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Fu Y, Fan P, Wang L, Shu Z, Zhu S, Feng S, Li X, Qiu X, Zhao S, Liu X. Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data. J Anim Sci 2021; 99:skab018. [PMID: 33493272 PMCID: PMC7885162 DOI: 10.1093/jas/skab018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 01/21/2021] [Indexed: 12/27/2022] Open
Abstract
Despite the broad variety of available microRNA (miRNA) research tools and methods, their application to the identification, annotation, and target prediction of miRNAs in nonmodel organisms is still limited. In this study, we collected nearly all public sRNA-seq data to improve the annotation for known miRNAs and identify novel miRNAs that have not been annotated in pigs (Sus scrofa). We newly annotated 210 mature sequences in known miRNAs and found that 43 of the known miRNA precursors were problematic due to redundant/missing annotations or incorrect sequences. We also predicted 811 novel miRNAs with high confidence, which was twice the current number of known miRNAs for pigs in miRBase. In addition, we proposed a correlation-based strategy to predict target genes for miRNAs by using a large amount of sRNA-seq and RNA-seq data. We found that the correlation-based strategy provided additional evidence of expression compared with traditional target prediction methods. The correlation-based strategy also identified the regulatory pairs that were controlled by nonbinding sites with a particular pattern, which provided abundant complementarity for studying the mechanism of miRNAs that regulate gene expression. In summary, our study improved the annotation of known miRNAs, identified a large number of novel miRNAs, and predicted target genes for all pig miRNAs by using massive public data. This large data-based strategy is also applicable for other nonmodel organisms with incomplete annotation information.
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Affiliation(s)
- Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, PR China
| | - Pengyu Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Lu Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Ziqiang Shu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Shilin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Siyuan Feng
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Xiaotian Qiu
- National Animal Husbandry Service, Beijing, PR China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
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52
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Gwam C, Mohammed N, Ma X. Stem cell secretome, regeneration, and clinical translation: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:70. [PMID: 33553363 PMCID: PMC7859812 DOI: 10.21037/atm-20-5030] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Regenerative medicine is a field growing in popularity due to high hopes for stimulating in situ tissue restoration. Stem cell therapy remain at the center of regenerative medicine, due to early reports on its pluripotent differentiating capability. However, more recent reports suggest the paracrine activity of stem cells, and not direct differentiation, as the cause of its therapeutic effects. This paracrine activity can be harnessed in the form of conditioned media. Despite these capabilities, the clinical translation of stem cell conditioned media (i.e., secretome) is precluded by a variety of factors. These limitations include standardization of stem cell-conditioned media formulation, characterization of bioactive factors in conditioned media and dosing, optimizing modes of delivery, and uncovering of mechanisms of action of stem cell conditioned media. The purpose of this review is to provide a focused narration on the aforementioned preclusions pertaining to the clinical translation of stem cell conditioned media. Specifically, we will report on commonly use methodologies for the development of stem cell conditioned media, modalities for conditioned media characterization, modes of delivery, and postulated mechanisms of action for stem cell conditioned media in regenerative medicine.
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Affiliation(s)
- Chukwuweike Gwam
- Department of Orthopedic Surgery, Wake Forest School of Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Nequesha Mohammed
- Department of Orthopedic Surgery, Wake Forest School of Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Xue Ma
- Department of Orthopedic Surgery, Wake Forest School of Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
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53
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Cho WC, Kim M, Park JW, Jeong SY, Ku JL. Exosomal miR-193a and let-7g accelerate cancer progression on primary colorectal cancer and paired peritoneal metastatic cancer. Transl Oncol 2020; 14:101000. [PMID: 33352502 PMCID: PMC7758376 DOI: 10.1016/j.tranon.2020.101000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023] Open
Abstract
A metastasis of colorectal cancer is difficult to diagnose, and has a poor prognosis. Therefore, we tried to elucidate the possibility of a diagnostic and prognostic marker. Exosomal miR-193a and let-7g were sorted by miRNA microarray. The expression of miR-193a in the PTM group was lower than that of the primary CRC group, and the expression of let-7g was higher than that of the primary CRC. MMP16 and CDKN1A expression was confirmed respectively for target genes of two miRNAs. When the mimics of these miRNAs were treated with cell lines, both MMP16 and CDKN1A decreased intracellular expression. Cell invasiveness and proliferation were decreased by miR-193a and increased by let-7g. The differences in expression of exosomal miR-193a and let-7g extracted from the plasma of patients were classified as cancer progression indicators. Furthermore, the survival rate decreased in the group with low miR-193a expression and high let-7g expression. Our study confirmed the possibility of using this as a diagnostic and prognostic marker for colorectal cancer by measuring the expression levels of exosomal miR-193a and let-7g in blood.
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Affiliation(s)
- Woo-Cheol Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
| | - Minjung Kim
- Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Korea
| | - Ji Won Park
- Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Korea
| | - Seung-Yong Jeong
- Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea; Division of Colorectal Surgery, Department of Surgery, Seoul National University Hospital, Seoul 03080, Korea.
| | - Ja-Lok Ku
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea; Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea.
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54
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Alexandri C, Daniel A, Bruylants G, Demeestere I. The role of microRNAs in ovarian function and the transition toward novel therapeutic strategies in fertility preservation: from bench to future clinical application. Hum Reprod Update 2020; 26:174-196. [PMID: 32074269 DOI: 10.1093/humupd/dmz039] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/02/2019] [Accepted: 10/01/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND New therapeutic approaches in oncology have converted cancer from a certain death sentence to a chronic disease. However, there are still challenges to be overcome regarding the off-target toxicity of many of these treatments. Oncological therapies can lead to future infertility in women. Given this negative impact on long-term quality of life, fertility preservation is highly recommended. While gamete and ovarian tissue cryopreservation are the usual methods offered, new pharmacological-based options aiming to reduce ovarian damage during oncological treatment are very attractive. In this vein, advances in the field of transcriptomics and epigenomics have brought small noncoding RNAs, called microRNAs (miRNAs), into the spotlight in oncology. MicroRNAs also play a key role in follicle development as regulators of follicular growth, atresia and steroidogenesis. They are also involved in DNA damage repair responses and they can themselves be modulated during chemotherapy. For these reasons, miRNAs may be an interesting target to develop new protective therapies during oncological treatment. This review summarizes the physiological role of miRNAs in reproduction. Considering recently developed strategies based on miRNA therapy in oncology, we highlight their potential interest as a target in fertility preservation and propose future strategies to make the transition from bench to clinic. OBJECTIVE AND RATIONALE How can miRNA therapeutic approaches be used to develop new adjuvant protective therapies to reduce the ovarian damage caused by cytotoxic oncological treatments? SEARCH METHODS A systematic search of English language literature using PubMed and Google Scholar databases was performed through to 2019 describing the role of miRNAs in the ovary and their use for diagnosis and targeted therapy in oncology. Personal data illustrate miRNA therapeutic strategies to target the gonads and reduce chemotherapy-induced follicular damage. OUTCOMES This review outlines the importance of miRNAs as gene regulators and emphasizes the fact that insights in oncology can inspire new adjuvant strategies in the field of onco-fertility. Recent improvements in nanotechnology offer the opportunity for drug development using next-generation miRNA-nanocarriers. WIDER IMPLICATIONS Although there are still some barriers regarding the immunogenicity and toxicity of these treatments and there is still room for improvement concerning the specific delivery of miRNAs into the ovaries, we believe that, in the future, miRNAs can be developed as powerful and non-invasive tools for fertility preservation.
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Affiliation(s)
- C Alexandri
- Research Laboratory in Human Reproduction, Faculty of Medicine, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - A Daniel
- Research Laboratory in Human Reproduction, Faculty of Medicine, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium.,Université de Tours, Faculty of Science and Technology, 37200 Tours, France
| | - G Bruylants
- Engineering of Molecular NanoSystems, Ecole Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - I Demeestere
- Research Laboratory in Human Reproduction, Faculty of Medicine, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium.,Fertility Clinic, CUB-Erasme, 1070 Brussels, Belgium
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55
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Diener C, Hart M, Kehl T, Rheinheimer S, Ludwig N, Krammes L, Pawusch S, Lenhof K, Tänzer T, Schub D, Sester M, Walch-Rückheim B, Keller A, Lenhof HP, Meese E. Quantitative and time-resolved miRNA pattern of early human T cell activation. Nucleic Acids Res 2020; 48:10164-10183. [PMID: 32990751 PMCID: PMC7544210 DOI: 10.1093/nar/gkaa788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/14/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
T cells are central to the immune response against various pathogens and cancer cells. Complex networks of transcriptional and post-transcriptional regulators, including microRNAs (miRNAs), coordinate the T cell activation process. Available miRNA datasets, however, do not sufficiently dissolve the dynamic changes of miRNA controlled networks upon T cell activation. Here, we established a quantitative and time-resolved expression pattern for the entire miRNome over a period of 24 h upon human T-cell activation. Based on our time-resolved datasets, we identified central miRNAs and specified common miRNA expression profiles. We found the most prominent quantitative expression changes for miR-155-5p with a range from initially 40 molecules/cell to 1600 molecules/cell upon T-cell activation. We established a comprehensive dynamic regulatory network of both the up- and downstream regulation of miR-155. Upstream, we highlight IRF4 and its complexes with SPI1 and BATF as central for the transcriptional regulation of miR-155. Downstream of miR-155-5p, we verified 17 of its target genes by the time-resolved data recorded after T cell activation. Our data provide comprehensive insights into the range of stimulus induced miRNA abundance changes and lay the ground to identify efficient points of intervention for modifying the T cell response.
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Affiliation(s)
- Caroline Diener
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Martin Hart
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | | | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Lena Krammes
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Sarah Pawusch
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Kerstin Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Tanja Tänzer
- Institute of Virology and Center of Human and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - David Schub
- Department of Transplant and Infection Immunology, Saarland University, 66421 Homburg, Germany
| | - Martina Sester
- Department of Transplant and Infection Immunology, Saarland University, 66421 Homburg, Germany
| | - Barbara Walch-Rückheim
- Institute of Virology and Center of Human and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
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56
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Barbieri E, Hill C, Quesnel-Vallières M, Zucco AJ, Barash Y, Gardini A. Rapid and Scalable Profiling of Nascent RNA with fastGRO. Cell Rep 2020; 33:108373. [PMID: 33176136 PMCID: PMC7702699 DOI: 10.1016/j.celrep.2020.108373] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/15/2020] [Accepted: 10/19/2020] [Indexed: 12/20/2022] Open
Abstract
Genome-wide profiling of nascent RNA has become a fundamental tool to study transcription regulation. Unlike steady-state RNA-sequencing (RNA-seq), nascent RNA profiling mirrors real-time activity of RNA polymerases and provides an accurate readout of transcriptome-wide variations. Some species of nuclear RNAs (i.e., large intergenic noncoding RNAs [lincRNAs] and eRNAs) have a short half-life and can only be accurately gauged by nascent RNA techniques. Furthermore, nascent RNA-seq detects post-cleavage RNA at termination sites and promoter-associated antisense RNAs, providing insights into RNA polymerase II (RNAPII) dynamics and processivity. Here, we present a run-on assay with 4-thio ribonucleotide (4-S-UTP) labeling, followed by reversible biotinylation and affinity purification via streptavidin. Our protocol allows streamlined sample preparation within less than 3 days. We named the technique fastGRO (fast Global Run-On). We show that fastGRO is highly reproducible and yields a more complete and extensive coverage of nascent RNA than comparable techniques can. Importantly, we demonstrate that fastGRO is scalable and can be performed with as few as 0.5 × 106 cells. Barbieri et al. developed fastGRO, a nascent RNA-sequencing technique based on nuclear run-on. Using a streamlined, under-3-days protocol, fastGRO tracks the activity of RNA polymerase for differential gene expression analysis, polymerase kinetic studies, and profiling of lowly expressed and unstable RNA species. A low-input fastGRO protocol profiles nascent RNA in as little as 0.5 × 106 cells.
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Affiliation(s)
- Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Connor Hill
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Avery J Zucco
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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57
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Woods S, Charlton S, Cheung K, Hao Y, Soul J, Reynard LN, Crowe N, Swingler TE, Skelton AJ, Piróg KA, Miles CG, Tsompani D, Jackson RM, Dalmay T, Clark IM, Barter MJ, Young DA. microRNA-seq of cartilage reveals an overabundance of miR-140-3p which contains functional isomiRs. RNA (NEW YORK, N.Y.) 2020; 26:1575-1588. [PMID: 32660984 PMCID: PMC7566571 DOI: 10.1261/rna.075176.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/06/2020] [Indexed: 05/15/2023]
Abstract
miR-140 is selectively expressed in cartilage. Deletion of the entire Mir140 locus in mice results in growth retardation and early-onset osteoarthritis-like pathology; however, the relative contribution of miR-140-5p or miR-140-3p to the phenotype remains to be determined. An unbiased small RNA sequencing approach identified miR-140-3p as significantly more abundant (>10-fold) than miR-140-5p in human cartilage. Analysis of these data identified multiple miR-140-3p isomiRs differing from the miRBase annotation at both the 5' and 3' end, with >99% having one of two seed sequences (5' bases 2-8). Canonical (miR-140-3p.2) and shifted (miR-140-3p.1) seed isomiRs were overexpressed in chondrocytes and transcriptomics performed to identify targets. miR-140-3p.1 and miR-140-3p.2 significantly down-regulated 694 and 238 genes, respectively, of which only 162 genes were commonly down-regulated. IsomiR targets were validated using 3'UTR luciferase assays. miR-140-3p.1 targets were enriched within up-regulated genes in rib chondrocytes of Mir140-null mice and within down-regulated genes during human chondrogenesis. Finally, through imputing the expression of miR-140 from the expression of the host gene WWP2 in 124 previously published data sets, an inverse correlation with miR-140-3p.1 predicted targets was identified. Together these data suggest the novel seed containing isomiR miR-140-3p.1 is more functional than original consensus miR-140-3p seed containing isomiR.
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Affiliation(s)
- Steven Woods
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Sarah Charlton
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Kat Cheung
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Yao Hao
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
- Orthopedics Department, First Hospital of Shanxi Medical University, Yingze District, Taiyuan, 030000, China
| | - Jamie Soul
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Louise N Reynard
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Natalie Crowe
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Tracey E Swingler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Andrew J Skelton
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Katarzyna A Piróg
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Colin G Miles
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Dimitra Tsompani
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Robert M Jackson
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Ian M Clark
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Matt J Barter
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - David A Young
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
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58
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Furlan M, Galeota E, Gaudio ND, Dassi E, Caselle M, de Pretis S, Pelizzola M. Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling. Genome Res 2020; 30:1492-1507. [PMID: 32978246 PMCID: PMC7605262 DOI: 10.1101/gr.260984.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022]
Abstract
The quantification of the kinetic rates of RNA synthesis, processing, and degradation are largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT−, a computational method based on the mathematical modeling of premature and mature RNA expression that is able to quantify kinetic rates from steady-state or time course total RNA-seq data without requiring any information on nascent transcripts. Our approach outperforms available solutions, closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcript half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions in which nascent transcription cannot be readily profiled. Finally, we applied INSPEcT− to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady-state or time course data, with or without the profiling of nascent RNA.
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Affiliation(s)
- Mattia Furlan
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy.,Physics Department and INFN, University of Turin, 10125 Turin, Italy
| | - Eugenia Galeota
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Nunzio Del Gaudio
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Erik Dassi
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Michele Caselle
- Physics Department and INFN, University of Turin, 10125 Turin, Italy
| | - Stefano de Pretis
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
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59
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Nazari-Shafti TZ, Neuber S, Duran AG, Exarchos V, Beez CM, Meyborg H, Krüger K, Wolint P, Buschmann J, Böni R, Seifert M, Falk V, Emmert MY. MiRNA Profiles of Extracellular Vesicles Secreted by Mesenchymal Stromal Cells-Can They Predict Potential Off-Target Effects? Biomolecules 2020; 10:biom10091353. [PMID: 32971982 PMCID: PMC7565205 DOI: 10.3390/biom10091353] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/06/2020] [Accepted: 09/16/2020] [Indexed: 12/14/2022] Open
Abstract
The cardioprotective properties of extracellular vesicles (EVs) derived from mesenchymal stromal cells (MSCs) are currently being investigated in preclinical studies. Although microRNAs (miRNAs) encapsulated in EVs have been identified as one component responsible for the cardioprotective effect of MSCs, their potential off-target effects have not been sufficiently characterized. In the present study, we aimed to investigate the miRNA profile of EVs isolated from MSCs that were derived from cord blood (CB) and adipose tissue (AT). The identified miRNAs were then compared to known targets from the literature to discover possible adverse effects prior to clinical use. Our data show that while many cardioprotective miRNAs such as miR-22-3p, miR-26a-5p, miR-29c-3p, and miR-125b-5p were present in CB- and AT-MSC-derived EVs, a large number of known oncogenic and tumor suppressor miRNAs such as miR-16-5p, miR-23a-3p, and miR-191-5p were also detected. These findings highlight the importance of quality assessment for therapeutically applied EV preparations.
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Affiliation(s)
- Timo Z. Nazari-Shafti
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany; (S.N.); (A.G.D.); (V.E.); (H.M.); (V.F.)
- German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany; (C.M.B.); (M.S.)
- Correspondence: (T.Z.N.-S.); (M.Y.E.); Tel.: +49-304-593-2024 (T.Z.N.-S.); +49-304-593-2030 (M.Y.E.)
| | - Sebastian Neuber
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany; (S.N.); (A.G.D.); (V.E.); (H.M.); (V.F.)
- German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany; (C.M.B.); (M.S.)
| | - Ana G. Duran
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany; (S.N.); (A.G.D.); (V.E.); (H.M.); (V.F.)
- Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany; (C.M.B.); (M.S.)
- Berlin-Brandenburg School for Regenerative Therapies, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Vasileios Exarchos
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany; (S.N.); (A.G.D.); (V.E.); (H.M.); (V.F.)
- Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Christien M. Beez
- Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany; (C.M.B.); (M.S.)
| | - Heike Meyborg
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany; (S.N.); (A.G.D.); (V.E.); (H.M.); (V.F.)
| | - Katrin Krüger
- Clinic for Cardiovascular Surgery, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany;
| | - Petra Wolint
- Department of Plastic Surgery and Hand Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (P.W.); (J.B.)
| | - Johanna Buschmann
- Department of Plastic Surgery and Hand Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (P.W.); (J.B.)
| | - Roland Böni
- White House Center for Liposuction, 8044 Zurich, Switzerland;
| | - Martina Seifert
- Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany; (C.M.B.); (M.S.)
- Institute of Medical Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
| | - Volkmar Falk
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany; (S.N.); (A.G.D.); (V.E.); (H.M.); (V.F.)
- German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany; (C.M.B.); (M.S.)
- Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
- Clinic for Cardiovascular Surgery, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany;
| | - Maximilian Y. Emmert
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany; (S.N.); (A.G.D.); (V.E.); (H.M.); (V.F.)
- German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, 13353 Berlin, Germany; (C.M.B.); (M.S.)
- Institute for Regenerative Medicine, University of Zurich, 8044 Zurich, Switzerland
- Wyss Zurich, University of Zurich and ETH Zurich, 8092 Zurich, Switzerland
- Correspondence: (T.Z.N.-S.); (M.Y.E.); Tel.: +49-304-593-2024 (T.Z.N.-S.); +49-304-593-2030 (M.Y.E.)
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Navarro-Martín L, Martyniuk CJ, Mennigen JA. Comparative epigenetics in animal physiology: An emerging frontier. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100745. [PMID: 33126028 DOI: 10.1016/j.cbd.2020.100745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.
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Affiliation(s)
- Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON K1N6N5, Canada
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Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs that are evolutionarily conserved across many different species. miRNA regulation of gene expression, specifically in the context of the mammalian brain, has been well characterized; however, the regulation of miRNA degradation is still a focus of ongoing research. This review focuses on recent findings concerning the cellular mechanisms that govern miRNA degradation, with an emphasis on target-mediated miRNA degradation and how this phenomenon is uniquely poised to maintain homeostasis in neuronal systems.
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Affiliation(s)
- Chun K Kim
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois
| | - Toni R Pak
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois
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Tajiri A, Hirota T, Kawano S, Yonamine A, Ieiri I. Regulation of Organic Anion Transporting Polypeptide 2B1 Expression by MicroRNA in the Human Liver. Mol Pharm 2020; 17:2821-2830. [PMID: 32602343 DOI: 10.1021/acs.molpharmaceut.0c00193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Organic anion transporting polypeptide 2B1 (OATP2B1, SLCO2B1) is an uptake transporter expressed in several tissues, including the liver, intestine, brain, kidney, and skeletal muscle. Hepatocyte nuclear factor 4 alpha (HNF4α) is known as an important transcriptional factor of OATP2B1 in the liver. It has been reported that there are large interindividual differences in OATP2B1 mRNA and protein expressions in human livers. The mechanism causing the interindividual differences in OATP2B1 expression is still unclear. MicroRNAs (miRNAs) control gene expression by leading translational repression and/or degradation of the target mRNA. There is no significant correlation between OATP2B1 mRNA and protein expression, suggesting that post-transcriptional regulating mechanisms, such as miRNAs, play an important role in the interindividual differences in OATP2B1 expression. In this study, we hypothesized that certain miRNAs cause the interindividual differences in OATP2B1 expression in the human liver. In silico analysis showed that miR-24 was a candidate miRNA regulating OATP2B1 expression. It has been reported that miR-24 degrades HNF4α mRNA expression. We revealed that the miR-24 expression level was negatively correlated with OATP2B1 mRNA, protein, and HNF4α mRNA expression levels in human livers. Transfection by the miR-24 precursor decreased the luciferase activity in the transfected cells with the vector containing the OATP2B1 3' untranslated region (3'UTR) or SLCO2B1 promoter region. In HepaRG cells, miR-24 decreased the OATP2B1 and HNF4α expression levels. These results suggest that miR-24 represses not only the translation of OATP2B1 but also the transcription of OATP2B1 by HNF4α mRNA degradation.
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Affiliation(s)
- Ayaka Tajiri
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Hirota
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Sasagu Kawano
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akira Yonamine
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ichiro Ieiri
- Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Differential Stability of miR-9-5p and miR-9-3p in the Brain Is Determined by Their Unique Cis- and Trans-Acting Elements. eNeuro 2020; 7:ENEURO.0094-20.2020. [PMID: 32376600 PMCID: PMC7294468 DOI: 10.1523/eneuro.0094-20.2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/21/2020] [Accepted: 04/25/2020] [Indexed: 12/14/2022] Open
Abstract
microRNAs (miRs) are fundamental regulators of protein coding genes. In the CNS, miR-9 is highly enriched and critical for neuronal development and function. Mature miRs are derived from a duplex precursor, and the -5p strand ("guide") is preferentially incorporated into an RNA-induced silencing complex (RISC) to exert its regulatory functions, while the complementary -3p strand ("passenger") is thought to be rapidly degraded. By contrast, both strands of the miR-9 duplex have unique functions critical for neuronal physiology, yet their respective degradation rates and mechanisms governing degradation are not well understood. Therefore, we determined the degradation kinetics of miR-9-5p and miR-9-3p and investigated the cis and trans elements that affected their stability in the brain. Using a combination of homogeneous neuronal/astrocyte cell models and heterogeneous brain tissue lysate, we demonstrate the novel finding that miR-9-3p was more stable than the miR-9-5p guide strand in all models tested. Moreover, the degradation kinetics of both miR-9-5p and miR-9-3p were brain-region specific, suggesting that each brain region was differentially enriched for specific degradation factors. We also determined that the 3' nucleotides harbor important cis elements required to not only maintain stability, but also to recruit potential protein degradation factors. We used mass spectrometry to assess the miR-9 interacting proteins and found that the -5p and -3p strands were associated with functionally distinct proteins. Overall, these studies revealed unique miR-9-5p and miR-9-3p degradation kinetics in the brain and proposed critical nucleotide sequences and protein partners that could contribute to this differential stability.
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Yang A, Shao TJ, Bofill-De Ros X, Lian C, Villanueva P, Dai L, Gu S. AGO-bound mature miRNAs are oligouridylated by TUTs and subsequently degraded by DIS3L2. Nat Commun 2020; 11:2765. [PMID: 32488030 PMCID: PMC7265490 DOI: 10.1038/s41467-020-16533-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 04/30/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) associated with Argonaute proteins (AGOs) regulate gene expression in mammals. miRNA 3' ends are subject to frequent sequence modifications, which have been proposed to affect miRNA stability. However, the underlying mechanism is not well understood. Here, by genetic and biochemical studies as well as deep sequencing analyses, we find that AGO mutations disrupting miRNA 3' binding are sufficient to trigger extensive miRNA 3' modifications in HEK293T cells and in cancer patients. Comparing these modifications in TUT4, TUT7 and DIS3L2 knockout cells, we find that TUT7 is more robust than TUT4 in oligouridylating mature miRNAs, which in turn leads to their degradation by the DIS3L2 exonuclease. Our findings indicate a decay machinery removing AGO-associated miRNAs with an exposed 3' end. A set of endogenous miRNAs including miR-7, miR-222 and miR-769 are targeted by this machinery presumably due to target-directed miRNA degradation.
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Affiliation(s)
- Acong Yang
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Tie-Juan Shao
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xavier Bofill-De Ros
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Chuanjiang Lian
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,State Key Laboratory of Veterinary Biotechnology and Heilongjiang Province Key Laboratory for Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Patricia Villanueva
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Lisheng Dai
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section; RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
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Lanfranconi S, Scola E, Bertani GA, Zarino B, Pallini R, d'Alessandris G, Mazzon E, Marino S, Carriero MR, Scelzo E, Faragò G, Castori M, Fusco C, Petracca A, d'Agruma L, Tassi L, d'Orio P, Lampugnani MG, Nicolis EB, Vasamì A, Novelli D, Torri V, Meessen JMTA, Al-Shahi Salman R, Dejana E, Latini R. Propranolol for familial cerebral cavernous malformation (Treat_CCM): study protocol for a randomized controlled pilot trial. Trials 2020; 21:401. [PMID: 32398113 PMCID: PMC7218540 DOI: 10.1186/s13063-020-4202-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/24/2020] [Indexed: 12/21/2022] Open
Abstract
Background Cerebral cavernous malformations (CCMs) are vascular malformations characterized by clusters of enlarged leaky capillaries in the central nervous system. They may result in intracranial haemorrhage, epileptic seizure(s), or focal neurological deficits, and potentially lead to severe disability. Globally, CCMs represent the second most common intracranial vascular malformation in humans, and their familial form (FCCMs) accounts for one-fifth of cases. Neurosurgical excision, and perhaps stereotactic radiosurgery, is the only available therapeutic option. Case reports suggest that propranolol might modify disease progression. Methods Treat_CCM is a prospective, randomized, open-label, blinded endpoint (PROBE), parallel-group trial involving six Italian clinical centres with central reading of brain magnetic resonance imaging (MRI) and adverse events. Patients with symptomatic FCCMs are randomized (2:1 ratio) either to propranolol (40–80 mg twice daily) in addition to standard care or to standard care alone (i.e. anti-epileptic drugs or headache treatments). The primary outcome is intracranial haemorrhage or focal neurological deficit attributable to CCMs. The secondary outcomes are MRI changes over time (i.e. de novo CCM lesions, CCM size and signal characteristics, iron deposition, and vascular leakage as assessed by quantitative susceptibility mapping and dynamic contrast enhanced permeability), disability, health-related quality of life, depression severity, and anxiety (SF-36, BDI-II, State-Trait Anxiety Inventory). Discussion Treat_CCM will evaluate the safety and efficacy of propranolol for CCMs following promising case reports in a randomized controlled trial. The direction of effect on the primary outcome and the consistency of effects on the secondary outcomes (even if none of them yield statistically significant differences) of this external pilot study may lead to a larger sample size in a definitive phase 2 trial. Trial registration ClinicalTrails.gov, NCT03589014. Retrospectively registered on 17 July 2018.
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Affiliation(s)
- Silvia Lanfranconi
- Department of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Padiglione Monteggia-piano 3, Via Francesco Sforza 35, 20122, Milan, Italy.
| | - Elisa Scola
- Department of Neuroradiology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Giulio Andrea Bertani
- Department of Neurosurgery, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Barbara Zarino
- Department of Neurosurgery, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Roberto Pallini
- Department of Neurosurgery, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Giorgio d'Alessandris
- Department of Neurosurgery, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi "Bonino Pulejo", Contrada Casazza, 98124, Messina, Italy
| | - Silvia Marino
- IRCCS Centro Neurolesi "Bonino Pulejo", Contrada Casazza, 98124, Messina, Italy
| | - Maria Rita Carriero
- Cerebrovascular Disease Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Giovanni Celoria 11, 20133, Milan, Italy
| | - Emma Scelzo
- Cerebrovascular Disease Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Giovanni Celoria 11, 20133, Milan, Italy
| | - Giuseppe Faragò
- Department of Neuroradiology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Giovanni Celoria 11, 20133, Milan, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 2, 71013, San Giovanni Rotondo, Italy
| | - Carmela Fusco
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 2, 71013, San Giovanni Rotondo, Italy
| | - Antonio Petracca
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 2, 71013, San Giovanni Rotondo, Italy
| | - Leonardo d'Agruma
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 2, 71013, San Giovanni Rotondo, Italy
| | - Laura Tassi
- "Claudio Munari" Epilepsy Surgery Centre, ASST Grande Ospedale Metropolitano Niguarda, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - Piergiorgio d'Orio
- "Claudio Munari" Epilepsy Surgery Centre, ASST Grande Ospedale Metropolitano Niguarda, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - Maria Grazia Lampugnani
- Laboratory of Vascular Biology, IFOM, Firc Institute for Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Enrico Bjorn Nicolis
- Laboratory of Cardiovascular Clinical Pharmacology, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri, 2, 20156, Milan, Italy
| | - Antonella Vasamì
- Laboratory of Cardiovascular Clinical Pharmacology, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri, 2, 20156, Milan, Italy
| | - Deborah Novelli
- Laboratory of Cardiovascular Clinical Pharmacology, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri, 2, 20156, Milan, Italy
| | - Valter Torri
- Laboratory of Research Methodology, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri, 2, 20156, Milan, Italy
| | - Jennifer Marie Theresia Anna Meessen
- Laboratory of Cardiovascular Clinical Pharmacology, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri, 2, 20156, Milan, Italy
| | - Rustam Al-Shahi Salman
- Centre for Clinical Brain Sciences, University of Edinburgh, Little France Crescent 49, Edinburgh, EH16 4SB, UK
| | - Elisabetta Dejana
- Laboratory of Vascular Biology, IFOM, Firc Institute for Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Roberto Latini
- Laboratory of Cardiovascular Clinical Pharmacology, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri, 2, 20156, Milan, Italy
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Szabo EX, Reichert P, Lehniger MK, Ohmer M, de Francisco Amorim M, Gowik U, Schmitz-Linneweber C, Laubinger S. Metabolic Labeling of RNAs Uncovers Hidden Features and Dynamics of the Arabidopsis Transcriptome. THE PLANT CELL 2020; 32:871-887. [PMID: 32060173 PMCID: PMC7145469 DOI: 10.1105/tpc.19.00214] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 01/14/2020] [Accepted: 02/11/2020] [Indexed: 05/05/2023]
Abstract
Transcriptome analysis by RNA sequencing (RNA-seq) has become an indispensable research tool in modern plant biology. Virtually all RNA-seq studies provide a snapshot of the steady state transcriptome, which contains valuable information about RNA populations at a given time but lacks information about the dynamics of RNA synthesis and degradation. Only a few specialized sequencing techniques, such as global run-on sequencing, have been used to provide information about RNA synthesis rates in plants. Here, we demonstrate that RNA labeling with the modified, nontoxic uridine analog 5-ethynyl uridine (5-EU) in Arabidopsis (Arabidopsis thaliana) seedlings provides insight into plant transcriptome dynamics. Pulse labeling with 5-EU revealed nascent and unstable RNAs, RNA processing intermediates generated by splicing, and chloroplast RNAs. Pulse-chase experiments with 5-EU allowed us to determine RNA stabilities without the need for chemical transcription inhibitors such as actinomycin and cordycepin. Inhibitor-free, genome-wide analysis of polyadenylated RNA stability via 5-EU pulse-chase experiments revealed RNAs with shorter half-lives than those reported after chemical inhibition of transcription. In summary, our results indicate that the Arabidopsis nascent transcriptome contains unstable RNAs and RNA processing intermediates and suggest that polyadenylated RNAs have low stability in plants. Our technique lays the foundation for easy, affordable, nascent transcriptome analysis and inhibitor-free analysis of RNA stability in plants.
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Affiliation(s)
- Emese Xochitl Szabo
- Institute for Biology and Environmental Science, University of Oldenburg, 26129 Oldenburg, Germany
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
| | - Philipp Reichert
- Institute for Biology and Environmental Science, University of Oldenburg, 26129 Oldenburg, Germany
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
| | | | - Marilena Ohmer
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
| | | | - Udo Gowik
- Institute for Biology and Environmental Science, University of Oldenburg, 26129 Oldenburg, Germany
| | | | - Sascha Laubinger
- Institute for Biology and Environmental Science, University of Oldenburg, 26129 Oldenburg, Germany
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Bedi K, Paulsen MT, Wilson TE, Ljungman M. Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing. NAR Genom Bioinform 2020; 2:lqz014. [PMID: 31709421 PMCID: PMC6824518 DOI: 10.1093/nargab/lqz014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/07/2019] [Accepted: 10/26/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are key contributors to gene regulatory networks. Because miRNAs are processed from RNA polymerase II transcripts, insight into miRNA regulation requires a comprehensive understanding of the regulation of primary miRNA transcripts. We used Bru-seq nascent RNA sequencing and hidden Markov model segmentation to map primary miRNA transcription units (TUs) across 32 human cell lines, allowing us to describe TUs encompassing 1443 miRNAs from miRBase and 438 from MirGeneDB. We identified TUs for 61 miRNAs with an unknown CAGE TSS signal for MirGeneDB miRNAs. Many primary transcripts containing miRNA sequences failed to generate mature miRNAs, suggesting that miRNA biosynthesis is under both transcriptional and post-transcriptional control. In addition to constitutive and cell-type specific TU expression regulated by differential promoter usage, miRNA synthesis can be regulated by transcription past polyadenylation sites (transcriptional read through) and promoter divergent transcription (PROMPTs). We identified 197 miRNA TUs with novel promoters, 97 with transcriptional read-throughs and 3 miRNA TUs that resemble PROMPTs in at least one cell line. The miRNA TU annotation data resource described here reveals a greater complexity in miRNA regulation than previously known and provides a framework for identifying cell-type specific differences in miRNA transcription in cancer and cell transition states.
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Affiliation(s)
- Karan Bedi
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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Biasini A, Marques AC. A Protocol for Transcriptome-Wide Inference of RNA Metabolic Rates in Mouse Embryonic Stem Cells. Front Cell Dev Biol 2020; 8:97. [PMID: 32175319 PMCID: PMC7056730 DOI: 10.3389/fcell.2020.00097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/07/2020] [Indexed: 12/16/2022] Open
Abstract
The relative ease of mouse Embryonic Stem Cells (mESCs) culture and the potential of these cells to differentiate into any of the three primary germ layers: ectoderm, endoderm and mesoderm (pluripotency), makes them an ideal and frequently used ex vivo system to dissect how gene expression changes impact cell state and differentiation. These efforts are further supported by the large number of constitutive and inducible mESC mutants established with the aim of assessing the contributions of different pathways and genes to cell homeostasis and gene regulation. Gene product abundance is controlled by the modulation of the rates of RNA synthesis, processing, and degradation. The ability to determine the relative contribution of these different RNA metabolic rates to gene expression control using standard RNA-sequencing approaches, which only capture steady state abundance of transcripts, is limited. In contrast, metabolic labeling of RNA with 4-thiouridine (4sU) coupled with RNA-sequencing, allows simultaneous and reproducible inference of transcriptome wide synthesis, processing, and degradation rates. Here we describe, a detailed protocol for 4sU metabolic labeling in mESCs that requires short 4sU labeling times at low concentration and minimally impacts cellular homeostasis. This approach presents a versatile method for in-depth characterization of the gene regulatory strategies governing gene steady state abundance in mESC.
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Affiliation(s)
- Adriano Biasini
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ana Claudia Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
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How Complementary Targets Expose the microRNA 3' End for Tailing and Trimming during Target-Directed microRNA Degradation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:179-183. [PMID: 32019864 DOI: 10.1101/sqb.2019.84.039321] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
microRNAs (miRNAs) are crucial for posttranscriptional regulation of messenger RNAs. "Classical" miRNA targets predominantly interact with the miRNA seed sequence located near the miRNA 5' end. Interestingly, certain transcripts that exhibit extensive complementarity to the miRNAs 3' region, instead of being subjected to regulation, induce miRNA decay in a process termed target-directed miRNA degradation (TDMD). Here, we review recent advances in understanding the molecular mechanisms of TDMD. Specifically, we discuss how extensive miRNA complementarity to TDMD-inducing targets results in displacement of the miRNA 3' end from its protective pocket in the Argonaute protein. Unprotected miRNA 3' ends are then available for enzymatic attack by still-unidentified cellular enzymes. Identification of these cellular enzymes and discovery of additional TDMD-inducing transcripts are subjects for future research.
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Gregersen LH, Mitter R, Svejstrup JQ. Using TT chem-seq for profiling nascent transcription and measuring transcript elongation. Nat Protoc 2020; 15:604-627. [PMID: 31915390 DOI: 10.1038/s41596-019-0262-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/29/2019] [Indexed: 01/08/2023]
Abstract
The dynamics of transcription can be studied genome wide by high-throughput sequencing of nascent and newly synthesized RNA. 4-thiouridine (4SU) labeling in vivo enables the specific capture of such new transcripts, with 4SU residues being tagged by biotin linkers and captured using streptavidin beads before library production and high-throughput sequencing. To achieve high-resolution profiles of transcribed regions, an RNA fragmentation step before biotin tagging was introduced, in an approach known as transient transcriptome sequencing (TT-seq). We recently introduced a chemical approach for RNA fragmentation that we refer to as TTchem-seq. We describe how TTchem-seq can be used in combination with transient inhibition of early elongation using the reversible CDK9 inhibitor, 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB), to measure RNA polymerase II (RNAPII) elongation rates in vivo, a technique we call DRB/TTchem-seq. Here, we provide detailed protocols for carrying out TTchem-seq and DRB/TTchem-seq, including computational analysis. Experiments and data analysis can be performed over a period of 10-13 d and require molecular biology and bioinformatics skills.
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Affiliation(s)
- Lea H Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK.
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71
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Abstract
MicroRNAs as critical regulators of gene expression important for functions including neuronal development, synapse formation, and synaptic plasticity have been linked with the regulation of neurobiological systems that underlie anxiety processing in the brain. In this chapter, we give an update on associative evidence linking regulation of microRNAs with anxiety- and trauma-related disorders. Moving beyond correlative research, functional studies have emerged recently that explore causal relationships between microRNA expression and anxiety-like behavior. It has been demonstrated that experimental up- or downregulation of the candidate microRNAs in important nodes of the anxiety neurocircuitry can indeed modulate anxiety-related behavior in animal models. Improved methodologies for assessing microRNA-mediated modulation have aided such functional studies, revealing a number of anxiety-regulating microRNAs including miR-15a, miR-17-92, miR-34, miR-101, miR-124, miR-135, and miR-155. Important functional target genes of these identified microRNAs are associated with specific neurotransmitter/neuromodulator signaling, neurotrophin (e.g., BDNF) expression and other aspects of synaptic plasticity, as well as with stress-regulatory/hypothalamic-pituitary-axis function. Furthermore, microRNAs have been revealed that are regulated in distinct brain regions following various anxiety-attenuating strategies. These include pharmacological treatments such as antidepressants and other drugs, as well as non-pharmacological interventions such as fear extinction/exposure therapy or positive stimuli such as exposure to environmental enrichment. These are first indications for a role for microRNAs in the mechanism of action of anxiolytic treatments. As research continues, there is much hope that a deeper understanding of the microRNA-mediated mechanisms underlying anxiety-related disorders could open up possibilities for future novel biomarker and treatment strategies.
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72
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Abstract
In this issue of Molecular Cell, two complementary studies illuminate miRNA biology with unprecedented depth and breadth. Reichholf et al. (2019) present a quantitative view of miRNA biogenesis and turnover, while Becker et al. (2019) describe an exhaustive evaluation of miRNA target recognition.
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Affiliation(s)
- Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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73
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Singh AK, Singh N, Kumar S, Kumari J, Singh R, Gaba S, Yadav MC, Grover M, Chaurasia S, Kumar R. Identification and evolutionary analysis of polycistronic miRNA clusters in domesticated and wild wheat. Genomics 2020; 112:2334-2348. [PMID: 31926215 DOI: 10.1016/j.ygeno.2020.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 12/31/2022]
Abstract
MicroRNAs are ~22 nucleotide long non-coding RNAs that regulate gene expression at posttranscriptional level. Genome-wide analysis was performed to identify polycistronic miRNAs from wheat. Total 89 polycistronic miRNAs were identified in bread wheat which were distributed on three component sub-genomes (A = 26, B = 33 and D = 30). Except some, most of the identified polycistronic miRNAs were also present in other cultivated and wild wheat species. Expression of 11 identified polycistronic miRNAs could be validated using previously assembled transcriptomes, RNA-seq/s-RNA seq data of cultivated and wild wheats and RT-PCR. Polycistronic miRNAs orthologs were also localized on rice and Brachypodium genomes. As a case study, we also analyzed molecular evolution of miR395 family polycistrons in wheat. Both tandem and segmental duplications contributed to expansion of miR395 family polycistrons. Our findings provide a comprehensive view on wheat polycitronic miRNAs that will enable their in-depth functional analysis in the future.
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Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India.
| | - Nidhi Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Sundeep Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Jyoti Kumari
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Sonam Gaba
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Mahesh C Yadav
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Monendra Grover
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Shiksha Chaurasia
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Rajesh Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
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74
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van der Kwast RV, Quax PH, Nossent AY. An Emerging Role for isomiRs and the microRNA Epitranscriptome in Neovascularization. Cells 2019; 9:cells9010061. [PMID: 31881725 PMCID: PMC7017316 DOI: 10.3390/cells9010061] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Therapeutic neovascularization can facilitate blood flow recovery in patients with ischemic cardiovascular disease, the leading cause of death worldwide. Neovascularization encompasses both angiogenesis, the sprouting of new capillaries from existing vessels, and arteriogenesis, the maturation of preexisting collateral arterioles into fully functional arteries. Both angiogenesis and arteriogenesis are highly multifactorial processes that require a multifactorial regulator to be stimulated simultaneously. MicroRNAs can regulate both angiogenesis and arteriogenesis due to their ability to modulate expression of many genes simultaneously. Recent studies have revealed that many microRNAs have variants with altered terminal sequences, known as isomiRs. Additionally, endogenous microRNAs have been identified that carry biochemically modified nucleotides, revealing a dynamic microRNA epitranscriptome. Both types of microRNA alterations were shown to be dynamically regulated in response to ischemia and are able to influence neovascularization by affecting the microRNA’s biogenesis, or even its silencing activity. Therefore, these novel regulatory layers influence microRNA functioning and could provide new opportunities to stimulate neovascularization. In this review we will highlight the formation and function of isomiRs and various forms of microRNA modifications, and discuss recent findings that demonstrate that both isomiRs and microRNA modifications directly affect neovascularization and vascular remodeling.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul H.A. Quax
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Laboratory Medicine and Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
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75
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Abstract
Since their serendipitous discovery in nematodes, microRNAs (miRNAs) have emerged as key regulators of biological processes in animals. These small RNAs form complex networks that regulate cell differentiation, development and homeostasis. Deregulation of miRNA function is associated with an increasing number of human diseases, particularly cancer. Recent discoveries have expanded our understanding of the control of miRNA function. Here, we review the mechanisms that modulate miRNA activity, stability and cellular localization through alternative processing and maturation, sequence editing, post-translational modifications of Argonaute proteins, viral factors, transport from the cytoplasm and regulation of miRNA-target interactions. We conclude by discussing intriguing, unresolved research questions.
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Affiliation(s)
- Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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76
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Schreiner WP, Pagliuso DC, Garrigues JM, Chen JS, Aalto AP, Pasquinelli AE. Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock. Nucleic Acids Res 2019; 47:9829-9841. [PMID: 31396626 PMCID: PMC6765114 DOI: 10.1093/nar/gkz693] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023] Open
Abstract
Elevated temperatures activate a heat shock response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor heat shock factor 1 (HSF-1), which binds heat shock elements (HSEs) in the promoters of genes induced by heat shock (HS). The upregulation of protein-coding genes (PCGs), such as heat shock proteins and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to HS has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that in Caenorhabditis elegans HS induces up- and downregulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene and repeat elements. Moreover, some ncRNA genes appear to be direct targets of the HSR, as they contain HSF-1 bound HSEs in their promoters and their expression is regulated by this factor during HS. These results demonstrate that multiple ncRNA genes respond to HS, some as direct HSF-1 targets, providing new candidates that may contribute to organismal survival during this stress.
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Affiliation(s)
- William P Schreiner
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Delaney C Pagliuso
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Jacob M Garrigues
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Jerry S Chen
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Antti P Aalto
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
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77
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Conditional Deletion of Dicer in Adult Mice Impairs Skeletal Muscle Regeneration. Int J Mol Sci 2019; 20:ijms20225686. [PMID: 31766249 PMCID: PMC6887938 DOI: 10.3390/ijms20225686] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle has a remarkable regenerative capacity, which is orchestrated by multiple processes, including the proliferation, fusion, and differentiation of the resident stem cells in muscle. MicroRNAs (miRNAs) are small noncoding RNAs that mediate the translational repression or degradation of mRNA to regulate diverse biological functions. Previous studies have suggested that several miRNAs play important roles in myoblast proliferation and differentiation in vitro. However, their potential roles in skeletal muscle regeneration in vivo have not been fully established. In this study, we generated a mouse in which the Dicer gene, which encodes an enzyme essential in miRNA processing, was knocked out in a tamoxifen-inducible way (iDicer KO mouse) and determined its regenerative potential after cardiotoxin-induced acute muscle injury. Dicer mRNA expression was significantly reduced in the tibialis anterior muscle of the iDicer KO mice, whereas the expression of muscle-enriched miRNAs was only slightly reduced in the Dicer-deficient muscles. After cardiotoxin injection, the iDicer KO mice showed impaired muscle regeneration. We also demonstrated that the number of PAX7+ cells, cell proliferation, and the myogenic differentiation capacity of the primary myoblasts did not differ between the wild-type and the iDicer KO mice. Taken together, these data demonstrate that Dicer is a critical factor for muscle regeneration in vivo.
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78
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Vizitiu AC, Stambouli D, Pavel AG, Muresan MC, Anastasiu DM, Bejinar C, Alexa A, Marian C, Sirbu IO, Sima L. Mature miR-99a Upregulation in the Amniotic Fluid Samples from Female Fetus Down Syndrome Pregnancies: A Pilot Study. ACTA ACUST UNITED AC 2019; 55:medicina55110728. [PMID: 31703316 PMCID: PMC6915350 DOI: 10.3390/medicina55110728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
Abstract
Background and Objective: Although Down syndrome is the most frequent aneuploidy, its pathogenic molecular mechanisms are not yet fully understood. The aim of our study is to quantify-by qRT-PCR-the expression levels of both the mature forms and the pri-miRNAs of the microRNAs resident on chromosome 21 (miR(21)) in the amniotic fluid samples from Down syndrome singleton pregnancies and to estimate the impact of the differentially expressed microRNAs on Down syndrome fetal heart and amniocytes transcriptomes. Materials and methods: We collected amniotic fluid samples harvested by trained obstetricians as part of the second trimester screening/diagnostic procedure for aneuploidies to assess the trisomy 21 status by QF-PCR and karyotyping. Next, we evaluated-by Taqman qRT-PCR-the expression levels of both the mature forms and the pri-miRNA precursors of the microRNAs resident on chromosome 21 in amniotic fluid samples from singleton Down syndrome and euploid pregnancies. Further, we combined miRWalk 3.0 microRNA target prediction with GEO DataSets analysis to estimate the impact of hsa-miR-99a abnormal expression on Down syndrome heart and amniocytes transcriptome. Results: We found a statistically significant up-regulation of the mature form of miR-99a, but not pri-miR-99a, in the amniotic fluid samples from Down syndrome pregnancies with female fetuses. GATHER functional enrichment analysis of miRWalk3.0-predicted targets from Down syndrome amniocytes and fetal hearts transcriptome GEODataSets outlined both focal adhesion and cytokine-cytokine receptor interaction signaling as novel signaling pathways impacted by miR-99a and associated with cardiac defects in female Down syndrome patients. Conclusions: The significant overexpression of miR-99a, but not pri-miR-99a, points towards an alteration of the post-transcriptional mechanisms of hsa-miR-99a maturation and/or stability in the female trisomic milieu, with a potential impact on signaling pathways important for proper development of the heart.
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Affiliation(s)
- Anda-Cornelia Vizitiu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Nr. 2, Timisoara 300041, Romania;
| | - Danae Stambouli
- CytoGenomic Medical Laboratory, Calea Floreasca Nr. 35, Sector 1, Bucharest 014451, Romania; (D.S.); (A.-G.P.)
| | - Anca-Gabriela Pavel
- CytoGenomic Medical Laboratory, Calea Floreasca Nr. 35, Sector 1, Bucharest 014451, Romania; (D.S.); (A.-G.P.)
| | - Maria-Cezara Muresan
- Obstetrics and Gynecology Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania (D.M.A.)
| | - Diana Maria Anastasiu
- Obstetrics and Gynecology Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania (D.M.A.)
| | - Cristina Bejinar
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania; (C.B.); (A.A.); (C.M.)
| | - Anda Alexa
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania; (C.B.); (A.A.); (C.M.)
| | - Catalin Marian
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania; (C.B.); (A.A.); (C.M.)
| | - Ioan Ovidiu Sirbu
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania; (C.B.); (A.A.); (C.M.)
- Correspondence: ; Tel.: +40-756-136-272
| | - Laurentiu Sima
- Surgical Semiology Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania;
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79
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Chen Y, Shen Y, Lin P, Tong D, Zhao Y, Allesina S, Shen X, Wu CI. Gene regulatory network stabilized by pervasive weak repressions: microRNA functions revealed by the May-Wigner theory. Natl Sci Rev 2019; 6:1176-1188. [PMID: 34691996 PMCID: PMC8291590 DOI: 10.1093/nsr/nwz076] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 01/01/2023] Open
Abstract
Food web and gene regulatory networks (GRNs) are large biological networks, both of which can be analyzed using the May-Wigner theory. According to the theory, networks as large as mammalian GRNs would require dedicated gene products for stabilization. We propose that microRNAs (miRNAs) are those products. More than 30% of genes are repressed by miRNAs, but most repressions are too weak to have a phenotypic consequence. The theory shows that (i) weak repressions cumulatively enhance the stability of GRNs, and (ii) broad and weak repressions confer greater stability than a few strong ones. Hence, the diffuse actions of miRNAs in mammalian cells appear to function mainly in stabilizing GRNs. The postulated link between mRNA repression and GRN stability can be seen in a different light in yeast, which do not have miRNAs. Yeast cells rely on non-specific RNA nucleases to strongly degrade mRNAs for GRN stability. The strategy is suited to GRNs of small and rapidly dividing yeast cells, but not the larger mammalian cells. In conclusion, the May-Wigner theory, supplanting the analysis of small motifs, provides a mathematical solution to GRN stability, thus linking miRNAs explicitly to 'developmental canalization'.
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Affiliation(s)
- Yuxin Chen
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yang Shen
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
- Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach an der Riß, Germany
| | - Pei Lin
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ding Tong
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT 06520, UK
| | - Yixin Zhao
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Stefano Allesina
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, UK
| | - Xu Shen
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chung-I Wu
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, UK
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80
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Kingston ER, Bartel DP. Global analyses of the dynamics of mammalian microRNA metabolism. Genome Res 2019; 29:1777-1790. [PMID: 31519739 PMCID: PMC6836734 DOI: 10.1101/gr.251421.119] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/29/2019] [Indexed: 12/30/2022]
Abstract
Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 110 ± 50 copies/cell/min, which exceeds rates reported for any mRNAs. These duplexes are rapidly loaded into Argonaute, with <30 min typically required for duplex loading and silencing-complex maturation. Within Argonaute, guide strands have stabilities that vary by 100-fold. Half-lives also vary globally between cell lines, with median values ranging from 11 to 34 h in mESCs and contact-inhibited MEFs, respectively. Moreover, relative half-lives for individual miRNAs vary between cell types, implying the influence of cell-specific factors in dictating turnover rate. The apparent influence of miRNA regions most important for targeting, together with the effect of one target on miR-7 accumulation, suggest that targets fulfill this role. Analysis of the tailing and trimming of miRNA 3' termini showed that the flux was typically greatest through the isoform tailed with a single uridine, although changes in this flux did not correspond to changes in stability, which suggested that the processes of tailing and trimming might be independent from that of decay. Together, these results establish a framework for describing the dynamics and regulation of miRNAs throughout their life cycle.
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Affiliation(s)
- Elena R Kingston
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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81
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Grau Ribes A, De Decker Y, Rongy L. Connecting gene expression to cellular movement: A transport model for cell migration. Phys Rev E 2019; 100:032412. [PMID: 31639952 DOI: 10.1103/physreve.100.032412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Indexed: 12/13/2022]
Abstract
The adhesion properties and the mobility of biological cells play key roles in the propagation of cancer. These properties are expected to depend on intracellular processes and on the concentrations of chemicals inside the cell. While most existing reaction-diffusion models for cell migration consider that cell mobility and proliferation rate are constant or depend on an external diffusing species, they do not include the gene expression dynamics taking place in moving cells that affect cellular transport. In this work, we propose a multiscale model where mobility and proliferation depend explicitly on the cell's internal state. We focus more specifically on the case of cellular mobility in epithelial tissues. Wound-healing experiments have demonstrated that the loss of a key protein, E-cadherin, results in a significant increase in both mobility and invasiveness of epithelial cells, with dramatic consequences on cancer progression. We can reproduce the results of these experiments under various genetic conditions with a single set of parameters.
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Affiliation(s)
- Alexis Grau Ribes
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Yannick De Decker
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Laurence Rongy
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
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82
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Simmonds RE. Transient up-regulation of miR-155-3p by lipopolysaccharide in primary human monocyte-derived macrophages results in RISC incorporation but does not alter TNF expression. Wellcome Open Res 2019; 4:43. [PMID: 31641696 PMCID: PMC6790912 DOI: 10.12688/wellcomeopenres.15065.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background: The innate immune response is a tightly regulated process that reacts rapidly in response to pathogen-associated molecular patterns (PAMPs) such as lipopolysaccharide (LPS). Evidence is accumulating that microRNAs contribute to this, although few studies have examined the early events that constitute the “primary” response. Methods: LPS-dependent changes to miRNA expression were studied in primary human monocyte-derived macrophages (1°MDMs). An unbiased screen by microarray was validated by qPCR and a method for the absolute quantitation of miRNAs was also developed, utilising 5’ phosphorylated RNA oligonucleotide templates. RNA immunoprecipitation was performed to explore incorporation of miRNAs into the RNA-induced silencing complex (RISC). The effect of miRNA functional inhibition on TNF expression (mRNA and secretion) was investigated. Results: Of the 197 miRNAs expressed in 1°MDMs, only five were induced >1.5-fold. The most strongly induced was miR-155-3p, the partner strand to miR-155-5p, which are both derived from the MIR155HG/BIC gene (pri-miR-155). The abundance of miR-155-3p was induced transiently ~250-fold at 2-4hrs and then returned towards baseline, mirroring pri-miR-155. Other PAMPs, IL-1β, and TNF caused similar responses. IL-10, NF-κB, and JNK inhibition reduced these responses, unlike cytokine-suppressing mycolactone. Absolute quantitation revealed that miRNA abundance varies widely from donor-to-donor, and showed that miR-155-3p abundance is substantially less than miR-155-5p in unstimulated cells. However, at its peak there were 446-1,113 copies/cell, and miR-155-3p was incorporated into the RISC with an efficiency similar to miR-16-5p and miR-155-5p. Inhibition of neither miRNA affected TNF secretion after 2hrs in 1°MDMs, but technical challenges here are noted. Conclusions: Dynamic regulation of miRNAs during the primary response is rare, with the exception of miR-155-3p. Further work is required to establish whether its low abundance, even at the transient peak, is sufficient for biological activity and to determine whether there are specific mechanisms determining its biogenesis from miR-155 precursors
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Affiliation(s)
- Rachel E Simmonds
- Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK.,Cytokine and Signal Transduction Laboratory, Kennedy Institute of Rheumatology, London, W6 8LH, UK
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83
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Hosseinpour S, He Y, Nanda A, Ye Q. MicroRNAs Involved in the Regulation of Angiogenesis in Bone Regeneration. Calcif Tissue Int 2019; 105:223-238. [PMID: 31175386 DOI: 10.1007/s00223-019-00571-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/01/2019] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) as a newly founded and thriving non-coding endogenous class of molecules which regulate many cellular pathways after transcription have been extensively investigated in regenerative medicine. In this systematic review, we sought to analyze miRNAs-mediated therapeutic approaches for influencing angiogenesis in bone tissue/bone regeneration. An electronic search in MEDLINE, Scopus, EMBASE, Cochrane library, web of science, and google scholar with no time limit were done on English publications. All types of original articles which a miRNA for angiogenesis in bone regeneration were included in our review. In the process of reviewing, we used PRISMA guideline and, SYRCLE's and science in risk assessment and policy tools for analyzing risk of bias. Among 751 initial retrieved records, 16 studies met the inclusion criteria and were fully assessed in this review. 275 miRNAs, one miRNA 195~497 cluster, and one Cysteine-rich 61 short hairpin RNA were differentially expressed during bone regeneration with 24 predicted targets reported in these studies. Among these miRNAs, miRNA-7b, -9, -21, -26a, -27a, -210, -378, -195~497 cluster, -378 and -675 positively promoted both angiogenesis and osteogenesis, whereas miRNA-10a, -222 and -494 inhibited both processes. The most common target was vasculoendothelial growth factor-signaling pathway. Recent evidence has demonstrated that miRNAs actively participated in angio-osteogenic coupling that can improve their therapeutic potentials for the treatment of bone-related diseases and bone regeneration. However, there is still need for further research to unravel the exact mechanisms.
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Affiliation(s)
- Sepanta Hosseinpour
- School of Dentistry, The University of Queensland, Herston, Brisbane, QLD, 4006, Australia
| | - Yan He
- School of Dentistry, The University of Queensland, Herston, Brisbane, QLD, 4006, Australia
| | - Ashwin Nanda
- School of Dentistry, The University of Queensland, Herston, Brisbane, QLD, 4006, Australia
| | - Qingsong Ye
- School of Dentistry, The University of Queensland, Herston, Brisbane, QLD, 4006, Australia.
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84
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MicroRNA (miRNA)-to-miRNA Regulation of Programmed Cell Death 4 (PDCD4). Mol Cell Biol 2019; 39:MCB.00086-19. [PMID: 31235478 PMCID: PMC6712940 DOI: 10.1128/mcb.00086-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/08/2019] [Indexed: 12/11/2022] Open
Abstract
The regulation of tumor suppressor genes by microRNAs (miRNAs) is often demonstrated as a one-miRNA-to-one-target relationship. However, given the large number of miRNA sites within a 3' untranslated region (UTR), most targets likely undergo miRNA cooperation or combinatorial action. Programmed cell death 4 (PDCD4), an important tumor suppressor, prevents neoplastic events and is commonly downregulated in cancer. This study investigates the relationship between miRNA 21 (miR-21) and miR-499 in regulating PDCD4. This was explored using miRNA overexpression, mutational analysis of the PDCD4 3' UTR to assess regulation at each miRNA site, and 50% inhibitory concentration (IC50) calculations for combinatorial behavior. We demonstrate that the first miR-499 binding site within PDCD4 is inactive, but the two remaining sites are both required for PDCD4 suppression. Additionally, the binding of miR-21 to PDCD4 influenced miR-499 activity through an increase in its silencing potency and stabilization of its mature form. Furthermore, adjoining miRNA sites more than 35 nucleotides (nt) apart could potentially regulate thousands of 3' UTRs, similar to that observed between miR-21 and miR-499. The regulation of PDCD4 serves as a unique example of regulatory action by multiple miRNAs. This relationship was predicted to occur on thousands of targets and may represent a wider mode of miRNA regulation.
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85
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Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S, Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ. Structural Basis for Target-Directed MicroRNA Degradation. Mol Cell 2019; 75:1243-1255.e7. [PMID: 31353209 DOI: 10.1016/j.molcel.2019.06.019] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/08/2019] [Accepted: 06/14/2019] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) broadly regulate gene expression through association with Argonaute (Ago), which also protects miRNAs from degradation. However, miRNA stability is known to vary and is regulated by poorly understood mechanisms. A major emerging process, termed target-directed miRNA degradation (TDMD), employs specialized target RNAs to selectively bind to miRNAs and induce their decay. Here, we report structures of human Ago2 (hAgo2) bound to miRNAs and TDMD-inducing targets. miRNA and target form a bipartite duplex with an unpaired flexible linker. hAgo2 cannot physically accommodate the RNA, causing the duplex to bend at the linker and display the miRNA 3' end for enzymatic attack. Altering 3' end display by changing linker flexibility, changing 3' end complementarity, or mutationally inducing 3' end release impacts TDMD efficiency, leading to production of distinct 3'-miRNA isoforms in cells. Our results uncover the mechanism driving TDMD and reveal 3' end display as a key determinant regulating miRNA activity via 3' remodeling and/or degradation.
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Affiliation(s)
- Jessica Sheu-Gruttadauria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Shannon M Klum
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sonia Wang
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Therese A Yario
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Nicole T Schirle Oakdale
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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86
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Reichholf B, Herzog VA, Fasching N, Manzenreither RA, Sowemimo I, Ameres SL. Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis. Mol Cell 2019; 75:756-768.e7. [PMID: 31350118 DOI: 10.1016/j.molcel.2019.06.018] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 11/27/2022]
Abstract
Argonaute-bound microRNAs silence mRNA expression in a dynamic and regulated manner to control organismal development, physiology, and disease. We employed metabolic small RNA sequencing for a comprehensive view on intracellular microRNA kinetics in Drosophila. Based on absolute rate of biogenesis and decay, microRNAs rank among the fastest produced and longest-lived cellular transcripts, disposing up to 105 copies per cell at steady-state. Mature microRNAs are produced within minutes, revealing tight intracellular coupling of biogenesis that is selectively disrupted by pre-miRNA-uridylation. Control over Argonaute protein homeostasis generates a kinetic bottleneck that cooperates with non-coding RNA surveillance to ensure faithful microRNA loading. Finally, regulated small RNA decay enables the selective rapid turnover of Ago1-bound microRNAs, but not of Ago2-bound small interfering RNAs (siRNAs), reflecting key differences in the robustness of small RNA silencing pathways. Time-resolved small RNA sequencing opens new experimental avenues to deconvolute the timescales, molecular features, and regulation of small RNA silencing pathways in living cells.
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Affiliation(s)
- Brian Reichholf
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Veronika A Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Nina Fasching
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | | | - Ivica Sowemimo
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
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87
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Chiu HS, Martínez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A. The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Res 2019; 46:4354-4369. [PMID: 29684207 PMCID: PMC5961349 DOI: 10.1093/nar/gky286] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/04/2018] [Indexed: 12/14/2022] Open
Abstract
microRNAs (miRNAs) play key roles in cancer, but their propensity to couple their targets as competing endogenous RNAs (ceRNAs) has only recently emerged. Multiple models have studied ceRNA regulation, but these models did not account for the effects of co-regulation by miRNAs with many targets. We modeled ceRNA and simulated its effects using established parameters for miRNA/mRNA interaction kinetics while accounting for co-regulation by multiple miRNAs with many targets. Our simulations suggested that co-regulation by many miRNA species is more likely to produce physiologically relevant context-independent couplings. To test this, we studied the overlap of inferred ceRNA networks from four tumor contexts-our proposed pan-cancer ceRNA interactome (PCI). PCI was composed of interactions between genes that were co-regulated by nearly three-times as many miRNAs as other inferred ceRNA interactions. Evidence from expression-profiling datasets suggested that PCI interactions are predictive of gene expression in 12 independent tumor- and non-tumor contexts. Biochemical assays confirmed ceRNA couplings for two PCI subnetworks, including oncogenes CCND1, HIF1A and HMGA2, and tumor suppressors PTEN, RB1 and TP53. Our results suggest that PCI is enriched for context-independent interactions that are coupled by many miRNA species and are more likely to be context independent.
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Affiliation(s)
- Hua-Sheng Chiu
- Texas Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Elena V Komissarova
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Pathology and Cell Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - David Llobet-Navas
- Bellvitge Biomedical Research Institute (IDIBELL), Gran via de l'Hospitalet, 199, L'Hospitalet de Llobregat 08908, Spain
| | - Mukesh Bansal
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Evan O Paull
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - José Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pavel Sumazin
- Texas Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Califano
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Biomedical Informatics, and Department of Biochemistry and Molecular Biophysics, and Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
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88
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Over-expression of miR-34a induces rapid cognitive impairment and Alzheimer's disease-like pathology. Brain Res 2019; 1721:146327. [PMID: 31295467 DOI: 10.1016/j.brainres.2019.146327] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/28/2019] [Accepted: 07/07/2019] [Indexed: 01/24/2023]
Abstract
Autosomal dominant Alzheimer disease (AD) is caused by rare mutations in one of three specific genes. This is in contrast to idiopathic, late-onset AD (LOAD), which has a more polygenetic risk profile and represents more than 95% of cases. Previously, we have demonstrated that increased expression of microRNA (miRNA)-34a (miR-34a) in AD brain targets genes linked to synaptic plasticity, energy metabolism, and resting state network activity. Here we report the generation of a heterozygous, conditional miR-34a overexpression mouse (miR-34a+/-(TetR-TetO-miR-34a) Transgenic Mice). Doxycycline-treated mice of either sex exhibited profound behavioral impairment compared to untreated groups with only 1-2 months of over-expression of miR-34a. Cognitive impairment of individual mice in T- and Y-maze tasks correlated with elevated miR-34a expression in many parts of the brain including the hippocampus and prefrontal cortex, regions which are known to be involved in this task and implicated in LOAD dysfunction. Immunocytochemistry of brain sections from mice show high amyloid β and phosphorylated tau-specific staining in the hippocampus and cortex. Analysis of protein samples from these mice revealed that miR-34a targets specific genes involved in memory formation, amyloid precursor protein (APP) metabolism and phosphorylation-dephosphorylation of tau. Thus, our results suggest that the polygenetic dysfunction caused by miR-34a may occur in LOAD and disclose miR-34a as a potential therapeutic target. SIGNIFICANCE STATEMENT: Late-onset Alzheimer disease (LOAD) is associated with multiple gene alleles, a polygenetic profile of risk factors that is difficult to model in animals. Our approach to modeling LOAD was to produce a conditional over-expressing, miR-34a mouse using doxycycline-induction to activate expression. We observed that miR-34a over-expression results in a rapid cognitive impairment, associated with accumulation of intracellular Aβ and tau hyperphosphorylation in multiple brain regions. Targets for miR-34a, including ADAM10, NMDAR 2B, and SIRT1 RNAs, were profoundly reduced by miR-34a over-expression. Collectively, these results indicate that a rapid, profound cognitive decline and Alzheimer's disease neuropathology can be induced with miR-34a over-expression, suggesting that this animal model may represent a polygenetic risk factor model for LOAD.
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89
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Wong RS, Chen YY, Smolke CD. Regulation of T cell proliferation with drug-responsive microRNA switches. Nucleic Acids Res 2019; 46:1541-1552. [PMID: 29244152 PMCID: PMC5815133 DOI: 10.1093/nar/gkx1228] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/30/2017] [Indexed: 11/21/2022] Open
Abstract
As molecular and cellular therapies advance in the clinic, the role of genetic regulation is becoming increasingly important for controlling therapeutic potency and safety. The emerging field of mammalian synthetic biology provides promising tools for the construction of regulatory platforms that can intervene with endogenous pathways and control cell behavior. Recent work has highlighted the development of synthetic biological systems that integrate sensing of molecular signals to regulated therapeutic function in various disease settings. However, the toxicity and limited dosing of currently available molecular inducers have largely inhibited translation to clinical settings. In this work, we developed synthetic microRNA-based genetic systems that are controlled by the pharmaceutical drug leucovorin, which is readily available and safe for prolonged administration in clinical settings. We designed microRNA switches to target endogenous cytokine receptor subunits (IL-2Rβ and γc) that mediate various signaling pathways in T cells. We demonstrate the function of these control systems by effectively regulating T cell proliferation with the drug input. Each control system produced unique functional responses, and combinatorial targeting of multiple receptor subunits exhibited greater repression of cell growth. This work highlights the potential use of drug-responsive genetic control systems to improve the management and safety of cellular therapeutics.
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Affiliation(s)
- Remus S Wong
- Department of Bioengineering, 443 Via Ortega, MC 4245, Stanford University, Stanford, CA 94305, USA
| | - Yvonne Y Chen
- Department of Chemical and Biomolecular Engineering, 420 Westwood Plaza, Boelter Hall 5531, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Christina D Smolke
- Department of Bioengineering, 443 Via Ortega, MC 4245, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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90
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Oncogenic Biogenesis of pri-miR-17∼92 Reveals Hierarchy and Competition among Polycistronic MicroRNAs. Mol Cell 2019; 75:340-356.e10. [PMID: 31253575 DOI: 10.1016/j.molcel.2019.05.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/26/2019] [Accepted: 05/23/2019] [Indexed: 01/07/2023]
Abstract
The microRNAs encoded by the miR-17∼92 polycistron are commonly overexpressed in cancer and orchestrate a wide range of oncogenic functions. Here, we identify a mechanism for miR-17∼92 oncogenic function through the disruption of endogenous microRNA (miRNA) processing. We show that, upon oncogenic overexpression of the miR-17∼92 primary transcript (pri-miR-17∼92), the microprocessor complex remains associated with partially processed intermediates that aberrantly accumulate. These intermediates reflect a series of hierarchical and conserved steps in the early processing of the pri-miR-17∼92 transcript. Encumbrance of the microprocessor by miR-17∼92 intermediates leads to the broad but selective downregulation of co-expressed polycistronic miRNAs, including miRNAs derived from tumor-suppressive miR-34b/c and from the Dlk1-Dio3 polycistrons. We propose that the identified steps of polycistronic miR-17∼92 biogenesis contribute to the oncogenic re-wiring of gene regulation networks. Our results reveal previously unappreciated functional paradigms for polycistronic miRNAs in cancer.
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91
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Layne TR, Green RA, Lewis CA, Nogales F, Dawson Cruz TC, Zehner ZE, Seashols-Williams SJ. microRNA Detection in Blood, Urine, Semen, and Saliva Stains After Compromising Treatments. J Forensic Sci 2019; 64:1831-1837. [PMID: 31184791 DOI: 10.1111/1556-4029.14113] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023]
Abstract
Evaluation of microRNA (miRNA) expression as a potential method for forensic body fluid identification has been the subject of investigation over the past several years. Because of their size and encapsulation within proteins and lipids, miRNAs are inherently less susceptible to degradation than other RNAs. In this work, blood, urine, semen, and saliva were exposed to environmental and chemical conditions mimicking sample compromise at the crime scene. For many treated samples, including 100% of blood samples, miRNAs remained detectable, comparable to the untreated control. Sample degradation varied by body fluid and treatment, with blood remarkably resistant, while semen and saliva are more susceptible to environmental insult. Body fluid identification using relative miRNA expression of blood and semen of the exposed samples was 100% and 94%, respectively. Given the overall robust results herein, the case is strengthened for the use of miRNAs as a molecular method for body fluid identification.
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Affiliation(s)
- Tiffany R Layne
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Raquel A Green
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Carolyn A Lewis
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Francy Nogales
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Tracey C Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Zendra E Zehner
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Box 980614, Richmond, Virginia, 23298-0614
| | - Sarah J Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
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92
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Crosby P, Hamnett R, Putker M, Hoyle NP, Reed M, Karam CJ, Maywood ES, Stangherlin A, Chesham JE, Hayter EA, Rosenbrier-Ribeiro L, Newham P, Clevers H, Bechtold DA, O'Neill JS. Insulin/IGF-1 Drives PERIOD Synthesis to Entrain Circadian Rhythms with Feeding Time. Cell 2019; 177:896-909.e20. [PMID: 31030999 PMCID: PMC6506277 DOI: 10.1016/j.cell.2019.02.017] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/26/2018] [Accepted: 02/11/2019] [Indexed: 01/21/2023]
Abstract
In mammals, endogenous circadian clocks sense and respond to daily feeding and lighting cues, adjusting internal ∼24 h rhythms to resonate with, and anticipate, external cycles of day and night. The mechanism underlying circadian entrainment to feeding time is critical for understanding why mistimed feeding, as occurs during shift work, disrupts circadian physiology, a state that is associated with increased incidence of chronic diseases such as type 2 (T2) diabetes. We show that feeding-regulated hormones insulin and insulin-like growth factor 1 (IGF-1) reset circadian clocks in vivo and in vitro by induction of PERIOD proteins, and mistimed insulin signaling disrupts circadian organization of mouse behavior and clock gene expression. Insulin and IGF-1 receptor signaling is sufficient to determine essential circadian parameters, principally via increased PERIOD protein synthesis. This requires coincident mechanistic target of rapamycin (mTOR) activation, increased phosphoinositide signaling, and microRNA downregulation. Besides its well-known homeostatic functions, we propose insulin and IGF-1 are primary signals of feeding time to cellular clocks throughout the body. Insulin and IGF-1 are a systemic synchronizing cue for circadian rhythms in mammals Insulin and IGF-1 signaling rapidly upregulates translation of PERIOD clock proteins Coincident signaling facilitates selective induction of PERIOD synthesis Circadian disruption is recapitulated by mistimed insulin in cell and animal models
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Affiliation(s)
- Priya Crosby
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Ryan Hamnett
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Marrit Putker
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Hubrecht Institute, Utrecht 3584 CT, the Netherlands
| | | | - Martin Reed
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | | | | | - Edward A Hayter
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | | | - Peter Newham
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge CB4 0FZ, UK
| | - Hans Clevers
- Hubrecht Institute, Utrecht 3584 CT, the Netherlands; Princess Máxima Centre, Utrecht 3584 CS, the Netherlands
| | - David A Bechtold
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - John S O'Neill
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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93
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Vechetti IJ, Wen Y, Chaillou T, Murach KA, Alimov AP, Figueiredo VC, Dal-Pai-Silva M, McCarthy JJ. Life-long reduction in myomiR expression does not adversely affect skeletal muscle morphology. Sci Rep 2019; 9:5483. [PMID: 30940834 PMCID: PMC6445125 DOI: 10.1038/s41598-019-41476-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 03/11/2019] [Indexed: 12/20/2022] Open
Abstract
We generated an inducible, skeletal muscle-specific Dicer knockout mouse to deplete microRNAs in adult skeletal muscle. Following tamoxifen treatment, Dicer mRNA expression was significantly decreased by 87%. Wild-type (WT) and Dicer knockout (KO) mice were subjected to either synergist ablation or hind limb suspension for two weeks. There was no difference in muscle weight with hypertrophy or atrophy between WT and KO groups; however, even with the significant loss of Dicer expression, myomiR (miR-1, -133a and -206) expression was only reduced by 38% on average. We next aged WT and KO mice for ~22 months following Dicer inactivation to determine if myomiR expression would be further reduced over a prolonged timeframe and assess the effects of myomiR depletion on skeletal muscle phenotype. Skeletal muscle Dicer mRNA expression remained significantly decreased by 80% in old KO mice and sequencing of cloned Dicer mRNA revealed the complete absence of the floxed exons in KO skeletal muscle. Despite a further reduction of myomiR expression to ~50% of WT, no change was observed in muscle morphology between WT and KO groups. These results indicate the life-long reduction in myomiR levels did not adversely affect skeletal muscle phenotype and suggest the possibility that microRNA expression is uniquely regulated in skeletal muscle.
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Affiliation(s)
- Ivan J Vechetti
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
- Department of Morphology, São Paulo State University, Institute of Biosciences, Botucatu, Brazil
| | - Yuan Wen
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
| | - Thomas Chaillou
- Örebro University, School of Health Sciences, Örebro, Sweden
| | - Kevin A Murach
- Department of Rehabilitation Sciences, College of Health Sciences, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
| | - Alexander P Alimov
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
| | - Vandre C Figueiredo
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA
- Department of Rehabilitation Sciences, College of Health Sciences, Kentucky, USA
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA
| | - Maeli Dal-Pai-Silva
- Department of Morphology, São Paulo State University, Institute of Biosciences, Botucatu, Brazil
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Kentucky, USA.
- Center for Muscle Biology University of Kentucky, Lexington, Kentucky, USA.
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94
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Nogimori T, Furutachi K, Ogami K, Hosoda N, Hoshino SI. A novel method for stabilizing microRNA mimics. Biochem Biophys Res Commun 2019; 511:422-426. [PMID: 30799083 DOI: 10.1016/j.bbrc.2019.02.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that negatively regulate gene expression at post-transcriptional level via translational repression and/or mRNA degradation. miRNAs are associated with many cellular processes, and down-regulation of miRNAs causes numerous diseases including cancer, neurological disorders, inflammation, and cardiovascular diseases, for which miRNA replacement therapy has emerged as a promising approach. This approach aims to restore down-regulated miRNAs using synthetic miRNA mimics. However, it remains a critical issue that miRNA mimics are unstable and transient in cells. Here, we first show that miRNA mimics are rapidly degraded by a mechanism different from Tudor-staphylococcal/micrococcal-like nuclease (TSN)-mediated miRNA decay, which degrades endogenous miRNAs, and newly identified 2'-5'-oligoadenylate synthetase (OAS)/RNase L as key factors responsible for the degradation of miRNA mimics in human cells. Our results suggest that the OAS1 recognizes miRNA mimics and produces 2'-5'-oligoadenylates (2-5A), which leads to the activation of latent endoribonuclease RNase L to degrade miRNA mimics. A small-molecule inhibitor that blocks RNase L can stabilize miRNA mimics. These findings provide a promising method for the stabilization of miRNA mimics, as well as for the efficient miRNA replacement therapy.
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Affiliation(s)
- Takuto Nogimori
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Kazuya Furutachi
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Koichi Ogami
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Nao Hosoda
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Shin-Ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
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95
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Synthetic Cannabinoids Influence the Invasion of Glioblastoma Cell Lines in a Cell- and Receptor-Dependent Manner. Cancers (Basel) 2019; 11:cancers11020161. [PMID: 30709059 PMCID: PMC6406558 DOI: 10.3390/cancers11020161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 01/10/2023] Open
Abstract
The current treatment of glioblastoma is not sufficient, since they are heterogeneous and often resistant to chemotherapy. Earlier studies demonstrated effects of specific cannabinoid receptor (CB) agonists on the invasiveness of glioblastoma cell lines, but the exact mechanism remained unclear. Three human glioblastoma cell lines were treated with synthetic CB ligands. The effect of cannabinoids on microRNAs (miRs), Akt, and on the expression of proliferation and apoptosis markers were analyzed. Furthermore, in a model of organotypic hippocampal slice cultures cannabinoid mediated changes in the invasiveness were assessed. MicroRNAs and the activation of Akt which are related to cell migration, apoptosis, and proliferation were evaluated and found not to be associated with changes in the invasiveness after treatment with CB ligands. Also proliferation and/or apoptosis were not altered after treatment. The effects of cannabinoids on invasiveness could be blocked by the application of receptor antagonists and are likely mediated via CB₁/CB₂. In conclusion, our results suggest that cannabinoids can influence glioblastoma cell invasion in a receptor and cell type specific manner that is independent of proliferation and apoptosis. Thus, cannabinoids can potentially be used in the future as an addition to current therapy.
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96
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Arai T, Kojima S, Yamada Y, Sugawara S, Kato M, Yamazaki K, Naya Y, Ichikawa T, Seki N. Pirin: a potential novel therapeutic target for castration-resistant prostate cancer regulated by miR-455-5p. Mol Oncol 2018; 13:322-337. [PMID: 30444038 PMCID: PMC6360383 DOI: 10.1002/1878-0261.12405] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/16/2018] [Accepted: 10/27/2018] [Indexed: 12/11/2022] Open
Abstract
Androgen deprivation therapy is frequently used to treat prostate cancer (PCa), but resistance can occur, a condition known as castration‐resistant prostate cancer (CRPC). Thus, novel approaches for identification of CRPC are important for designing effective PCa treatments. Analysis of microRNA (miRNA) expression signatures by RNA sequencing showed that both passenger and guide strands of the miR‐455‐duplex (miR‐455‐5p and miR‐455‐3p, respectively) acted as antitumor miRNAs in PCa cells. The involvement of miRNA passenger strands in cancer pathogenesis is a novel concept for miRNA functionality. Based on a large patient cohort in The Cancer Genome Atlas, expression of eight miR‐455‐5p/‐3p target genes (PIR: P = 0.0137, LRP8: P = 0.0495, IGFBP3: P = 0.0172, DMBX1: P = 0.0175, CCDC64: P = 0.0446, TUBB1: P = 0.0149, KIF21B: P = 0.0336, and NFAM1: P = 0.0013) was significantly associated with poor prognosis of PCa patients. Here, we focused on PIR (pirin), a highly conserved member of the cupin superfamily. PIR expression was directly regulated by miR‐455‐5p, and PIR overexpression was detected in hormone‐sensitive prostate cancer (HSPC) surgical specimens and CRPC autopsy specimens. Loss‐of‐function assays using siRNA or an inhibitor (bisamide) showed that downregulation of PIR expression blocked cancer cell migration and invasion. Moreover, the miR‐455‐5p/PIR axis contributed to cancer cell aggressiveness. These results suggest that PIR might be a promising diagnostic marker for HSPC and CRPC. Furthermore, CRPC treatment strategies targeting PIR may be possible in the future. Identification of antitumor miRNAs, including miRNA passenger strands, may contribute to the development of new diagnostic markers and therapeutic strategies for CRPC.
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Affiliation(s)
- Takayuki Arai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Japan
| | - Satoko Kojima
- Department of Urology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Yasutaka Yamada
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Japan
| | - Sho Sugawara
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Japan
| | - Mayuko Kato
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Japan
| | - Kazuto Yamazaki
- Department of Pathology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Yukio Naya
- Department of Urology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Tomohiko Ichikawa
- Department of Urology, Chiba University Graduate School of Medicine, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Japan
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97
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Fuchs Wightman F, Giono LE, Fededa JP, de la Mata M. Target RNAs Strike Back on MicroRNAs. Front Genet 2018; 9:435. [PMID: 30333855 PMCID: PMC6175985 DOI: 10.3389/fgene.2018.00435] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are extensively studied regulatory non-coding small RNAs that silence animal genes throughout most biological processes, typically doing so by binding to partially complementary sequences within target RNAs. A plethora of studies has described detailed mechanisms for microRNA biogenesis and function, as well as their temporal and spatial regulation during development. By inducing translational repression and/or degradation of their target RNAs, microRNAs can contribute to achieve highly specific cell- or tissue-specific gene expression, while their aberrant expression can lead to disease. Yet an unresolved aspect of microRNA biology is how such small RNA molecules are themselves cleared from the cell, especially under circumstances where fast microRNA turnover or specific degradation of individual microRNAs is required. In recent years, it was unexpectedly found that binding of specific target RNAs to microRNAs with extensive complementarity can reverse the outcome, triggering degradation of the bound microRNAs. This emerging pathway, named TDMD for Target RNA-Directed MicroRNA Degradation, leads to microRNA 3'-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3' end, and highly specific microRNA loss, providing a new layer of microRNA regulation. Originally described in flies and known to be triggered by viral RNAs, novel endogenous instances of TDMD have been uncovered and are now starting to be understood. Here, we review our current knowledge of this pathway and its potential role in the control and diversification of microRNA expression patterns.
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Affiliation(s)
- Federico Fuchs Wightman
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciana E Giono
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Juan Pablo Fededa
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Manuel de la Mata
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
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98
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Controlled Non-Viral Gene Delivery in Cartilage and Bone Repair: Current Strategies and Future Directions. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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99
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Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation. Nat Commun 2018; 9:3119. [PMID: 30087332 PMCID: PMC6081425 DOI: 10.1038/s41467-018-05182-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/19/2018] [Indexed: 01/19/2023] Open
Abstract
Little is known about miRNA decay. A target-directed miRNA degradation mechanism (TDMD) has been suggested, but further investigation on endogenous targets is necessary. Here, we identify hundreds of targets eligible for TDMD and show that an endogenous RNA (Serpine1) controls the degradation of two miRNAs (miR-30b-5p and miR-30c-5p) in mouse fibroblasts. In our study, TDMD occurs when the target is expressed at relatively low levels, similar in range to those of its miRNAs (100-200 copies per cell), and becomes more effective at high target:miRNA ratios (>10:1). We employ CRISPR/Cas9 to delete the miR-30 responsive element within Serpine1 3'UTR and interfere with TDMD. TDMD suppression increases miR-30b/c levels and boosts their activity towards other targets, modulating gene expression and cellular phenotypes (i.e., cell cycle re-entry and apoptosis). In conclusion, a sophisticated regulatory layer of miRNA and gene expression mediated by specific endogenous targets exists in mammalian cells.
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100
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Zhou L, Lim MYT, Kaur P, Saj A, Bortolamiol-Becet D, Gopal V, Tolwinski N, Tucker-Kellogg G, Okamura K. Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development. eLife 2018; 7:e38389. [PMID: 30024380 PMCID: PMC6066331 DOI: 10.7554/elife.38389] [Citation(s) in RCA: 26] [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: 05/16/2018] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Mature microRNAs (miRNAs) are processed from primary transcripts (pri-miRNAs), and their expression is controlled at transcriptional and post-transcriptional levels. However, how regulation at multiple levels achieves precise control remains elusive. Using published and new datasets, we profile a time course of mature and pri-miRNAs in Drosophila embryos and reveal the dynamics of miRNA production and degradation as well as dynamic changes in pri-miRNA isoform selection. We found that 5' nucleotides influence stability of mature miRNAs. Furthermore, distinct half-lives of miRNAs from the mir-309 cluster shape their temporal expression patterns, and the importance of rapid degradation of the miRNAs in gene regulation is detected as distinct evolutionary signatures at the target sites in the transcriptome. Finally, we show that rapid degradation of miR-3/-309 may be important for regulation of the planar cell polarity pathway component Vang. Altogether, the results suggest that complex mechanisms regulate miRNA expression to support normal development.
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Affiliation(s)
- Li Zhou
- Temasek Life Sciences LaboratorySingaporeSingapore
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Mandy Yu Theng Lim
- Temasek Life Sciences LaboratorySingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Prameet Kaur
- Division of ScienceYale-NUS CollegeSingaporeSingapore
| | - Abil Saj
- Cancer Therapeutics and Stratified OncologyGenome Institute of SingaporeSingaporeSingapore
| | | | - Vikneswaran Gopal
- Department of Statistics and Applied Probability, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Nicholas Tolwinski
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
- Division of ScienceYale-NUS CollegeSingaporeSingapore
| | - Greg Tucker-Kellogg
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Katsutomo Okamura
- Temasek Life Sciences LaboratorySingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
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