1
|
Lobo V, Nowak I, Fernandez C, Correa Muler AI, Westholm JO, Huang HC, Fabrik I, Huynh HT, Shcherbinina E, Poyraz M, Härtlova A, Benhalevy D, Angeletti D, Sarshad AA. Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference. Nucleic Acids Res 2024:gkae589. [PMID: 38994560 DOI: 10.1093/nar/gkae589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024] Open
Abstract
In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 cells, evident by changes in cell morphology, increased cell proliferation, and oncogenic miRNA expression. Moreover, AGO fPAR-CLIP in Lamin A KO SHSY5Y cells revealed significantly reduced RNAi activity. Further exploration of the nuclear AGO interactome by mass spectrometry identified FAM120A, an RNA-binding protein and known interactor of AGO2. Subsequent FAM120A fPAR-CLIP, revealed that FAM120A co-binds AGO targets and that this competition reduces the RNAi activity. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, FAM120A mediated RNAi impairment, and upregulation of oncogenic miRNAs, facilitating cancer cell proliferation.
Collapse
Affiliation(s)
- Vivian Lobo
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Iwona Nowak
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Carola Fernandez
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ana Iris Correa Muler
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Jakub O Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Hsiang-Chi Huang
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Hang T Huynh
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Evgeniia Shcherbinina
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Melis Poyraz
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Anetta Härtlova
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Daniel Benhalevy
- Lab of Cellular RNA Biology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- SciLifeLab, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Aishe A Sarshad
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| |
Collapse
|
2
|
Mauro M, Berretta M, Palermo G, Cavalieri V, La Rocca G. The Multiplicity of Argonaute Complexes in Mammalian Cells. J Pharmacol Exp Ther 2023; 384:1-9. [PMID: 35667689 PMCID: PMC9827513 DOI: 10.1124/jpet.122.001158] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/12/2023] Open
Abstract
Argonautes (AGOs) are a highly conserved family of proteins found in most eukaryotes and involved in mechanisms of gene regulation, both at the transcriptional and post-transcriptional level. Among other functions, AGO proteins associate with microRNAs (miRNAs) to mediate the post-transcriptional repression of protein-coding genes. In this process, AGOs associate with members of the trinucleotide repeat containing 6 protein (TNRC6) family to form the core of the RNA-induced silencing complex (RISC), the effector machinery that mediates miRNA function. However, the description of the exact composition of the RISC has been a challenging task due to the fact the AGO's interactome is dynamically regulated in a cell type- and condition-specific manner. Here, we summarize some of the most significant studies that have identified AGO complexes in mammalian cells, as well as the approaches used to characterize them. Finally, we discuss possible opportunities to exploit what we have learned on the properties of the RISC to develop novel anti-cancer therapies. SIGNIFICANCE STATEMENT: The RNA-induced silencing complex (RISC) is the molecular machinery that mediates miRNA function in mammals. Studies over the past two decades have shed light on important biochemical and functional properties of this complex. However, many aspects of this complex await further elucidation, mostly due to technical limitations that have hindered full characterization. Here, we summarize some of the most significant studies on the mammalian RISC and discuss possible sources of biases in the approaches used to characterize it.
Collapse
Affiliation(s)
- Maurizio Mauro
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Massimiliano Berretta
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Giuseppe Palermo
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Vincenzo Cavalieri
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Gaspare La Rocca
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| |
Collapse
|
3
|
Yang J, Zhang M, Yang D, Ma Y, Tang Y, Xing M, Li L, Chen L, Jin Y, Ma C. m 6A-mediated upregulation of AC008 promotes osteoarthritis progression through the miR-328-3p‒AQP1/ANKH axis. Exp Mol Med 2021; 53:1723-1734. [PMID: 34737423 PMCID: PMC8640060 DOI: 10.1038/s12276-021-00696-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important regulators of osteoarthritis (OA), but the biological roles and clinical significance of most lncRNAs in OA are not fully understood. Microarray analysis was performed to identify differentially expressed lncRNAs, mRNAs, and miRNAs between normal and osteoarthritic cartilage. We found that AC008440.5 (abbreviated AC008), as well as AQP1 and ANKH, were highly expressed in osteoarthritic cartilage, whereas miR-328-3p was expressed at a low level in osteoarthritic cartilage. Functional assays showed that ectopic expression of AC008, AQP1, and ANKH significantly decreased chondrocyte viability and promoted chondrocyte apoptosis and extracellular matrix (ECM) degradation, whereas knockdown of AC008, AQP1, and ANKH resulted in the opposite effects. Moreover, miR-328-3p overexpression increased chondrocyte viability and attenuated chondrocyte apoptosis and ECM degradation, whereas inhibition of miR-328-3p resulted in the opposite effects. Bioinformatics analysis, RNA immunoprecipitation (RIP), and luciferase assays revealed that AC008 functioned as a competing endogenous RNA (ceRNA) to regulate miR-328-3p, which specifically targeted the AQP1 and ANKH genes. In addition, miR-328-3p significantly ameliorated MIA-induced OA, whereas AC008 accelerated OA progression in vivo. Furthermore, fat mass and obesity-associated (FTO)-mediated N6-methyladenosine demethylation downregulated AC008 transcription, while lower FTO expression led to upregulation of AC008 transcription in OA. In conclusion, our data reveal that AC008 plays a critical role in OA pathogenesis via the miR-328-3p‒AQP1/ANKH pathway, suggesting that AC008 may be a potential therapeutic target for OA.
Collapse
Affiliation(s)
- Jiashu Yang
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, P.R. China
- Department of Medical Genetics, Nanjing Medical University, Nanjing, P.R. China
| | - Ming Zhang
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, P.R. China
- Department of Medical Genetics, Nanjing Medical University, Nanjing, P.R. China
| | - Dawei Yang
- Department of Orthopaedic Surgery, Nanjing First Hospital, Nanjing, P.R. China
| | - Yunfei Ma
- Department of Medical Genetics, Nanjing Medical University, Nanjing, P.R. China
| | - Yuting Tang
- Department of Medical Genetics, Nanjing Medical University, Nanjing, P.R. China
| | - Mengying Xing
- Department of Medical Genetics, Nanjing Medical University, Nanjing, P.R. China
| | - Lingyun Li
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, P.R. China
- Department of Medical Genetics, Nanjing Medical University, Nanjing, P.R. China
| | - Li Chen
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, P.R. China
- Department of Endocrinology and Metabolism, Endocrine Research Laboratory (KMEB), Odense University Hospital and University of Southern Denmark, Odense, Denmark
| | - Yucui Jin
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, P.R. China.
- Department of Medical Genetics, Nanjing Medical University, Nanjing, P.R. China.
| | - Changyan Ma
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, P.R. China.
- Department of Medical Genetics, Nanjing Medical University, Nanjing, P.R. China.
| |
Collapse
|
4
|
Bryzgunova O, Konoshenko M, Zaporozhchenko I, Yakovlev A, Laktionov P. Isolation of Cell-Free miRNA from Biological Fluids: Influencing Factors and Methods. Diagnostics (Basel) 2021; 11:865. [PMID: 34064927 PMCID: PMC8151063 DOI: 10.3390/diagnostics11050865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
A vast wealth of recent research has seen attempts of using microRNA (miRNA) found in biological fluids in clinical research and medicine. One of the reasons behind this trend is the apparent their high stability of cell-free miRNA conferred by small size and packaging in supramolecular complexes. However, researchers in both basic and clinical settings often face the problem of selecting adequate methods to extract appropriate quality miRNA preparations for use in specific downstream analysis pipelines. This review outlines the variety of different methods of miRNA isolation from biofluids and examines the key determinants of their efficiency, including, but not limited to, the structural properties of miRNA and factors defining their stability in the extracellular environment.
Collapse
Affiliation(s)
- Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Ivan Zaporozhchenko
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Alexey Yakovlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| |
Collapse
|
5
|
Nowak I, Sarshad AA. Argonaute Proteins Take Center Stage in Cancers. Cancers (Basel) 2021; 13:cancers13040788. [PMID: 33668654 PMCID: PMC7918559 DOI: 10.3390/cancers13040788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The dysregulation of RNA interference (RNAi) has often been observed in cancers, where the main focus of research has been on the small RNA molecules directing RNAi. In this review, we focus on the activity of Argonaute proteins, central components of RNAi, in tumorigenesis, and also highlight their potential applications in grading tumors and anti-cancer therapies. Abstract Argonaute proteins (AGOs) play crucial roles in RNA-induced silencing complex (RISC) formation and activity. AGOs loaded with small RNA molecules (miRNA or siRNA) either catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and target destabilization. miRNAs are well characterized and broadly studied in tumorigenesis; nevertheless, the functions of the AGOs in cancers have lagged behind. Here, we discuss the current state of knowledge on the role of AGOs in tumorigenesis, highlighting canonical and non-canonical functions of AGOs in cancer cells, as well as the biomarker potential of AGO expression in different of tumor types. Furthermore, we point to the possible application of the AGOs in development of novel therapeutic approaches.
Collapse
Affiliation(s)
- Iwona Nowak
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Aishe A. Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
| |
Collapse
|
6
|
Tiny miRNAs Play a Big Role in the Treatment of Breast Cancer Metastasis. Cancers (Basel) 2021; 13:cancers13020337. [PMID: 33477629 PMCID: PMC7831489 DOI: 10.3390/cancers13020337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary MicroRNAs (miRNAs) have emerged as important regulators of tumour progression and metastasis in breast cancer. Through a review of multiple studies, this paper has identified the key regulatory roles of oncogenic miRNAs in breast cancer metastasis including the potentiation of angiogenesis, epithelial-mesenchymal transition, the Warburg effect, and the tumour microenvironment. Several approaches have been studied for selective targeting of breast tumours by miRNAs, ranging from delivery systems such as extracellular vesicles and liposomes to the use of prodrugs and functionally modified vehicle-free miRNAs. While promising, these miRNA-based therapies face challenges including toxicity and immunogenicity, and greater research on their safety profiles must be performed before progressing to clinical trials. Abstract Distant organ metastases accounts for the majority of breast cancer deaths. Given the prevalence of breast cancer in women, it is imperative to understand the underlying mechanisms of its metastatic progression and identify potential targets for therapy. Since their discovery in 1993, microRNAs (miRNAs) have emerged as important regulators of tumour progression and metastasis in various cancers, playing either oncogenic or tumour suppressor roles. In the following review, we discuss the roles of miRNAs that potentiate four key areas of breast cancer metastasis—angiogenesis, epithelial-mesenchymal transition, the Warburg effect and the tumour microenvironment. We then evaluate the recent developments in miRNA-based therapies in breast cancer, which have shown substantial promise in controlling tumour progression and metastasis. Yet, certain challenges must be overcome before these strategies can be implemented in clinical trials.
Collapse
|
7
|
Tng PYL, Carabajal Paladino L, Verkuijl SAN, Purcell J, Merits A, Leftwich PT, Fragkoudis R, Noad R, Alphey L. Cas13b-dependent and Cas13b-independent RNA knockdown of viral sequences in mosquito cells following guide RNA expression. Commun Biol 2020; 3:413. [PMID: 32737398 PMCID: PMC7395101 DOI: 10.1038/s42003-020-01142-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/09/2020] [Indexed: 12/26/2022] Open
Abstract
Aedes aegypti and Aedes albopictus mosquitoes are vectors of the RNA viruses chikungunya (CHIKV) and dengue that currently have no specific therapeutic treatments. The development of new methods to generate virus-refractory mosquitoes would be beneficial. Cas13b is an enzyme that uses RNA guides to target and cleave RNA molecules and has been reported to suppress RNA viruses in mammalian and plant cells. We investigated the potential use of the Prevotella sp. P5-125 Cas13b system to provide viral refractoriness in mosquito cells, using a virus-derived reporter and a CHIKV split replication system. Cas13b in combination with suitable guide RNAs could induce strong suppression of virus-derived reporter RNAs in insect cells. Surprisingly, the RNA guides alone (without Cas13b) also gave substantial suppression. Our study provides support for the potential use of Cas13b in mosquitoes, but also caution in interpreting CRISPR/Cas data as we show that guide RNAs can have Cas-independent effects.
Collapse
Affiliation(s)
- Priscilla Ying Lei Tng
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, Hertfordshire, AL9 7TA, UK
| | | | - Sebald Alexander Nkosana Verkuijl
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Jessica Purcell
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Andres Merits
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Philip Thomas Leftwich
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Rennos Fragkoudis
- Arbovirus Pathogenesis, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington, Loughborough, LE12 5RD, UK
| | - Rob Noad
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, Hertfordshire, AL9 7TA, UK
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| |
Collapse
|
8
|
Unal O, Akkoc Y, Kocak M, Nalbat E, Dogan-Ekici AI, Yagci Acar H, Gozuacik D. Treatment of breast cancer with autophagy inhibitory microRNAs carried by AGO2-conjugated nanoparticles. J Nanobiotechnology 2020; 18:65. [PMID: 32345308 PMCID: PMC7189576 DOI: 10.1186/s12951-020-00615-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Nanoparticle based gene delivery systems holds great promise. Superparamagnetic iron oxide nanoparticles (SPIONs) are being heavily investigated due to good biocompatibility and added diagnostic potential, rendering such nanoparticles theranostic. Yet, commonly used cationic coatings for efficient delivery of such anionic cargos, results in significant toxicity limiting translation of the technology to the clinic. Here, we describe a highly biocompatible, small and non-cationic SPION-based theranostic nanoparticles as novel gene therapy agents. We propose for the first-time, the usage of the microRNA machinery RISC complex component Argonaute 2 (AGO2) protein as a microRNA stabilizing agent and a delivery vehicle. In this study, AGO2 protein-conjugated, anti-HER2 antibody-linked and fluorophore-tagged SPION nanoparticles were developed (SP-AH nanoparticles) and used as a carrier for an autophagy inhibitory microRNA, MIR376B. These functionalized nanoparticles selectively delivered an effective amount of the microRNA into HER2-positive breast cancer cell lines in vitro and in a xenograft nude mice model of breast cancer in vivo, and successfully blocked autophagy. Furthermore, combination of the chemotherapy agent cisplatin with MIR376B-loaded SP-AH nanoparticles increased the efficacy of the anti-cancer treatment both in vitro in cells and in vivo in the nude mice. Therefore, we propose that AGO2 protein conjugated SPIONs are a new class of theranostic nanoparticles and can be efficiently used as innovative, non-cationic, non-toxic gene therapy tools for targeted therapy of cancer.
Collapse
Affiliation(s)
- Ozlem Unal
- Koc University, Graduate School of Material Science and Engineering, Rumelifeneri Yolu Sarıyer, 34450, Istanbul, Turkey
| | - Yunus Akkoc
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Department of Biotechnology, Tuzla, 34956, Istanbul, Turkey
| | - Muhammed Kocak
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Department of Biotechnology, Tuzla, 34956, Istanbul, Turkey
| | - Esra Nalbat
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Department of Biotechnology, Tuzla, 34956, Istanbul, Turkey
| | - Asiye Isin Dogan-Ekici
- Acıbadem Mehmet Ali Aydınlar University, School of Medicine Department of Pathology, Ataşehir, 34755, Istanbul, Turkey
| | - Havva Yagci Acar
- Koc University, Graduate School of Material Science and Engineering, Rumelifeneri Yolu Sarıyer, 34450, Istanbul, Turkey. .,Koc University, Department of Chemistry, Rumelifeneri Yolu Sarıyer, 34450, Istanbul, Turkey. .,Koc University Surface Science and Technology Center (KUYTAM), Rumelifeneri Yolu Sarıyer, 34450, Istanbul, Turkey.
| | - Devrim Gozuacik
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Department of Biotechnology, Tuzla, 34956, Istanbul, Turkey. .,Koç University, School of Medicine, Koç University Research Center for Translational Medicine (KUTTAM), Topkapı, 34010, Istanbul, Turkey.
| |
Collapse
|
9
|
Van Meter EN, Onyango JA, Teske KA. A review of currently identified small molecule modulators of microRNA function. Eur J Med Chem 2020; 188:112008. [DOI: 10.1016/j.ejmech.2019.112008] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022]
|
10
|
Ledda B, Ottaggio L, Izzotti A, Sukkar SG, Miele M. Small RNAs in eucaryotes: new clues for amplifying microRNA benefits. Cell Biosci 2020; 10:1. [PMID: 31911829 PMCID: PMC6942390 DOI: 10.1186/s13578-019-0370-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/23/2019] [Indexed: 12/31/2022] Open
Abstract
miRNAs, the smallest nucleotide molecules able to regulate gene expression at post transcriptional level, are found in both animals and plants being involved in fundamental processes for growth and development of living organisms. The number of miRNAs has been hypothesized to increase when some organisms specialized the process of mastication and grinding of food. Further to the vertical transmission, miRNAs can undergo horizontal transmission among different species, in particular between plants and animals. In the last years, an increasing number of studies reported that miRNA passage occurs through feeding, and that in animals, plant miRNAs can survive the gastro intestinal digestion and transferred by blood into host cells, where they can exert their functions modulating gene expression. The present review reports studies on miRNAs during evolution, with particular focus on biogenesis and mechanisms regulating their stability in plants and animals. The different biogenesis and post biogenesis modifications allow to discriminate miRNAs of plant origin from those of animal origin, and make it possible to better clarify the controversial question on whether a possible cross-kingdom miRNA transfer through food does exist. The majority of human medicines and supplements derive from plants and a regular consumption of plant food is suggested for their beneficial effects in the prevention of metabolic diseases, cancers, and dietary related disorders. So far, these beneficial effects have been generally attributed to the content of secondary metabolites, whereas mechanisms regarding other components remain unclear. Therefore, in light of the above reported studies miRNAs could result another component for the medical properties of plants. miRNAs have been mainly studied in mammals characterizing their sequences and molecular targets as available in public databases. The herein presented studies provide evidences that miRNA situation is much more complex than the static situation reported in databases. Indeed, miRNAs may have redundant activities, variable sequences, different methods of biogenesis, and may be differently influenced by external and environmental factors. In-depth knowledge of mechanisms of synthesis, regulation and transfer of plant miRNAs to other species can open new frontiers in the therapy of many human diseases, including cancer.
Collapse
Affiliation(s)
- Bernardetta Ledda
- 1Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16132 Genoa, Italy
| | - Laura Ottaggio
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, L.Go R. Benzi, 10, Genoa, Italy
| | - Alberto Izzotti
- 1Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16132 Genoa, Italy.,Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, L.Go R. Benzi, 10, Genoa, Italy
| | - Samir G Sukkar
- UOD Dietetic and Clinical Nutrition, IRCCS Ospedale Policlinico San Martino, L.Go R. Benzi, 10, Genoa, Italy
| | - Mariangela Miele
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, L.Go R. Benzi, 10, Genoa, Italy
| |
Collapse
|
11
|
Temoche-Diaz MM, Shurtleff MJ, Nottingham RM, Yao J, Fadadu RP, Lambowitz AM, Schekman R. Distinct mechanisms of microRNA sorting into cancer cell-derived extracellular vesicle subtypes. eLife 2019; 8:e47544. [PMID: 31436530 PMCID: PMC6728143 DOI: 10.7554/elife.47544] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) encompass a variety of vesicles secreted into the extracellular space. EVs have been implicated in promoting tumor metastasis, but the molecular composition of tumor-derived EV sub-types and the mechanisms by which molecules are sorted into EVs remain mostly unknown. We report the separation of two small EV sub-populations from a metastatic breast cancer cell line, with biochemical features consistent with different sub-cellular origins. These EV sub-types use different mechanisms of miRNA sorting (selective and non-selective), suggesting that sorting occurs via fundamentally distinct processes, possibly dependent on EV origin. Using biochemical and genetic tools, we identified the Lupus La protein as mediating sorting of selectively packaged miRNAs. We found that two motifs embedded in miR-122 are responsible for high-affinity binding to Lupus La and sorting into vesicles formed in a cell-free reaction. Thus, tumor cells can simultaneously deploy multiple EV species using distinct sorting mechanisms that may enable diverse functions in normal and cancer biology.
Collapse
Affiliation(s)
- Morayma M Temoche-Diaz
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Matthew J Shurtleff
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Ryan M Nottingham
- Department of Molecular Biosciences, Institute for Cellular and Molecular BiologyUniversity of TexasAustinUnited States
| | - Jun Yao
- Department of Molecular Biosciences, Institute for Cellular and Molecular BiologyUniversity of TexasAustinUnited States
| | - Raj P Fadadu
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Alan M Lambowitz
- Department of Molecular Biosciences, Institute for Cellular and Molecular BiologyUniversity of TexasAustinUnited States
| | - Randy Schekman
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| |
Collapse
|
12
|
Casey MC, Prakash A, Holian E, McGuire A, Kalinina O, Shalaby A, Curran C, Webber M, Callagy G, Bourke E, Kerin MJ, Brown JA. Quantifying Argonaute 2 (Ago2) expression to stratify breast cancer. BMC Cancer 2019; 19:712. [PMID: 31324173 PMCID: PMC6642579 DOI: 10.1186/s12885-019-5884-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 06/26/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Argonaute-2 (Ago2) is an essential component of microRNA biogenesis implicated in tumourigenesis. However Ago2 expression and localisation in breast cancer remains undetermined. The aim was to define Ago2 expression (mRNA and protein) and localisation in breast cancer, and investigate associations with clinicopathological details. METHODS Ago2 protein was stained in breast cancer cell lines and tissue microarrays (TMAs), with intensity and localization assessed. Staining intensity was correlated with clinicopathological details. Using independent databases, Ago2 mRNA expression and gene alterations in breast cancer were investigated. RESULTS In the breast cancer TMAs, 4 distinct staining intensities were observed (Negative, Weak, Moderate, Strong), with 64.2% of samples stained weak or negatively for Ago2 protein. An association was found between strong Ago2 staining and, the Her2 positive or basal subtypes, and between Ago2 intensity and receptor status (Estrogen or Progesterone). In tumours Ago2 mRNA expression correlated with reduced relapse free survival. Conversely, Ago2 mRNA was expressed significantly lower in SK-BR-3 (HER2 positive) and BT-20 (Basal/Triple negative) cell lines. Interestingly, high levels of Ago2 gene amplification (10-27%) were observed in breast cancer across multiple patient datasets. Importantly, knowledge of Ago2 expression improves predictions of breast cancer subtype by 20%, ER status by 15.7% and PR status by 17.5%. CONCLUSIONS Quantification of Ago2 improves the stratification of breast cancer and suggests a differential role for Ago2 in breast cancer subtypes, based on levels and cellular localisation. Further investigation of the mechanisms affecting Ago2 dysregulation will reveal insights into the molecular differences underpinning breast cancer subtypes.
Collapse
Affiliation(s)
- M C Casey
- Discipline of Surgery, School of Medicine, Lambe institute for Translational Research, National University of Ireland, Galway, Ireland
| | - A Prakash
- Discipline of Pathology, School of Medicine, Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland
| | - E Holian
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - A McGuire
- Discipline of Surgery, School of Medicine, Lambe institute for Translational Research, National University of Ireland, Galway, Ireland
| | - O Kalinina
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - A Shalaby
- Discipline of Pathology, School of Medicine, Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland
| | - C Curran
- Discipline of Surgery, School of Medicine, Lambe institute for Translational Research, National University of Ireland, Galway, Ireland
| | - M Webber
- Discipline of Pathology, School of Medicine, Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland
| | - G Callagy
- Discipline of Pathology, School of Medicine, Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland
| | - E Bourke
- Discipline of Pathology, School of Medicine, Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland
| | - M J Kerin
- Discipline of Surgery, School of Medicine, Lambe institute for Translational Research, National University of Ireland, Galway, Ireland
| | - J A Brown
- Discipline of Surgery, School of Medicine, Lambe institute for Translational Research, National University of Ireland, Galway, Ireland.
| |
Collapse
|
13
|
Zhang Y, Zhang H. RNAa Induced by TATA Box-Targeting MicroRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 28639194 DOI: 10.1007/978-981-10-4310-9_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent studies reveal that some nuclear microRNAs (miRNA) and synthesized siRNAs target gene promoters to activate gene transcription (RNAa). Interestingly, our group identified a novel HIV-1-encoded miRNA, miR-H3, which targets specifically the core promoter TATA box of HIV-1 and activates viral gene expression. Depletion of miR-H3 significantly impaired the replication of HIV-1. miR-H3 mimics could activate viruses from CD4+ T cells isolated from patients receiving suppressive highly active antiretroviral therapy, which is very intriguing for reducing HIV-1 latent reservoir. Further study revealed that many cellular miRNAs also function like miR-H3. For instance, let-7i targets the TATA box of the interleukin-2 (IL-2) promoter and upregulates IL-2 expression in T-lymphocytes. In RNAa induced by TATA box-targeting miRNAs, Argonaute (AGO) proteins are needed, but there is no evidence for the involvement of promoter-associated transcripts or epigenetic modifications. We propose that the binding of small RNA-AGO complex to TATA box could facilitate the assembly of RNA Polymerase II transcription preinitiation complex. In addition, synthesized small RNAs targeting TATA box can also efficiently activate transcription of interested genes, such as insulin, IL-2, and c-Myc. The discovery of RNAa induced by TATA box-targeting miRNA provides an easy-to-use tool for activating gene expression.
Collapse
Affiliation(s)
- Yijun Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| |
Collapse
|
14
|
Yao Q, Chen Y, Wu F, Wu F, Liu C, Hong T, Li W, Chen Y, Zhou X. Efficient Self‐Assembled DNA Nanoparticles through Rolling Circle Amplification for siRNA Delivery
in
v
itro. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qian Yao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| | - Chaoxing Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| | - Tingting Hong
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| | - Wei Li
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| | - Yi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and ImmunologyWuhan University Wuhan Hubei 430072 China
| |
Collapse
|
15
|
Acetylation of AGO2 promotes cancer progression by increasing oncogenic miR-19b biogenesis. Oncogene 2018; 38:1410-1431. [PMID: 30305728 PMCID: PMC6372475 DOI: 10.1038/s41388-018-0530-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/03/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022]
Abstract
Argonaute2 (AGO2) is an effector of small RNA mediated gene silencing. Increasing evidence show that post-translational modifications of AGO2 can change miRNA activity at specific or global levels. Among the six mature miRNAs that are encoded by miR-17-92, miR-19b1 is the most powerful to exert the oncogenic properties of the entire cluster. Here we identify that AGO2 can be acetylated by P300/CBP and deacetylated by HDAC7, and that acetylation occurs at three sites K720, K493, and K355. Mutation of K493R/K720R, but not K355R at AGO2, inhibits miR-19b biogenesis. We demonstrate that acetylation of AGO2 specifically increases its recruiting pre-miR-19b1 to form the miPDC (miRNA precursor deposit complex), thereby to enhance miR-19b maturation. The motif UGUGUG in the terminal-loop of pre-miR-19b1, as a specific processing feature that is recognized and bound by acetylated AGO2, is essential for the assembly of miRISC (miRNA-induced silencing complex) loading complex. Analyses on public clinical data, xenograft mouse models, and IHC and ISH staining of lung cancer tissues, further confirm that the high levels of both AGO2 acetylation and miR-19b correlate with poor prognosis in lung cancer patients. Our finding reveals a novel function of AGO2 acetylation in increasing oncogenic miR-19b biogenesis and suggests that modulation of AGO2 acetylation has potential clinical implications.
Collapse
|
16
|
Structurally modulated codelivery of siRNA and Argonaute 2 for enhanced RNA interference. Proc Natl Acad Sci U S A 2018; 115:E2696-E2705. [PMID: 29432194 DOI: 10.1073/pnas.1719565115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Small interfering RNA (siRNA) represents a promising class of inhibitors in both fundamental research and the clinic. Numerous delivery vehicles have been developed to facilitate siRNA delivery. Nevertheless, achieving highly potent RNA interference (RNAi) toward clinical translation requires efficient formation of RNA-induced gene-silencing complex (RISC) in the cytoplasm. Here we coencapsulate siRNA and the central RNAi effector protein Argonaute 2 (Ago2) via different delivery carriers as a platform to augment RNAi. The physical clustering between siRNA and Ago2 is found to be indispensable for enhanced RNAi. Moreover, by utilizing polyamines bearing the same backbone but distinct cationic side-group arrangements of ethylene diamine repeats as the delivery vehicles, we find that the molecular structure of these polyamines modulates the degree of siRNA/Ago2-mediated improvement of RNAi. We apply this strategy to silence the oncogene STAT3 and significantly prolong survival in mice challenged with melanoma. Our findings suggest a paradigm for RNAi via the synergistic coassembly of RNA with helper proteins.
Collapse
|
17
|
Qu H, Zheng L, Song H, Jiao W, Li D, Fang E, Wang X, Mei H, Pu J, Huang K, Tong Q. microRNA-558 facilitates the expression of hypoxia-inducible factor 2 alpha through binding to 5'-untranslated region in neuroblastoma. Oncotarget 2018; 7:40657-40673. [PMID: 27276678 PMCID: PMC5130034 DOI: 10.18632/oncotarget.9813] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/20/2016] [Indexed: 11/25/2022] Open
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. Our previous studies have shown that hypoxia-inducible factor 2 alpha (HIF-2α), one member of the bHLH-PAS transcription factor family, facilitates the progression of NB under non-hypoxic conditions. However, the mechanisms underlying HIF-2α expression in NB still remain largely unknown. Herein, through analyzing the computational algorithm programs, we identified microRNA-558 (miR-558) as a crucial regulator of HIF-2α expression in NB. We demonstrated that miR-558 promoted the expression of HIF-2α at translational levels in NB cells through recruiting Argonaute 2 (AGO2). Mechanistically, miR-558 directly bound with its complementary site within 5′-untranslated region (5′-UTR) to facilitate the binding of AGO2 to eukaryotic translation initiation factor 4E (eIF4E) binding protein 1, resulting in increased eIF4E enrichment and HIF-2α translation. In addition, miR-558 promoted the growth, invasion, metastasis, and angiogenesis of NB cells in vitro and in vivo, and these biological features were rescued by knockdown of AGO2, eIF4E, or HIF-2α. In clinical NB specimens, miR-558, AGO2, and eIF4E were highly expressed and positively correlated with HIF-2α expression. Patients with high miR-558, HIF-2α, AGO2, or eIF4E levels had lower survival probability. Taken together, these results demonstrate that miR-558 facilitates the expression of HIF-2α through bindingto its 5′-UTR, thus promoting the tumorigenesis and aggressiveness of NB.
Collapse
Affiliation(s)
- Hongxia Qu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China.,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Huajie Song
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Wanju Jiao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Erhu Fang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Xiaojing Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Hong Mei
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Jiarui Pu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Kai Huang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China.,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, P. R. China
| |
Collapse
|
18
|
Bottini S, Hamouda-Tekaya N, Tanasa B, Zaragosi LE, Grandjean V, Repetto E, Trabucchi M. From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data. Nucleic Acids Res 2017; 45:e71. [PMID: 28108660 PMCID: PMC5435922 DOI: 10.1093/nar/gkx007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/03/2017] [Indexed: 12/20/2022] Open
Abstract
Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq). Since the quality of peaks is of pivotal importance for the final output of the proposed method, we provide a comprehensive benchmarking of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, on four publicly available Ago2-HITS-CLIP datasets and one unpublished in-house Ago2-dataset in stem cells. We measured the sensitivity, the specificity and the position accuracy toward miRNA binding sites identification, and the agreement with TargetScan. Secondly, we developed a new pipeline, called miRBShunter, to identify canonical and non-canonical miRNA-binding sites based on de novo motif identification from Ago2 peaks and prediction of miRNA::RNA heteroduplexes. miRBShunter was tested and experimentally validated on the in-house Ago2-dataset and on an Ago2-PAR-CLIP dataset in human stem cells. Overall, we provide guidelines to choose a suitable peak detection program and a new method for miRNA-target identification.
Collapse
Affiliation(s)
- Silvia Bottini
- Université Côte d'Azur, Inserm, C3M, Nice, 06204, France
| | | | - Bogdan Tanasa
- Stanford University School of Medicine, 265 Campus Drive, LLSCR Building, Stanford, CA 94305, USA
| | | | | | | | | |
Collapse
|
19
|
Reactivity of human AGO2 monoclonal antibody 11A9 with the SWI/SNF complex: A case study for rigorously defining antibody selectivity. Sci Rep 2017; 7:7278. [PMID: 28779093 PMCID: PMC5544689 DOI: 10.1038/s41598-017-07539-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
In this study, we originally aimed to characterize the potential role of Argonaute 2 (AGO2) in the nucleus, a key protein of the miRNA machinery. We combined Chromatin Immunoprecipitation (ChIP) with high throughput sequencing (ChIP-seq) and quantitative mass spectrometry (ChIP-MS) using the broadly used AGO2 11A9 antibody to determine interactions with chromatin and nuclear proteins. We found a previously described interaction between AGO2 and SWI/SNF on chromatin with ChIP-MS and observed enrichment at enhancers and transcription start sites using ChIP-seq. However, antibody specificity issues can produce misleading results for ChIP, RNA-seq and Mass spectrometry. Therefore, we developed a CRISPR/Cas9 engineered AGO2−/− HEK293T cell line to validate our findings. ChIP-qPCR and immunoprecipitation combined with MS (IP-MS) showed that the 11A9 antibody associates with chromatin and SWI/SNF in the absence of AGO2. Furthermore, stoichiometry, IP-MS and co-IP analysis suggests a direct interaction of this antibody with SMARCC1, a component of the SWI/SNF complex. For this reason, particular care should be taken in performing and interpreting experiments in which the 11A9 antibody is used to study a nuclear role of AGO2.
Collapse
|
20
|
Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| |
Collapse
|
21
|
Zealy RW, Wrenn SP, Davila S, Min KW, Yoon JH. microRNA-binding proteins: specificity and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [DOI: 10.1002/wrna.1414] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/14/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Richard W. Zealy
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| | - Samuel P. Wrenn
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| | - Sylvia Davila
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| | - Kyung-Won Min
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, College of Medicine; Medical University of South Carolina; Charleston SC USA
| |
Collapse
|
22
|
Ismael H, Altmeyer S, Stahl H. Regulation of the U3-, U8-, and U13snoRNA Expression by the DEAD Box Proteins Ddx5/Ddx17 with Consequences for Cell Proliferation and Survival. Noncoding RNA 2016; 2:ncrna2040011. [PMID: 29657268 PMCID: PMC5831926 DOI: 10.3390/ncrna2040011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/22/2016] [Accepted: 08/09/2016] [Indexed: 12/17/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) in cooperation with their associated proteins (snoRNPs) contribute to the maturation of ribosomal RNA, transfer RNA, and other transcripts. Most snoRNPs mediate chemical base modifications of their RNA substrates, and a few others, like those formed by the C/D snoRNAs U3, U8, and U13, are needed for the structural organization and maturation of primary transcripts. The U3-, U8-, and U13snoRNAs are encoded by autonomous genes, and our knowledge about their expression regulation is limited. In this study, a significant increase in the concentrations of U3-, U8-, and U13snoRNA after a knockdown of DEAD box proteins Ddx5/Ddx17 in HeLa cells is observed. These alterations are shown to be caused by transcriptional suppression mediated by Ddx5/Ddx17 via histone deacetylase 1 in a promoter-dependent way. The biological function of this expression control may be related to the role of Ddx5/Ddx17 in cell proliferation. The U3snoRNA is shown here to be essential for the proliferation and viability of human cells. Moreover, it was found that U3snoRNA interacts with Argonaute 2 in the RNA-induced silencing complexes (RISC), pointing to a microRNA-like function. For this reason, the 3′ untranslated region of the A-kinase anchor protein 9 (AKAP9)-mRNA could be identified as a potential target.
Collapse
Affiliation(s)
- Hala Ismael
- Department of Medical Biochemistry and Molecular Biology, University of Saarland, Medical Center, Building 45, 66421 Homburg, Germany.
| | - Simone Altmeyer
- Department of Medical Biochemistry and Molecular Biology, University of Saarland, Medical Center, Building 45, 66421 Homburg, Germany.
| | - Hans Stahl
- Department of Medical Biochemistry and Molecular Biology, University of Saarland, Medical Center, Building 45, 66421 Homburg, Germany.
| |
Collapse
|
23
|
Mukherjee K, Ghoshal B, Ghosh S, Chakrabarty Y, Shwetha S, Das S, Bhattacharyya SN. Reversible HuR-microRNA binding controls extracellular export of miR-122 and augments stress response. EMBO Rep 2016; 17:1184-203. [PMID: 27402548 PMCID: PMC4967961 DOI: 10.15252/embr.201541930] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/09/2016] [Indexed: 01/10/2023] Open
Abstract
microRNAs (miRNAs), the tiny but stable regulatory RNAs in metazoan cells, can undergo selective turnover in presence of specific internal and external cues to control cellular response against the changing environment. We have observed reduction in cellular miR-122 content, due to their accelerated extracellular export in human hepatic cells starved for small metabolites including amino acids. In this context, a new role of human ELAV protein HuR has been identified. HuR, a negative regulator of miRNA function, accelerates extracellular vesicle (EV)-mediated export of miRNAs in human cells. In stressed cells, HuR replaces miRNPs from target messages and is both necessary and sufficient for the extracellular export of corresponding miRNAs. HuR could reversibly bind miRNAs to replace them from Ago2 and subsequently itself gets freed from bound miRNAs upon ubiquitination. The ubiquitinated form of HuR is predominantly associated with multivesicular bodies (MVB) where HuR-unbound miRNAs also reside. These MVB-associated pool of miRNAs get exported out via EVs thereby delimiting cellular miR-122 level during starvation. Therefore, by modulating extracellular export of miR-122, HuR could control stress response in starved human hepatic cells.
Collapse
Affiliation(s)
- Kamalika Mukherjee
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Bartika Ghoshal
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Souvik Ghosh
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Yogaditya Chakrabarty
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shivaprasad Shwetha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Suvendra N Bhattacharyya
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| |
Collapse
|
24
|
Azlan A, Dzaki N, Azzam G. Argonaute: The executor of small RNA function. J Genet Genomics 2016; 43:481-94. [PMID: 27569398 DOI: 10.1016/j.jgg.2016.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/08/2016] [Accepted: 06/17/2016] [Indexed: 01/06/2023]
Abstract
The discovery of small non-coding RNAs - microRNA (miRNA), short interfering RNA (siRNA) and PIWI-interacting RNA (piRNA) - represents one of the most exciting frontiers in biology specifically on the mechanism of gene regulation. In order to execute their functions, these small RNAs require physical interactions with their protein partners, the Argonaute (AGO) family proteins. Over the years, numerous studies have made tremendous progress on understanding the roles of AGO in gene silencing in various organisms. In this review, we summarize recent progress of AGO-mediated gene silencing and other cellular processes in which AGO proteins have been implicated with a particular focus on progress made in flies, humans and other model organisms as compliment.
Collapse
Affiliation(s)
- Azali Azlan
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Najat Dzaki
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia; Advance Medical and Dental Institute, Universiti Sains Malaysia, Penang 11800, Malaysia.
| |
Collapse
|
25
|
Atwood BL, Woolnough JL, Lefevre GM, Saint Just Ribeiro M, Felsenfeld G, Giles KE. Human Argonaute 2 Is Tethered to Ribosomal RNA through MicroRNA Interactions. J Biol Chem 2016; 291:17919-28. [PMID: 27288410 DOI: 10.1074/jbc.m116.725051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 11/06/2022] Open
Abstract
The primary role of the RNAi machinery is to promote mRNA degradation within the cytoplasm in a microRNA-dependent manner. However, both Dicer and the Argonaute protein family have expanded roles in gene regulation within the nucleus. To further our understanding of this role, we have identified chromatin binding sites for AGO2 throughout the 45S region of the human rRNA gene. The location of these sites was mirrored by the positions of AGO2 cross-linking sites identified via PAR-CLIP-seq. AGO2 binding to the rRNA within the nucleus was confirmed by RNA immunoprecipitation and quantitative-PCR. To explore a possible mechanism by which AGO2 could be recruited to the rRNA, we identified 1174 regions within the 45S rRNA transcript that have the ability to form a perfect duplex with position 2-6 (seed sequence) of each microRNA expressed in HEK293T cells. Of these potential AGO2 binding sites, 479 occurred within experimentally verified AGO2-rRNA cross-linking sites. The ability of AGO2 to cross-link to rRNA was almost completely lost in a DICER knock-out cell line. The transfection of miR-92a-2-3p into the noDICE cell line facilitated AGO2 cross-linking at a region of the rRNA that has a perfect seed match at positions 3-8, including a single G-U base pair. Knockdown of AGO2 within HEK293T cells causes a slight, but statistically significant increase in the overall rRNA synthesis rate but did not impact the ratio of processing intermediates or the recruitment of the Pol I transcription factor UBTF.
Collapse
Affiliation(s)
- Blake L Atwood
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Jessica L Woolnough
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Gaelle M Lefevre
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Mariana Saint Just Ribeiro
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Keith E Giles
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| |
Collapse
|
26
|
Re-evaluation of the roles of DROSHA, Export in 5, and DICER in microRNA biogenesis. Proc Natl Acad Sci U S A 2016; 113:E1881-9. [PMID: 26976605 DOI: 10.1073/pnas.1602532113] [Citation(s) in RCA: 309] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Export in 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of each of these maturation steps, we deleted DROSHA, XPO5, and DICER in the same human cell line, and analyzed their effects on miRNA biogenesis. Canonical miRNA production was completely abolished in DROSHA-deleted cells, whereas we detected a few DROSHA-independent miRNAs including three previously unidentified noncanonical miRNAs (miR-7706, miR-3615, and miR-1254). In contrast to DROSHA knockout, many canonical miRNAs were still detected without DICER albeit at markedly reduced levels. In the absence of DICER, pre-miRNAs are loaded directly onto AGO and trimmed at the 3' end, yielding miRNAs from the 5' strand (5p miRNAs). Interestingly, in XPO5 knockout cells, most miRNAs are affected only modestly, suggesting that XPO5 is necessary but not critical for miRNA maturation. Our study demonstrates an essential role of DROSHA and an important contribution of DICER in the canonical miRNA pathway, and reveals that the function of XPO5 can be complemented by alternative mechanisms. Thus, this study allows us to understand differential contributions of key biogenesis factors, and provides with valuable resources for miRNA research.
Collapse
|
27
|
Zhang X, Devany E, Murphy MR, Glazman G, Persaud M, Kleiman FE. PARN deadenylase is involved in miRNA-dependent degradation of TP53 mRNA in mammalian cells. Nucleic Acids Res 2015; 43:10925-38. [PMID: 26400160 PMCID: PMC4678859 DOI: 10.1093/nar/gkv959] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 09/13/2015] [Indexed: 01/10/2023] Open
Abstract
mRNA deadenylation is under the control of cis-acting regulatory elements, which include AU-rich elements (AREs) and microRNA (miRNA) targeting sites, within the 3' untranslated region (3' UTRs) of eukaryotic mRNAs. Deadenylases promote miRNA-induced mRNA decay through their interaction with miRNA-induced silencing complex (miRISC). However, the role of poly(A) specific ribonuclease (PARN) deadenylase in miRNA-dependent mRNA degradation has not been elucidated. Here, we present evidence that not only ARE- but also miRNA-mediated pathways are involved in PARN-mediated regulation of the steady state levels of TP53 mRNA, which encodes the tumor suppressor p53. Supporting this, Argonaute-2 (Ago-2), the core component of miRISC, can coexist in complexes with PARN resulting in the activation of its deadenylase activity. PARN regulates TP53 mRNA stability through not only an ARE but also an adjacent miR-504/miR-125b-targeting site in the 3' UTR. More importantly, we found that miR-125b-loaded miRISC contributes to the specific recruitment of PARN to TP53 mRNA, and that can be reverted by the ARE-binding protein HuR. Together, our studies provide new insights into the role of PARN in miRNA-dependent control of mRNA decay and into the mechanisms behind the regulation of p53 expression.
Collapse
Affiliation(s)
- Xiaokan Zhang
- Chemistry Department, Belfer Research Building, Hunter College and Graduate Center, City University of New York, New York, NY 10021, USA
| | - Emral Devany
- Chemistry Department, Belfer Research Building, Hunter College and Graduate Center, City University of New York, New York, NY 10021, USA Department of Biological Sciences, Kingsborough Community College, City University of New York, 2001 Oriental Boulevard, Brooklyn, NY 11235, USA
| | - Michael R Murphy
- Chemistry Department, Belfer Research Building, Hunter College and Graduate Center, City University of New York, New York, NY 10021, USA
| | - Galina Glazman
- Chemistry Department, Belfer Research Building, Hunter College and Graduate Center, City University of New York, New York, NY 10021, USA
| | - Mirjana Persaud
- Chemistry Department, Belfer Research Building, Hunter College and Graduate Center, City University of New York, New York, NY 10021, USA
| | - Frida E Kleiman
- Chemistry Department, Belfer Research Building, Hunter College and Graduate Center, City University of New York, New York, NY 10021, USA
| |
Collapse
|
28
|
Moore MJ, Scheel TKH, Luna JM, Park CY, Fak JJ, Nishiuchi E, Rice CM, Darnell RB. miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity. Nat Commun 2015; 6:8864. [PMID: 26602609 PMCID: PMC4674787 DOI: 10.1038/ncomms9864] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 10/12/2015] [Indexed: 12/19/2022] Open
Abstract
microRNAs (miRNAs) act as sequence-specific guides for Argonaute (AGO) proteins, which mediate posttranscriptional silencing of target messenger RNAs. Despite their importance in many biological processes, rules governing AGO–miRNA targeting are only partially understood. Here we report a modified AGO HITS-CLIP strategy termed CLEAR (covalent ligation of endogenous Argonaute-bound RNAs)-CLIP, which enriches miRNAs ligated to their endogenous mRNA targets. CLEAR-CLIP mapped ∼130,000 endogenous miRNA–target interactions in mouse brain and ∼40,000 in human hepatoma cells. Motif and structural analysis define expanded pairing rules for over 200 mammalian miRNAs. Most interactions combine seed-based pairing with distinct, miRNA-specific patterns of auxiliary pairing. At some regulatory sites, this specificity confers distinct silencing functions to miRNA family members with shared seed sequences but divergent 3′-ends. This work provides a means for explicit biochemical identification of miRNA sites in vivo, leading to the discovery that miRNA 3′-end pairing is a general determinant of AGO binding specificity. microRNAs (miRNAs) act as sequence-specific guides for Argonaute (AGO) proteins. By using a modified AGO HITS-CLIP strategy that enriches miRNAs ligated to their endogenous mRNA targets, here the authors show that miRNA 3' end pairing is a general determinant of AGO binding specificity.
Collapse
Affiliation(s)
- Michael J Moore
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, Box 226, New York, New York 10065, USA
| | - Troels K H Scheel
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, New York 10065, USA.,Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, 2650 Hvidovre, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Joseph M Luna
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, Box 226, New York, New York 10065, USA.,Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, New York 10065, USA
| | - Christopher Y Park
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, Box 226, New York, New York 10065, USA.,New York Genome Center, 101 Avenue of the Americas, New York, New York 10013, USA
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, Box 226, New York, New York 10065, USA
| | - Eiko Nishiuchi
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, New York 10065, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, New York 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, Box 226, New York, New York 10065, USA.,New York Genome Center, 101 Avenue of the Americas, New York, New York 10013, USA
| |
Collapse
|
29
|
Yoon JH, Jo MH, White EJF, De S, Hafner M, Zucconi BE, Abdelmohsen K, Martindale JL, Yang X, Wood WH, Shin YM, Song JJ, Tuschl T, Becker KG, Wilson GM, Hohng S, Gorospe M. AUF1 promotes let-7b loading on Argonaute 2. Genes Dev 2015; 29:1599-604. [PMID: 26253535 PMCID: PMC4536308 DOI: 10.1101/gad.263749.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Yoon et al. discovered that RBP AU-rich-binding factor 1 (AUF1) promotes let-7b loading onto Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex (RISC). In turn, AGO2–let-7 triggered target mRNA decay. Eukaryotic gene expression is tightly regulated post-transcriptionally by RNA-binding proteins (RBPs) and microRNAs. The RBP AU-rich-binding factor 1 (AUF1) isoform p37 was found to have high affinity for the microRNA let-7b in vitro (Kd = ∼6 nM) in cells. Ribonucleoprotein immunoprecipitation, in vitro association, and single-molecule-binding analyses revealed that AUF1 promoted let-7b loading onto Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex (RISC). In turn, AGO2–let-7 triggered target mRNA decay. Our findings uncover a novel mechanism by which AUF1 binding and transfer of microRNA let-7 to AGO2 facilitates let-7-elicited gene silencing.
Collapse
Affiliation(s)
- Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Myung Hyun Jo
- Department of Physics and Astronomy, Institute of Applied Physics, National Center for Creative Research Initiatives, Seoul National University, Seoul 151-747, Korea
| | - Elizabeth J F White
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases-Intramural Research Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Beth E Zucconi
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Xiaoling Yang
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - William H Wood
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Yu Mi Shin
- Cancer Metastasis Control Center, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-338, Korea
| | - Ji-Joon Song
- Cancer Metastasis Control Center, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-338, Korea
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York 10065, USA
| | - Kevin G Becker
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Sungchul Hohng
- Department of Physics and Astronomy, Institute of Applied Physics, National Center for Creative Research Initiatives, Seoul National University, Seoul 151-747, Korea
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| |
Collapse
|
30
|
Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis. Mol Cell Biol 2015; 35:2278-94. [PMID: 25918241 DOI: 10.1128/mcb.00076-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To further our understanding of the RNAi machinery within the human nucleus, we analyzed the chromatin and RNA binding of Argonaute 2 (AGO2) within human cancer cell lines. Our data indicated that AGO2 binds directly to nascent tRNA and 5S rRNA, and to the genomic loci from which these RNAs are transcribed, in a small RNA- and DICER-independent manner. AGO2 chromatin binding was not observed at non-TFIIIC-dependent RNA polymerase III (Pol III) genes or at extra-TFIIIC (ETC) sites, indicating that the interaction is specific for TFIIIC-dependent Pol III genes. A genome-wide analysis indicated that loss of AGO2 caused a global increase in mRNA expression level among genes that flank AGO2-bound tRNA genes. This effect was shown to be distinct from that of the disruption of DICER, DROSHA, or CTCF. We propose that AGO2 binding to tRNA genes has a novel and important regulatory role in human cells.
Collapse
|
31
|
Modzelewski AJ, Hilz S, Crate EA, Schweidenback CTH, Fogarty EA, Grenier JK, Freire R, Cohen PE, Grimson A. Dgcr8 and Dicer are essential for sex chromosome integrity during meiosis in males. J Cell Sci 2015; 128:2314-27. [PMID: 25934699 PMCID: PMC4487015 DOI: 10.1242/jcs.167148] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/21/2015] [Indexed: 12/22/2022] Open
Abstract
Small RNAs play crucial roles in regulating gene expression during mammalian meiosis. To investigate the function of microRNAs (miRNAs) and small interfering RNAs (siRNAs) during meiosis in males, we generated germ-cell-specific conditional deletions of Dgcr8 and Dicer in mice. Analysis of spermatocytes from both conditional knockout lines revealed that there were frequent chromosomal fusions during meiosis, always involving one or both sex chromosomes. RNA sequencing indicates upregulation of Atm in spermatocytes from miRNA-deficient mice, and immunofluorescence imaging demonstrates an increased abundance of activated ATM kinase and mislocalization of phosphorylated MDC1, an ATM phosphorylation substrate. The Atm 3′UTR contains many potential microRNA target sites, and, notably, target sites for several miRNAs depleted in both conditional knockout mice were highly effective at promoting repression. RNF8, a telomere-associated protein whose localization is controlled by the MDC1–ATM kinase cascade, normally associates with the sex chromosomes during pachytene, but in both conditional knockouts redistributed to the autosomes. Taken together, these results suggest that Atm dysregulation in microRNA-deficient germ lines contributes to the redistribution of proteins involved in chromosomal stability from the sex chromosomes to the autosomes, resulting in sex chromosome fusions during meiotic prophase I. Highlighted Article: miRNA-deficient spermatocytes display frequent sex chromosome fusions and fail to progress through meiosis in a process that is probably mediated by dysregulation of Atm.
Collapse
Affiliation(s)
| | - Stephanie Hilz
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth A Crate
- Departments of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Jennifer K Grenier
- Departments of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Raimundo Freire
- Unidad de Investigacion, Hospital Universitario de Canarias, Ofra s/n, La Cuesta, La Laguna, Tenerife 38320, Spain
| | - Paula E Cohen
- Departments of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Grimson
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
32
|
Smalheiser NR, Gomes OLA. Mammalian Argonaute-DNA binding? Biol Direct 2014; 10:27. [PMID: 25472905 PMCID: PMC4258305 DOI: 10.1186/s13062-014-0027-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/19/2014] [Indexed: 12/21/2022] Open
Abstract
When a field shares the consensus that a particular phenomenon does NOT occur, this may reflect extensive experimental investigations with negative outcomes, or may represent the “common sense” position based on current knowledge and established ways of thinking. The current consensus of the RNA field is that eukaryotic Argonaute (Ago) proteins employ RNA guides and target other RNAs. The alternative -- that eukaryotic Ago has biologically important interactions with DNA in vivo – has not been seriously considered, in part because the only role contemplated for DNA was as a guide strand, and in part because it did not seem plausible that any natural source of suitable DNAs exists in eukaryotic cells. However, eukaryotic Argonaute domains bind DNA in the test tube, and several articles report that small inhibitory double-stranded DNAs do have the ability to silence target RNAs in a sequence-dependent (though poorly characterized) manner. A search of the literature identified potential DNA binding partners for Ago, including (among others) single-stranded DNAs residing in extracellular vesicles, and cytoplasmic satellite-repeat DNA fragments that are associated with the plasma membrane and transcribed by Pol II. It is interesting to note that both cytoplasmic and extracellular vesicle DNA are expressed at greatly elevated levels in cancer cells relative to normal cells. In such a pathological scenario, if not under normal conditions, there may be appreciable binding of Ago to DNA despite its lower affinity compared to RNA. If so, DNA might displace Ago from binding to its normal partners (miRNAs, siRNAs and other short ncRNAs), disrupting tightly controlled post-transcriptional gene silencing processes that are vital to correct functioning of a normal cell. The possible contribution to cancer pathogenesis is a strong motivator for further investigation of Ago-DNA binding. More generally, this case underscores the need for better informatics tools to allow investigators to analyze the state of a given scientific question at a high-level and to identify possible new research directions. Reviewers: This article was reviewed by Eugene Koonin, Kira S. Makarova, Alexander Maxwell Burroughs (nominated by L Aravind), and Isidore Rigoutsos. Open peer review: Reviewed by Eugene Koonin, Kira S. Makarova, Alexander Maxwell Burroughs (nominated by L Aravind), and Isidore Rigoutsos. For the full reviews, please go to the Reviewers’ comments section.
Collapse
|
33
|
Zhang Y, Fan M, Zhang X, Huang F, Wu K, Zhang J, Liu J, Huang Z, Luo H, Tao L, Zhang H. Cellular microRNAs up-regulate transcription via interaction with promoter TATA-box motifs. RNA (NEW YORK, N.Y.) 2014; 20:1878-89. [PMID: 25336585 PMCID: PMC4238354 DOI: 10.1261/rna.045633.114] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The TATA box represents one of the most prevalent core promoters where the pre-initiation complexes (PICs) for gene transcription are assembled. This assembly is crucial for transcription initiation and well regulated. Here we show that some cellular microRNAs (miRNAs) are associated with RNA polymerase II (Pol II) and TATA box-binding protein (TBP) in human peripheral blood mononuclear cells (PBMCs). Among them, let-7i sequence specifically binds to the TATA-box motif of interleukin-2 (IL-2) gene and elevates IL-2 mRNA and protein production in CD4(+) T-lymphocytes in vitro and in vivo. Through direct interaction with the TATA-box motif, let-7i facilitates the PIC assembly and transcription initiation of IL-2 promoter. Several other cellular miRNAs, such as mir-138, mir-92a or mir-181d, also enhance the promoter activities via binding to the TATA-box motifs of insulin, calcitonin or c-myc, respectively. In agreement with the finding that an HIV-1-encoded miRNA could enhance viral replication through targeting the viral promoter TATA-box motif, our data demonstrate that the interaction with core transcription machinery is a novel mechanism for miRNAs to regulate gene expression.
Collapse
Affiliation(s)
- Yijun Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Miaomiao Fan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Xue Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Feng Huang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Kang Wu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Junsong Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Zhuoqiong Huang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Haihua Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Liang Tao
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| |
Collapse
|
34
|
Batsché E, Ameyar-Zazoua M. The influence of Argonaute proteins on alternative RNA splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:141-56. [DOI: 10.1002/wrna.1264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Eric Batsché
- Institut Pasteur, Dpt Biologie du Développement et Cellules Souches; Unité de Régulation Epigénétique; 75015 Paris France
- URA2578; CNRS
| | - Maya Ameyar-Zazoua
- Institut Pasteur, Dpt Biologie du Développement et Cellules Souches; Unité de Régulation Epigénétique; 75015 Paris France
- URA2578; CNRS
- Laboratoire Epigénétique et Destin Cellulaire, CNRS UMR7216; Université Paris Diderot, Cité Sorbonne Paris; Paris France
| |
Collapse
|
35
|
Abstract
Microribonucleic acids, best known as microRNAs or miRNAs, are small, non-coding RNAs with important regulatory roles in eukaryotic cells. Here, I present a broad review on highly relevant but generally non-depicted features of miRNAs, among which stand out the non-conventional miRNA seed sites, the unusual messenger RNA (mRNA) target regions, the non-canonical miRNA-guided mechanisms of gene expression regulation, and the recently identified new class of miRNA ligands. Furthermore, I address the miRNA uncommon genomic location, transcription, and subcellular localization. Altogether, these unusual features and roles place the miRNA system as a very diverse, complex, and intriguing biological mechanism.
Collapse
Affiliation(s)
- Gabriel A Cipolla
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná Curitiba, Brazil
| |
Collapse
|
36
|
Liu X, Zheng Q, Vrettos N, Maragkakis M, Alexiou P, Gregory BD, Mourelatos Z. A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis. Mol Cell 2014; 55:868-879. [PMID: 25175028 DOI: 10.1016/j.molcel.2014.07.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 06/17/2014] [Accepted: 07/24/2014] [Indexed: 11/18/2022]
Abstract
MicroRNAs (miRNAs) are essential for regulation of gene expression. Though numerous miRNAs have been identified by high-throughput sequencing, few precursor miRNAs (pre-miRNAs) are experimentally validated. Here we report a strategy for constructing high-throughput sequencing libraries enriched for full-length pre-miRNAs. We find widespread and extensive uridylation of Argonaute (Ago)-bound pre-miRNAs, which is primarily catalyzed by two terminal uridylyltransferases: TUT7 and TUT4. Uridylation by TUT7/4 not only polishes pre-miRNA 3' ends, but also facilitates their degradation by the exosome, preventing clogging of Ago with defective species. We show that the exosome exploits distinct substrate preferences of DIS3 and RRP6, its two catalytic subunits, to distinguish productive from defective pre-miRNAs. Furthermore, we identify a positive feedback loop formed by the exosome and TUT7/4 in triggering uridylation and degradation of Ago-bound pre-miRNAs. Our study reveals a pre-miRNA surveillance system that comprises TUT7, TUT4, and the exosome in quality control of miRNA synthesis.
Collapse
Affiliation(s)
- Xuhang Liu
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qi Zheng
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas Vrettos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian D Gregory
- PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
37
|
Guo YE, Steitz JA. 3'-Biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells. RNA (NEW YORK, N.Y.) 2014; 20:985-988. [PMID: 24821854 PMCID: PMC4114695 DOI: 10.1261/rna.045054.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 04/02/2014] [Indexed: 06/03/2023]
Abstract
Synthetic 3'-biotin-tagged microRNAs (miRNAs) have often been used to select interacting messenger RNA (mRNA) and noncoding RNA (ncRNA) targets. Here, we examined the extent of association of 3'-end biotinylated miR-27 with Argonaute (Ago) proteins in transfected human cells using a coimmunoprecipitation assay followed by Northern blot analysis. We report that biotinylated miR-27 does not efficiently associate with Ago compared to unmodified miR-27. These results suggest that 3'-end biotin-modified miRNAs are questionable monitors of miRNA function in cells.
Collapse
Affiliation(s)
- Yang Eric Guo
- Department of Cell Biology
- Department of Molecular Biophysics and Biochemistry
| | - 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
| |
Collapse
|
38
|
Chak LL, Okamura K. Argonaute-dependent small RNAs derived from single-stranded, non-structured precursors. Front Genet 2014; 5:172. [PMID: 24959173 PMCID: PMC4050365 DOI: 10.3389/fgene.2014.00172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/22/2014] [Indexed: 12/31/2022] Open
Abstract
A general feature of Argonaute-dependent small RNAs is their base-paired precursor structures, and precursor duplex structures are often required for confident annotation of miRNA genes. However, this rule has been broken by discoveries of functional small RNA species whose precursors lack a predictable double-stranded (ds-) RNA structure, arguing that duplex structures are not prerequisite for small RNA loading to Argonautes. The biological significance of single-stranded (ss-) RNA loading has been recognized particularly in systems where active small RNA amplification mechanisms are involved, because even a small amount of RNA molecules can trigger the production of abundant RNA species leading to profound biological effects. However, even in the absence of small RNA amplification mechanisms, recent studies have demonstrated that potent gene silencing can be achieved using chemically modified synthetic ssRNAs that are resistant to RNases in mice. Therefore, such ssRNA-mediated gene regulation may have broader roles than previously recognized, and the findings have opened the door for further research to optimize the design of ss-siRNAs toward future pharmaceutical and biomedical applications of gene silencing technologies. In this review, we will summarize studies about endogenous ssRNA species that are bound by Argonaute proteins and how ssRNA precursors are recognized by various small RNA pathways.
Collapse
Affiliation(s)
- Li-Ling Chak
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore Singapore, Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore Singapore, Singapore ; School of Biological Sciences, Nanyang Technological University Singapore, Singapore
| |
Collapse
|
39
|
Peng Y, Yu S, Li H, Xiang H, Peng J, Jiang S. MicroRNAs: emerging roles in adipogenesis and obesity. Cell Signal 2014; 26:1888-96. [PMID: 24844591 DOI: 10.1016/j.cellsig.2014.05.006] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/06/2014] [Accepted: 05/09/2014] [Indexed: 12/31/2022]
Abstract
Obesity is a serious health problem worldwide associated with an increased risk of life-threatening diseases such as type 2 diabetes, atherosclerosis, and certain types of cancer. Understanding the molecular basis of adipogenesis and fat cell development in obesity is essential to identify new biomarkers and therapeutic targets for the development of anti-obesity drugs. Recent computational and experimental studies have shown that microRNAs (miRNAs) appear to play regulatory roles in many biological processes associated with obesity, including adipocyte differentiation and lipid metabolism. In addition, many miRNAs are dysregulated in metabolic tissues from obese animals and humans, which potentially contributes to the pathogenesis of obesity-associated complications. The discovery of circulating miRNAs has highlighted their potential as both endocrine signaling molecules and disease markers. The potential of miRNA based therapeutics targeting obesity is highlighted as well as recommendations for future research which could lead to a breakthrough in the treatment of obesity.
Collapse
Affiliation(s)
- Yongdong Peng
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shulong Yu
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Huanan Li
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Hong Xiang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jian Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Siwen Jiang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
| |
Collapse
|
40
|
Chu YD, Wang WC, Chen SAA, Hsu YT, Yeh MW, Slack FJ, Chan SP. RACK-1 regulates let-7 microRNA expression and terminal cell differentiation in Caenorhabditis elegans. Cell Cycle 2014; 13:1995-2009. [PMID: 24776851 PMCID: PMC4111763 DOI: 10.4161/cc.29017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The let-7 microRNA (miRNA) regulates cell cycle exit and terminal differentiation in the C. elegans heterochronic gene pathway. Low expression of let-7 results in retarded vulva and hypodermal cell development in C. elegans and has been associated with several human cancers. Previously, the versatile scaffold protein receptor for activated C kinase 1 (RACK1) was proposed to facilitate recruitment of the miRNA-induced silencing complex (miRISC) to the polysome and to be required for miRNA function in C. elegans and humans. Here, we show that depletion of C. elegans RACK-1 by RNAi increases let-7 miRNA levels and suppresses the retarded terminal differentiation of lateral hypodermal seam cells in mutants carrying the hypomorphic let-7(n2853) allele or lacking the let-7 family miRNA genes mir-48 and mir-241. Depletion of RACK-1 also increases the levels of precursor let-7 miRNA. When Dicer is knocked down and pre-miRNA processing is inhibited, depletion of RACK-1 still leads to increased levels of pre-let-7, suggesting that RACK-1 affects a biogenesis mechanism upstream of Dicer. No changes in the activity of the let-7 promoter or the levels of primary let-7 miRNA are associated with depletion of RACK-1, suggesting that RACK-1 affects let-7 miRNA biogenesis at the post-transcriptional level. Interestingly, rack-1 knockdown also increases the levels of a few other precursor miRNAs. Our results reveal that RACK-1 controls the biogenesis of a subset of miRNAs, including let-7, and in this way plays a role in the heterochronic gene pathway during C. elegans development.
Collapse
Affiliation(s)
- Yu-De Chu
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan
| | - Wei-Chieh Wang
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan
| | - Shi-An A Chen
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan; Genome and Systems Biology Degree Program; College of Life Science; National Taiwan University; Taipei, Taiwan
| | - Yen-Ting Hsu
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan
| | - Meng-Wei Yeh
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan
| | - Frank J Slack
- Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven, CT USA
| | - Shih-Peng Chan
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan; Genome and Systems Biology Degree Program; College of Life Science; National Taiwan University; Taipei, Taiwan; Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven, CT USA
| |
Collapse
|
41
|
Berkhout B, Liu YP. Towards improved shRNA and miRNA reagents as inhibitors of HIV1 replication. Future Microbiol 2014; 9:561-71. [DOI: 10.2217/fmb.14.5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT: miRNAs are the key players of the RNAi mechanism, which regulates the expression of a large number of mRNAs in human cells. shRNAs are man-made synthetic miRNA mimics that exploit similar intracellular RNA processing routes. Massive amounts of data derived from next-generation sequencing have revealed miRNA species that are derived from alternative biosynthesis pathways. Here, we review recent progress in our understanding of these noncanonical routes of miRNA and shRNA biosynthesis. We focus on ways to use these novel insights for the design of more potent and specific RNAi reagents for therapeutic applications, including the AgoshRNA design, which is processed differently than regular shRNAs. We will also discuss the development of a durable gene therapy against HIV1.
Collapse
Affiliation(s)
- Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection & Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection & Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
- Current address: uniQure biopharma BV, Department of Research & Development, The Netherlands
| |
Collapse
|
42
|
Cox EM, Sagan SM, Mortimer SA, Doudna JA, Sarnow P. Enhancement of hepatitis C viral RNA abundance by precursor miR-122 molecules. RNA (NEW YORK, N.Y.) 2013; 19:1825-1832. [PMID: 24106328 PMCID: PMC3884667 DOI: 10.1261/rna.040865.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 09/11/2013] [Indexed: 06/02/2023]
Abstract
The hepatitis C viral RNA genome forms a complex with liver-specific microRNA (miR-122) at the extreme 5' end of the viral RNA. This complex is essential to stabilize the viral RNA in infected cultured cells and in the liver of humans. The abundances of primary and precursor forms of miR-122, but not the abundance of mature miR-122, are regulated in a circadian rhythm in the liver of animals, suggesting a possible independent function of precursor molecules of miR-122 in regulating viral gene expression. Modified precursor molecules of miR-122 were synthesized that were refractory to cleavage by Dicer. These molecules were found to enhance the abundance of HCV RNA. Furthermore, they diminished the expression of mRNAs that contained binding sites for miR-122 in their 3' noncoding regions. By use of duplex and precursor miR-122 mimetic molecules that carried mutations in the passenger strand of miR-122, the effects on viral and reporter gene expression could be pinpointed to the action of precursor miR-122 molecules. Targeting the circadian expression of precursor miR-122 by specific compounds likely provides novel therapeutic strategies.
Collapse
Affiliation(s)
- Erica Machlin Cox
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Selena M. Sagan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Stefanie A.W. Mortimer
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
43
|
Khudayberdiev SA, Zampa F, Rajman M, Schratt G. A comprehensive characterization of the nuclear microRNA repertoire of post-mitotic neurons. Front Mol Neurosci 2013; 6:43. [PMID: 24324399 PMCID: PMC3840315 DOI: 10.3389/fnmol.2013.00043] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/07/2013] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with important functions in the development and plasticity of post-mitotic neurons. In addition to the well-described cytoplasmic function of miRNAs in post-transcriptional gene regulation, recent studies suggested that miRNAs could also be involved in transcriptional and post-transcriptional regulatory processes in the nuclei of proliferating cells. However, whether miRNAs localize to and function within the nucleus of post-mitotic neurons is unknown. Using a combination of microarray hybridization and small RNA deep sequencing, we identified a specific subset of miRNAs which are enriched in the nuclei of neurons. Nuclear enrichment of specific candidate miRNAs (miR-25 and miR-92a) could be independently validated by Northern blot, quantitative real-time PCR (qRT-PCR) and fluorescence in situ hybridization (FISH). By cross-comparison to published reports, we found that nuclear accumulation of miRNAs might be linked to a down-regulation of miRNA expression during in vitro development of cortical neurons. Importantly, by generating a comprehensive isomiR profile of the nuclear and cytoplasmic compartments, we found a significant overrepresentation of guanine nucleotides (nt) at the 3′-terminus of nuclear-enriched isomiRs, suggesting the presence of neuron-specific mechanisms involved in miRNA nuclear localization. In conclusion, our results provide a starting point for future studies addressing the nuclear function of specific miRNAs and the detailed mechanisms underlying subcellular localization of miRNAs in neurons and possibly other polarized cell types.
Collapse
Affiliation(s)
- Sharof A Khudayberdiev
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg Marburg, Germany
| | | | | | | |
Collapse
|
44
|
MacKay CR, Wang JP, Kurt-Jones EA. Dicer's role as an antiviral: still an enigma. Curr Opin Immunol 2013; 26:49-55. [PMID: 24556400 DOI: 10.1016/j.coi.2013.10.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/21/2013] [Accepted: 10/28/2013] [Indexed: 12/31/2022]
Abstract
Dicer is a multifunctional protein that is essential across species for the generation of microRNAs, a function that is highly conserved across the plant and animal kingdoms. Intriguingly, Dicer exhibits antiviral functions in lower organisms including Drosophila melanogaster and Caenorhabditis elegans. Antiviral activity occurs via small interfering RNA production following cytoplasmic sensing of viral dsRNA. Notably, such antiviral activity has not yet been clearly demonstrated in higher organisms such as mammals. Here, we review the evidence for Dicer as an innate antiviral across species.
Collapse
Affiliation(s)
- Christopher R MacKay
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jennifer P Wang
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Evelyn A Kurt-Jones
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
| |
Collapse
|
45
|
Profiling circulating microRNA expression in experimental sepsis using cecal ligation and puncture. PLoS One 2013; 8:e77936. [PMID: 24205035 PMCID: PMC3813489 DOI: 10.1371/journal.pone.0077936] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 09/05/2013] [Indexed: 12/23/2022] Open
Abstract
The levels of circulating microRNAs (miRNAs) in mice with experimental sepsis induced by cecal ligation and puncture (CLP) were determined using whole blood samples obtained from C57BL/6 mice at 4, 8, and 24 h after CLP; miRNA expression analysis was performed in these samples using an miRNA array. Microarray analysis revealed upregulation of 10 miRNA targets (miR-16, miR-17, miR-20a, miR-20b, miR-26a, miR-26b, miR-106a, miR-106b, miR-195, and miR-451). The expression of these miRNA targets in the whole blood, serum, and white blood cells (WBCs) of CLP mice was quantified using quantitative real-time PCR; these values were compared to those in sham-operated C57BL/6 mice, and the results indicated that these miRNA targets were significantly up-regulated in the whole blood and serum but not in the WBCs. In addition, the levels of these 10 miRNA targets in the serum of Tlr2-/-, Tlr4-/-, and NF-κB-/- mice at 8 h after CLP did not decrease significantly., which indicated that the transcription of these miRNAs was not directly mediated by the TLR2/NF-κB or TLR4/NF-κB pathway, and pathways induced by exposure to the gram-positive or gram-negative bacteria. Immunoprecipitation with the Argonaute 2 ribonucleoprotein complex revealed significantly increased expression of the 10 miRNA targets in the serum of mice after CLP, and the levels of 6 (miR-16, miR-17, miR-20a, miR-20b, miR-26a, and miR-26b) of these 10 miRNA targets increased significantly in exosomes isolated using ExoQuick precipitation solution. In this study, we identified circulating miRNAs that were up-regulated after CLP and determined the increase in the levels of these miRNAs, and our results suggest that circulating Ago2 complexes and exosomes may be responsible for the stability of miRNAs in the serum.
Collapse
|
46
|
Lu J, Miao J, Su T, Liu Y, He R. Formaldehyde induces hyperphosphorylation and polymerization of Tau protein both in vitro and in vivo. Biochim Biophys Acta Gen Subj 2013; 1830:4102-16. [DOI: 10.1016/j.bbagen.2013.04.028] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/07/2013] [Accepted: 04/18/2013] [Indexed: 12/29/2022]
|
47
|
Smibert P, Yang JS, Azzam G, Liu JL, Lai EC. Homeostatic control of Argonaute stability by microRNA availability. Nat Struct Mol Biol 2013; 20:789-95. [PMID: 23708604 PMCID: PMC3702675 DOI: 10.1038/nsmb.2606] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/10/2013] [Indexed: 12/18/2022]
Abstract
Homeostatic mechanisms regulate the abundance of several components in small-RNA pathways. We used Drosophila and mammalian systems to demonstrate a conserved homeostatic system in which the status of miRNA biogenesis controls Argonaute protein stability. Clonal analyses of multiple mutants of core Drosophila miRNA factors revealed that stability of the miRNA effector AGO1 is dependent on miRNA biogenesis. Reciprocally, ectopic transcription of miRNAs within in vivo clones induced accumulation of AGO1, as did genetic interference with the ubiquitin-proteasome system. In mouse cells, we found that the stability of Ago2 declined in Dicer-knockout cells and was rescued by proteasome blockade or introduction of either Dicer plasmid or Dicer-independent miRNA constructs. Notably, Dicer-dependent miRNA constructs generated pre-miRNAs that bound Ago2 but did not rescue Ago2 stability. We conclude that Argonaute levels are finely tuned by cellular availability of mature miRNAs and the ubiquitin-proteasome system.
Collapse
Affiliation(s)
- Peter Smibert
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, USA
| | | | | | | | | |
Collapse
|
48
|
An unsolved mystery: the target-recognizing RNA species of microRNA genes. Biochimie 2013; 95:1663-76. [PMID: 23685275 DOI: 10.1016/j.biochi.2013.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/06/2013] [Indexed: 11/21/2022]
Abstract
MicroRNAs (miRNAs) are an abundant class of endogenous ∼21-nucleotide (nt) RNAs. These small RNAs are produced from long primary miRNA transcripts - pri-miRNAs - through sequential endonucleolytic maturation steps that yield precursor miRNA (pre-miRNA) intermediates and then the mature miRNAs. The mature miRNAs are loaded into the RNA-induced silencing complexes (RISC), and guide RISC to target mRNAs for cleavage and/or translational repression. This paradigm, which represents one of major discoveries of modern molecular biology, is built on the assumption that mature miRNAs are the only species produced from miRNA genes that recognize targets. This assumption has guided the miRNA field for more than a decade and has led to our current understanding of the mechanisms of target recognition and repression by miRNAs. Although progress has been made, fundamental questions remain unanswered with regard to the principles of target recognition and mechanisms of repression. Here I raise questions about the assumption that mature miRNAs are the only target-recognizing species produced from miRNA genes and discuss the consequences of working under an incomplete or incorrect assumption. Moreover, I present evolution-based and experimental evidence that support the roles of pri-/pre-miRNAs in target recognition and repression. Finally, I propose a conceptual framework that integrates the functions of pri-/pre-miRNAs and mature miRNAs in target recognition and repression. The integrated framework opens experimental enquiry and permits interpretation of fundamental problems that have so far been precluded.
Collapse
|
49
|
Li F, Li P, Yang L, Tang B. Simple and sensitive fluorescence detection of the RNA endonuclease activity of mammalian argonaute2 protein based on an RNA molecular beacon. Chem Commun (Camb) 2013; 48:12192-4. [PMID: 23145433 DOI: 10.1039/c2cc36404b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A new strategy for determining the RNA endonuclease activity of mammalian argonaute2 (Ago2) protein has been developed, which combines the unique cleavage function of Ago2 protein with an RNA molecular beacon (RMB). Through the fluorescence restoration of the RMB, simple and sensitive detection of Ago2 is achieved.
Collapse
Affiliation(s)
- Feng Li
- College of Chemistry, Chemical Engineering and Materials Science, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Key Laboratory of Molecular and Nano Probes, Shandong Normal University, Jinan 250014, China
| | | | | | | |
Collapse
|
50
|
Martinez NJ, Gregory RI. Argonaute2 expression is post-transcriptionally coupled to microRNA abundance. RNA (NEW YORK, N.Y.) 2013; 19:605-12. [PMID: 23485552 PMCID: PMC3677276 DOI: 10.1261/rna.036434.112] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/13/2013] [Indexed: 05/17/2023]
Abstract
Argonaute proteins are essential components of microRNA (miRNA)- and small interfering (siRNA)-mediated post-transcriptional gene-silencing pathways. In mammals, Argonaute2 (Ago2) is the catalytic center of the RNA-induced silencing complex (RISC) that recognizes and endonucleolytically cleaves messenger RNAs of complementary sequence. Although Ago2 is essential for RISC activity, the mechanisms regulating Argonaute protein expression are largely unknown. Here we report that Ago2 expression is dependent on miRNA abundance and that unloaded Ago2 protein is unstable. We observed a low level of Ago2 protein in Dicer- or DGCR8-deficent mouse embryonic stem cells (ESCs) that could be rescued by reintroduction of the respective cDNAs or by transfection of miRNAs or siRNAs. We found expression of Ago2 protein from a transgene to be similarly regulated, further supporting a post-transcriptional control mechanism. Inhibition of Hsc70/Hsp90 led to decreased Ago2 expression consistent with the reported role of this chaperone complex in RISC assembly. We furthermore found that the degradation of Ago2 was specifically blocked by inhibition of the lysosome, but not the proteasome. Our results illuminate a novel feedback mechanism that post-transcriptionally couples Ago2 protein levels with small RNA abundance with implications for RNA-interference (RNAi) and miRNA function.
Collapse
|