1
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Li S, Chu Y, Guo X, Mao C, Xiao SJ. Circular RNA oligonucleotides: enzymatic synthesis and scaffolding for nanoconstruction. NANOSCALE HORIZONS 2024. [PMID: 39042106 DOI: 10.1039/d4nh00236a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
We report the efficient synthesis of monomeric circular RNAs (circRNAs) in the size range of 16-44 nt with a novel DNA dumbbell splinting plus T4 DNA ligation strategy. Such a DNA dumbbell splinting strategy was developed by one group among ours recently for near-quantitative conversion of short linear DNAs into monomeric circular ones. Furthermore, using the 44 nt circRNA as scaffold strands, we constructed hybrid RNA:DNA and pure RNA:RNA double crossover tiles and their assemblies of nucleic acid nanotubes and flat arrays.
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Affiliation(s)
- Shijie Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Yanxin Chu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Xin Guo
- Bruker (Beijing) Scientific Technology Co. Ltd, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Shou-Jun Xiao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
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2
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Sharma NK, Dwivedi P, Bhushan R, Maurya PK, Kumar A, Dakal TC. Engineering circular RNA for molecular and metabolic reprogramming. Funct Integr Genomics 2024; 24:117. [PMID: 38918231 DOI: 10.1007/s10142-024-01394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
The role of messenger RNA (mRNA) in biological systems is extremely versatile. However, it's extremely short half-life poses a fundamental restriction on its application. Moreover, the translation efficiency of mRNA is also limited. On the contrary, circular RNAs, also known as circRNAs, are a common and stable form of RNA found in eukaryotic cells. These molecules are synthesized via back-splicing. Both synthetic circRNAs and certain endogenous circRNAs have the potential to encode proteins, hence suggesting the potential of circRNA as a gene expression machinery. Herein, we aim to summarize all engineering aspects that allow exogenous circular RNA (circRNA) to prolong the time that proteins are expressed from full-length RNA signals. This review presents a systematic engineering approach that have been devised to efficiently assemble circRNAs and evaluate several aspects that have an impact on protein production derived from. We have also reviewed how optimization of the key components of circRNAs, including the topology of vector, 5' and 3' untranslated sections, entrance site of the internal ribosome, and engineered aptamers could be efficiently impacting the translation machinery for molecular and metabolic reprogramming. Collectively, molecular and metabolic reprogramming present a novel way of regulating distinctive cellular features, for instance growth traits to neoplastic cells, and offer new possibilities for therapeutic inventions.
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Affiliation(s)
- Narendra Kumar Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India.
| | - Pragya Dwivedi
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India
| | - Ravi Bhushan
- Department of Zoology, M.S. College, Motihari, Bihar, India
| | - Pawan Kumar Maurya
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
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3
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Choi SW, Nam JW. Optimal design of synthetic circular RNAs. Exp Mol Med 2024; 56:1281-1292. [PMID: 38871815 PMCID: PMC11263348 DOI: 10.1038/s12276-024-01251-w] [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: 12/24/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs are an unusual class of single-stranded RNAs whose ends are covalently linked via back-splicing. Due to their versatility, the need to express circular RNAs in vivo and in vitro has increased. Efforts have been made to efficiently and precisely synthesize circular RNAs. However, a review on the optimization of the processes of circular RNA design, synthesis, and delivery is lacking. Our review highlights the multifaceted aspects considered when producing optimal circular RNAs and summarizes the available options for each step of exogenous circular RNA design and synthesis, including circularization strategies. Additionally, this review describes several potential applications of circular RNAs.
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Affiliation(s)
- Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seoul, 04763, Republic of Korea.
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4
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Huang W, Paul D, Calin GA, Bayraktar R. miR-142: A Master Regulator in Hematological Malignancies and Therapeutic Opportunities. Cells 2023; 13:84. [PMID: 38201290 PMCID: PMC10778542 DOI: 10.3390/cells13010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/29/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
MicroRNAs (miRNAs) are a type of non-coding RNA whose dysregulation is frequently associated with the onset and progression of human cancers. miR-142, an ultra-conserved miRNA with both active -3p and -5p mature strands and wide-ranging physiological targets, has been the subject of countless studies over the years. Due to its preferential expression in hematopoietic cells, miR-142 has been found to be associated with numerous types of lymphomas and leukemias. This review elucidates the multifaceted role of miR-142 in human physiology, its influence on hematopoiesis and hematopoietic cells, and its intriguing involvement in exosome-mediated miR-142 transport. Moreover, we offer a comprehensive exploration of the genetic and molecular landscape of the miR-142 genomic locus, highlighting its mutations and dysregulation within hematological malignancies. Finally, we discuss potential avenues for harnessing the therapeutic potential of miR-142 in the context of hematological malignancies.
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Affiliation(s)
- Wilson Huang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (W.H.); (G.A.C.)
| | - Doru Paul
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA;
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (W.H.); (G.A.C.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Recep Bayraktar
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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5
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Chen X, Wang C, Lu Y. Tactics targeting circular mRNA biosynthesis. Biotechnol Bioeng 2023. [PMID: 37126367 DOI: 10.1002/bit.28410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 05/02/2023]
Abstract
Faced with the development of mRNA technology in the field of medicine and vaccine, circular mRNA (circmRNA) becomes a strong alternative to mRNA for its circular secondary structure and higher stability. At present, the synthesis of circmRNAs has been realized by ligating linear mRNA precursors and is limited by poor efficiency. To solve this challenge, this study started with ribozyme catalysis and enzymatic reaction to explore different circmRNA biosynthesis strategies. In terms of ribozyme method, by screening different group I intron self-splicing system sequences, the sequence from thymidylate synthase (Td) gene of phage T4 showed the highest ligation efficiency. In terms of enzyme method, with the help of 20-bp homologous arm, T4 Rnl 2 was determined as the ligation method with the highest ligation efficiency. By comparing the two ligation methods, the expression level of circmRNA ligated by T4 Rnl 2 was 86% higher than that ligated by Td ribozyme. Based on these ligation methods, the screening results of internal ribosome entry site (IRES) sequences showed that mud crab dicistrovirus IRES was an IRES sequence with high ribosome binding ability and could be widely used in circmRNAs for efficient and stable translation in mammalian cells. These results should provide positive guidance for the industrial production of circmRNAs and the development of mRNA vaccines. Eventually, circmRNAs could widely function in the field of biomedicine.
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Affiliation(s)
- Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Chen Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
- Department of Chemical Engineering, Tsinghua University, Beijing, China
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6
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Kameda S, Ohno H, Saito H. Synthetic circular RNA switches and circuits that control protein expression in mammalian cells. Nucleic Acids Res 2023; 51:e24. [PMID: 36642090 PMCID: PMC9976894 DOI: 10.1093/nar/gkac1252] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
Synthetic messenger RNA (mRNA) has been focused on as an emerging application for mRNA-based therapies and vaccinations. Recently, synthetic circular RNAs (circRNAs) have shown promise as a new class of synthetic mRNA that enables superior stability and persistent gene expression in cells. However, translational control of circRNA remained challenging. Here, we develop 'circRNA switches' capable of controlling protein expression from circRNA by sensing intracellular RNA or proteins. We designed microRNA (miRNA) and protein-responsive circRNA switches by inserting miRNA-binding or protein-binding sequences into untranslated regions (UTRs), or Coxsackievirus B3 Internal Ribosome Entry Site (CVB3 IRES), respectively. Engineered circRNAs efficiently expressed reporter proteins without inducing severe cell cytotoxicity and immunogenicity, and responded to target miRNAs or proteins, controlling translation levels from circRNA in a cell type-specific manner. Moreover, we constructed circRNA-based gene circuits that selectively activated translation by detecting endogenous miRNA, by connecting miRNA and protein-responsive circRNAs. The designed circRNA circuits performed better than the linear mRNA-based circuits in terms of persistent expression levels. Synthetic circRNA devices provide new insights into RNA engineering and have a potential for RNA synthetic biology and therapies.
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Affiliation(s)
- Shigetoshi Kameda
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan.,Graduate School of Medicine, Kyoto University,Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hirohisa Ohno
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan
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7
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Wu H, Zheng S, He Q, Li Y. Recent Advances of Circular RNAs as Biomarkers for Osteosarcoma. Int J Gen Med 2023; 16:173-183. [PMID: 36687163 PMCID: PMC9850833 DOI: 10.2147/ijgm.s380834] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 11/30/2022] [Indexed: 01/15/2023] Open
Abstract
Osteosarcoma is the most common primary malignant bone tumor in young adult, which is prone to early metastasis and poor prognosis. The current treatment methods need to be improved. Circular RNA is a covalently blocked circular, non-coding RNA that plays an essential role in the occurrence, development, clinical diagnosis, and treatment of various diseases. Recently, an increasing number of circRNAs have been identified in osteosarcoma. Understanding its role in osteosarcoma is conducive to the early detection, diagnosis, and treatment of osteosarcoma. In this paper, we reviewed the mechanism of action of circular RNA in the occurrence and development of osteosarcoma and its clinical application in recent years.
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Affiliation(s)
- Hongliang Wu
- Department of Orthopedics, Fuzhou Second Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, People’s Republic of China,Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, People’s Republic of China,Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Sihang Zheng
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Qun He
- Department of Bioinformatics, School of Life Sciences, China Medical University, Shenyang, People’s Republic of China
| | - Yan Li
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, People’s Republic of China,Correspondence: Yan Li; Qun He, Email ;
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8
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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9
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Wang W, Sun L, Huang MT, Quan Y, Jiang T, Miao Z, Zhang Q. Regulatory circular RNAs in viral diseases: applications in diagnosis and therapy. RNA Biol 2023; 20:847-858. [PMID: 37882652 PMCID: PMC10730172 DOI: 10.1080/15476286.2023.2272118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 10/27/2023] Open
Abstract
Circular RNA (circRNA) forms closed loops via back-splicing in precursor mRNA, resisting exonuclease degradation. In higher eukaryotes, protein-coding genes create circRNAs through exon back-splicing. Unlike mRNAs, circRNAs possess unique production and structural traits, bestowing distinct cellular functions and biomedical potential. In this review, we explore the pivotal roles of viral circRNAs and associated RNA in various biological processes. Analysing the interactions between viral circRNA and host cellular machinery yields fresh insights into antiviral immunity, catalysing the development of potential therapeutics. Furthermore, circRNAs serve as enduring biomarkers in viral diseases due to their stable translation within specific tissues. Additionally, a deeper understanding of translational circRNA could expedite the establishment of circRNA-based expression platforms, meeting the rising demand for broad-spectrum viral vaccines. We also highlight the applications of circular RNA in biomarker studies as well as circRNA-based therapeutics. Prospectively, we expect a technological revolution in combating viral infections using circRNA.
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Affiliation(s)
- Wei Wang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Lei Sun
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Meng-Ting Huang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yun Quan
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Tao Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Zhichao Miao
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qiong Zhang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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10
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Kristensen LS, Jakobsen T, Hager H, Kjems J. The emerging roles of circRNAs in cancer and oncology. Nat Rev Clin Oncol 2022; 19:188-206. [PMID: 34912049 DOI: 10.1038/s41571-021-00585-y] [Citation(s) in RCA: 435] [Impact Index Per Article: 217.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
Over the past decade, circular RNAs (circRNAs) have emerged as a large class of primarily non-coding RNA molecules, many of which have key roles in cancer development and progression through diverse mechanisms of action. CircRNAs often have tissue-restricted and cancer-specific expression patterns, and accumulating data suggest that these molecules are of potential clinical relevance and utility. In particular, circRNAs have strong potential as diagnostic, prognostic and predictive biomarkers, which is underscored by their detectability in liquid biopsy samples such as in plasma, saliva and urine. However, technical issues in the detection and assessment of circRNAs as well as biological knowledge gaps need to be addressed to move this relatively young field of research forward and bring circRNAs to the forefront of clinical practice. Herein, we review the current knowledge regarding circRNA biogenesis, regulation and functions in cancer as well as their clinical potential as biomarkers, therapeutic agents and drug targets.
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Affiliation(s)
| | | | - Henrik Hager
- Department of Clinical Pathology, Vejle Hospital, Vejle, Denmark.,Danish Colorectal Cancer Center South, Vejle Hospital, Vejle, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus C, Denmark. .,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark.
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11
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Obi P, Chen YG. The design and synthesis of circular RNAs. Methods 2021; 196:85-103. [PMID: 33662562 PMCID: PMC8670866 DOI: 10.1016/j.ymeth.2021.02.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of RNAs distinguished by their single-stranded, covalently-closed topology. Although initially perceived as rare byproducts of aberrant splicing, circRNAs are now recognized as ubiquitously expressed and functionally significant. These discoveries have led to a growing need for ways to model circRNAs in living cells to advance our understanding of their biogenesis, regulation, and function, and to adopt them as new technologies for application within research and medicine. In this review, we provide an updated summary of approaches used to produce circRNAs in vitro and in vivo, the latter of which has grown considerably in recent years. Given increased interest in the unique functions carried out by individual circRNAs, we further dedicate a section on how to customize synthesized circRNAs for specific biological roles. We focus on the most common applications, including designing circRNAs for protein delivery, to target miRNAs and proteins, to act as fluorescent reporters, and to modulate cellular immunity.
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Affiliation(s)
- Prisca Obi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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12
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Chen X, Lu Y. Circular RNA: Biosynthesis in vitro. Front Bioeng Biotechnol 2021; 9:787881. [PMID: 34917603 PMCID: PMC8670002 DOI: 10.3389/fbioe.2021.787881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a unique type of noncoding RNA molecule. Compared with traditional linear RNA, circRNA is a covalently closed circle produced by a process called backsplicing. CircRNA is abundant in many cells and has rich functions in cells, such as acting as miRNA sponge, protein sponge, protein scaffold, and mRNA regulator. With the continuous development of circRNA study, circRNA has also played an important role in medical applications, including circRNA vaccines and gene therapy. In this review, we illustrate the synthesis of circRNAs in vitro. We focus on biological ligation methods, such as enzymatic ligation from the bacteriophage T4 and ribozyme method. In addition, we summarize the current challenges in the design, synthesis, application, and production of circRNAs, and propose possible solutions in the future. CircRNA is expected to play an essential role in basic research and medical applications.
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Affiliation(s)
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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13
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Rausch JW, Heinz WF, Payea MJ, Sherpa C, Gorospe M, Le Grice SFJ. Characterizing and circumventing sequence restrictions for synthesis of circular RNA in vitro. Nucleic Acids Res 2021; 49:e35. [PMID: 33406226 DOI: 10.1093/nar/gkaa1256] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/27/2020] [Accepted: 12/18/2020] [Indexed: 01/10/2023] Open
Abstract
Just as eukaryotic circular RNA (circRNA) is a product of intracellular backsplicing, custom circRNA can be synthesized in vitro using a transcription template in which transposed halves of a split group I intron flank the sequence of the RNA to be circularized. Such permuted intron-exon (PIE) constructs have been used to produce circRNA versions of ribozymes, mimics of viral RNA motifs, a streptavidin aptamer, and protein expression vectors for genetic engineering and vaccine development. One limitation of this approach is the obligatory incorporation of small RNA segments (E1 and E2) into nascent circRNA at the site of end-joining. This restriction may preclude synthesis of small circRNA therapeutics and RNA nanoparticles that are sensitive to extraneous sequence, as well as larger circRNA mimics whose sequences must precisely match those of the native species on which they are modelled. In this work, we used serial mutagenesis and in vitro selection to determine how varying E1 and E2 sequences in a thymidylate synthase (td) group I intron PIE transcription template construct affects circRNA synthesis yield. Based on our collective findings, we present guidelines for the design of custom-tailored PIE transcription templates from which synthetic circRNAs of almost any sequence may be efficiently synthesized.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew J Payea
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
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14
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The GAUGAA Motif Is Responsible for the Binding between circSMARCA5 and SRSF1 and Related Downstream Effects on Glioblastoma Multiforme Cell Migration and Angiogenic Potential. Int J Mol Sci 2021; 22:ijms22041678. [PMID: 33562358 PMCID: PMC7915938 DOI: 10.3390/ijms22041678] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/26/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
Circular RNAs (circRNAs) are a large class of RNAs with regulatory functions within cells. We recently showed that circSMARCA5 is a tumor suppressor in glioblastoma multiforme (GBM) and acts as a decoy for Serine and Arginine Rich Splicing Factor 1 (SRSF1) through six predicted binding sites (BSs). Here we characterized RNA motifs functionally involved in the interaction between circSMARCA5 and SRSF1. Three different circSMARCA5 molecules (Mut1, Mut2, Mut3), each mutated in two predicted SRSF1 BSs at once, were obtained through PCR-based replacement of wild-type (WT) BS sequences and cloned in three independent pcDNA3 vectors. Mut1 significantly decreased its capability to interact with SRSF1 as compared to WT, based on the RNA immunoprecipitation assay. In silico analysis through the “Find Individual Motif Occurrences” (FIMO) algorithm showed GAUGAA as an experimentally validated SRSF1 binding motif significantly overrepresented within both predicted SRSF1 BSs mutated in Mut1 (q-value = 0.0011). U87MG and CAS-1, transfected with Mut1, significantly increased their migration with respect to controls transfected with WT, as revealed by the cell exclusion zone assay. Immortalized human brain microvascular endothelial cells (IM-HBMEC) exposed to conditioned medium (CM) harvested from U87MG and CAS-1 transfected with Mut1 significantly sprouted more than those treated with CM harvested from U87MG and CAS-1 transfected with WT, as shown by the tube formation assay. qRT-PCR showed that the intracellular pro- to anti-angiogenic Vascular Endothelial Growth Factor A (VEGFA) mRNA isoform ratio and the amount of total VEGFA mRNA secreted in CM significantly increased in Mut1-transfected CAS-1 as compared to controls transfected with WT. Our data suggest that GAUGAA is the RNA motif responsible for the interaction between circSMARCA5 and SRSF1 as well as for the circSMARCA5-mediated control of GBM cell migration and angiogenic potential.
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Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key Players In Vivoand In Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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16
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Gnanamony M, Demirkhanyan L, Ge L, Sojitra P, Bapana S, Norton JA, Gondi CS. Circular dumbbell miR-34a-3p and -5p suppresses pancreatic tumor cell-induced angiogenesis and activates macrophages. Oncol Lett 2021; 21:75. [PMID: 33365086 PMCID: PMC7716711 DOI: 10.3892/ol.2020.12336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
Angiogenesis is a tightly regulated biological process by which new blood vessels are formed from pre-existing blood vessels. This process is also critical in diseases such as cancer. Therefore, angiogenesis has been explored as a drug target for cancer therapy. The future of effective anti-angiogenic therapy lies in the intelligent combination of multiple targeting agents with novel modes of delivery to maximize therapeutic effects. Therefore, a novel approach is proposed that utilizes dumbbell RNA (dbRNA) to target pathological angiogenesis by simultaneously targeting multiple molecules and processes that contribute to angiogenesis. In the present study, a plasmid expressing miR-34a-3p and -5p dbRNA (db34a) was constructed using the permuted intron-exon method. A simple protocol to purify dbRNA from bacterial culture with high purity was also developed by modification of the RNASwift method. To test the efficacy of db34a, pancreatic cancer cell lines PANC-1 and MIA PaCa-2 were used. Functional validation of the effect of db34a on angiogenesis was performed on human umbilical vein endothelial cells using a tube formation assay, in which cells transfected with db34a exhibited a significant reduction in tube formation compared with cells transfected with scrambled dbRNA. These results were further validated in vivo using a zebrafish angiogenesis model. In conclusion, the present study demonstrates an approach for blocking angiogenesis using db34a. The data also show that this approach may be used to targeting multiple molecules and pathways.
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Affiliation(s)
- Manu Gnanamony
- Department of Pediatrics, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Lusine Demirkhanyan
- Department of Internal Medicine, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Liang Ge
- University of Pittsburgh Medical Center, Presbyterian University Hospital, Pittsburgh, PA 15213, USA
| | - Paresh Sojitra
- Sanford Center for Digestive Health, Sioux Falls, SD 57105, USA
| | - Sneha Bapana
- Department of Internal Medicine, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Joseph A. Norton
- Department of Internal Medicine, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Christopher S. Gondi
- Department of Internal Medicine, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
- Department of Surgery, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
- Department of Pathology, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
- Correspondence to: Dr Christopher S. Gondi, Department of Internal Medicine, University of Illinois College of Medicine Peoria, 1 Illini Drive, Peoria, IL 61605, USA, E-mail:
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17
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Sui Z, An R, Komiyama M, Liang X. Stepwise Strategy for One-Pot Synthesis of Single-Stranded DNA Rings from Multiple Short Fragments. Chembiochem 2020; 22:1005-1011. [PMID: 33124728 DOI: 10.1002/cbic.202000738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 12/24/2022]
Abstract
Cyclic rings of single-stranded (ss) DNA have various unique properties, but wider applications have been hampered by their poor availability. This paper reports a convenient one-pot method in which these rings are efficiently synthesized by using T4 DNA ligase through convergent cyclization of easily available short DNA fragments. The key to the present method is to separate all the splint oligonucleotides into several sets, and add each set sequentially at an appropriate interval to the solutions containing all the short DNA fragments. Compared with simple one-pot strategies involving simultaneous addition of all the splints at the beginning of the reaction, both the selectivity and the yields of target ssDNA rings are greatly improved. This convergent method is especially useful for preparing large-sized rings that are otherwise hard to obtain. By starting from six short DNA fragments (71-82 nt), prepared by a DNA synthesizer, a ssDNA ring of 452-nt size was synthesized in 35 mol % yield and in high selectivity. Satisfactorily pure DNA rings were obtainable simply by treating the crude products with exonuclease.
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Affiliation(s)
- Zhe Sui
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, P. R. China
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18
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Ho-Xuan H, Glažar P, Latini C, Heizler K, Haase J, Hett R, Anders M, Weichmann F, Bruckmann A, Van den Berg D, Hüttelmaier S, Rajewsky N, Hackl C, Meister G. Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts. Nucleic Acids Res 2020; 48:10368-10382. [PMID: 32955563 PMCID: PMC7544230 DOI: 10.1093/nar/gkaa704] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 08/07/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) encompass a widespread and conserved class of RNAs, which are generated by back-splicing of downstream 5' to upstream 3' splice sites. CircRNAs are tissue-specific and have been implicated in diseases including cancer. They can function as sponges for microRNAs (miRNAs) or RNA binding proteins (RBPs), for example. Moreover, some contain open reading frames (ORFs) and might be translated. The functional relevance of such peptides, however, remains largely elusive. Here, we report that the ORF of circZNF609 is efficiently translated when expressed from a circZNF609 overexpression construct. However, endogenous proteins could not be detected. Moreover, initiation of circZNF609 translation is independent of m6A-generating enzyme METTL3 or RNA sequence elements such as internal ribosome entry sites (IRESs). Surprisingly, a comprehensive mutational analysis revealed that deletion constructs, which are deficient in producing circZNF609, still generate the observed protein products. This suggests that the apparent circZNF609 translation originates from trans-splicing by-products of the overexpression plasmids and underline that circRNA overexpression constructs need to be evaluated carefully, particularly when functional studies are performed.
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Affiliation(s)
- Hung Ho-Xuan
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Petar Glažar
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Claudia Latini
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Kevin Heizler
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Jacob Haase
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Protein Center, 06120 Halle, Germany
| | - Robert Hett
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Marvin Anders
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Franziska Weichmann
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Debbie Van den Berg
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin-Luther-University Halle-Wittenberg, Charles Tanford Protein Center, 06120 Halle, Germany
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Christina Hackl
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
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Rostain W, Shen S, Cordero T, Rodrigo G, Jaramillo A. Engineering a Circular Riboregulator in Escherichia coli. BIODESIGN RESEARCH 2020; 2020:1916789. [PMID: 37849901 PMCID: PMC10521646 DOI: 10.34133/2020/1916789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/17/2020] [Indexed: 10/19/2023] Open
Abstract
RNAs of different shapes and sizes, natural or synthetic, can regulate gene expression in prokaryotes and eukaryotes. Circular RNAs have recently appeared to be more widespread than previously thought, but their role in prokaryotes remains elusive. Here, by inserting a riboregulatory sequence within a group I permuted intron-exon ribozyme, we created a small noncoding RNA that self-splices to produce a circular riboregulator in Escherichia coli. We showed that the resulting riboregulator can trans-activate gene expression by interacting with a cis-repressed messenger RNA. We characterized the system with a fluorescent reporter and with an antibiotic resistance marker, and we modeled this novel posttranscriptional mechanism. This first reported example of a circular RNA regulating gene expression in E. coli adds to an increasing repertoire of RNA synthetic biology parts, and it highlights that topological molecules can play a role in the case of prokaryotic regulation.
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Affiliation(s)
- William Rostain
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
- Institute of Systems and Synthetic Biology, CNRS-Université d’Évry Val-d’Essonne, 91000 Évry, France
| | - Shensi Shen
- Institute of Systems and Synthetic Biology, CNRS-Université d’Évry Val-d’Essonne, 91000 Évry, France
| | - Teresa Cordero
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Guillermo Rodrigo
- Institute of Systems and Synthetic Biology, CNRS-Université d’Évry Val-d’Essonne, 91000 Évry, France
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, 46022 Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980 Paterna, Spain
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
- Institute of Systems and Synthetic Biology, CNRS-Université d’Évry Val-d’Essonne, 91000 Évry, France
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980 Paterna, Spain
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20
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Abstract
Exonic circular RNAs (circRNAs) have been discovered in all kingdoms of life. In many cases, the details of circRNA function and their involvement in cellular processes and diseases are not yet fully understood. However, the past few years have seen significant developments in bioinformatics and in experimental protocols that advance the ongoing research in this still-emerging field. Sophisticated methods for circRNA generation in vitro and in vivo have been developed, allowing model studies into circRNA function and application. We here review the ongoing circRNA research, giving special attention to recent progress in the field.
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Affiliation(s)
| | - Theodor Schnarr
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
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21
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Chen H, Cheng K, Liu X, An R, Komiyama M, Liang X. Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand. Nucleic Acids Res 2020; 48:e54. [PMID: 32232357 PMCID: PMC7229815 DOI: 10.1093/nar/gkaa181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/04/2020] [Accepted: 03/11/2020] [Indexed: 12/04/2022] Open
Abstract
Rings of single-stranded RNA are promising for many practical applications, but the methods to prepare them in preparative scale have never been established. Previously, RNA circularization was achieved by T4 RNA ligase 2 (Rnl2, a dsRNA ligase) using splints, but the yield was low due to concurrent intermolecular polymerization. Here, various functional RNAs (siRNA, miRNA, ribozyme, etc.) are dominantly converted by Rnl2 to the rings without significant limitations in sizes and sequences. The key is to design a precursor RNA, which is highly activated for the efficient circularization without any splint. First, secondary structure of target RNA ring is simulated by Mfold, and then hypothetically cut at one site so that a few intramolecular base pairs are formed at the terminal. Simply by treating this RNA with Rnl2, the target ring was selectively and efficiently produced. Unexpectedly, circular RNA can be obtained in high yield (>90%), even when only 2 bp form in the 3'-OH side and no full match base pair forms in the 5'-phosphate side. Formation of polymeric by-products was further suppressed by diluting conventional Rnl2 buffer to abnormally low concentrations. Even at high-RNA concentrations (e.g. 50 μM), enormously high selectivity (>95%) was accomplished.
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Affiliation(s)
- Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiaoli Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
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22
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Lavenniah A, Luu TDA, Li YP, Lim TB, Jiang J, Ackers-Johnson M, Foo RSY. Engineered Circular RNA Sponges Act as miRNA Inhibitors to Attenuate Pressure Overload-Induced Cardiac Hypertrophy. Mol Ther 2020; 28:1506-1517. [PMID: 32304667 PMCID: PMC7264434 DOI: 10.1016/j.ymthe.2020.04.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/16/2020] [Accepted: 04/04/2020] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) sequester microRNAs (miRNAs) and repress their endogenous activity. We hypothesized that artificial circRNA sponges (circmiRs) can be constructed to target miRNAs therapeutically, with a low dosage requirement and extended half-lives compared to current alternatives. This could present a new treatment approach for critical global pathologies, including cardiovascular disease. Here, we constructed a circmiR sponge to target known cardiac pro-hypertrophic miR-132 and -212. Expressed circmiRs competitively inhibited miR-132 and -212 activity in luciferase rescue assays and showed greater stability than linear sponges. A design containing 12 bulged binding sites with 12 nucleotides spacing was determined to be optimal. Adeno-associated viruses (AAVs) were used to deliver circmiRs to cardiomyocytes in vivo in a transverse aortic constriction (TAC) mouse model of cardiac disease. Hypertrophic disease characteristics were attenuated, and cardiac function was preserved in treated mice, demonstrating the potential of circmiRs as novel therapeutic tools. Subsequently, group I permutated intron-exon sequences were used to directly synthesize exogenous circmiRs, which showed greater in vitro efficacy than the current gold standard antagomiRs in inhibiting miRNA function. Engineered circRNAs thus offer exciting potential as future therapeutics.
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Affiliation(s)
- Annadoray Lavenniah
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Cardiovascular Research Institute, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Tuan Danh Anh Luu
- Cardiovascular Research Institute, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Yiqing Peter Li
- Cardiovascular Research Institute, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Tingsen Benson Lim
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Cardiovascular Research Institute, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Jianming Jiang
- Cardiovascular Research Institute, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Matthew Ackers-Johnson
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Cardiovascular Research Institute, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Roger S-Y Foo
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Cardiovascular Research Institute, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore.
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23
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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Kikuchi Y, Umekage S. Extracellular nucleic acids of the marine bacterium Rhodovulum sulfidophilum and recombinant RNA production technology using bacteria. FEMS Microbiol Lett 2019; 365:4705897. [PMID: 29228187 DOI: 10.1093/femsle/fnx268] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
Extracellular nucleic acids of high molecular weight are detected ubiquitously in seawater. Recent studies have indicated that these nucleic acids are, at least in part, derived from active production by some bacteria. The marine bacterium Rhodovulum sulfidophilum is one of those bacteria. Rhodovulumsulfidophilum is a non-sulfur phototrophic marine bacterium that is known to form structured communities of cells called flocs, and to produce extracellular nucleic acids in culture media. Recently, it has been revealed that this bacterium produces gene transfer agent-like particles and that this particle production may be related to the extracellular nucleic acid production mechanism. This review provides a summary of recent physiological and genetic studies of these phenomena and also introduces a new method for extracellular production of artificial and biologically functional RNAs using this bacterium. In addition, artificial RNA production using Escherichia coli, which is related to this topic, will also be described.
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Affiliation(s)
- Yo Kikuchi
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
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25
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Litke JL, Jaffrey SR. Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts. Nat Biotechnol 2019; 37:667-675. [PMID: 30962542 PMCID: PMC6554452 DOI: 10.1038/s41587-019-0090-6] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022]
Abstract
RNA aptamers and RNA aptamer-based devices can be genetically encoded and expressed in cells to probe and manipulate cellular function. However, their usefulness in the mammalian cell is limited by low expression and rapid degradation. Here we describe the Tornado (Twister-optimized RNA for durable overexpression) expression system for achieving rapid RNA circularization, resulting in RNA aptamers with high stability and expression levels. Tornado-expressed transcripts contain an RNA of interest flanked by Twister ribozymes. The ribozymes rapidly undergo autocatalytic cleavage, leaving termini that are ligated by the ubiquitous endogenous RNA ligase RtcB. Using this approach, protein-binding aptamers that otherwise have minimal effects in cells become potent inhibitors of cellular signaling. Additionally, an RNA-based fluorescent metabolite biosensor for S-adenosyl methionine (SAM) that is expressed at low levels when expressed as a linear RNA achieves levels sufficient for detection of intracellular SAM dynamics when expressed as a circular RNA. The Tornado expression system thus markedly enhances the utility of RNA-based approaches in the mammalian cell.
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Affiliation(s)
- Jacob L Litke
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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26
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Holdt LM, Kohlmaier A, Teupser D. Circular RNAs as Therapeutic Agents and Targets. Front Physiol 2018; 9:1262. [PMID: 30356745 PMCID: PMC6189416 DOI: 10.3389/fphys.2018.01262] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/21/2018] [Indexed: 12/26/2022] Open
Abstract
It has recently been reported that thousands of covalently linked circular RNAs (circRNAs) are expressed from human genomes. circRNAs emerge during RNA splicing. circRNAs are circularized in a reaction termed "backsplicing," whereby the spliceosome fuses a splice donor site in a downstream exon to a splice acceptor site in an upstream exon. Although a young field of research, first studies indicate that backsplicing is not an erroneous reaction of the spliceosome. Instead, circRNAs are produced in cells with high cell-type specificity and can exert biologically meaningful and specific functions. These observations and the finding that circRNAs are stable against exonucleolytic decay are raising the question whether circRNAs may be relevant as therapeutic agents and targets. In this review, we start out with a short introduction into classification, biogenesis and general molecular mechanisms of circRNAs. We then describe reports, where manipulating circRNA abundance has been shown to have therapeutic value in animal disease models in vivo, with a focus on cardiovascular disease (CVD). Starting from existing approaches, we outline particular challenges and opportunities for future circRNA-based therapeutic approaches that exploit stability and molecular effector functions of native circRNAs. We end with considerations which designer functions could be engineered into artificial therapeutic circular RNAs.
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Affiliation(s)
| | | | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, Ludwig Maximilian University of Munich (LMU), Munich, Germany
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Jost I, Shalamova LA, Gerresheim GK, Niepmann M, Bindereif A, Rossbach O. Functional sequestration of microRNA-122 from Hepatitis C Virus by circular RNA sponges. RNA Biol 2018; 15:1032-1039. [PMID: 29486652 PMCID: PMC6161685 DOI: 10.1080/15476286.2018.1435248] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Circular RNAs (circRNAs) were recently described as a novel class of cellular RNAs. Two circRNAs were reported to function as molecular sponges, sequestering specific microRNAs, thereby de-repressing target mRNAs. Due to their elevated stability in comparison to linear RNA, circRNAs may be an interesting tool in molecular medicine and biology. In this study, we provide a proof-of-principle that circRNAs can be engineered as microRNA sponges. As a model system, we used the Hepatitis C Virus (HCV), which requires cellular microRNA-122 for its life cycle. We produced artificial circRNA sponges in vitro that efficiently sequester microRNA-122, thereby inhibiting viral protein production in an HCV cell culture system. These circRNAs are more stable than their linear counterparts, and localize both to the cytoplasm and to the nucleus, opening up a wide range of potential applications.
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Affiliation(s)
- Isabelle Jost
- a Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, Heinrich-Buff-Ring 17 , Giessen , Germany
| | - Lyudmila A Shalamova
- a Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, Heinrich-Buff-Ring 17 , Giessen , Germany.,b Institute of Biochemistry, Faculty of Medicine, University of Giessen , Friedrichstrasse 24, Giessen , Germany
| | - Gesche K Gerresheim
- a Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, Heinrich-Buff-Ring 17 , Giessen , Germany.,b Institute of Biochemistry, Faculty of Medicine, University of Giessen , Friedrichstrasse 24, Giessen , Germany
| | - Michael Niepmann
- b Institute of Biochemistry, Faculty of Medicine, University of Giessen , Friedrichstrasse 24, Giessen , Germany
| | - Albrecht Bindereif
- a Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, Heinrich-Buff-Ring 17 , Giessen , Germany
| | - Oliver Rossbach
- a Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, Heinrich-Buff-Ring 17 , Giessen , Germany
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Abstract
This chapter describes a simple and straightforward way to obtain single-stranded circular RNA sequences in vitro. Linear RNA that is phosphorylated at the 5' end is first prepared by a chemical or enzymatic method, then circularized using ligase. The function of the prepared circular RNA molecule, such as an ability to induce translation, can then be investigated.
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Affiliation(s)
- Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Ayumi Kodama
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.
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29
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Fang PY, Bowman JC, Gómez Ramos L, Hsiao C, Williams LD. RNA: packaged and protected by VLPs. RSC Adv 2018; 8:21399-21406. [PMID: 35539947 PMCID: PMC9080931 DOI: 10.1039/c8ra02084a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023] Open
Abstract
VLP packaging is most efficient for compact RNA, and protects RNA against assault by small diffusible damaging agents.
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Affiliation(s)
- Po-Yu Fang
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Lizzette M. Gómez Ramos
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemical and Biomolecular Engineering
| | - Chiaolong Hsiao
- Institute of Biochemical Sciences
- National Taiwan University
- Taipei 10617
- Republic of China
| | - Loren Dean Williams
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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30
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Hu X, Zhu M, Zhang X, Liu B, Liang Z, Huang L, Xu J, Yu L, Li K, Zar MS, Xue R, Cao G, Gong C. Identification and characterization of circular RNAs in the silkworm midgut following Bombyx mori cytoplasmic polyhedrosis virus infection. RNA Biol 2017; 15:292-301. [PMID: 29268657 DOI: 10.1080/15476286.2017.1411461] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection is unclear, although accumulating evidence indicates that circular RNAs (circRNAs), which act as competing endogenous RNAs or positive regulators, play important roles in regulating gene expression in eukaryotes and, thus, may play a role in BmCPV infections. To explore the expression and biological functions of circRNAs in the silkworm midgut following BmCPV infection, silkworm circRNA expression profiles of normal midgut tissue (control) and BmCPV-infected midgut tissue (test) were determined using high-through sequencing. A total of 9,753 and 7,475circRNAs were detected from the control and test samples, respectively. The two samples shared 6,085 circRNAs, while 646 and 737 circRNAs were expressed specifically in the control and test samples, respectively. A total of 3,638 circRNAs were shown to be differentially expressed, and 400 circRNAs were substantially differentially expressed with a fold-change ≥ 2.0 (p< 0.05 and a false discover rate < 0.05), of which 294 were up-regulated and 106 were down-regulated following infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted to determine the principal functions of the substantially differentially regulated genes. circRNA-miRNA interaction networks were constructed based on a correlation analysis between the differentially expressed circRNAs and the nature of their microRNA (miRNA) binding sites. The network inferred that 13 miRNAs interacting with 193 circRNAs were among the 300 most abundant relationships. bmo-miR-3389-5p, bmo-miR-745-3p, and bmo-miR-3262 were related to 30, 34, and 34 circRNAs, respectively. circRNA_8115, circRNA_9444, circRNA_4553, circRNA_0827, and circRNA_6649 contained six, five, four, four, and four miRNA binding sites, respectively. We further found that alternative circularization of circRNAs is a common feature in silkworms and that the junction sites of many silkworm circRNAs are flanked by canonical GT/AG splicing signals. Our study is the first to show the circRNA response to virus infection. Thus, it provides a novel perspective on circRNA-miRNA interactions during BmCPV pathogenesis, and it lays the foundation for future research of the potential roles of circRNAs in BmCPV pathogenesis.
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Affiliation(s)
- Xiaolong Hu
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Min Zhu
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Xing Zhang
- b Department of Infectious Disease , First Affiliated Hospital of Soochow University , Suzhou , China
| | - Bo Liu
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Zi Liang
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Lixu Huang
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Jian Xu
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Lei Yu
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Kun Li
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Mian Sahib Zar
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China
| | - Renyu Xue
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China.,c Institute of Agricultural Biotechnology and Ecological Research, Soochow University , Suzhou , China
| | - Guangli Cao
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China.,c Institute of Agricultural Biotechnology and Ecological Research, Soochow University , Suzhou , China
| | - Chengliang Gong
- a School of Biology & Basic Medical Science, Soochow University , Suzhou , China.,c Institute of Agricultural Biotechnology and Ecological Research, Soochow University , Suzhou , China
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31
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Balke D, Hieronymus R, Müller S. Challenges and Perspectives in Nucleic Acid Enzyme Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 170:21-35. [DOI: 10.1007/10_2017_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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32
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Nunes ARD, Chavante SF, Rocha HAO, Lanza DCF. "In-House" Production of Single Stranded Oligodeoxyribonucleotides. Nucleic Acid Ther 2017; 27:115-120. [PMID: 28051347 DOI: 10.1089/nat.2016.0625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The most widely used technique for the production of DNA aptamers/oligonucleotides is chemical synthesis. Despite its effectiveness, this technique cannot be performed "in house", making the user fully dependent on a supplier. In this work, we present a simplified method by which it is possible to enzymatically produce DNA aptamers "in house". This new method uses the rolling circle replication followed by a unique cleavage step using the SchI endonuclease. Potentially, any oligonucleotide can be produced by the enzymatic method proposed in this study. To illustrate, we present the production of three variations of the 31-TBA aptamer, a single stranded DNA which has anticoagulant action.
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Affiliation(s)
- Allan R D Nunes
- 1 Laboratório de Biologia Molecular Aplicada-LAPLIC, Departamento de Bioquímica, Centro de Biocieências Universidade Federal do Rio Grande do Norte , Natal, Brazil .,2 Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Centro de Biocieências Universidade Federal do Rio Grande do Norte , Natal, Brazil
| | - Suely F Chavante
- 2 Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Centro de Biocieências Universidade Federal do Rio Grande do Norte , Natal, Brazil
| | - Hugo A O Rocha
- 2 Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Centro de Biocieências Universidade Federal do Rio Grande do Norte , Natal, Brazil
| | - Daniel C F Lanza
- 1 Laboratório de Biologia Molecular Aplicada-LAPLIC, Departamento de Bioquímica, Centro de Biocieências Universidade Federal do Rio Grande do Norte , Natal, Brazil .,2 Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Centro de Biocieências Universidade Federal do Rio Grande do Norte , Natal, Brazil
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Abstract
Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.
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Affiliation(s)
- Sabine Müller
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
| | - Bettina Appel
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
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34
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Pereira P, Pedro AQ, Tomás J, Maia CJ, Queiroz JA, Figueiras A, Sousa F. Advances in time course extracellular production of human pre-miR-29b from Rhodovulum sulfidophilum. Appl Microbiol Biotechnol 2016; 100:3723-34. [DOI: 10.1007/s00253-016-7350-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 01/12/2016] [Accepted: 01/23/2016] [Indexed: 02/08/2023]
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35
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Petkovic S, Badelt S, Block S, Flamm C, Delcea M, Hofacker I, Müller S. Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM. RNA (NEW YORK, N.Y.) 2015; 21:1249-1260. [PMID: 25999318 PMCID: PMC4478344 DOI: 10.1261/rna.047670.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/07/2015] [Indexed: 06/04/2023]
Abstract
Reversible chemistry allowing for assembly and disassembly of molecular entities is important for biological self-organization. Thus, ribozymes that support both cleavage and formation of phosphodiester bonds may have contributed to the emergence of functional diversity and increasing complexity of regulatory RNAs in early life. We have previously engineered a variant of the hairpin ribozyme that shows how ribozymes may have circularized or extended their own length by forming concatemers. Using the Vienna RNA package, we now optimized this hairpin ribozyme variant and selected four different RNA sequences that were expected to circularize more efficiently or form longer concatemers upon transcription. (Two-dimensional) PAGE analysis confirms that (i) all four selected ribozymes are catalytically active and (ii) high yields of cyclic species are obtained. AFM imaging in combination with RNA structure prediction enabled us to calculate the distributions of monomers and self-concatenated dimers and trimers. Our results show that computationally optimized molecules do form reasonable amounts of trimers, which has not been observed for the original system so far, and we demonstrate that the combination of theoretical prediction, biochemical and physical analysis is a promising approach toward accurate prediction of ribozyme behavior and design of ribozymes with predefined functions.
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Affiliation(s)
- Sonja Petkovic
- Institute for Biochemistry, Ernst-Moritz-Arndt University Greifswald, 17487 Greifswald, Germany
| | - Stefan Badelt
- Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria
| | - Stephan Block
- ZIK HIKE-Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, Ernst-Moritz-Arndt University Greifswald, 17489 Greifswald, Germany
| | - Christoph Flamm
- Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria
| | - Mihaela Delcea
- ZIK HIKE-Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, Ernst-Moritz-Arndt University Greifswald, 17489 Greifswald, Germany
| | - Ivo Hofacker
- Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, University of Vienna, A-1090 Vienna, Austria
| | - Sabine Müller
- Institute for Biochemistry, Ernst-Moritz-Arndt University Greifswald, 17487 Greifswald, Germany
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Petkovic S, Müller S. RNA circularization strategies in vivo and in vitro. Nucleic Acids Res 2015; 43:2454-65. [PMID: 25662225 PMCID: PMC4344496 DOI: 10.1093/nar/gkv045] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
In the plenitude of naturally occurring RNAs, circular RNAs (circRNAs) and their biological role were underestimated for years. However, circRNAs are ubiquitous in all domains of life, including eukaryotes, archaea, bacteria and viruses, where they can fulfill diverse biological functions. Some of those functions, as for example playing a role in the life cycle of viral and viroid genomes or in the maturation of tRNA genes, have been elucidated; other putative functions still remain elusive. Due to the resistance to exonucleases, circRNAs are promising tools for in vivo application as aptamers, trans-cleaving ribozymes or siRNAs. How are circRNAs generated in vivo and what approaches do exist to produce ring-shaped RNAs in vitro? In this review we illustrate the occurrence and mechanisms of RNA circularization in vivo, survey methods for the generation of circRNA in vitro and provide appropriate protocols.
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Affiliation(s)
- Sonja Petkovic
- Institut für Biochemie, Ernst Moritz Arndt Universität Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst Moritz Arndt Universität Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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37
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Hassall J, MacDonald P, Cordero T, Rostain W, Jaramillo A. Design and Characterization of Topological Small RNAs. Methods Mol Biol 2015; 1316:149-167. [PMID: 25967060 DOI: 10.1007/978-1-4939-2730-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA can self-assemble into complex structures through base pairing, as well as encode information and bind with proteins to induce enzymatic activity. Furthermore, RNA can possess intrinsic enzymatic-like (ribozymatic) activity, a property that, if necessary, can be activated only upon the binding of a small molecule or another RNA (as is the case in aptazymes). As such, RNA could be of use in nanotechnology as a programmable polymer capable of self-assembling into complex topological structures. In this chapter we describe a method for designing advanced topological structures using self-circulating RNA, exemplified by three tiers of topologically manipulated self-assembling synthetic RNA systems. The first tier of topological manipulation, the RNA knot is a physically locked structure, formed by circularizing one monomer of knotted single-stranded RNA left with loose ends (an "open" knot). The second tier, a two interlocking ring system, is made by interlocking two circular RNA components: a circular RNA target, and an RNA lasso designed to intercalate the target before circularizing. The third tier naturally extends this system into a string of topologically locked circular RNA molecules (an RNA chain). We detail the methodology used for designing such topologically complex RNAs, including computational predictions of secondary structure, and where appropriate, RNA-RNA interactions, illustrated by examples. We then describe the experimental methods used for characterizing such structures, and provide sequences of building blocks that can be used for topological manipulation of RNA.
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Affiliation(s)
- Jack Hassall
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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38
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Tay FC, Lim JK, Zhu H, Hin LC, Wang S. Using artificial microRNA sponges to achieve microRNA loss-of-function in cancer cells. Adv Drug Deliv Rev 2015; 81:117-27. [PMID: 24859534 DOI: 10.1016/j.addr.2014.05.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 04/18/2014] [Accepted: 05/15/2014] [Indexed: 12/19/2022]
Abstract
Widely observed dysregulation of microRNAs (miRNAs) in human cancer has led to substantial speculation regarding possible functions of these short, non-coding RNAs in cancer development and manipulation of miRNA expression to treat cancer. To achieve miRNA loss-of-function, miRNA sponge technology has been developed to use plasmid or viral vectors for intracellular expression of tandemly arrayed, bulged miRNA binding sites complementary to a miRNA target to saturate its ability to regulate natural mRNAs. A strong viral promoter can be used in miRNA sponge vectors to generate high-level expression of the competitive inhibitor transcripts for either transient or long-term inhibition of miRNA function. Taking the advantage of sharing a common seed sequence by members of a miRNA family, this technology is especially useful in knocking down the expression of a family of miRNAs, providing a powerful means for simultaneous inhibition of multiple miRNAs of interest with a single inhibitor. Knockdown of overexpressed oncogenic miRNAs with the technology can be a rational therapeutic strategy for cancer, whereas inhibition of tumor-suppressive miRNAs by the sponges will be useful in deciphering functions of miRNAs in oncogenesis. Herein, we discuss the design of miRNA sponge expression vectors and the use of the vectors to gain better understanding of miRNA's roles in cancer biology and as an alternative tool for anticancer gene therapy.
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RETRACTED: Construction of circular miRNA sponges targeting miR-21 or miR-221 and demonstration of their excellent anticancer effects on malignant melanoma cells. Int J Biochem Cell Biol 2013; 45:2643-50. [DOI: 10.1016/j.biocel.2013.09.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 08/31/2013] [Accepted: 09/02/2013] [Indexed: 11/19/2022]
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40
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Ponchon L, Catala M, Seijo B, El Khouri M, Dardel F, Nonin-Lecomte S, Tisné C. Co-expression of RNA-protein complexes in Escherichia coli and applications to RNA biology. Nucleic Acids Res 2013; 41:e150. [PMID: 23804766 PMCID: PMC3753655 DOI: 10.1093/nar/gkt576] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
RNA has emerged as a major player in many cellular processes. Understanding these processes at the molecular level requires homogeneous RNA samples for structural, biochemical and pharmacological studies. We previously devised a generic approach that allows efficient in vivo expression of recombinant RNA in Escherichia coli. In this work, we have extended this method to RNA/protein co-expression. We have engineered several plasmids that allow overexpression of RNA–protein complexes in E. coli. We have investigated the potential of these tools in many applications, including the production of nuclease-sensitive RNAs encapsulated in viral protein pseudo-particles, the co-production of non-coding RNAs with chaperone proteins, the incorporation of a post-transcriptional RNA modification by co-production with the appropriate modifying enzyme and finally the production and purification of an RNA–His-tagged protein complex by nickel affinity chromatography. We show that this last application easily provides pure material for crystallographic studies. The new tools we report will pave the way to large-scale structural and molecular investigations of RNA function and interactions with proteins.
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Affiliation(s)
- Luc Ponchon
- CNRS, UMR 8015, Laboratoire de Cristallographie et RMN biologiques, 4 avenue de l'Observatoire, 75006 Paris, France and Université Paris Descartes, Sorbonne Paris Cité, UMR 8015, Laboratoire de Cristallographie et RMN biologiques, 4 avenue de l'Observatoire, 75006 Paris, France
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41
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Petkovic S, Müller S. RNA self-processing: formation of cyclic species and concatemers from a small engineered RNA. FEBS Lett 2013; 587:2435-40. [PMID: 23796421 DOI: 10.1016/j.febslet.2013.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/05/2013] [Accepted: 06/05/2013] [Indexed: 01/08/2023]
Abstract
We have engineered a self-processing RNA, derived from the hairpin ribozyme that runs through a cascade of cleavage and ligation reactions thereby changing its topology. The first two cleavage events leave the resulting RNA with a 5'-OH group and a 2',3'-cyclic phosphate. Thus, upon refolding, intramolecular ligation delivers a cyclic species. In addition, we demonstrate formation of concatemers resulting from multiple intermolecular ligations. Our results demonstrate the potential of RNA for self-supported topology changes and support the suggestion of 2',3'-cyclic phosphates being suitable activated building blocks for reversible phosphodiester bond formation in the RNA world.
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Affiliation(s)
- Sonja Petkovic
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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42
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Umekage S, Kikuchi Y. In vivo circular RNA production using a constitutive promoter for high-level expression. J Biosci Bioeng 2010; 108:354-6. [PMID: 19716528 DOI: 10.1016/j.jbiosc.2009.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 04/09/2009] [Accepted: 04/13/2009] [Indexed: 11/16/2022]
Abstract
The permuted intron-exon (PIE) method based on group I intron self-splicing is the only methodology currently available for production of circular RNA in vivo. Here, we report improvement of the circular RNA expression method based on an induction-free vector system utilizing the highly efficient constitutive lpp promoter.
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Affiliation(s)
- So Umekage
- Department of Ecological Engineering, Toyohashi University of Technology, Tempaku-cho, Aichi, Japan.
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43
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Kikuchi Y. Extracellular Nucleic Acids of the Marine Phototrophic Bacterium Rhodovulum sulfidophilum and Related Bacteria: Physiology and Biotechnology. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2010. [DOI: 10.1007/978-3-642-12617-8_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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44
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Extracellular production of an RNA aptamer by ribonuclease-free marine bacteria harboring engineered plasmids: a proposal for industrial RNA drug production. Appl Environ Microbiol 2009; 76:786-93. [PMID: 19966026 DOI: 10.1128/aem.01971-09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Natural noncoding small RNAs have been shown to be involved in a number of cellular processes as regulators. Using the mechanisms thus elucidated, artificial small interfering RNAs (siRNAs), ribozymes, and RNA aptamers are also expected to be potential candidates for RNA therapeutic agents. However, current techniques are too costly for industrial production of these RNAs for use as drugs. Here, we propose a new method for in vivo production of artificial RNAs using the marine phototrophic bacterium Rhodovulum sulfidophilum. Using engineered plasmids and this bacterium, which produces extracellular nucleic acids in nature, we developed a method for extracellular production of a streptavidin RNA aptamer. As the bacterium does not produce any RNases in the culture medium, at least within the cultivation period tested, the designed RNA itself is produced and retained in the culture medium of the bacterium without any specific mechanism for protection against degradation by nucleases. Here, we report that the streptavidin RNA aptamer is produced in the culture medium and retains its specific function. This is the first demonstration of extracellular production of a functional artificial RNA in vivo, which will pave the way for inexpensive production of RNA drugs.
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