | - Zhasmina Mihaylova
- Clinic of Medical Oncology, Military Medical Academy, 1000 Sofia, Bulgaria;
| | - Ivan Donev
- Clinic of Medical Oncology, Hospital Nadezhda, 1000 Sofia, Bulgaria
| |
Collapse
|
6
|
Wu R, Guo F, Wang CH, Qian B, Shen F, Huang F, Xu W. Bibliometric Analysis of Global Circular RNA Research Trends from 2007 to 2018. CELL JOURNAL 2021; 23:238-246. [PMID: 34096225 PMCID: PMC8181316 DOI: 10.22074/cellj.2021.7143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/08/2020] [Indexed: 11/14/2022]
Abstract
Objective Circular RNA (circRNA) is of significant interest in genetic research. The aim of this study was to assess
global trends in circRNA research production in order to shed new light on future research frontiers. Materials and Methods In this retrospective study, we conducted a literature search using the Web of Science Core
Collection (WoSCC) database on March 21, 2019 to retrieve publications from 2007 to 2018. Excel 2013, CiteSpace
V, and VOSviewer were used to evaluate bibliometric features that included publication output, countries/regions,
institutions, journals, citation frequency, H-index, and research hotspots. Results Global cumulative publication output on circRNA consisted of 998 papers with a total citation of 28 595 during
2007-2018. China, the US, and Germany were the most prolific countries. China ranked first in H-index (60 times) and
citations (13 333 times). The most productive institution was Nanjing Medical University with 73 papers. Biochemical
and Biophysical Research Communications (impact factor [IF]2017:2.559) ranked first among journals in the number
of publications (64 papers). The keywords shifted from "sequence", "intron", and "splice-site" to "transcriptome",
"microRNA sponge", "exon circularization", and "circRNA biogenesis" overtime. The burst keywords "transcriptome",
"microRNA sponge", "exon circularization", and "circRNA biogenesis" were the latest frontiers by 2018. Conclusion This is a relatively novel bibliometric analysis to inspect research related to circRNA. The results show
that publications have continuously increased in the past decade. China, the US, and Germany were the leading
countries/regions in terms of quantity. Recent studies on topics related to circRNA biogenesis and function should be
closely followed in this field.
Collapse
Affiliation(s)
- Ran Wu
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fei Guo
- Department of Transfusion Medicine, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - C Hen Wang
- Department of Orthopaedics, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Baohua Qian
- Department of Transfusion Medicine, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Fuming Shen
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fang Huang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Weidong Xu
- Department of Orthopaedics, Changhai Hospital, Second Military Medical University, Shanghai, China.
| |
Collapse
|
7
|
Saw PE, Xu X, Chen J, Song EW. Non-coding RNAs: the new central dogma of cancer biology. SCIENCE CHINA-LIFE SCIENCES 2020; 64:22-50. [PMID: 32930921 DOI: 10.1007/s11427-020-1700-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
The central dogma of molecular biology states that the functions of RNA revolve around protein translation. Until the last decade, most researches were geared towards characterization of RNAs as intermediaries in protein translation, namely, messenger RNAs (mRNAs) as temporary copies of genetic information, ribosomal RNAs (rRNAs) as a main component of ribosome, or translators of codon sequence (tRNAs). The statistical reality, however, is that these processes account for less than 2% of the genome, and insufficiently explain the functionality of 98% of transcribed RNAs. Recent discoveries have unveiled thousands of unique non-coding RNAs (ncRNAs) and shifted the perception of them from being "junk" transcriptional products to "yet to be elucidated"-and potentially monumentally important-RNAs. Most ncRNAs are now known as key regulators in various networks in which they could lead to specific cellular responses and fates. In major cancers, ncRNAs have been identified as both oncogenic drivers and tumor suppressors, indicating a complex regulatory network among these ncRNAs. Herein, we provide a comprehensive review of the various ncRNAs and their functional roles in cancer, and the pre-clinical and clinical development of ncRNA-based therapeutics. A deeper understanding of ncRNAs could facilitate better design of personalized therapeutics.
Collapse
Affiliation(s)
- Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Jianing Chen
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Er-Wei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China. .,Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| |
Collapse
|
8
|
Jin J, He X, Silva E. Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties. BMC Genomics 2020; 21:287. [PMID: 32264855 PMCID: PMC7137253 DOI: 10.1186/s12864-020-6687-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/18/2020] [Indexed: 12/31/2022] Open
Abstract
Background Stable introns and intronic fragments make up the largest population of RNA in the oocyte nucleus of the frog Xenopus tropicalis. These stable intronic sequence RNAs (sisRNAs) persist through the onset of zygotic transcription when synchronous cell division has ended, and the developing embryo consists of approximately 8000 cells. Despite their abundance, the sequence properties and biological function of sisRNAs are just beginning to be understood. Results To characterize this population of non-coding RNA, we identified all of the sisRNAs in the X. tropicalis oocyte nucleus using published high-throughput RNA sequencing data. Our analysis revealed that sisRNAs, have an average length of ~ 360 nt, are widely expressed from genes with multiple introns, and are derived from specific regions of introns that are GC and TG rich, while CpG poor. They are enriched in introns at both ends of transcripts but preferentially at the 3′ end. The consensus binding sites of specific transcription factors such as Stat3 are enriched in sisRNAs, suggesting an association between sisRNAs and transcription factors involved in early development. Evolutionary conservation analysis of sisRNA sequences in seven vertebrate genomes indicates that sisRNAs are as conserved as other parts of introns, but much less conserved than exons. Conclusion In total, our results indicate sisRNAs are selected intron regions with distinct properties and may play a role in gene expression regulation.
Collapse
Affiliation(s)
- Jing Jin
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.,Department of Biology, Georgetown University, 37th and O Sts, NW, Washington DC, 20057, USA
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Elena Silva
- Department of Biology, Georgetown University, 37th and O Sts, NW, Washington DC, 20057, USA.
| |
Collapse
|
9
|
Mehta SL, Dempsey RJ, Vemuganti R. Role of circular RNAs in brain development and CNS diseases. Prog Neurobiol 2020; 186:101746. [PMID: 31931031 PMCID: PMC7024016 DOI: 10.1016/j.pneurobio.2020.101746] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/13/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
In mammals, many classes of noncoding RNAs (ncRNAs) are expressed at a much higher level in the brain than in other organs. Recent studies have identified a new class of ncRNAs called circular RNAs (circRNAs), which are produced by back-splicing and fusion of either exons, introns, or both exon-intron into covalently closed loops. The circRNAs are also highly enriched in the brain and increase continuously from the embryonic to the adult stage. Although the functional significance and mechanism of action of circRNAs are still being actively explored, they are thought to regulate the transcription of their host genes and sequestration of miRNAs and RNA binding proteins. Some circRNAs are also shown to have translation potential to form peptides. The expression and abundance of circRNAs seem to be spatiotemporally maintained in a normal brain. Altered expression of circRNAs is also thought to mediate several disorders, including brain-tumor growth, and acute and chronic neurodegenerative disorders by affecting mechanisms such as angiogenesis, neuronal plasticity, autophagy, apoptosis, and inflammation. This review discusses the involvement of various circRNAs in brain development and CNS diseases. A better understanding of the circRNA function will help to develop novel therapeutic strategies to treat CNS complications.
Collapse
Affiliation(s)
- Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States
| | - Robert J Dempsey
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States; William S. Middleton Veterans Hospital, Madison, WI, United States.
| |
Collapse
|
10
|
Broen JCA, van Laar JM. Mycophenolate mofetil, azathioprine and tacrolimus: mechanisms in rheumatology. Nat Rev Rheumatol 2020; 16:167-178. [PMID: 32055040 DOI: 10.1038/s41584-020-0374-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2020] [Indexed: 02/08/2023]
Abstract
The introduction of biologic DMARDs into rheumatology has resulted in a substantial reduction of the burden of many rheumatic diseases. In the slipstream of the success achieved with these biologic DMARDs, some conventional immunosuppressive drugs have also found use in new indications. Notably, mycophenolate mofetil, azathioprine and tacrolimus have made their way from solid organ transplantation drugs to become useful assets in rheumatology practice. Mycophenolate mofetil and azathioprine inhibit the purine pathway and subsequently diminish cell proliferation. Both drugs have a pivotal role in the treatment of various rheumatic diseases, including lupus nephritis. Tacrolimus inhibits lymphocyte activation by inhibiting the calcineurin pathway. Mycophenolate mofetil and tacrolimus are, among other indications, increasingly being recognized as useful drugs in the treatment of interstitial lung disease in systemic rheumatic diseases and skin fibrosis in systemic sclerosis. A broad array of trials with mycophenolate mofetil, azathioprine and/or tacrolimus are ongoing within the field of rheumatology that might provide further novel avenues for the use of these drugs. In this Review, we discuss the historical perspective, pharmacodynamics, clinical indications and novel avenues for mycophenolate mofetil, azathioprine and tacrolimus in rheumatology.
Collapse
Affiliation(s)
- Jasper C A Broen
- Regional Rheumatology Center, Máxima Medical Center, Eindhoven and Veldhoven, Eindhoven, the Netherlands
| | - Jacob M van Laar
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands.
| |
Collapse
|
11
|
Fusion of multiple heterogeneous networks for predicting circRNA-disease associations. Sci Rep 2019; 9:9605. [PMID: 31270357 PMCID: PMC6610109 DOI: 10.1038/s41598-019-45954-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs (circRNAs) are a newly identified type of non-coding RNA (ncRNA) that plays crucial roles in many cellular processes and human diseases, and are potential disease biomarkers and therapeutic targets in human diseases. However, experimentally verified circRNA-disease associations are very rare. Hence, developing an accurate and efficient method to predict the association between circRNA and disease may be beneficial to disease prevention, diagnosis, and treatment. Here, we propose a computational method named KATZCPDA, which is based on the KATZ method and the integrations among circRNAs, proteins, and diseases to predict circRNA-disease associations. KATZCPDA not only verifies existing circRNA-disease associations but also predicts unknown associations. As demonstrated by leave-one-out and 10-fold cross-validation, KATZCPDA achieves AUC values of 0.959 and 0.958, respectively. The performance of KATZCPDA was substantially higher than those of previously developed network-based methods. To further demonstrate the effectiveness of KATZCPDA, we apply KATZCPDA to predict the associated circRNAs of Colorectal cancer, glioma, breast cancer, and Tuberculosis. The results illustrated that the predicted circRNA-disease associations could rank the top 10 of the experimentally verified associations.
Collapse
|
12
|
Li X, Yang L, Chen LL. The Biogenesis, Functions, and Challenges of Circular RNAs. Mol Cell 2018; 71:428-442. [PMID: 30057200 DOI: 10.1016/j.molcel.2018.06.034] [Citation(s) in RCA: 1309] [Impact Index Per Article: 218.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/18/2018] [Accepted: 06/22/2018] [Indexed: 12/21/2022]
Abstract
Covalently closed circular RNAs (circRNAs) are produced by precursor mRNA back-splicing of exons of thousands of genes in eukaryotes. circRNAs are generally expressed at low levels and often exhibit cell-type-specific and tissue-specific patterns. Recent studies have shown that their biogenesis requires spliceosomal machinery and can be modulated by both cis complementary sequences and protein factors. The functions of most circRNAs remain largely unexplored, but known functions include sequestration of microRNAs or proteins, modulation of transcription and interference with splicing, and even translation to produce polypeptides. However, challenges exist at multiple levels to understanding of the regulation of circRNAs because of their circular conformation and sequence overlap with linear mRNA counterparts. In this review, we survey the recent progress on circRNA biogenesis and function and discuss technical obstacles in circRNA studies.
Collapse
Affiliation(s)
- Xiang Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
| |
Collapse
|
13
|
Jia Ng SS, Zheng RT, Osman I, Pek JW. Generation of Drosophila sisRNAs by Independent Transcription from Cognate Introns. iScience 2018; 4:68-75. [PMID: 30240754 PMCID: PMC6146417 DOI: 10.1016/j.isci.2018.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/25/2018] [Accepted: 05/14/2018] [Indexed: 01/26/2023] Open
Abstract
Although stable intronic sequence RNAs (sisRNAs) are conserved in plants and animals, their functional significance is still unclear. We identify a pool of polyadenylated maternally deposited sisRNAs in Drosophila melanogaster. These sisRNAs can be generated by independent transcription from the cognate introns. The ovary-specific poly(A) polymerase Wispy mediates the polyadenylation of maternal sisRNAs and confers their stability as maternal transcripts. A developmentally regulated sisRNA sisR-3 represses the expression of a long noncoding RNA CR44148 and is required during development. Our results expand the pool of sisRNAs and suggest that sisRNAs perform regulatory functions during development in Drosophila. Identification of polyadenylated sisRNAs sisRNAs can be produced from independent transcription sisR-3 regulates a long noncoding RNA sisR-3 is required during development
Collapse
Affiliation(s)
- Sharon Si Jia Ng
- Temasek Polytechnic, 21 Tampines Avenue 1, Singapore 529757, Singapore
| | - Ruther Teo Zheng
- Ngee Ann Polytechnic, 535 Clementi Road, Singapore 599489, Singapore
| | - Ismail Osman
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore 117543, Singapore, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
| |
Collapse
|
14
|
Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
Collapse
Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
| |
Collapse
|
15
|
Yao T, Chen Q, Fu L, Guo J. Circular RNAs: Biogenesis, properties, roles, and their relationships with liver diseases. Hepatol Res 2017; 47:497-504. [PMID: 28185365 DOI: 10.1111/hepr.12871] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/31/2017] [Accepted: 02/08/2017] [Indexed: 02/08/2023]
Abstract
Circular RNAs (circRNAs) are a class of new-found RNA molecules that have a special covalent loop structure without a 5' cap and 3' tail. Researchers have found that circRNAs may be generated by intron-pairing-driven or lariat-driven circularization. They are cleared up by way of extracellular vesicles. They have some advantages such as stability, conservation, and tissue specificity. By serving as sponges of microRNAs, interacting with long non-coding RNAs, mRNA, or proteins, circRNAs regulate gene expression at transcriptional and post-transcriptional levels and contribute to carcinogenesis. In recent years, circRNAs have been found to be correlated with many cancers including hepatocellular carcinoma, one of the most common cancers with high mortality. This article will first introduce the biogenesis, properties, and functions of circRNAs. Then we focus on the molecular mechanisms underlying some circRNAs, including hsa_circ_0001649, hsa_circ_0005075, and cerebellar degeneration-related protein 1 antisense, on hepatocellular carcinoma metastasis.
Collapse
Affiliation(s)
- Ting Yao
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
| | - Qingqing Chen
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
| | - Liyun Fu
- Ningbo No. 2 Hospital and the Affiliated Hospital, Medical School of Ningbo University, Ningbo, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
| |
Collapse
|
16
|
Osman I, Tay MLI, Pek JW. Stable intronic sequence RNAs (sisRNAs): a new layer of gene regulation. Cell Mol Life Sci 2016; 73:3507-19. [PMID: 27147469 PMCID: PMC11108444 DOI: 10.1007/s00018-016-2256-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 02/05/2023]
Abstract
Upon splicing, introns are rapidly degraded. Hence, RNAs derived from introns are commonly deemed as junk sequences. However, the discoveries of intronic-derived small nucleolar RNAs (snoRNAs), small Cajal body associated RNAs (scaRNAs) and microRNAs (miRNAs) suggested otherwise. These non-coding RNAs are shown to play various roles in gene regulation. In this review, we highlight another class of intron-derived RNAs known as stable intronic sequence RNAs (sisRNAs). sisRNAs have been observed since the 1980 s; however, we are only beginning to understand their biological significance. Recent studies have shown or suggested that sisRNAs regulate their own host's gene expression, function as molecular sinks or sponges, and regulate protein translation. We propose that sisRNAs function as an additional layer of gene regulation in the cells.
Collapse
Affiliation(s)
- Ismail Osman
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Mandy Li-Ian Tay
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
| |
Collapse
|
17
|
Qu S, Zhong Y, Shang R, Zhang X, Song W, Kjems J, Li H. The emerging landscape of circular RNA in life processes. RNA Biol 2016; 14:992-999. [PMID: 27617908 PMCID: PMC5680710 DOI: 10.1080/15476286.2016.1220473] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNA that assumes a covalently closed continuous conformation. CircRNAs were previously thought to be the byproducts of splicing errors caused by low abundance and the technological limitations. With the recent development of high-throughput sequencing technology, numerous circRNAs have been discovered in many species. Recent studies have revealed that circRNAs are stable and widely expressed, and often exhibit cell type-specific or tissue-specific expression. Most circRNAs can be generated from exons, introns, or both. Remarkably, emerging evidence indicates that some circRNAs can serve as microRNA (miRNA) sponges, regulate transcription or splicing, and can interact with RNA binding proteins (RBPs). Moreover, circRNAs have been reported to play essential roles in myriad life processes, such as aging, insulin secretion, tissue development, atherosclerotic vascular disease risk, cardiac hypertrophy and cancer. Although circRNAs are ancient molecules, they represent a newly appreciated form of noncoding RNA and as such have great potential implications in clinical and research fields. Here, we review the current understanding of circRNA classification, function and significance in physiological and pathological processes. We believe that future research will increase our understanding of the regulation and function of these novel molecules.
Collapse
Affiliation(s)
- Shibin Qu
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Yue Zhong
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China.,b Department of General Surgery , The Second People's Hospital of Shaanxi Province , Xi'an , China
| | - Runze Shang
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Xuan Zhang
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Wenjie Song
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Jørgen Kjems
- c Department of Molecular Biology and Genetics (MBG) and Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Aarhus , Denmark
| | - Haimin Li
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| |
Collapse
|
18
|
Li LJ, Huang Q, Pan HF, Ye DQ. Circular RNAs and systemic lupus erythematosus. Exp Cell Res 2016; 346:248-54. [DOI: 10.1016/j.yexcr.2016.07.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/20/2016] [Indexed: 01/01/2023]
|
19
|
Chen W, Schuman E. Circular RNAs in Brain and Other Tissues: A Functional Enigma. Trends Neurosci 2016; 39:597-604. [PMID: 27445124 DOI: 10.1016/j.tins.2016.06.006] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 01/20/2023]
Abstract
Circular RNAs (circRNAs) are RNAs with a covalently closed loop structure that have recently regained the attention of biologists. Using deep RNA sequencing (RNA-seq) coupled with novel bioinformatic approaches, genome-wide studies have detected a large number of circRNAs, many of which are abundant, stable, and well conserved during evolution. With few exceptions, the function of most circRNAs remains elusive. Several recent studies have shown that circRNAs are more enriched in neuronal tissues and are often derived from genes specific for neuronal and synaptic function. Moreover, circRNA expression is regulated during neuronal development and by synaptic plasticity, suggesting specific neuronal functions. In this review, we discuss recent advances in the detection, biogenesis, and potential functions of circRNAs, with a particular focus on brain tissues.
Collapse
Affiliation(s)
- Wei Chen
- Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany; Department of Biology, South University of Science and Technology of China, Shenzhen, China.
| | - Erin Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany.
| |
Collapse
|
20
|
Abstract
Unlike linear RNAs terminated with 5' caps and 3' tails, circular RNAs are characterized by covalently closed loop structures with neither 5' to 3' polarity nor polyadenylated tail. This intrinsic characteristic has led to the general under-estimation of the existence of circular RNAs in previous polyadenylated transcriptome analyses. With the advent of specific biochemical and computational approaches, a large number of circular RNAs from back-spliced exons (circRNAs) have been identified in various cell lines and across different species. Recent studies have uncovered that back-splicing requires canonical spliceosomal machinery and can be facilitated by both complementary sequences and specific protein factors. In this review, we highlight our current understanding of the regulation of circRNA biogenesis, including both the competition between splicing and back-splicing and the previously under-appreciated alternative circularization.
Collapse
Affiliation(s)
- Ling-Ling Chen
- a State Key Laboratory of Molecular Biology; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences ; Shanghai , China
| | | |
Collapse
|
21
|
Chen X, Fan S, Song E. Noncoding RNAs: New Players in Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 927:1-47. [PMID: 27376730 DOI: 10.1007/978-981-10-1498-7_1] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The world of noncoding RNAs (ncRNAs) has gained widespread attention in recent years due to their novel and crucial potency of biological regulation. Noncoding RNAs play essential regulatory roles in a broad range of developmental processes and diseases, notably human cancers. Regulatory ncRNAs represent multiple levels of structurally and functionally distinct RNAs, including the best-known microRNAs (miRNAs), the complicated long ncRNAs (lncRNAs), and the newly identified circular RNAs (circRNAs). However, the mechanisms by which they act remain elusive. In this chapter, we will review the current knowledge of the ncRNA field, discussing the genomic context, biological functions, and mechanisms of action of miRNAs, lncRNAs, and circRNAs. We also highlight the implications of the biogenesis and gene expression dysregulation of different ncRNA subtypes in the initiation and development of human malignancies.
Collapse
Affiliation(s)
- Xueman Chen
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China
| | - Siting Fan
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China
| | - Erwei Song
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China.
| |
Collapse
|
22
|
Pek JW, Okamura K. Regulatory RNAs discovered in unexpected places. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:671-86. [DOI: 10.1002/wrna.1309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/14/2015] [Accepted: 08/21/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Jun Wei Pek
- Temasek Life Sciences Laboratory; 1 Research Link, National University of Singapore; Singapore Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory; 1 Research Link, National University of Singapore; Singapore Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
| |
Collapse
|
23
|
Chen I, Chen CY, Chuang TJ. Biogenesis, identification, and function of exonic circular RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:563-79. [PMID: 26230526 PMCID: PMC5042038 DOI: 10.1002/wrna.1294] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/11/2015] [Accepted: 06/16/2015] [Indexed: 01/20/2023]
Abstract
Circular RNAs (circRNAs) arise during post-transcriptional processes, in which a single-stranded RNA molecule forms a circle through covalent binding. Previously, circRNA products were often regarded to be splicing intermediates, by-products, or products of aberrant splicing. But recently, rapid advances in high-throughput RNA sequencing (RNA-seq) for global investigation of nonco-linear (NCL) RNAs, which comprised sequence segments that are topologically inconsistent with the reference genome, leads to renewed interest in this type of NCL RNA (i.e., circRNA), especially exonic circRNAs (ecircRNAs). Although the biogenesis and function of ecircRNAs are mostly unknown, some ecircRNAs are abundant, highly expressed, or evolutionarily conserved. Some ecircRNAs have been shown to affect microRNA regulation, and probably play roles in regulating parental gene transcription, cell proliferation, and RNA-binding proteins, indicating their functional potential for development as diagnostic tools. To date, thousands of ecircRNAs have been identified in multiple tissues/cell types from diverse species, through analyses of RNA-seq data. However, the detection of ecircRNA candidates involves several major challenges, including discrimination between ecircRNAs and other types of NCL RNAs (e.g., trans-spliced RNAs and genetic rearrangements); removal of sequencing errors, alignment errors, and in vitro artifacts; and the reconciliation of heterogeneous results arising from the use of different bioinformatics methods or sequencing data generated under different treatments. Such challenges may severely hamper the understanding of ecircRNAs. Herein, we review the biogenesis, identification, properties, and function of ecircRNAs, and discuss some unanswered questions regarding ecircRNAs. We also evaluate the accuracy (in terms of sensitivity and precision) of some well-known circRNA-detecting methods.
Collapse
Affiliation(s)
- Iju Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | |
Collapse
|
24
|
Qu S, Yang X, Li X, Wang J, Gao Y, Shang R, Sun W, Dou K, Li H. Circular RNA: A new star of noncoding RNAs. Cancer Lett 2015; 365:141-8. [PMID: 26052092 DOI: 10.1016/j.canlet.2015.06.003] [Citation(s) in RCA: 1277] [Impact Index Per Article: 141.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/01/2015] [Accepted: 06/01/2015] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are a novel type of RNA that, unlike linear RNAs, form a covalently closed continuous loop and are highly represented in the eukaryotic transcriptome. Recent studies have discovered thousands of endogenous circRNAs in mammalian cells. CircRNAs are largely generated from exonic or intronic sequences, and reverse complementary sequences or RNA-binding proteins (RBPs) are necessary for circRNA biogenesis. The majority of circRNAs are conserved across species, are stable and resistant to RNase R, and often exhibit tissue/developmental-stage-specific expression. Recent research has revealed that circRNAs can function as microRNA (miRNA) sponges, regulators of splicing and transcription, and modifiers of parental gene expression. Emerging evidence indicates that circRNAs might play important roles in atherosclerotic vascular disease risk, neurological disorders, prion diseases and cancer; exhibit aberrant expression in colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC); and serve as diagnostic or predictive biomarkers of some diseases. Similar to miRNAs and long noncoding RNAs (lncRNAs), circRNAs are becoming a new research hotspot in the field of RNA and could be widely involved in the processes of life. Herein, we review the formation and properties of circRNAs, their functions, and their potential significance in disease.
Collapse
Affiliation(s)
- Shibin Qu
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Xisheng Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Xiaolei Li
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Jianlin Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Yuan Gao
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Runze Shang
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Wei Sun
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Kefeng Dou
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Haimin Li
- Department of Hepatobiliary Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China.
| |
Collapse
|
25
|
A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation. Nat Commun 2015; 6:6966. [PMID: 25923108 PMCID: PMC4421845 DOI: 10.1038/ncomms7966] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/20/2015] [Indexed: 02/07/2023] Open
Abstract
Estrogen receptor-α (ER)-positive breast cancer cells undergo hormone-independent proliferation after deprivation of oestrogen, leading to endocrine therapy resistance. Up-regulation of the ER gene (ESR1) is critical for this process, but the underlying mechanisms remain unclear. Here we show that the combination of transcriptome and fluorescence in situ hybridization analyses revealed that oestrogen deprivation induced a cluster of noncoding RNAs that defined a large chromatin domain containing the ESR1 locus. We termed these RNAs as Eleanors (ESR1 locus enhancing and activating noncoding RNAs). Eleanors were present in ER-positive breast cancer tissues and localized at the transcriptionally active ESR1 locus to form RNA foci. Depletion of one Eleanor, upstream (u)-Eleanor, impaired cell growth and transcription of intragenic Eleanors and ESR1 mRNA, indicating that Eleanors cis-activate the ESR1 gene. Eleanor-mediated gene activation represents a new type of locus control mechanism and plays an essential role in the adaptation of breast cancer cells. Estrogen-receptor-positive breast cancer cells undergo hormone-independent proliferation after long-term oestrogen deprivation and become resistant to endocrine therapies. Here, the authors report a cluster of noncoding RNAs important for this adaptation process.
Collapse
|
26
|
Abstract
It is now clear that there is a diversity of circular RNAs in biological systems. Circular RNAs can be produced by the direct ligation of 5' and 3' ends of linear RNAs, as intermediates in RNA processing reactions, or by "backsplicing," wherein a downstream 5' splice site (splice donor) is joined to an upstream 3' splice site (splice acceptor). Circular RNAs have unique properties including the potential for rolling circle amplification of RNA, the ability to rearrange the order of genomic information, protection from exonucleases, and constraints on RNA folding. Circular RNAs can function as templates for viroid and viral replication, as intermediates in RNA processing reactions, as regulators of transcription in cis, as snoRNAs, and as miRNA sponges. Herein, we review the breadth of circular RNAs, their biogenesis and metabolism, and their known and anticipated functions.
Collapse
Affiliation(s)
- Erika Lasda
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
| |
Collapse
|
27
|
Gardner EJ, Nizami ZF, Talbot CC, Gall JG. Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. Genes Dev 2013; 26:2550-9. [PMID: 23154985 DOI: 10.1101/gad.202184.112] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To compare nuclear and cytoplasmic RNA from a single cell type, free of cross-contamination, we studied the oocyte of the frog Xenopus tropicalis, a giant cell with an equally giant nucleus. We isolated RNA from manually dissected nuclei and cytoplasm of mature oocytes and subjected it to deep sequencing. Cytoplasmic mRNA consisted primarily of spliced exons derived from ∼6700 annotated genes. Nearly all of these genes were represented in the nucleus by intronic sequences. However, unspliced nascent transcripts were not detected. Inhibition of transcription or splicing for 1-2 d had little or no effect on the abundance of nuclear intronic sequences, demonstrating that they are unusually stable. RT-PCR analysis showed that these stable intronic sequences are transcribed from the coding strand and that a given intron can be processed into more than one molecule. Stable intronic sequence RNA (sisRNA) from the oocyte nucleus constitutes a new class of noncoding RNA. sisRNA is detectable by RT-PCR in samples of total RNA from embryos up to the mid-blastula stage, when zygotic transcription begins. Storage of sisRNA in the oocyte nucleus and its transmission to the developing embryo suggest that it may play important regulatory roles during oogenesis and/or early embryogenesis.
Collapse
Affiliation(s)
- Eugene J Gardner
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | | | | | | |
Collapse
|
28
|
Ou SA, Chang E, Lee S, So K, Wu CT, Morris JR. Effects of chromosomal rearrangements on transvection at the yellow gene of Drosophila melanogaster. Genetics 2009; 183:483-96. [PMID: 19667134 PMCID: PMC2766311 DOI: 10.1534/genetics.109.106559] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 08/05/2009] [Indexed: 11/18/2022] Open
Abstract
Homologous chromosomes are paired in somatic cells of Drosophila melanogaster. This pairing can lead to transvection, which is a process by which the proximity of homologous genes can lead to a change in gene expression. At the yellow gene, transvection is the basis for several examples of intragenic complementation involving the enhancers of one allele acting in trans on the promoter of a paired second allele. Using complementation as our assay, we explored the chromosomal requirements for pairing and transvection at yellow. Following a protocol established by Ed Lewis, we generated and characterized chromosomal rearrangements to define a region in cis to yellow that must remain intact for complementation to occur. Our data indicate that homolog pairing at yellow is efficient, as complementation was disrupted only in the presence of chromosomal rearrangements that break
Collapse
Affiliation(s)
- Sharon A Ou
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | |
Collapse
|
29
|
Parks AL, Shalaby NA, Muskavitch MAT. Notch and suppressor of Hairless regulate levels but not patterns of Delta expression in Drosophila. Genesis 2008; 46:265-75. [PMID: 18442047 DOI: 10.1002/dvg.20391] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Notch signal transduction pathway is highly conserved and governs many developmental decisions in metazoans. The ligand Delta, and its receptor Notch, are often expressed in complementary patterns during Drosophila postembryonic development. Notch signaling is thought to play a role in generation of these complementary patterns through feedback mechanisms that regulate Delta and Notch expression. We have examined Delta expression during postembryonic development, following global alteration of Notch-dependent or Su(H)-dependent transcriptional regulation. We find that Notch and Su(H) regulate Delta expression in a manner that varies by context. Surprisingly, we find that wild type Delta expression levels are influenced by Su(H)-dependent mechanisms only in regions of high Delta/low Notch expression. In contrast, Delta expression levels in regions of low Delta/high Notch expression appear to be unaffected by Su(H)-mediated regulation. We conclude that Notch pathway feedback regulation is unlikely to contribute to the generation of complementary patterns in the contexts examined.
Collapse
Affiliation(s)
- Annette L Parks
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA
| | | | | |
Collapse
|
30
|
Williams BR, Bateman JR, Novikov ND, Wu CT. Disruption of topoisomerase II perturbs pairing in drosophila cell culture. Genetics 2007; 177:31-46. [PMID: 17890361 PMCID: PMC2013714 DOI: 10.1534/genetics.107.076356] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 06/22/2007] [Indexed: 12/16/2022] Open
Abstract
Homolog pairing refers to the alignment and physical apposition of homologous chromosomal segments. Although commonly observed during meiosis, homolog pairing also occurs in nonmeiotic cells of several organisms, including humans and Drosophila. The mechanism underlying nonmeiotic pairing, however, remains largely unknown. Here, we explore the use of established Drosophila cell lines for the analysis of pairing in somatic cells. Using fluorescent in situ hybridization (FISH), we assayed pairing at nine regions scattered throughout the genome of Kc167 cells, observing high levels of homolog pairing at all six euchromatic regions assayed and variably lower levels in regions in or near centromeric heterochromatin. We have also observed extensive pairing in six additional cell lines representing different tissues of origin, different ploidies, and two different species, demonstrating homolog pairing in cell culture to be impervious to cell type or culture history. Furthermore, by sorting Kc167 cells into G1, S, and G2 subpopulations, we show that even progression through these stages of the cell cycle does not significantly change pairing levels. Finally, our data indicate that disrupting Drosophila topoisomerase II (Top2) gene function with RNAi and chemical inhibitors perturbs homolog pairing, suggesting Top2 to be a gene important for pairing.
Collapse
Affiliation(s)
- Benjamin R Williams
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | |
Collapse
|
31
|
Bouaynaya N, Schonfeld D. The genomic structure: proof of the role of non-coding DNA. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2006; 2006:4544-4547. [PMID: 17947097 DOI: 10.1109/iembs.2006.259446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We prove that the introns play the role of a decoy in absorbing mutations in the same way hollow uninhabited structures are used by the military to protect important installations. Our approach is based on a probability of error analysis, where errors are mutations which occur in the exon sequences. We derive the optimal exon length distribution, which minimizes the probability of error in the genome. Furthermore, to understand how can Nature generate the optimal distribution, we propose a diffusive random walk model for exon generation throughout evolution. This model results in an alpha stable exon length distribution, which is asymptotically equivalent to the optimal distribution. Experimental results show that both distributions accurately fit the real data. Given that introns also drive biological evolution by increasing the rate of unequal crossover between genes, we conclude that the role of introns is to maintain a genius balance between stability and adaptability in eukaryotic genomes.
Collapse
|
32
|
Wilkie GS, Zimyanin V, Kirby R, Korey C, Francis-Lang H, Van Vactor D, Davis I. Small bristles, the Drosophila ortholog of NXF-1, is essential for mRNA export throughout development. RNA (NEW YORK, N.Y.) 2001; 7:1781-1792. [PMID: 11780634 PMCID: PMC1370217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We identified a temperature-sensitive allele of small bristles (sbr), the Drosophila ortholog of human TAP/NXF-1 and yeast Mex67, in a screen for mutants defective in mRNA export. We show that sbr is essential for the nuclear export of all mRNAs tested in a wide range of tissues and times in development. High resolution and sensitive in situ hybridization detect the rapid accumulation of individual mRNA species in sbr mutant nuclei in particles that are distinct from nascent transcript foci and resemble wild-type export intermediates. The particles become more numerous and intense with increasing time at the restrictive temperature and are exported very rapidly after shifting back to the permissive temperature. The mRNA export block is not due indirectly to a defect in splicing, nuclear protein import, or aberrant nuclear ultrastructure, suggesting that in sbr mutants, mRNA is competent for export but fails to dock or translocate through NPCs. We conclude that NXF-1 is an essential ubiquitous export factor for all mRNAs throughout development in higher eukaryotes.
Collapse
Affiliation(s)
- G S Wilkie
- Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Scotland, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
33
|
Pipes GC, Lin Q, Riley SE, Goodman CS. The Beat generation: a multigene family encoding IgSF proteins related to the Beat axon guidance molecule in Drosophila. Development 2001; 128:4545-52. [PMID: 11714679 DOI: 10.1242/dev.128.22.4545] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A previous genetic screen led to the identification of the beaten path (beat Ia) gene in Drosophila. Beat Ia contains two immunoglobulin (Ig) domains and appears to function as an anti-adhesive factor secreted by specific growth cones to promote axon defasciculation. We identify a family of 14 beat-like genes in Drosophila. In contrast to beat Ia, four novel Beat-family genes encode membrane-bound proteins. Moreover, mutations in each gene lead to much more subtle guidance phenotypes than observed in beat Ia. Genetic interactions between beat Ic and beat Ia reveal complementary functions. Our data suggest a model whereby Beat Ic (and perhaps other membrane-bound family members) functions in a pro-adhesive fashion to regulate fasciculation, while Beat Ia (the original secreted Beat) functions in an anti-adhesive fashion to regulate defasciculation.
Collapse
Affiliation(s)
- G C Pipes
- Howard Hughes Medical Institute, Division of Neurobiology, Department of Molecular and Cell Biology, 519 LSA, University of California, Berkeley, CA 94720, USA.
| | | | | | | |
Collapse
|
34
|
Clement JQ, Maiti S, Wilkinson MF. Localization and stability of introns spliced from the Pem homeobox gene. J Biol Chem 2001; 276:16919-30. [PMID: 11278282 DOI: 10.1074/jbc.m005104200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA splicing generates two products in equal molar amounts, mature mRNAs and spliced introns. Although the mechanism of RNA splicing and the fate of the spliced mRNA products have been well studied, very little is known about the fate and stability of most spliced introns. Research in this area has been hindered by the widely held view that most vertebrate introns are too unstable to be detectable. Here, we report that we are able to detect all three spliced introns from the coding region of the Pem homeobox gene. By using a tetracycline (tet)-regulated promoter, we found that the half-lives of these Pem introns ranged from 9 to 29 min, comparable with those of short lived mRNAs such as those encoding c-fos and c-myc. The half-lives of the Pem introns correlated with both their length and 5' to 3' orientation in the Pem gene. Subcellular fractionation analysis revealed that spliced Pem introns and pre-mRNA accumulated in the nuclear matrix, high salt-soluble, and DNase-sensitive fractions within the nucleus. Surprisingly, we found that all three of the spliced Pem introns were also in the cytoplasmic fraction, whereas Pem pre-mRNAs, U6 small nuclear RNA, and a spliced intron from another gene were virtually excluded from this fraction. This indicates either that spliced Pem introns are uniquely exported to the cytoplasm for degradation or they reside in a unique soluble nuclear fraction. Our study has implications for understanding the regulation of RNA metabolism, as the stability of introns and the location of their degradation may dictate the following: (i) the stability of nearby mRNAs that compete with spliced introns for rate-limiting nucleases, (ii) the rate at which free nucleotides are available for further rounds of transcription, and (iii) the rate at which splicing factors are recycled.
Collapse
Affiliation(s)
- J Q Clement
- Department of Immunology, the University of Texas, M. D. Anderson Cancer Center, Houston, Texas 77030, USA
| | | | | |
Collapse
|
35
|
Verheyen EM, Mirkovic I, MacLean SJ, Langmann C, Andrews BC, MacKinnon C. The tissue polarity gene nemo carries out multiple roles in patterning during Drosophila development. Mech Dev 2001; 101:119-32. [PMID: 11231065 DOI: 10.1016/s0925-4773(00)00574-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Drosophila nemo was first identified as a gene required for tissue polarity during ommatidial development. We have extended the analysis of nemo and found that it participates in multiple developmental processes. It is required during wing development for wing shape and vein patterning. We observe genetic interactions between nemo and mutations in the Notch, Wingless, Frizzled and Decapentaplegic pathways. Our data support the findings from other organisms that Nemo proteins act as negative regulators of Wingless signaling. nemo mutations cause polarity defects in the adult wing and overexpression of nemo leads to abdominal polarity defects. The expression of nemo during embryogenesis is dynamic and dsRNA inhibition and ectopic expression studies indicate that nemo is essential during embryogenesis.
Collapse
MESH Headings
- Alleles
- Animals
- Blotting, Northern
- Body Patterning
- DNA, Complementary/metabolism
- Drosophila/embryology
- Drosophila Proteins
- Frizzled Receptors
- In Situ Hybridization
- Insect Proteins/genetics
- Membrane Proteins/genetics
- Microscopy, Electron, Scanning
- Mitogen-Activated Protein Kinases/physiology
- Models, Biological
- Models, Genetic
- Mutation
- Phenotype
- Photoreceptor Cells, Invertebrate/embryology
- Photoreceptor Cells, Invertebrate/physiology
- RNA/metabolism
- RNA, Messenger/metabolism
- Receptors, G-Protein-Coupled
- Receptors, Notch
- Signal Transduction
- Wings, Animal/embryology
- Wings, Animal/physiology
Collapse
Affiliation(s)
- E M Verheyen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, B.C., V5A 1S6, Burnaby, Canada.
| | | | | | | | | | | |
Collapse
|
36
|
Melcák I, Cermanová S, Jirsová K, Koberna K, Malínský J, Raska I. Nuclear pre-mRNA compartmentalization: trafficking of released transcripts to splicing factor reservoirs. Mol Biol Cell 2000; 11:497-510. [PMID: 10679009 PMCID: PMC14788 DOI: 10.1091/mbc.11.2.497] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In the present study, the spatial organization of intron-containing pre-mRNAs of Epstein-Barr virus (EBV) genes relative to location of splicing factors is investigated. The intranuclear position of transcriptionally active EBV genes, as well as of nascent transcripts, is found to be random with respect to the speckled accumulations of splicing factors (SC35 domains) in Namalwa cells, arguing against the concept of the locus-specific organization of mRNA genes with respect to the speckles. Microclusters of splicing factors are, however, frequently superimposed on nascent transcript sites. The transcript environment is a dynamic structure consisting of both nascent and released transcripts, i.e., the track-like transcript environment. Both EBV sequences of the chromosome 1 homologue are usually associated with the track, are transcriptionally active, and exhibit in most cases a polar orientation. In contrast to nascent transcripts (in the form of spots), the association of a post-transcriptional pool of viral pre-mRNA (in the form of tracks) with speckles is not random and is further enhanced in transcriptionally silent cells when splicing factors are sequestered in enlarged accumulations. The transcript environment reflects the intranuclear transport of RNA from the sites of transcription to SC35 domains, as shown by concomitant mapping of DNA, RNA, and splicing factors. No clear vectorial intranuclear trafficking of transcripts from the site of synthesis toward the nuclear envelope for export into the cytoplasm is observed. Using Namalwa and Raji cell lines, a correlation between the level of viral gene transcription and splicing factor accumulation within the viral transcript environment has been observed. This supports a concept that the level of transcription can alter the spatial relationship among intron-containing genes, their transcripts, and speckles attributable to various levels of splicing factors recruited from splicing factor reservoirs. Electron microscopic in situ hybridization studies reveal that the released transcripts are directed toward reservoirs of splicing factors organized in clusters of interchromatin granules. Our results point to the bidirectional intranuclear movement of macromolecular complexes between intron-containing genes and splicing factor reservoirs: the recruitment of splicing factors to transcription sites and movement of released transcripts from DNA loci to reservoirs of splicing factors.
Collapse
MESH Headings
- Biological Transport
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cell Nucleus/ultrastructure
- Cell Nucleus/virology
- DNA, Viral/genetics
- DNA, Viral/metabolism
- DNA-Directed RNA Polymerases/antagonists & inhibitors
- DNA-Directed RNA Polymerases/metabolism
- Genes, Viral/genetics
- Genome, Viral
- Herpesvirus 4, Human/genetics
- Heterogeneous-Nuclear Ribonucleoproteins
- Humans
- Introns/genetics
- Microscopy, Confocal
- Microscopy, Electron
- Microscopy, Fluorescence
- Nuclear Proteins/metabolism
- Plasmids/genetics
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Ribonucleoproteins/metabolism
- Serine-Arginine Splicing Factors
- Spliceosomes/genetics
- Spliceosomes/metabolism
- Spliceosomes/ultrastructure
- Transcription, Genetic/genetics
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- I Melcák
- Department of Cell Biology, Institute of Experimental Medicine, Academy of Sciences of Czech Republic, Czech Republic
| | | | | | | | | | | |
Collapse
|
37
|
Affiliation(s)
- A Pàldi
- INSERM U257, Institut Cochin de Génétique Moléculaire, Paris, France
| | | |
Collapse
|
38
|
Clement JQ, Qian L, Kaplinsky N, Wilkinson MF. The stability and fate of a spliced intron from vertebrate cells. RNA (NEW YORK, N.Y.) 1999; 5:206-220. [PMID: 10024173 PMCID: PMC1369753 DOI: 10.1017/s1355838299981190] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Introns constitute most of the length of typical pre-mRNAs in vertebrate cells. Thus, the turnover rate of introns may significantly influence the availability of ribonucleotides and splicing factors for further rounds of transcription and RNA splicing, respectively. Given the importance of intron turnover, it is surprising that there have been no reports on the half-life of introns from higher eukaryotic cells. Here, we determined the stability of IVS1Cbeta1, the first intron from the constant region of the mouse T-cell receptor-beta, (TCR-beta) gene. Using a tetracycline (tet)-regulated promoter, we demonstrate that spliced IVS1Cbeta1 and its pre-mRNA had half-lives of 6.0+/-1.4 min and 3.7+/-1.0 min, respectively. We also examined the half-lives of these transcripts by using actinomycin D (Act.D). Act.D significantly stabilized IVS1Cbeta1 and its pre-mRNA, suggesting that Act.D not only blocks transcription but exerts rapid and direct posttranscriptional effects in the nucleus. We observed that in vivo spliced IVS1Cbeta1 accumulated predominantly as lariat molecules that use a consensus branchpoint nucleotide. The accumulation of IVS1Cbeta1 as a lariat did not result from an intrinsic inability to be debranched, as it could be debranched in vitro, albeit somewhat less efficiently than an adenovirus intron. Subcellular-fractionation and sucrose-gradient analyses showed that most spliced IVS1Cbeta1 lariats cofractionated with pre-mRNA, but not always with mRNA in the nucleus. Some IVS1Cbeta1 also appeared to be selectively exported to the cytoplasm, whereas TCR-beta pre-mRNA remained in the nucleus. This study constitutes the first detailed analysis of the stability and fate of a spliced nuclear intron in vivo.
Collapse
Affiliation(s)
- J Q Clement
- Department of Immunology, The University of Texas M.D. Anderson Cancer Center, Houston 77030, USA
| | | | | | | |
Collapse
|
39
|
Abstract
We examined the effect of cell cycle progression on various levels of chromosome organization in Drosophila. Using bromodeoxyuridine incorporation and DNA quantitation in combination with fluorescence in situ hybridization, we detected gross chromosomal movements in diploid interphase nuclei of larvae. At the onset of S-phase, an increased separation was seen between proximal and distal positions of a long chromsome arm. Progression through S-phase disrupted heterochromatic associations that have been correlated with gene silencing. Additionally, we have found that large-scale G1 nuclear architecture is continually dynamic. Nuclei display a Rabl configuration for only approximately 2 h after mitosis, and with further progression of G1-phase can establish heterochromatic interactions between distal and proximal parts of the chromosome arm. We also find evidence that somatic pairing of homologous chromosomes is disrupted during S-phase more rapidly for a euchromatic than for a heterochromatic region. Such interphase chromosome movements suggest a possible mechanism that links gene regulation via nuclear positioning to the cell cycle: delayed maturation of heterochromatin during G1-phase delays establishment of a silent chromatin state.
Collapse
Affiliation(s)
- A K Csink
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.
| | | |
Collapse
|
40
|
Beumer KJ, Pimpinelli S, Golic KG. Induced chromosomal exchange directs the segregation of recombinant chromatids in mitosis of Drosophila. Genetics 1998; 150:173-88. [PMID: 9725837 PMCID: PMC1460302 DOI: 10.1093/genetics/150.1.173] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In meiosis, the segregation of chromosomes at the reductional division is accomplished by first linking homologs together. Genetic exchange generates the bivalents that direct regular chromosome segregation. We show that genetic exchange in mitosis also generates bivalents and that these bivalents direct mitotic chromosome segregation. After FLP-mediated homologous recombination in G2 of the cell cycle, recombinant chromatids consistently segregate away from each other (x segregation). This pattern of segregation also applies to exchange between heterologs. Most, or all, cases of non-x segregation are the result of exchange in G1. Cytological evidence is presented that confirms the existence of the bivalents that direct this pattern of segregation. Our results implicate sister chromatid cohesion in maintenance of the bivalent. The pattern of chromatid segregation can be altered by providing an additional FRT at a more proximal site on one chromosome. We propose that sister chromatid exchange occurs at the more proximal site, allowing the recombinant chromatids to segregate together. This also allowed the recovery of reciprocal translocations following FLP-mediated heterologous recombination. The observation that exchange can generate a bivalent in mitotic divisions provides support for a simple evolutionary relationship between mitosis and meiosis.
Collapse
Affiliation(s)
- K J Beumer
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
| | | | | |
Collapse
|
41
|
Long AD, Lyman RF, Langley CH, Mackay TF. Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster. Genetics 1998; 149:999-1017. [PMID: 9611209 PMCID: PMC1460197 DOI: 10.1093/genetics/149.2.999] [Citation(s) in RCA: 150] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A restriction enzyme survey of a 57-kb region including the gene Delta uncovered 53 polymorphic molecular markers in a sample of 55 naturally occurring chromosomes. A permutation test, which assesses the significance of the molecular marker with the largest effect on bristle variation in four genetic backgrounds relative to permuted data-sets, found two sites that were independently associated with variation in bristle number. A common site in the second intron of Delta affected only sternopleural bristle number, and another common site in the fifth intron affected only abdominal bristle number in females. Under an additive genetic model, the polymorphism in the second intron may account for 12% of the total genetic variation in sternopleural bristle number due to third chromosomes, and the site in the fifth intron may account for 6% of the total variation in female abdominal bristle number due to the third chromosomes. These results suggest the following: (1) models that incorporate balancing selection are more consistent with observations than deleterious mutation-selection equilibrium models, (2) mapped quantitative trait loci of large effect may not represent a single variable site at a genetic locus, and (3) linkage disequilibrium can be used as a tool for understanding the molecular basis of quantitative variation.
Collapse
Affiliation(s)
- A D Long
- Center for Population Biology, University of California, Davis, California 95616, USA.
| | | | | | | |
Collapse
|
42
|
Martin-Morris LE, Csink AK, Dorer DR, Talbert PB, Henikoff S. Heterochromatic trans-inactivation of Drosophila white transgenes. Genetics 1997; 147:671-7. [PMID: 9335603 PMCID: PMC1208188 DOI: 10.1093/genetics/147.2.671] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Position effect variegation of most Drosophila melanogaster genes, including the white eye pigment gene is recessive. We find that this is not always the case for white transgenes. Three examples are described in which a lesion causing variegation is capable of silencing the white transgene on the paired homologue (trans-inactivation). These examples include two different transgene constructs inserted at three distinct genomic locations. The lesions that cause variegation of white minimally disrupt the linear order of genes on the chromosomes, permitting close homologous pairing. At one of these sites, trans-inactivation has also been extended to include a vital gene in the vicinity of the white transgene insertion. These findings suggest that many Drosophila genes, in many positions in the genome, can sense the heterochromatic state of a paired homologue.
Collapse
Affiliation(s)
- L E Martin-Morris
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
| | | | | | | | | |
Collapse
|
43
|
Henikoff S. Nuclear organization and gene expression: homologous pairing and long-range interactions. Curr Opin Cell Biol 1997; 9:388-95. [PMID: 9159074 DOI: 10.1016/s0955-0674(97)80012-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genetic studies have demonstrated that pairing interactions between homologous chromosomes and long-range associations between nonhomologous sites can influence gene expression. Recent work has revealed that such influences are widespread in eukaryotes and that chromosome architecture is likely to be of fundamental importance for nuclear structure and function.
Collapse
Affiliation(s)
- S Henikoff
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA.
| |
Collapse
|
44
|
Parks AL, Huppert SS, Muskavitch MA. The dynamics of neurogenic signalling underlying bristle development in Drosophila melanogaster. Mech Dev 1997; 63:61-74. [PMID: 9178257 DOI: 10.1016/s0925-4773(97)00675-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have examined expression of the neurogenic gene, Delta (Dl), and the regulatory relationships between the Delta-Notch signalling pathway and the proneural gene, achaete, during microchaeta development in Drosophila. Delta is expressed in all microchaeta proneural cells and microchaeta sensory organ precursors (SOPs) and is expressed dynamically in SOP progeny. We find that Delta expression in microchaeta proneural cells is detected prior to the onset of achaete expression and arises normally in the absence of achaete/scute function, indicating that initial Delta expression in the notum is not dependent on proneural gene function. Activation of the Delta-Notch pathway results in loss of Delta protein accumulation, suggesting that Delta expression is regulated, in part, by Delta-Notch signalling activity. We find that Delta signalling is required for correct delineation of early proneural gene expression in developing nota. Within microchaeta proneural stripes, we demonstrate that Delta-Notch signalling prohibits adoption of the SOP fate by repressing expression of proneural genes.
Collapse
Affiliation(s)
- A L Parks
- Department of Biology, Indiana University, Bloomington 47405, USA
| | | | | |
Collapse
|
45
|
Cherbas L, Cherbas P. "Parahomologous" gene targeting in Drosophila cells: an efficient, homology-dependent pathway of illegitimate recombination near a target site. Genetics 1997; 145:349-58. [PMID: 9071589 PMCID: PMC1207800 DOI: 10.1093/genetics/145.2.349] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Drosophila cells in culture can be transformed by introducing exogenous DNA carrying a selectable marker. Here we report on the fate of plasmids that contain an extended fragment of Drosophila DNA in addition to the selectable marker. A small minority of the resulting transformants appear to arise from homologous recombination at the chromosomal target. However, the majority of the insertions are the products of illegitimate events in the vicinity of the target DNA, and they often cause mutations in the targeted region. The efficiency of this process, its homology dependence, and the clustering of the products define a novel transformation pathway that we call "parahomologous targeting."
Collapse
Affiliation(s)
- L Cherbas
- Department of Biology, Indiana University, Bloomington 47405, USA.
| | | |
Collapse
|
46
|
Fambrough D, Pan D, Rubin GM, Goodman CS. The cell surface metalloprotease/disintegrin Kuzbanian is required for axonal extension in Drosophila. Proc Natl Acad Sci U S A 1996; 93:13233-8. [PMID: 8917574 PMCID: PMC24076 DOI: 10.1073/pnas.93.23.13233] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
It has long been suspected that proteolytic activity associated with advancing growth cones may be required for axon extension. We have isolated mutations in the kuzbanian (kuz) gene, which is expressed in the nervous system and encodes a putative zinc metalloprotease with a disintegrin domain. Drosophila embryos with loss-of-function mutations in kuz have dramatic defects in the development of central nervous system axon pathways, with many axons stalling and failing to extend through the nerve cord. This phenotype is rescued by panneural expression of kuz mRNA in the embryo. These results show that the Kuz metalloprotease is required for axon extension, suggesting a requirement for proteolytic activity at the growth cone surface.
Collapse
Affiliation(s)
- D Fambrough
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
| | | | | | | |
Collapse
|
47
|
Zachow KR, Bentley D. Blackjack, a novel protein associated with microtubules in embryonic neurons. J Cell Sci 1996; 109 ( Pt 6):1497-507. [PMID: 8799836 DOI: 10.1242/jcs.109.6.1497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microtubule-associated proteins can influence the organization, stability and dynamics of microtubules. We characterize a novel protein that associates with microtubules as assessed by immunofluorescence, immunoelectron microscopy, and co-sedimentation. The protein is expressed heavily in embryonic neurons and, to a lesser extent, in epithelial and mesodermal cells. The cDNA sequence predicts a protein of 1,547 amino acids and approximately 170 kDa. Immunoblot of embryo lysate demonstrates bands of approximately 240 and 260 kDa. The predicted amino acid sequence contains 77 potential serine/threonine phosphorylation sites. A distinctive feature is a predicted alpha-helical central domain comprising 21 identical repeats of an 11 amino acid sequence (PLEELRKDAAE). The protein is thermostable and has two major charge-domains: the amino-terminal 80% has an estimated pI of 4.0 and the carboxy-terminal 20%, a pI of 12.2. The protein shares several general biochemical and molecular features of MAPs, but its sequence is not similar to that of any described MAP.
Collapse
Affiliation(s)
- K R Zachow
- Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
| | | |
Collapse
|
48
|
Golic MM, Golic KG. A quantitative measure of the mitotic pairing of alleles in Drosophila melanogaster and the influence of structural heterozygosity. Genetics 1996; 143:385-400. [PMID: 8722790 PMCID: PMC1207271 DOI: 10.1093/genetics/143.1.385] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In Drosophila there exist several examples of gene expression that can be modified by an interaction between alleles; this effect is known as transvection. The inference that alleles interact comes from the observations that homologous chromosomes pair in mitotically dividing cells, and that chromosome rearrangements can alter the phenotype produced by a pair of alleles. It is thought that heterozygous rearrangements impede the ability of alleles to pair and interact. However, because the existing data are inconsistent, this issue is not fully settled. By measuring the frequency of site-specific recombination between homologous chromosomes, we show that structural heterozygosity inhibits the pairing of alleles that lie distal to a rearrangement breakpoint. We suggest that some of the apparent conflicts may owe to variations in cell-cycle lengths in the tissues where the relevant allelic interactions occur. Cells with a longer cell cycle have more time to establish the normal pairing relationships that have been disturbed by rearrangements. In support, we show that Minute mutations, which slow the rate of cell division, partially restore a transvection effect that is disrupted by inversion heterozygosity.
Collapse
Affiliation(s)
- M M Golic
- Department of Biology, University of Utah, Salt Lake City 84112, USA
| | | |
Collapse
|
49
|
Krueger NX, Van Vactor D, Wan HI, Gelbart WM, Goodman CS, Saito H. The transmembrane tyrosine phosphatase DLAR controls motor axon guidance in Drosophila. Cell 1996; 84:611-22. [PMID: 8598047 DOI: 10.1016/s0092-8674(00)81036-3] [Citation(s) in RCA: 284] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
DLAR is a receptor-like, transmembrane protein-tyrosine phosphatase in Drosophila that is expressed almost exclusively by developing neurons. Analysis of Dlar loss-of-function mutations shows that DLAR plays a key role during motoneuron growth cone guidance. Segmental nerve b (SNb) motor axons normally exit the common motor pathway, enter the ventral target region, and then synapse on specific ventral muscles. In Dlar mutant embryos, SNb axons bypass their normal target region and instead continue to extend along the common pathway. SNd motor axons also make pathfinding errors, while SNa and SNc axons appear normal. Thus, DLAR controls the ability of certain motor axons to navigate specific choices points in the developing Drosophila nervous system.
Collapse
Affiliation(s)
- N X Krueger
- Division of Tumor Immunology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | | | | | | | | | | |
Collapse
|
50
|
Henikoff S. A Pairing-Looping Model for Position-Effect Variegation in Drosophila. GENOMES OF PLANTS AND ANIMALS 1996. [DOI: 10.1007/978-1-4899-0280-1_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|