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Shen W, Hou Y, Yi Y, Li F, He C, Wang J. G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets. J Am Chem Soc 2024; 146:12778-12789. [PMID: 38679963 DOI: 10.1021/jacs.4c02901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
MicroRNAs (miRNAs) play indispensable roles in post-transcriptional gene regulation. The identification of target mRNAs is essential for dissecting the recognition basis, dynamics, and regulatory mechanism of miRNA-mRNA interactions. However, the lack of an unbiased method for detecting weak miRNA-mRNA interactions remains a long-standing obstacle for miRNA research. Here, we develop and provide proof-of-concept evidence demonstrating a chemical G-clamp-enhanced photo-cross-linking strategy for covalent capture of intracellular miRNA targets in different cell lines. This approach relies on an aryl-diazirine-G-clamp-modified-nucleoside (ARAGON) miRNA probe containing an alkynyl group that improves the thermal stability of miRNA-target mRNA duplex molecules and can rapidly cross-link with the complementary strand upon UV 365 nm activation, enhancing the transient capture of mRNA targets. After validating the accuracy and binding properties of ARAGON-based miRNA probes through the successful enrichment for the known targets of miR-106a, miR-21, and miR-101, we then extend ARAGON's application to screen for previously unknown targets of different miRNAs in various cell lines. Ultimately, results in this study uncover GAB1 as a target of miR-101 in H1299 lung cancer cells and show that miR-101 silencing of GAB1 can promote apoptosis in H1299 cells, suggesting an oncogenic mechanism of GAB1. This study thus provides a powerful and versatile tool for enhanced screening of global miRNA targets in cells to facilitate investigations of miRNA functions in fundamental cellular processes and disease pathogenesis.
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Affiliation(s)
- Weiguo Shen
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yongkang Hou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yunpeng Yi
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Fei Li
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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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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3
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Habib S, Singh M. Carbon-based Nanomaterials for delivery of small RNA molecules: a focus on potential cancer treatment applications. Pharm Nanotechnol 2022; 10:PNT-EPUB-124198. [PMID: 35670355 DOI: 10.2174/2211738510666220606102906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/17/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleic acid-mediated therapy holds immense potential in the treatment of recalcitrant human diseases such as cancer. This is underscored by advances in understanding the mechanisms of gene regulation. In particular, the endogenous protective mechanism of gene silencing known as RNA interference (RNAi) has been extensively exploited. METHODS We review here the developments from 2011 to 2021, in the use of nanographene oxide, carbon nanotubes, fullerenes, carbon nanohorns, carbon nanodots and nanodiamonds for the delivery of therapeutic small RNA molecules. RESULTS Appropriately designed effector molecules such as small interfering RNA (siRNA), can, in theory, silence the expression of any disease-causing gene. Alternatively, siRNA can be generated in vivo through the introduction of plasmid-based short hairpin RNA (shRNA) expression vectors. Other small RNAs such as micro RNA (miRNA) also function in post-transcriptional gene regulation and are aberrantly expressed under disease conditions. The miRNA-based therapy involves either restoration of miRNA function through the introduction of miRNA mimics; or the inhibition of miRNA function by delivering anti-miRNA oligomers. However, the large size, hydrophilicity, negative charge and nuclease-sensitivity of nucleic acids necessitate an appropriate carrier for their introduction as medicine into cells. CONCLUSION While numerous organic and inorganic materials have been investigated for this purpose, the perfect carrier agent remains elusive. In recent years, carbon-based nanomaterials have received widespread attention in biotechnology due to their tunable surface characteristics, mechanical, electrical, optical and chemical properties.
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Affiliation(s)
- Saffiya Habib
- Nano-Gene and Drug Delivery Laboratory, Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Moganavelli Singh
- Nano-Gene and Drug Delivery Laboratory, Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
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Wang Y, Soneson C, Malinowska AL, Laski A, Ghosh S, Kanitz A, Gebert LFR, Robinson MD, Hall J. MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome. Nucleic Acids Res 2021; 49:25-37. [PMID: 33300035 PMCID: PMC7797034 DOI: 10.1093/nar/gkaa1117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/04/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
Many microRNAs regulate gene expression via atypical mechanisms, which are difficult to discern using native cross-linking methods. To ascertain the scope of non-canonical miRNA targeting, methods are needed that identify all targets of a given miRNA. We designed a new class of miR-CLIP probe, whereby psoralen is conjugated to the 3p arm of a pre-microRNA to capture targetomes of miR-124 and miR-132 in HEK293T cells. Processing of pre-miR-124 yields miR-124 and a 5′-extended isoform, iso-miR-124. Using miR-CLIP, we identified overlapping targetomes from both isoforms. From a set of 16 targets, 13 were differently inhibited at mRNA/protein levels by the isoforms. Moreover, delivery of pre-miR-124 into cells repressed these targets more strongly than individual treatments with miR-124 and iso-miR-124, suggesting that isomirs from one pre-miRNA may function synergistically. By mining the miR-CLIP targetome, we identified nine G-bulged target-sites that are regulated at the protein level by miR-124 but not isomiR-124. Using structural data, we propose a model involving AGO2 helix-7 that suggests why only miR-124 can engage these sites. In summary, access to the miR-124 targetome via miR-CLIP revealed for the first time how heterogeneous processing of miRNAs combined with non-canonical targeting mechanisms expand the regulatory range of a miRNA.
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Affiliation(s)
- Yuluan Wang
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Charlotte Soneson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, 8057, Zurich, Switzerland
| | - Anna L Malinowska
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Artur Laski
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Souvik Ghosh
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark D Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, 8057, Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
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Orally Administered Exosomes Suppress Mouse Delayed-Type Hypersensitivity by Delivering miRNA-150 to Antigen-Primed Macrophage APC Targeted by Exosome-Surface Anti-Peptide Antibody Light Chains. Int J Mol Sci 2020; 21:ijms21155540. [PMID: 32748889 PMCID: PMC7432818 DOI: 10.3390/ijms21155540] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 07/29/2020] [Accepted: 08/01/2020] [Indexed: 12/16/2022] Open
Abstract
We previously discovered suppressor T cell-derived, antigen (Ag)-specific exosomes inhibiting mouse hapten-induced contact sensitivity effector T cells by targeting antigen-presenting cells (APCs). These suppressive exosomes acted Ag-specifically due to a coating of antibody free light chains (FLC) from Ag-activated B1a cells. Current studies are aimed at determining if similar immune tolerance could be induced in cutaneous delayed-type hypersensitivity (DTH) to the protein Ag (ovalbumin, OVA). Intravenous administration of a high dose of OVA-coupled, syngeneic erythrocytes similarly induced CD3+CD8+ suppressor T cells producing suppressive, miRNA-150-carrying exosomes, also coated with B1a cell-derived, OVA-specific FLC. Simultaneously, OVA-immunized B1a cells produced an exosome subpopulation, originally coated with Ag-specific FLC, that could be rendered suppressive by in vitro association with miRNA-150. Importantly, miRNA-150-carrying exosomes from both suppressor T cells and B1a cells efficiently induced prolonged DTH suppression after single systemic administration into actively immunized mice, with the strongest effect observed after oral treatment. Current studies also showed that OVA-specific FLC on suppressive exosomes bind OVA peptides suggesting that exosome-coating FLC target APCs by binding to peptide-Ag-major histocompatibility complexes. This renders APCs capable of inhibiting DTH effector T cells. Thus, our studies describe a novel immune tolerance mechanism mediated by FLC-coated, Ag-specific, miRNA-150-carrying exosomes that act on the APC and are particularly effective after oral administration.
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Chen L, Sun Y, Li J, Zhang Y. A photoactivatable microRNA probe for identification of microRNA targets and light-controlled suppression of microRNA target expression. Chem Commun (Camb) 2019; 56:627-630. [PMID: 31833483 DOI: 10.1039/c9cc08277h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here, we report a novel dual-functional microRNA (miRNA) probe, PA-miRNA, for miRNA target identification and light control of miRNA target expression. PA-miRNA is a miRNA mimic with a 3'-biotin tag linked via a photo-cleavable linker. Using PA-miR-34a, intracellular targets of miR-34a in HeLa cells were isolated and confirmed. Moreover, PA-miR-34a upon transfection into HeLa cells was inactive until light irradiation to break the photo-cleavable linker to release functional miR-34a. We demonstrated that miR-34a target expression as well as miR-34a-promoted cell apoptosis were regulated by PA-miR-34a in a photo-controllable manner.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China.
| | - Yu Sun
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China.
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China.
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China.
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Zhang P, Fu H, Du S, Wang F, Yang J, Cai W, Liu D. Click RNA for Rapid Capture and Identification of Intracellular MicroRNA Targets. Anal Chem 2019; 91:15740-15747. [PMID: 31714070 DOI: 10.1021/acs.analchem.9b03943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Rapid capture and identification of the intracellular target genes of microRNAs (miRNAs) are the key to understanding miRNA functions and development of RNA-based therapeutics. However, developing biochemical tools that can fish out the target genes of miRNAs in live cells is a significant technical challenge. Here, we report a remarkably simple yet powerful technology capable of loading virtually any miRNA into Ago2 of the RNA-induced silencing complexes (RISCs). This surprising discovery enables rapid capture and identification of target mRNAs and long noncoding RNAs. It is achieved by linking dibenzocyclooctyne (DBCO), a classical chemical moiety in copper-free click chemistry, to the 3' end of miRNAs. DBCO serves as a high-affinity tag to the Ago2 protein, thus boosting the formation of RISCs with miRNA target genes in living cells. Upon cell lysing, DBCO's routine function in click chemistry allows rapid enrichment of target genes for analysis without the need of additional molecular handles. A series of miR-21 and miR-27a target genes that were previously unknown were pulled down from various cell lines and identified with qRT-PCR, demonstrating the utility of this innovative technology in both transcriptomic research and RNA-based studies.
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Affiliation(s)
- Pengjuan Zhang
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , China.,Hebei University of Environmental Engineering , Qinhuangdao 066102 , Hebei , China
| | - Haohao Fu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , China
| | - Shuangli Du
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , China
| | - Fengchao Wang
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , China
| | - Jie Yang
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , China
| | - Wensheng Cai
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing , Nankai University , Tianjin 300071 , China
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8
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Recent progress in microRNA-based delivery systems for the treatment of human disease. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41544-019-0024-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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9
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Li J, Zhang Y. Current experimental strategies for intracellular target identification of microRNA. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41544-018-0002-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Kriegel AJ, Terhune SS, Greene AS, Noon KR, Pereckas MS, Liang M. Isomer-specific effect of microRNA miR-29b on nuclear morphology. J Biol Chem 2018; 293:14080-14088. [PMID: 30006350 DOI: 10.1074/jbc.ra117.001705] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 07/02/2018] [Indexed: 12/31/2022] Open
Abstract
Targeting mRNAs via seed region pairing is the canonical mechanism by which microRNAs (miRNAs) regulate cellular functions and disease processes. Emerging evidence suggests miRNAs might also act through other mechanisms. miRNA isomers that contain identical seed region sequences, such as miR-29a and miR-29b, provide naturally occurring, informative models for identifying those miRNA effects that are independent of seed region pairing. miR-29a and miR-29b are both expressed in HeLa cells, and miR-29b has been reported to localize to the nucleus in early mitosis because of unique nucleotide sequences on its 3' end. Here, we sought to better understand the mechanism of miR-29b nuclear localization and its function in cell division. We hypothesized that its nuclear localization may be facilitated by protein-miRNA interactions unique to miR-29b. Specific blockade of miR-29b resulted in striking nuclear irregularities not observed following miR-29a blockade. We also observed that miR-29b, but not miR-29a, is enriched in the nucleus and perinuclear clusters during mitosis. Targeted proteomic analysis of affinity-purified samples identified several proteins interacting with synthetic oligonucleotides mimicking miR-29b, but these proteins did not interact with miR-29a. One of these proteins, ADP/ATP translocase 2 (ANT2), known to be involved in mitotic spindle formation, colocalized with miR-29b in perinuclear clusters independently of Argonaute 2. Of note, ANT2 knockdown resulted in nuclear irregularities similar to those observed following miR-29b blockade and prevented nuclear uptake of endogenous miR-29b. Our findings reveal that miR-29 regulates nuclear morphology during mitosis and that this critical function is unique to the miR-29b isoform.
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Affiliation(s)
- Alison J Kriegel
- From the Department of Physiology, Center of Systems Molecular Medicine,
| | - Scott S Terhune
- the Department of Microbiology and Molecular Genetics, and.,the Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Andrew S Greene
- From the Department of Physiology, Center of Systems Molecular Medicine.,the Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Kathleen R Noon
- the Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Michael S Pereckas
- the Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Mingyu Liang
- From the Department of Physiology, Center of Systems Molecular Medicine,
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Nakamoto K, Akao Y, Ueno Y. Diazirine-containing tag-free RNA probes for efficient RISC-loading and photoaffinity labeling of microRNA targets. Bioorg Med Chem Lett 2018; 28:2906-2909. [PMID: 30021704 DOI: 10.1016/j.bmcl.2018.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/17/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022]
Abstract
We designed and synthesized a photo-reactive and tag-free RNA probe for the identification of microRNA (miRNA) targets. To synthesize the RNA probe, we designed a novel nucleoside analog 1-O-[3-ethynyl-5-(3-trifluoromethyl-3H-diazirine-3-yl)]benzyl-β-d-ribofuranose containing aryl trifluoromethyl diazirine and ethynyl moieties. The RNA probe containing this analog was observed to form crosslinks with complementary RNA by UV irradiation and was rapidly tagged by Cu-catalyzed azide alkyne cycloaddition (CuAAC). In addition, the tag-free and photo-reactive miRNA-145 probe showed comparable gene silencing activity to that of unmodified miRNA-145. Therefore, miRNA probes containing the nucleoside analog are promising candidates for the identification of target mRNAs of miRNAs.
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Affiliation(s)
- Kosuke Nakamoto
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yukihiro Akao
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, 1-1 Yanagido, Gifu 501-1193, Japan; Center of Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), 1-1 Yanagido, Gifu 501-1193, Japan.
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12
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Dash S, Balasubramaniam M, Dash C, Pandhare J. Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs. J Vis Exp 2018. [PMID: 29985341 DOI: 10.3791/57786] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally regulate cellular gene expression. MiRNAs bind to the 3' untranslated region (UTR) of target mRNA to inhibit protein translation or in some instances cause mRNA degradation. The binding of the miRNA to the 3' UTR of the target mRNA is mediated by a 2-8 nucleotide seed sequence at the 5' end of miRNA. While the role of miRNAs as cellular regulatory molecules is well established, identification of the target mRNAs with functional relevance remains a challenge. Bioinformatic tools have been employed to predict sequences within the 3' UTR of mRNAs as potential targets for miRNA binding. These tools have also been utilized to determine the evolutionary conservation of such sequences among related species in an attempt to predict functional role. However, these computational methods often generate false positive results and are limited to predicting canonical interaction between miRNA and mRNA. Therefore, experimental procedures that measure direct binding of miRNA to its mRNA target are necessary to establish functional interaction. In this report, we describe a sensitive method for validating direct interaction between the cellular miRNA miR-125b and the 3' UTR of PARP-1 mRNA. We elaborate a protocol in which synthetic biotinylated-miRNA mimics were transfected into mammalian cells and the miRNA-mRNA complex in the cellular lysate was pulled down with streptavidin-coated magnetic beads. Finally, the target mRNA in the pulled-down nucleic acid complex was quantified using a qPCR-based strategy.
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Affiliation(s)
- Sabyasachi Dash
- School of Biotechnology, Kalinga Institute of Industrial Technology University; 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College; Kalinga Institute of Industrial Technology University
| | - Muthukumar Balasubramaniam
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College
| | - Chandravanu Dash
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College;
| | - Jui Pandhare
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College;
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13
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Awan HM, Shah A, Rashid F, Wei S, Chen L, Shan G. Comparing two approaches of miR-34a target identification, biotinylated-miRNA pulldown vs miRNA overexpression. RNA Biol 2018; 15:55-61. [PMID: 29028450 PMCID: PMC5786020 DOI: 10.1080/15476286.2017.1391441] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 10/18/2022] Open
Abstract
microRNAs (miRNAs) are critical regulators of gene expression. For elucidating functional roles of miRNAs, it is critical to identify their direct targets. There are debates about whether pulldown of biotinylated miRNA mimics can be used to identify miRNA targets or not. Here we show that biotin-labelled miR-34a can be loaded to AGO2, and AGO2 immunoprecipitation can pulldown biotinylated miR-34a (Bio-miR pulldown). RNA-sequencing (RNA-seq) of the Bio-miR pulldown RNAs efficiently identified miR-34a mRNA targets, which could be verified with luciferase assays. In contrast to the approach of Bio-miR pulldown, RNA-seq of miR-34a overexpression samples had limited value in identifying direct targets of miR-34a. It seems that pulldown of 3'-Biotin-tagged miRNA can identify bona fide microRNA targets at least for miR-34a.
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Affiliation(s)
- Hassaan Mehboob Awan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Abdullah Shah
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Farooq Rashid
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shuai Wei
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Liang Chen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
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14
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Nakamoto K, Minami K, Akao Y, Ueno Y. Labeling of target mRNAs using a photo-reactive microRNA probe. Chem Commun (Camb) 2017; 52:6720-2. [PMID: 27117176 DOI: 10.1039/c6cc01360k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To identify target mRNAs of an miRNA, we synthesized photo-reactive miRNA probes, which contained a photo-reactive nucleoside analog, 1-O-[4-(3-trifluoromethyl-3H-diazirine-3-yl)]benzyl-β-d-ribofuranose, in the middle of the strand. The photo-reactive miRNA-145 probe was found to specifically label the target mRNAs, FSCN1 and KLF4, by UV-A irradiation in human colon cancer DLD-1 cells.
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Affiliation(s)
- Kosuke Nakamoto
- United Graduate School of Agricultural Science, Gifu University, Japan.
| | - Koichiro Minami
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Japan
| | - Yukihiro Akao
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Japan
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University, Japan. and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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15
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Huang L, Chen Y, Chen L, Xiao X, Wang X, Li J, Zhang Y. Photo-clickable microRNA for in situ fluorescence labeling and imaging of microRNA in living cells. Chem Commun (Camb) 2017; 53:6452-6455. [DOI: 10.1039/c7cc03328a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A photo-clickable microRNA was constructed for in situ fluorescence labeling and imaging of microRNA in living cells with spatiotemporal resolution.
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Affiliation(s)
- Lei Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Yingjie Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Lei Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Xiao Xiao
- State Key Laboratory of Analytical Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Xingxing Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
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16
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Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Methyltransferase-like protein 16 binds the 3'-terminal triple helix of MALAT1 long noncoding RNA. Proc Natl Acad Sci U S A 2016; 113:14013-14018. [PMID: 27872311 PMCID: PMC5150381 DOI: 10.1073/pnas.1614759113] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a cancer-promoting long noncoding RNA, accumulates in cells by using a 3'-triple-helical RNA stability element for nuclear expression (ENE). The ENE, a stem-loop structure containing a U-rich internal loop, interacts with a downstream A-rich tract (ENE+A) to form a blunt-ended triple helix composed of nine U•A-U triples interrupted by a C•G-C triple and C-G doublet. This unique structure prompted us to explore the possibility of protein binding. Native gel-shift assays revealed a shift in radiolabeled MALAT1 ENE+A RNA upon addition of HEK293T cell lysate. Competitive gel-shift assays suggested that protein binding depends not only on the triple-helical structure but also its nucleotide composition. Selection from the lysate using a biotinylated-RNA probe followed by mass spectrometry identified methyltransferase-like protein 16 (METTL16), a putative RNA methyltransferase, as an interacting protein of the MALAT1 ENE+A. Gel-shift assays confirmed the METTL16-MALAT1 ENE+A interaction in vitro: Binding was observed with recombinant METTL16, but diminished in lysate depleted of METTL16, and a supershift was detected after adding anti-METTL16 antibody. Importantly, RNA immunoprecipitation after in vivo UV cross-linking and an in situ proximity ligation assay for RNA-protein interactions confirmed an association between METTL16 and MALAT1 in cells. METTL16 is an abundant (∼5 × 105 molecules per cell) nuclear protein in HeLa cells. Its identification as a triple-stranded RNA binding protein supports the formation of RNA triple helices inside cells and suggests the existence of a class of triple-stranded RNA binding proteins, which may enable the discovery of additional cellular RNA triple helices.
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Affiliation(s)
- Jessica A Brown
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536
| | - Charles G Kinzig
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536
| | - Suzanne J DeGregorio
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536
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17
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Li J, Huang L, Xiao X, Chen Y, Wang X, Zhou Z, Zhang C, Zhang Y. Photoclickable MicroRNA for the Intracellular Target Identification of MicroRNAs. J Am Chem Soc 2016; 138:15943-15949. [DOI: 10.1021/jacs.6b08521] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School
of Chemistry and Chemical Engineering and ‡State Key Laboratory of Pharmaceutical
Biotechnology, Collaborative Innovation Center of Chemistry for Life
Sciences, Jiangsu Engineering Research Center for MicroRNA Biology
and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS),
School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Lei Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School
of Chemistry and Chemical Engineering and ‡State Key Laboratory of Pharmaceutical
Biotechnology, Collaborative Innovation Center of Chemistry for Life
Sciences, Jiangsu Engineering Research Center for MicroRNA Biology
and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS),
School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiao Xiao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School
of Chemistry and Chemical Engineering and ‡State Key Laboratory of Pharmaceutical
Biotechnology, Collaborative Innovation Center of Chemistry for Life
Sciences, Jiangsu Engineering Research Center for MicroRNA Biology
and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS),
School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yingjie Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School
of Chemistry and Chemical Engineering and ‡State Key Laboratory of Pharmaceutical
Biotechnology, Collaborative Innovation Center of Chemistry for Life
Sciences, Jiangsu Engineering Research Center for MicroRNA Biology
and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS),
School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xingxing Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School
of Chemistry and Chemical Engineering and ‡State Key Laboratory of Pharmaceutical
Biotechnology, Collaborative Innovation Center of Chemistry for Life
Sciences, Jiangsu Engineering Research Center for MicroRNA Biology
and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS),
School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhengquan Zhou
- State Key Laboratory of Analytical Chemistry for Life Sciences, School
of Chemistry and Chemical Engineering and ‡State Key Laboratory of Pharmaceutical
Biotechnology, Collaborative Innovation Center of Chemistry for Life
Sciences, Jiangsu Engineering Research Center for MicroRNA Biology
and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS),
School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chenyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School
of Chemistry and Chemical Engineering and ‡State Key Laboratory of Pharmaceutical
Biotechnology, Collaborative Innovation Center of Chemistry for Life
Sciences, Jiangsu Engineering Research Center for MicroRNA Biology
and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS),
School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School
of Chemistry and Chemical Engineering and ‡State Key Laboratory of Pharmaceutical
Biotechnology, Collaborative Innovation Center of Chemistry for Life
Sciences, Jiangsu Engineering Research Center for MicroRNA Biology
and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS),
School of Life Sciences, Nanjing University, Nanjing 210023, China
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18
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Shurtleff MJ, Temoche-Diaz MM, Karfilis KV, Ri S, Schekman R. Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction. eLife 2016; 5. [PMID: 27559612 PMCID: PMC5047747 DOI: 10.7554/elife.19276] [Citation(s) in RCA: 431] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022] Open
Abstract
Exosomes are small vesicles that are secreted from metazoan cells and may convey selected membrane proteins and small RNAs to target cells for the control of cell migration, development and metastasis. To study the mechanisms of RNA packaging into exosomes, we devised a purification scheme based on the membrane marker CD63 to isolate a single exosome species secreted from HEK293T cells. Using immunoisolated CD63-containing exosomes we identified a set of miRNAs that are highly enriched with respect to their cellular levels. To explore the biochemical requirements for exosome biogenesis and RNA packaging, we devised a cell-free reaction that recapitulates the species-selective enclosure of miR-223 in isolated membranes supplemented with cytosol. We found that the RNA-binding protein Y-box protein I (YBX1) binds to and is required for the sorting of miR-223 in the cell-free reaction. Furthermore, YBX1 serves an important role in the secretion of miRNAs in exosomes by HEK293T cells. DOI:http://dx.doi.org/10.7554/eLife.19276.001 Human cells release molecules into their surroundings via membrane-bound packets called exosomes. These molecules can then circulate throughout the body and are protected from degradation. Among the cargos carried by exosomes are small molecules of RNA known as microRNAs, which are involved in regulating gene activity. Only a select subset of the hundreds of microRNAs in a human cell end up packaged into exosomes. This suggests that there might be a specific mechanism that sorts those microRNAs that are destined for export. However, few proteins or other factors that might be involved in this sorting process had been identified to date. Shurtleff et al. set out to identify these factors and started by purifying exosomes from human cells grown in the laboratory and looking for microRNAs that were more abundant in the exosomes than the cells. One exosome-specific microRNA, called miR-223, was further studied via a test-tube based system that uses extracts from cells rather than cells themselves. These experiments confirmed that miR-223 is selectively packed into exosomes that formed in the test tube. Using this system, Shurtleff et al. then isolated a protein called Y-box Protein I (or YBX1 for short) that binds to RNA molecules and found that it was required for this selective packaging. YBX1 is known to be a constituent of exosomes released from intact cells and may therefore be required to sort other RNA molecules into exosomes. Future studies will explore how YBX1 recognizes those RNA molecules to be exported from cells via exosomes. Also, because exosomes have been implicated in some diseases such as cancer, it will be important to explore what role exosome-specific microRNAs play in both health and disease. DOI:http://dx.doi.org/10.7554/eLife.19276.002
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Affiliation(s)
- Matthew J Shurtleff
- Department of Plant and Microbial Biology, University of California, Berkeley, United States
| | - Morayma M Temoche-Diaz
- Department of Plant and Microbial Biology, University of California, Berkeley, United States
| | - Kate V Karfilis
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Sayaka Ri
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Randy Schekman
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
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19
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Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate the stability and expression of target RNAs in a sequence-dependent manner. Identifying miRNA-regulated genes is key to understanding miRNA function. Here, we describe an unbiased biochemical pulldown method to identify with high-specificity miRNA targets. Regulated transcripts are enriched in streptavidin-captured mRNAs that bind to a transfected biotinylated miRNA mimic. The method is relatively simple, does not involve cross-linking and can be performed with only a million cells. Addition of an on-bead RNase digestion step also identifies miRNA recognition elements (MRE).
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Affiliation(s)
- Shen Mynn Tan
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA
| | - Judy Lieberman
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA.
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20
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Abstract
Eukaryotic cells produce several classes of long and small noncoding RNA (ncRNA). Many DNA and RNA viruses synthesize their own ncRNAs. Like their host counterparts, viral ncRNAs associate with proteins that are essential for their stability, function, or both. Diverse biological roles--including the regulation of viral replication, viral persistence, host immune evasion, and cellular transformation--have been ascribed to viral ncRNAs. In this review, we focus on the multitude of functions played by ncRNAs produced by animal viruses. We also discuss their biogenesis and mechanisms of action.
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Affiliation(s)
- Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Yang Eric Guo
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Nara Lee
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Walter N Moss
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Tenaya K Vallery
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Mingyi Xie
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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21
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miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol 2014; 11:107-14. [PMID: 25531890 DOI: 10.1038/nchembio.1713] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 10/29/2014] [Indexed: 12/19/2022]
Abstract
Identifying the interaction partners of noncoding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA crosslinking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-crosslinking and Argonaute 2 immunopurification followed by streptavidin affinity purification of probe-linked RNAs provided selectivity in the capture of targets, which were identified by deep sequencing. miR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. miR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long noncoding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation, levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a 'sponge' for these miRNAs.
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