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Bahojb Mahdavi SZ, Jebelli A, Aghbash PS, Baradaran B, Amini M, Oroojalian F, Pouladi N, Baghi HB, de la Guardia M, Mokhtarzadeh AA. A comprehensive overview on the crosstalk between microRNAs and viral pathogenesis and infection. Med Res Rev 2024. [PMID: 39185567 DOI: 10.1002/med.22073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 04/11/2023] [Accepted: 08/04/2024] [Indexed: 08/27/2024]
Abstract
Infections caused by viruses as the smallest infectious agents, pose a major threat to global public health. Viral infections utilize different host mechanisms to facilitate their own propagation and pathogenesis. MicroRNAs (miRNAs), as small noncoding RNA molecules, play important regulatory roles in different diseases, including viral infections. They can promote or inhibit viral infection and have a pro-viral or antiviral role. Also, viral infections can modulate the expression of host miRNAs. Furthermore, viruses from different families evade the host immune response by producing their own miRNAs called viral miRNAs (v-miRNAs). Understanding the replication cycle of viruses and their relation with host miRNAs and v-miRNAs can help to find new treatments against viral infections. In this review, we aim to outline the structure, genome, and replication cycle of various viruses including hepatitis B, hepatitis C, influenza A virus, coronavirus, human immunodeficiency virus, human papillomavirus, herpes simplex virus, Epstein-Barr virus, Dengue virus, Zika virus, and Ebola virus. We also discuss the role of different host miRNAs and v-miRNAs and their role in the pathogenesis of these viral infections.
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Affiliation(s)
- Seyedeh Zahra Bahojb Mahdavi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Asiyeh Jebelli
- Department of Biological Science, Faculty of Basic Science, Higher Education Institute of Rab-Rashid, Tabriz, Iran
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Nasser Pouladi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Burjassot, Valencia, Spain
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2
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McJunkin K, Gottesman S. What goes up must come down: off switches for regulatory RNAs. Genes Dev 2024; 38:597-613. [PMID: 39111824 DOI: 10.1101/gad.351934.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Small RNAs base pair with and regulate mRNA translation and stability. For both bacterial small regulatory RNAs and eukaryotic microRNAs, association with partner proteins is critical for the stability and function of the regulatory RNAs. We review the mechanisms for degradation of these RNAs: displacement of the regulatory RNA from its protein partner (in bacteria) or destruction of the protein and its associated microRNAs (in eukaryotes). These mechanisms can allow specific destruction of a regulatory RNA via pairing with a decay trigger RNA or function as global off switches by disrupting the stability or function of the protein partner.
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Affiliation(s)
- Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, Maryland 20892, USA;
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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3
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Aghajani Mir M. Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105613. [PMID: 38844190 DOI: 10.1016/j.meegid.2024.105613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Babol University of Medical Sciences, Babol, Iran.
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4
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Ressel S, Kumar S, Bermúdez-Barrientos JR, Gordon K, Lane J, Wu J, Abreu-Goodger C, Schwarze J, Buck A. RNA-RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunity. Nucleic Acids Res 2024; 52:4872-4888. [PMID: 38412296 PMCID: PMC11109944 DOI: 10.1093/nar/gkae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 02/01/2024] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
microRNAs (miRNAs) regulate nearly all physiological processes but our understanding of exactly how they function remains incomplete, particularly in the context of viral infections. Here, we adapt a biochemical method (CLEAR-CLIP) and analysis pipeline to identify targets of miRNAs in lung cells infected with Respiratory syncytial virus (RSV). We show that RSV binds directly to miR-26 and miR-27 through seed pairing and demonstrate that these miRNAs target distinct gene networks associated with cell cycle and metabolism (miR-27) and antiviral immunity (miR-26). Many of the targets are de-repressed upon infection and we show that the miR-27 targets most sensitive to miRNA inhibition are those associated with cell cycle. Finally, we demonstrate that high confidence chimeras map to long noncoding RNAs (lncRNAs) and pseudogenes in transcriptional regulatory regions. We validate that a proportion of miR-27 and Argonaute 2 (AGO2) is nuclear and identify a long non-coding RNA (lncRNA) as a miR-27 target that is linked to transcriptional regulation of nearby genes. This work expands the target networks of miR-26 and miR-27 to include direct interactions with RSV and lncRNAs and implicate these miRNAs in regulation of key genes that impact the viral life cycle associated with cell cycle, metabolism, and antiviral immunity.
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Affiliation(s)
- Sarah Ressel
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sujai Kumar
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Katrina Gordon
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Julia Lane
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jin Wu
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jürgen Schwarze
- Child Life and Health, Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Amy H Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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5
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Kotagama K, Grimme AL, Braviner L, Yang B, Sakhawala R, Yu G, Benner LK, Joshua-Tor L, McJunkin K. Catalytic residues of microRNA Argonautes play a modest role in microRNA star strand destabilization in C. elegans. Nucleic Acids Res 2024; 52:4985-5001. [PMID: 38471816 PMCID: PMC11109956 DOI: 10.1093/nar/gkae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Many microRNA (miRNA)-guided Argonaute proteins can cleave RNA ('slicing'), even though miRNA-mediated target repression is generally cleavage-independent. Here we use Caenorhabditis elegans to examine the role of catalytic residues of miRNA Argonautes in organismal development. In contrast to previous work, mutations in presumed catalytic residues did not interfere with development when introduced by CRISPR. We find that unwinding and decay of miRNA star strands is weakly defective in the catalytic residue mutants, with the largest effect observed in embryos. Argonaute-Like Gene 2 (ALG-2) is more dependent on catalytic residues for unwinding than ALG-1. The miRNAs that displayed the greatest (albeit minor) dependence on catalytic residues for unwinding tend to form stable duplexes with their star strand, and in some cases, lowering duplex stability alleviates dependence on catalytic residues. While a few miRNA guide strands are reduced in the mutant background, the basis of this is unclear since changes were not dependent on EBAX-1, an effector of Target-Directed miRNA Degradation (TDMD). Overall, this work defines a role for the catalytic residues of miRNA Argonautes in star strand decay; future work should examine whether this role contributes to the selection pressure to conserve catalytic activity of miRNA Argonautes across the metazoan phylogeny.
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Affiliation(s)
- Kasuen Kotagama
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Acadia L Grimme
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
- Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Leah Braviner
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Bing Yang
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Rima M Sakhawala
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
- Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Guoyun Yu
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Lars Kristian Benner
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Leemor Joshua-Tor
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
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6
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Fuchs Wightman F, Lukin J, Giusti S, Soutschek M, Bragado L, Pozzi B, Pierelli M, González P, Fededa J, Schratt G, Fujiwara R, Wilusz J, Refojo D, de la Mata M. Influence of RNA circularity on Target RNA-Directed MicroRNA Degradation. Nucleic Acids Res 2024; 52:3358-3374. [PMID: 38381063 PMCID: PMC11014252 DOI: 10.1093/nar/gkae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
A subset of circular RNAs (circRNAs) and linear RNAs have been proposed to 'sponge' or block microRNA activity. Additionally, certain RNAs induce microRNA destruction through the process of Target RNA-Directed MicroRNA Degradation (TDMD), but whether both linear and circular transcripts are equivalent in driving TDMD is unknown. Here, we studied whether circular/linear topology of endogenous and artificial RNA targets affects TDMD. Consistent with previous knowledge that Cdr1as (ciRS-7) circular RNA protects miR-7 from Cyrano-mediated TDMD, we demonstrate that depletion of Cdr1as reduces miR-7 abundance. In contrast, overexpression of an artificial linear version of Cdr1as drives miR-7 degradation. Using plasmids that express a circRNA with minimal co-expressed cognate linear RNA, we show differential effects on TDMD that cannot be attributed to the nucleotide sequence, as the TDMD properties of a sequence often differ when in a circular versus linear form. By analysing RNA sequencing data of a neuron differentiation system, we further detect potential effects of circRNAs on microRNA stability. Our results support the view that RNA circularity influences TDMD, either enhancing or inhibiting it on specific microRNAs.
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Affiliation(s)
- Federico Fuchs Wightman
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires 1428, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
| | - Jerónimo Lukin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Buenos Aires 1425, Argentina
| | - Sebastián A Giusti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Buenos Aires 1425, Argentina
| | - Michael Soutschek
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich 8092, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, ETH Zürich 8092, Switzerland
| | - Laureano Bragado
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires 1428, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
| | - Berta Pozzi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires 1428, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | - María L Pierelli
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires 1428, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
| | - Paula González
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, Buenos Aires 1650, Argentina
| | - Juan P Fededa
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, Buenos Aires 1650, Argentina
| | - Gerhard Schratt
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich 8092, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, ETH Zürich 8092, Switzerland
| | - Rina Fujiwara
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX77030, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX77030, USA
| | - Damián Refojo
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Buenos Aires 1425, Argentina
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Manuel de la Mata
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires 1428, Argentina
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7
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Hiers NM, Li T, Traugot CM, Xie M. Target-directed microRNA degradation: Mechanisms, significance, and functional implications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1832. [PMID: 38448799 PMCID: PMC11098282 DOI: 10.1002/wrna.1832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a fundamental role in enabling miRNA-mediated target repression, a post-transcriptional gene regulatory mechanism preserved across metazoans. Loss of certain animal miRNA genes can lead to developmental abnormalities, disease, and various degrees of embryonic lethality. These short RNAs normally guide Argonaute (AGO) proteins to target RNAs, which are in turn translationally repressed and destabilized, silencing the target to fine-tune gene expression and maintain cellular homeostasis. Delineating miRNA-mediated target decay has been thoroughly examined in thousands of studies, yet despite these exhaustive studies, comparatively less is known about how and why miRNAs are directed for decay. Several key observations over the years have noted instances of rapid miRNA turnover, suggesting endogenous means for animals to induce miRNA degradation. Recently, it was revealed that certain targets, so-called target-directed miRNA degradation (TDMD) triggers, can "trigger" miRNA decay through inducing proteolysis of AGO and thereby the bound miRNA. This process is mediated in animals via the ZSWIM8 ubiquitin ligase complex, which is recruited to AGO during engagement with triggers. Since its discovery, several studies have identified that ZSWIM8 and TDMD are indispensable for proper animal development. Given the rapid expansion of this field of study, here, we summarize the key findings that have led to and followed the discovery of ZSWIM8-dependent TDMD. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Conner M Traugot
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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8
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Zhang C, Liu Y, Yang F, Liu Y, Wang N, Li Y, Liu Y, Qiu Z, Zhang L, You X, Gan L. MicroRNA-194-5p/Heparin-binding EGF-like growth factor signaling mediates dexamethasone-induced activation of pseudorabies virus in rat pheochromocytoma cells. Vet Microbiol 2024; 290:109974. [PMID: 38262115 DOI: 10.1016/j.vetmic.2023.109974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
Pseudorabies virus (PRV) is a neurotropic virus, which infects a wide range of mammals. The activity of PRV is gradually suppressed in hosts that have tolerated the primary infection. Increased glucocorticoid levels resulting from stressful stimuli overcome repression of PRV activity. However, the host cell mechanism involved in the activation processes under stressful conditions remains unclear. In this study, infection of rat PC-12 pheochromocytoma cells with neuronal properties using PRV at a multiplicity of infection (MOI) = 1 for 24 h made the activity of PRV be the relatively repressed state, and then incubation with 0.5 μM of the corticosteroid dexamethasone (DEX) for 4 h overcomes the relative repression of PRV activity. RNA-seq deep sequencing and bioinformatics analyses revealed different microRNA and mRNA profiles of PC-12 cells with/without PRV and/or DEX treatment. qRT-PCR and western blot analyses confirmed the negative regulatory relationship of miRNA-194-5p and its target heparin-binding EGF-like growth factor (Hbegf); a dual-luciferase reporter assay revealed that Hbegf is directly targeted by miRNA-194-5p. Further, miRNA-194-5p mock transfection contributed to PRV activation, Hbegf was downregulated in DEX-treated PRV infection cells, and Hbegf overexpression contributed to returning activated PRV to the repression state. Moreover, miRNA-194-5p overexpression resulted in reduced levels of HBEGF, c-JUN, and p-EGFR, whereas Hbegf overexpression suppressed the reduction caused by miRNA-194-5p overexpression. Overall, this study is the first to report that changes in the miR-194-5p-HBEGF/EGFR pathway in neurons are involved in DEX-induced activation of PRV, laying a foundation for the clinical prevention of stress-induced PRV activation.
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Affiliation(s)
- Chen Zhang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Yuxuan Liu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Fan Yang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Yifan Liu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Naixiu Wang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Yuhang Li
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Yanqing Liu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Zhiyun Qiu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Lin Zhang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Xiaoyan You
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture and Rural Affairs, Chongqing, China; Chongqing Key Laboratory of Pig Industry Sciences, Chongqing, China
| | - Ling Gan
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China.
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9
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Buhagiar AF, Kleaveland B. To kill a microRNA: emerging concepts in target-directed microRNA degradation. Nucleic Acids Res 2024; 52:1558-1574. [PMID: 38224449 PMCID: PMC10899785 DOI: 10.1093/nar/gkae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
MicroRNAs (miRNAs) guide Argonaute (AGO) proteins to bind mRNA targets. Although most targets are destabilized by miRNA-AGO binding, some targets induce degradation of the miRNA instead. These special targets are also referred to as trigger RNAs. All triggers identified thus far have binding sites with greater complementarity to the miRNA than typical target sites. Target-directed miRNA degradation (TDMD) occurs when trigger RNAs bind the miRNA-AGO complex and recruit the ZSWIM8 E3 ubiquitin ligase, leading to AGO ubiquitination and proteolysis and subsequent miRNA destruction. More than 100 different miRNAs are regulated by ZSWIM8 in bilaterian animals, and hundreds of trigger RNAs have been predicted computationally. Disruption of individual trigger RNAs or ZSWIM8 has uncovered important developmental and physiologic roles for TDMD across a variety of model organisms and cell types. In this review, we highlight recent progress in understanding the mechanistic basis and functions of TDMD, describe common features of trigger RNAs, outline best practices for validating trigger RNAs, and discuss outstanding questions in the field.
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Affiliation(s)
- Amber F Buhagiar
- Department of Pathology and Lab Medicine, Weill Cornell Medicine, New York, NY10065, USA
| | - Benjamin Kleaveland
- Department of Pathology and Lab Medicine, Weill Cornell Medicine, New York, NY10065, USA
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10
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Tucker EJ, Wong SW, Marri S, Ali S, Fedele AO, Michael MZ, Rojas-Canales D, Li JY, Lim CK, Gleadle JM. SARS-CoV-2 produces a microRNA CoV2-miR-O8 in patients with COVID-19 infection. iScience 2024; 27:108719. [PMID: 38226175 PMCID: PMC10788221 DOI: 10.1016/j.isci.2023.108719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024] Open
Abstract
Many viruses produce microRNAs (miRNAs), termed viral miRNAs (v-miRNAs), with the capacity to target host gene expression. Bioinformatic and cell culture studies suggest that SARS-CoV-2 can also generate v-miRNAs. This patient-based study defines the SARS-CoV-2 encoded small RNAs present in nasopharyngeal swabs of patients with COVID-19 infection using small RNA-seq. A specific conserved sequence (CoV2-miR-O8) is defined that is not expressed in other coronaviruses but is preserved in all SARS-CoV-2 variants. CoV2-miR-O8 is highly represented in nasopharyngeal samples from patients with COVID-19 infection, is detected by RT-PCR assays in patients, has features consistent with Dicer and Drosha generation as well as interaction with Argonaute and targets specific human microRNAs.
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Affiliation(s)
- Elise J. Tucker
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Soon Wei Wong
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Shashikanth Marri
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Saira Ali
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Anthony O. Fedele
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
| | - Michael Z. Michael
- College of Medicine and Public Health, Flinders University, SA, Australia
- Department of Gastroenterology, Flinders Medical Centre, SA, Australia
| | - Darling Rojas-Canales
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Jordan Y. Li
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Chuan Kok Lim
- Infectious Diseases Laboratories, SA Pathology, SA, Australia
| | - Jonathan M. Gleadle
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
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11
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Makarenkov N, Yoel U, Haim Y, Pincu Y, Bhandarkar NS, Shalev A, Shelef I, Liberty IF, Ben-Arie G, Yardeni D, Rudich A, Etzion O, Veksler-Lublinsky I. Circulating isomiRs May Be Superior Biomarkers Compared to Their Corresponding miRNAs: A Pilot Biomarker Study of Using isomiR-Ome to Detect Coronary Calcium-Based Cardiovascular Risk in Patients with NAFLD. Int J Mol Sci 2024; 25:890. [PMID: 38255963 PMCID: PMC10815227 DOI: 10.3390/ijms25020890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Circulating miRNAs are increasingly being considered as biomarkers in various medical contexts, but the value of analyzing isomiRs (isoforms of canonical miRNA sequences) has not frequently been assessed. Here we hypothesize that an in-depth analysis of the full circulating miRNA landscape could identify specific isomiRs that are stronger biomarkers, compared to their corresponding miRNA, for identifying increased CV risk in patients with non-alcoholic fatty liver disease (NAFLD)-a clinical unmet need. Plasma miRNAs were sequenced with next-generation sequencing (NGS). Liver fat content was measured with magnetic-resonance spectrometry (MRS); CV risk was determined, beyond using traditional biomarkers, by a CT-based measurement of coronary artery calcium (CAC) score and the calculation of a CAC score-based CV-risk percentile (CAC-CV%). This pilot study included n = 13 patients, age > 45 years, with an MRS-measured liver fat content of ≥5% (wt/wt), and free of overt CVD. NGS identified 1103 miRNAs and 404,022 different isomiRs, of which 280 (25%) and 1418 (0.35%), respectively, passed an abundance threshold. Eighteen (sixteen/two) circulating miRNAs correlated positively/negatively, respectively, with CAC-CV%, nine of which also significantly discriminated between high/low CV risk through ROC-AUC analysis. IsomiR-ome analyses uncovered 67 isomiRs highly correlated (R ≥ 0.55) with CAC-CV%. Specific isomiRs of miRNAs 101-3p, 144-3p, 421, and 484 exhibited stronger associations with CAC-CV% compared to their corresponding miRNA. Additionally, while miRNAs 140-3p, 223-3p, 30e-5p, and 342-3p did not correlate with CAC-CV%, specific isomiRs with altered seed sequences exhibited a strong correlation with coronary atherosclerosis burden. Their predicted isomiRs-specific targets were uniquely enriched (compared to their canonical miRNA sequence) in CV Disease (CVD)-related pathways. Two of the isomiRs exhibited discriminative ROC-AUC, and another two showed a correlation with reverse cholesterol transport from cholesterol-loaded macrophages to ApoB-depleted plasma. In summary, we propose a pipeline for exploring circulating isomiR-ome as an approach to uncover novel and strong CVD biomarkers.
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Affiliation(s)
- Nataly Makarenkov
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (N.M.); (U.Y.); (N.S.B.)
- Department of Software & Information Systems Engineering, Faculty of Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel;
| | - Uri Yoel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (N.M.); (U.Y.); (N.S.B.)
- The Endocrinology Unit, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - Yulia Haim
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (N.M.); (U.Y.); (N.S.B.)
| | - Yair Pincu
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (N.M.); (U.Y.); (N.S.B.)
| | - Nikhil S. Bhandarkar
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (N.M.); (U.Y.); (N.S.B.)
| | - Aryeh Shalev
- Cardiology Department, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - Ilan Shelef
- Department of Diagnostic Imaging, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - Idit F. Liberty
- Diabetes Clinic, Soroka University Medical Center, Beer-Sheva 84101, Israel;
| | - Gal Ben-Arie
- Department of Diagnostic Imaging, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - David Yardeni
- Department of Gastroenterology and Liver Diseases, Soroka University Medical Center, Beer-Sheva 84101, Israel (O.E.)
| | - Assaf Rudich
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (N.M.); (U.Y.); (N.S.B.)
| | - Ohad Etzion
- Department of Gastroenterology and Liver Diseases, Soroka University Medical Center, Beer-Sheva 84101, Israel (O.E.)
| | - Isana Veksler-Lublinsky
- Department of Software & Information Systems Engineering, Faculty of Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel;
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12
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Kotagama K, Grimme AL, Braviner L, Yang B, Sakhawala RM, Yu G, Benner LK, Joshua-Tor L, McJunkin K. The catalytic activity of microRNA Argonautes plays a modest role in microRNA star strand destabilization in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.19.524782. [PMID: 36711716 PMCID: PMC9882359 DOI: 10.1101/2023.01.19.524782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Many Argonaute proteins can cleave RNA ("slicing") as part of the microRNA-induced silencing complex (miRISC), even though miRNA-mediated target repression is generally independent of target cleavage. Here we use genome editing in C. elegans to examine the role of miRNA-guided slicing in organismal development. In contrast to previous work, slicing-inactivating mutations did not interfere with normal development when introduced by CRISPR. We find that unwinding and decay of miRNA star strands is weakly defective in the absence of slicing, with the largest effect observed in embryos. Argonaute-Like Gene 2 (ALG-2) is more dependent on slicing for unwinding than ALG-1. The miRNAs that displayed the greatest (albeit minor) dependence on slicing for unwinding tend to form stable duplexes with their star strand, and in some cases, lowering duplex stability alleviates dependence on slicing. Gene expression changes were consistent with negligible to moderate loss of function for miRNA guides whose star strand was upregulated, suggesting a reduced proportion of mature miRISC in slicing mutants. While a few miRNA guide strands are reduced in the mutant background, the basis of this is unclear since changes were not dependent on EBAX-1, a factor in the Target-Directed miRNA Degradation (TDMD) pathway. Overall, this work defines a role for miRNA Argonaute slicing in star strand decay; future work should examine whether this role could have contributed to the selection pressure to conserve catalytic activity of miRNA Argonautes across the metazoan phylogeny.
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Affiliation(s)
- Kasuen Kotagama
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Acadia L. Grimme
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
- Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Leah Braviner
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Bing Yang
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Rima M. Sakhawala
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
- Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Guoyun Yu
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Lars Kristian Benner
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
- Current address: Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Leemor Joshua-Tor
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
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13
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Shang R, Lee S, Senavirathne G, Lai EC. microRNAs in action: biogenesis, function and regulation. Nat Rev Genet 2023; 24:816-833. [PMID: 37380761 PMCID: PMC11087887 DOI: 10.1038/s41576-023-00611-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/30/2023]
Abstract
Ever since microRNAs (miRNAs) were first recognized as an extensive gene family >20 years ago, a broad community of researchers was drawn to investigate the universe of small regulatory RNAs. Although core features of miRNA biogenesis and function were revealed early on, recent years continue to uncover fundamental information on the structural and molecular dynamics of core miRNA machinery, how miRNA substrates and targets are selected from the transcriptome, new avenues for multilevel regulation of miRNA biogenesis and mechanisms for miRNA turnover. Many of these latest insights were enabled by recent technological advances, including massively parallel assays, cryogenic electron microscopy, single-molecule imaging and CRISPR-Cas9 screening. Here, we summarize the current understanding of miRNA biogenesis, function and regulation, and outline challenges to address in the future.
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Affiliation(s)
- Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Gayan Senavirathne
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
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14
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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15
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Shi CY, Elcavage LE, Chivukula RR, Stefano J, Kleaveland B, Bartel DP. ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development. Genome Res 2023; 33:1482-1496. [PMID: 37532519 PMCID: PMC10620050 DOI: 10.1101/gr.278073.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023]
Abstract
MicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the ZSWIM8 E3 ubiquitin ligase. Here, we report the function of ZSWIM8 in the mouse embryo. Zswim8 -/- embryos were smaller than their littermates and died near the time of birth. This highly penetrant perinatal lethality was apparently caused by a lung sacculation defect attributed to failed maturation of alveolar epithelial cells. Some mutant individuals also had heart ventricular septal defects. These developmental abnormalities were accompanied by aberrant accumulation of more than 50 miRNAs observed across 12 tissues, which often led to enhanced repression of their mRNA targets. These ZSWIM8-sensitive miRNAs were preferentially produced from genomic miRNA clusters, and in some cases, ZSWIM8 caused a switch in the dominant strand or isoform that accumulated from a miRNA hairpin-observations suggesting that TDMD provides a mechanism to uncouple coproduced miRNAs from each other. Overall, our findings indicate that the regulatory influence of ZSWIM8, and presumably TDMD, in mammalian biology is widespread and consequential, and posit the existence of many yet-unidentified transcripts that trigger miRNA degradation.
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Affiliation(s)
- Charlie Y Shi
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Lara E Elcavage
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Raghu R Chivukula
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Joanna Stefano
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Benjamin Kleaveland
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10021, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA;
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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16
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Jones BT, Han J, Zhang H, Hammer RE, Evers BM, Rakheja D, Acharya A, Mendell JT. Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals. Genes Dev 2023; 37:661-674. [PMID: 37553261 PMCID: PMC10499020 DOI: 10.1101/gad.350906.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutive or conditional deletion of Zswim8, which encodes an essential TDMD factor. Loss of Zswim8 resulted in developmental defects in the heart and lungs, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD and greatly expanded the known catalog of miRNAs regulated by this pathway. These experiments also uncovered novel features of TDMD-regulated miRNAs, including their enrichment in cotranscribed clusters and examples in which TDMD underlies "arm switching," a phenomenon wherein the dominant strand of a miRNA precursor changes in different tissues or conditions. Importantly, deletion of two miRNAs, miR-322 and miR-503, rescued growth of Zswim8-null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. These data illuminate the broad landscape and developmental role of TDMD in mammals.
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Affiliation(s)
- Benjamin T Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Robert E Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Bret M Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA;
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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17
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Jones BT, Han J, Zhang H, Hammer RE, Evers BM, Rakheja D, Acharya A, Mendell JT. Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546601. [PMID: 37425885 PMCID: PMC10327180 DOI: 10.1101/2023.06.26.546601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutive or conditional deletion of Zswim8 , which encodes an essential TDMD factor. Loss of Zswim8 resulted in developmental defects in heart and lung, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD and greatly expanded the known catalog of miRNAs regulated by this pathway. These experiments also uncovered novel features of TDMD-regulated miRNAs, including their enrichment in co-transcribed clusters and examples in which TDMD underlies 'arm switching', a phenomenon wherein the dominant strand of a miRNA precursor changes in different tissues or conditions. Importantly, deletion of two miRNAs, miR-322 and miR-503, rescued growth of Zswim8 null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. These data illuminate the broad landscape and developmental role of TDMD in mammals.
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Affiliation(s)
- Benjamin T Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert E. Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bret M. Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T. Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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18
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Simeone I, Ceccarelli M. Pan-cancer onco-signatures reveal a novel mitochondrial subtype of luminal breast cancer with specific regulators. J Transl Med 2023; 21:55. [PMID: 36717859 PMCID: PMC9885701 DOI: 10.1186/s12967-023-03907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Somatic alterations in cancer cause dysregulation of signaling pathways that control cell-cycle progression, apoptosis, and cell growth. The effect of individual alterations in these pathways differs between individual tumors and tumor types. Recognizing driver events is a complex task requiring integrating multiple molecular data, including genomics, epigenomics, and functional genomics. A common hypothesis is that these driver events share similar effects on the hallmarks of cancer. The availability of large-scale multi-omics studies allows for inferring these common effects from data. Once these effects are known, one can then deconvolve in every individual patient whether a given genomics alteration is a driver event. METHODS Here, we develop a novel data-driven approach to identify shared oncogenic expression signatures among tumors. We aim to identify gene onco-signature for classifying tumor patients in homogeneous subclasses with distinct prognoses and specific genomic alterations. We derive expression pan-cancer onco-signatures from TCGA gene expression data using a discovery set of 9107 primary pan-tumor samples together with respective matched mutational data and a list of known cancer-related genes from COSMIC database. RESULTS We use the derived ono-signatures to state their prognostic significance and apply them to the TCGA breast cancer dataset as proof of principle of our approach. We uncover a "mitochondrial" sub-group of Luminal patients characterized by its biological features and regulated by specific genetic modulators. Collectively, our results demonstrate the effectiveness of onco-signatures-based methodologies, and they also contribute to a comprehensive understanding of the metabolic heterogeneity of Luminal tumors. CONCLUSIONS These findings provide novel genomics evidence for developing personalized breast cancer patient treatments. The onco-signature approach, demonstrated here on breast cancer, is general and can be applied to other cancer types.
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Affiliation(s)
- Ines Simeone
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II", Via Claudio 21, 80128, Naples, Italy. .,Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II", Via Claudio 21, 80128, Naples, Italy. .,BIOGEM Institute of Molecular Biology and Genetics, Via Camporeale, 83031, Ariano Irpino, Italy.
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19
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Han J, Mendell JT. MicroRNA turnover: a tale of tailing, trimming, and targets. Trends Biochem Sci 2023; 48:26-39. [PMID: 35811249 PMCID: PMC9789169 DOI: 10.1016/j.tibs.2022.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) post-transcriptionally repress gene expression by guiding Argonaute (AGO) proteins to target mRNAs. While much is known about the regulation of miRNA biogenesis, miRNA degradation pathways are comparatively poorly understood. Although miRNAs generally exhibit slow turnover, they can be rapidly degraded through regulated mechanisms that act in a context- or sequence-specific manner. Recent work has revealed a particularly important role for specialized target interactions in controlling rates of miRNA degradation. Engagement of these targets is associated with the addition and removal of nucleotides from the 3' ends of miRNAs, a process known as tailing and trimming. Here we review these mechanisms of miRNA modification and turnover, highlighting the contexts in which they impact miRNA stability and discussing important questions that remain unanswered.
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Affiliation(s)
- Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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20
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Diggins NL, Hancock MH. Viral miRNA regulation of host gene expression. Semin Cell Dev Biol 2022; 146:2-19. [PMID: 36463091 PMCID: PMC10101914 DOI: 10.1016/j.semcdb.2022.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
Viruses have evolved a multitude of mechanisms to combat barriers to productive infection in the host cell. Virally-encoded miRNAs are one such means to regulate host gene expression in ways that benefit the virus lifecycle. miRNAs are small non-coding RNAs that regulate protein expression but do not trigger the adaptive immune response, making them powerful tools encoded by viruses to regulate cellular processes. Diverse viruses encode for miRNAs but little sequence homology exists between miRNAs of different viral species. Despite this, common cellular pathways are targeted for regulation, including apoptosis, immune evasion, cell growth and differentiation. Herein we will highlight the viruses that encode miRNAs and provide mechanistic insight into how viral miRNAs aid in lytic and latent infection by targeting common cellular processes. We also highlight how viral miRNAs can mimic host cell miRNAs as well as how viral miRNAs have evolved to regulate host miRNA expression. These studies dispel the myth that viral miRNAs are subtle regulators of gene expression, and highlight the critical importance of viral miRNAs to the virus lifecycle.
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Affiliation(s)
- Nicole L Diggins
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR, USA
| | - Meaghan H Hancock
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR, USA.
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21
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Herb S, Zeleznjak J, Hennig T, L'Hernault A, Lodha M, Jürges C, Trsan T, Juranic Lisnic V, Jonjic S, Erhard F, Krmpotic A, Dölken L. Two murine cytomegalovirus microRNAs target the major viral immediate early 3 gene. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Human cytomegalovirus is responsible for morbidity and mortality in immune compromised patients and is the leading viral cause of congenital infection. Virus-encoded microRNAs (miRNAs) represent interesting targets for novel antiviral agents. While many cellular targets that augment productive infection have been identified in recent years, regulation of viral genes such as the major viral immediate early protein 72 (IE72) by hcmv-miR-UL112-1 may contribute to both the establishment and the maintenance of latent infection. We employed photoactivated ribonucleotide-enhanced individual nucleotide resolution crosslinking (PAR-iCLIP) to identify murine cytomegalovirus (MCMV) miRNA targets during lytic infection. While the PAR-iCLIP data were of insufficient quality to obtain a comprehensive list of cellular and viral miRNA targets, the most prominent PAR-iCLIP peak in the MCMV genome mapped to the 3′ untranslated region of the major viral immediate early 3 (ie3) transcript. We show that this results from two closely positioned binding sites for the abundant MCMV miRNAs miR-M23-2-3p and miR-m01-2-3p. Their pre-expression significantly impaired viral plaque formation. However, mutation of the respective binding sites did not alter viral fitness during acute or subacute infection in vivo. Furthermore, no differences in the induction of virus-specific CD8+ T cells were observed. Future studies will probably need to go beyond studying immunocompetent laboratory mice housed in pathogen-free conditions to reveal the functional relevance of viral miRNA-mediated regulation of key viral immediate early genes.
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Affiliation(s)
- Stefanie Herb
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Jelena Zeleznjak
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Anne L'Hernault
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Manivel Lodha
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Christopher Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Tihana Trsan
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Vanda Juranic Lisnic
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Stipan Jonjic
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Astrid Krmpotic
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Lars Dölken
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), 97080 Würzburg, Germany
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
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22
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Davuluri KS, Chauhan DS. microRNAs associated with the pathogenesis and their role in regulating various signaling pathways during Mycobacterium tuberculosis infection. Front Cell Infect Microbiol 2022; 12:1009901. [PMID: 36389170 PMCID: PMC9647626 DOI: 10.3389/fcimb.2022.1009901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
Despite more than a decade of active study, tuberculosis (TB) remains a serious health concern across the world, and it is still the biggest cause of mortality in the human population. Pathogenic bacteria recognize host-induced responses and adapt to those hostile circumstances. This high level of adaptability necessitates a strong regulation of bacterial metabolic characteristics. Furthermore, the immune reponse of the host virulence factors such as host invasion, colonization, and survival must be properly coordinated by the pathogen. This can only be accomplished by close synchronization of gene expression. Understanding the molecular characteristics of mycobacterial pathogenesis in order to discover therapies that prevent or resolve illness relies on the bacterial capacity to adjust its metabolism and replication in response to various environmental cues as necessary. An extensive literature details the transcriptional alterations of host in response to in vitro environmental stressors, macrophage infection, and human illness. Various studies have recently revealed the finding of several microRNAs (miRNAs) that are believed to play an important role in the regulatory networks responsible for adaptability and virulence in Mycobacterium tuberculosis. We highlighted the growing data on the existence and quantity of several forms of miRNAs in the pathogenesis of M. tuberculosis, considered their possible relevance to disease etiology, and discussed how the miRNA-based signaling pathways regulate bacterial virulence factors.
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23
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Kingston ER, Blodgett LW, Bartel DP. Endogenous transcripts direct microRNA degradation in Drosophila, and this targeted degradation is required for proper embryonic development. Mol Cell 2022; 82:3872-3884.e9. [PMID: 36150386 PMCID: PMC9648618 DOI: 10.1016/j.molcel.2022.08.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/25/2022] [Accepted: 08/25/2022] [Indexed: 10/14/2022]
Abstract
MicroRNAs (miRNAs) typically direct degradation of their mRNA targets. However, some targets have unusual miRNA-binding sites that direct degradation of cognate miRNAs. Although this target-directed miRNA degradation (TDMD) is thought to shape the levels of numerous miRNAs, relatively few sites that endogenously direct degradation have been identified. Here, we identify six sites, five in mRNAs and one in a noncoding RNA named Marge, which serve this purpose in Drosophila cells or embryos. These six sites direct miRNA degradation without collateral target degradation, helping explain the effectiveness of this miRNA-degradation pathway. Mutations that disrupt this pathway are lethal, with many flies dying as embryos. Concomitant derepression of miR-3 and its paralog miR-309 appears responsible for some of this lethality, whereas the loss of Marge-directed degradation of miR-310 miRNAs causes defects in embryonic cuticle development. Thus, TDMD is implicated in the viability of an animal and is required for its proper development.
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Affiliation(s)
- Elena R Kingston
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute of Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lianne W Blodgett
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute of Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute of Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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24
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Donnelly BF, Yang B, Grimme AL, Vieux KF, Liu CY, Zhou L, McJunkin K. The developmentally timed decay of an essential microRNA family is seed-sequence dependent. Cell Rep 2022; 40:111154. [PMID: 35947946 PMCID: PMC9413084 DOI: 10.1016/j.celrep.2022.111154] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 06/04/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
MicroRNA (miRNA) abundance is tightly controlled by regulation of biogenesis and decay. Here, we show that the mir-35 miRNA family undergoes selective decay at the transition from embryonic to larval development in C. elegans. The seed sequence of the miRNA is necessary and largely sufficient for this regulation. Sequences outside the seed (3' end) regulate mir-35 abundance in the embryo but are not necessary for sharp decay at the transition to larval development. Enzymatic modifications of the miRNA 3' end are neither prevalent nor correlated with changes in decay, suggesting that miRNA 3' end display is not a core feature of this mechanism and further supporting a seed-driven decay model. Our findings demonstrate that seed-sequence-specific decay can selectively and coherently regulate all redundant members of a miRNA seed family, a class of mechanism that has great biological and therapeutic potential for dynamic regulation of a miRNA family's target repertoire.
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Affiliation(s)
- Bridget F Donnelly
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA; Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Bing Yang
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Acadia L Grimme
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA; Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Karl-Frédéric Vieux
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Chen-Yu Liu
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Lecong Zhou
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA.
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25
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Single-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2. Nat Commun 2022; 13:3825. [PMID: 35780145 PMCID: PMC9250533 DOI: 10.1038/s41467-022-31480-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
Human Argonaute 2 (hAgo2) constitutes the functional core of the RNA interference pathway. Guide RNAs direct hAgo2 to target mRNAs, which ultimately leads to hAgo2-mediated mRNA degradation or translational inhibition. Here, we combine site-specifically labeled hAgo2 with time-resolved single-molecule FRET measurements to monitor conformational states and dynamics of hAgo2 and hAgo2-RNA complexes in solution that remained elusive so far. We observe dynamic anchoring and release of the guide’s 3’-end from the PAZ domain during the stepwise target loading process even with a fully complementary target. We find differences in structure and dynamic behavior between partially and fully paired canonical hAgo2-guide/target complexes and the miRNA processing complex formed by hAgo2 and pre-miRNA451. Furthermore, we detect a hitherto unknown conformation of hAgo2-guide/target complexes that poises them for target-directed miRNA degradation. Taken together, our results show how the conformational flexibility of hAgo2-RNA complexes determines function and the fate of the ribonucleoprotein particle. Single-molecule FRET measurements provide detailed insights into the conformational states and dynamics of human Argonaute 2 that are required for its function at the core of the eukaryotic RNA silencing pathway.
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26
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Simeone I, Rubolino C, Noviello T, Farinello D, Cerulo L, Marzi M, Nicassio F. Prediction and pan-cancer analysis of mammalian transcripts involved in target directed miRNA degradation. Nucleic Acids Res 2022; 50:2019-2035. [PMID: 35137158 PMCID: PMC8887481 DOI: 10.1093/nar/gkac057] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
It is currently unknown how many RNA transcripts are able to induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD). We developed TDMDfinder, a computational pipeline that identifies 'high confidence' TDMD interactions in the Human and Mouse transcriptomes by combining sequence alignment and feature selection approaches. Our predictions suggested that TDMD is widespread, with potentially every miRNA controlled by endogenous targets. We experimentally tested 37 TDMDfinder predictions, of which 17 showed TDMD effects as measured by RT-qPCR and small RNA sequencing, linking the miR-17, miR-19, miR-30, miR-221, miR-26 and miR-23 families to novel endogenous TDMDs. In some cases, TDMD was found to affect different members of the same miRNA family selectively. Features like complementarity to the miRNA 3' region, bulge size and hybridization energy appeared to be the main factors determining sensitivity. Computational analyses performed using the multiomic TCGA platform substantiated the involvement of many TDMD transcripts in human cancer and highlighted 36 highly significant interactions, suggesting TDMD as a new potential oncogenic mechanism. In conclusion, TDMDfinder provides the first inventory of bona fide human and mouse TDMDs. Available as a free webtool, TDMDfinder allows users to search for any TDMD interaction of interest by customizing its selection criteria.
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Affiliation(s)
- Ines Simeone
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)—Via Adamello 16, 20139 Milan, Italy
| | - Carmela Rubolino
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)—Via Adamello 16, 20139 Milan, Italy
| | - Teresa Maria Rosaria Noviello
- Department of Electrical Engineering and Information Technology, University of Naples “Federico II”, Via Claudio 21, Naples 80128, Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Via Camporeale, Ariano Irpino (AV) 83031, Italy
| | - Diego Farinello
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)—Via Adamello 16, 20139 Milan, Italy
| | - Luigi Cerulo
- Dep. of Science and Technology, University of Sannio, via de Sanctis, 11, Benevento 82100, Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Via Camporeale, Ariano Irpino (AV) 83031, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)—Via Adamello 16, 20139 Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)—Via Adamello 16, 20139 Milan, Italy
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27
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McGeary SE, Bisaria N, Pham TM, Wang PY, Bartel DP. MicroRNA 3'-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position. eLife 2022; 11:e69803. [PMID: 35191832 PMCID: PMC8940178 DOI: 10.7554/elife.69803] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2-8), preferences of the miRNA 3' region are poorly understood, due to the sparsity of measured affinities for the many pairing possibilities. We used RNA bind-n-seq with purified AGO2-miRNA complexes to measure relative affinities of >1000 3'-pairing architectures for each miRNA. In some cases, optimal 3' pairing increased affinity by >500 fold. Some miRNAs had two high-affinity 3'-pairing modes-one of which included additional nucleotides bridging seed and 3' pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3' pairing is determined for each miRNA.
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Affiliation(s)
- Sean E McGeary
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Namita Bisaria
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Thy M Pham
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Peter Y Wang
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - David P Bartel
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
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28
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Wang D, Ye R, Cai Z, Xue Y. Emerging roles of RNA-RNA interactions in transcriptional regulation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1712. [PMID: 35042277 DOI: 10.1002/wrna.1712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/07/2021] [Accepted: 12/16/2021] [Indexed: 12/26/2022]
Abstract
Pervasive transcription of the human genome generates a massive amount of noncoding RNAs (ncRNAs) that lack protein-coding potential but play crucial roles in development, differentiation, and tumorigenesis. To achieve these biological functions, ncRNAs must first fold into intricate structures via intramolecular RNA-RNA interactions (RRIs) and then interact with different RNA substrates via intermolecular RRIs. RRIs are usually facilitated, stabilized, or mediated by RNA-binding proteins. With this guiding principle, several protein-based high-throughput methods have been developed for unbiased mapping of defined or all RNA-binding protein-mediated RRIs in various species and cell lines. In addition, some chemical-based approaches are also powerful to detect RRIs globally based on the fact that RNA duplex can be cross-linked by psoralen or its derivative 4'-aminomethyltrioxsalen. These efforts have significantly expanded our understanding of RRIs in determining the specificity and variability of gene regulation. Here, we review the current knowledge of the regulatory roles of RRI, focusing on their emerging roles in transcriptional regulation and nuclear body formation. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Di Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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29
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Abstract
MicroRNAs are RNAs of about 18-24 nucleotides in lengths, which are found in the small noncoding RNA class and have a crucial role in the posttranscriptional regulation of gene expression, cellular metabolic pathways, and developmental events. These small but essential molecules are first processed by Drosha and DGCR8 in the nucleus and then released into the cytoplasm, where they cleaved by Dicer to form the miRNA duplex. These duplexes are bound by the Argonaute (AGO) protein to form the RNA-induced silencing complex (RISC) in a process called RISC loading. Transcription of miRNAs, processing with Drosha and DGCR8 in the nucleus, cleavage by Dicer, binding to AGO proteins and forming RISC are the most critical steps in miRNA biogenesis. Additional molecules involved in biogenesis at these stages can enhance or inhibit these processes, which can radically change the fate of the cell. Biogenesis is regulated by many checkpoints at every step, primarily at the transcriptional level, in the nucleus, cytoplasm, with RNA regulation, RISC loading, miRNA strand selection, RNA methylation/uridylation, and turnover rate. Moreover, in recent years, different regulation mechanisms have been discovered in noncanonical Drosha or Dicer-independent pathways. This chapter seeks answers to how miRNA biogenesis and function are regulated through both canonical and non-canonical pathways.
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30
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Panzade G, Li L, Hebbar S, Veksler-Lublinsky I, Zinovyeva A. Global profiling and annotation of templated isomiRs dynamics across Caenorhabditis elegans development. RNA Biol 2022; 19:928-942. [PMID: 35848953 PMCID: PMC9298154 DOI: 10.1080/15476286.2022.2099646] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/05/2022] [Indexed: 11/11/2022] Open
Abstract
microRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through translational repression and mRNA destabilization. During canonical miRNA biogenesis, several miRNA isoforms, or isomiRs, are produced from a single precursor miRNA. Templated isomiRs are generated through Drosha or Dicer cleavage at alternate positions on either the primary or the precursor miRNAs, generating truncated or extended 5' and/or 3' miRNA ends. As changes to the mature miRNA sequence can alter miRNA gene target repertoire, we investigated the extent of templated isomiR prevalence, providing a profiling map for templated isomiRs across stages of C. elegans development. While most miRNA loci did not produce abundant templated isomiRs, a substantial number of miRNA loci produced isomiRs were just as, or more, abundant than their annotated canonical mature miRNAs. 3' end miRNA alterations were more frequent than the seed-altering 5' end extensions or truncations. However, we identified several miRNA loci that produced a considerable amount of isomiRs with 5' end alterations, predicted to target new, distinct sets of genes. Overall, the presented annotation of templated isomiR dynamics across C. elegans developmental stages provides a basis for further studies into miRNA biogenesis and the intriguing potential of functional miRNA diversification through isomiR production.
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Affiliation(s)
- Ganesh Panzade
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Li Li
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-sheva, Israel
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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31
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Nakanishi K. Are Argonaute-Associated Tiny RNAs Junk, Inferior miRNAs, or a New Type of Functional RNAs? Front Mol Biosci 2021; 8:795356. [PMID: 34926585 PMCID: PMC8678501 DOI: 10.3389/fmolb.2021.795356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/01/2021] [Indexed: 11/14/2022] Open
Abstract
The biosynthesis pathways of microRNAs (miRNAs) have been well characterized with the identification of the required components. miRNAs are synthesized from the transcripts of miRNA genes and other RNAs, such as introns, transfer RNAs, ribosomal RNAs, small nucleolar RNAs, and even viral miRNAs. These small RNAs are loaded into Argonaute (AGO) proteins and recruit the effector complexes to target mRNAs, repressing their gene expression post-transcriptionally. While mature miRNAs were defined as 19–23 nucleotides (nt), tiny RNAs (tyRNAs) shorter than 19 nt have been found to bind AGOs as equivalent or lesser miRNAs compared to their full-length mature miRNAs. In contrast, my recent study revealed that when human AGO3 loads 14 nt cleavage-inducing tyRNAs (cityRNAs), comprised of the first 14 nt of their corresponding mature miRNA, it can become a comparable slicer to AGO2. This observation raises the possibility that tyRNAs play distinct roles from their mature form. This minireview focuses on human AGO-associated tyRNAs shorter than 19 nt and discusses their possible biosynthesis pathways and physiological benefits, including how tyRNAs could avoid target-directed miRNA degradation accompanied by AGO polyubiquitination.
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Affiliation(s)
- Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States.,Center for RNA Biology, Columbus, OH, United States
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32
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Prodromidou K, Matsas R. Evolving features of human cortical development and the emerging roles of non-coding RNAs in neural progenitor cell diversity and function. Cell Mol Life Sci 2021; 79:56. [PMID: 34921638 PMCID: PMC11071749 DOI: 10.1007/s00018-021-04063-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
The human cerebral cortex is a uniquely complex structure encompassing an unparalleled diversity of neuronal types and subtypes. These arise during development through a series of evolutionary conserved processes, such as progenitor cell proliferation, migration and differentiation, incorporating human-associated adaptations including a protracted neurogenesis and the emergence of novel highly heterogeneous progenitor populations. Disentangling the unique features of human cortical development involves elucidation of the intricate developmental cell transitions orchestrated by progressive molecular events. Crucially, developmental timing controls the fine balance between cell cycle progression/exit and the neurogenic competence of precursor cells, which undergo morphological transitions coupled to transcriptome-defined temporal states. Recent advances in bulk and single-cell transcriptomic technologies suggest that alongside protein-coding genes, non-coding RNAs exert important regulatory roles in these processes. Interestingly, a considerable number of novel long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have appeared in human and non-human primates suggesting an evolutionary role in shaping cortical development. Here, we present an overview of human cortical development and highlight the marked diversification and complexity of human neuronal progenitors. We further discuss how lncRNAs and miRNAs constitute critical components of the extended epigenetic regulatory network defining intermediate states of progenitors and controlling cell cycle dynamics and fate choices with spatiotemporal precision, during human neurodevelopment.
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Affiliation(s)
- Kanella Prodromidou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece.
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece
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33
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nanoString evaluation of murine Cytomegalovirus transcription in vivo and in vitro. J Virol Methods 2021; 301:114436. [PMID: 34929204 DOI: 10.1016/j.jviromet.2021.114436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/28/2021] [Accepted: 12/15/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Next Generation Sequencing allows for deep analysis of transcriptional activity in cells and tissues, however it is still a cost intensive method that demands well versed data handling. Reverse transcription quantitative PCR (RT-qPCR) is the most commonly used method to measure gene expression levels, however the information gathered is quite small in comparison to NGS. A newer method called nanoString allows for highly multiplexed gene expression analysis by detecting mRNAs without the use of enzymes for reverse transcription or amplification even for single cells or low input material. The method can be done in 1.5 days and data are quickly analyzed by the accompanied user friendly software. Our aim was to investigate this new method and compare it to the existing alternatives, while investigating murine Cytomegalovirus (mCMV) infection and latency. METHODS mCMV infected murine embryonic fibroblasts (MEF), lung and salivary glands from BALB/c mice were evaluated at different stages of infection. A set of 30 custom designed nanoString probes were tested, 20 probes specific for mCMV genes, 6 probes for host genes known to be influenced by viral infection and 4 reference gene specific probes. nanoString counts were compared to published RNA-Seq RPKM. RESULTS We found that nanoString can be used for analysis of cytomegalovirus gene expression during acute infection in vitro and in vivo, both for virus specific and host genes. Although some transcripts show different expression rates in comparison to NGS data, the most abundant transcripts are comparable. When tissues are infected, there are significantly fewer transcripts than in MEFs, and consistent with previous work there are significant differences in relevant abundance between MEF and tissues. We were unable to detect our viral transcripts of interest in latently infected tissue. CONCLUSIONS For viruses with annotated transcriptomes, nanoString allows simultaneous quantitation of multiple virus and host genes. One huge advantage of the platform is rapid turnaround and simplicity of analysis. It should prove to be very useful to explore host virus interactions during acute infection, but it is unclear if it has adequate sensitivity for analysis during latency in immunocompetent mice.
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Iwakawa HO, Tomari Y. Life of RISC: Formation, action, and degradation of RNA-induced silencing complex. Mol Cell 2021; 82:30-43. [PMID: 34942118 DOI: 10.1016/j.molcel.2021.11.026] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 01/12/2023]
Abstract
Small RNAs regulate a wide variety of biological processes by repressing the expression of target genes at the transcriptional and post-transcriptional levels. To achieve these functions, small RNAs form RNA-induced silencing complex (RISC) together with a member of the Argonaute (AGO) protein family. RISC is directed by its bound small RNA to target complementary RNAs and represses their expression through mRNA cleavage, degradation, and/or translational repression. Many different factors fine-tune RISC activity and stability-from guide-target RNA complementarity to the recruitment of other protein partners to post-translational modifications of RISC itself. Here, we review recent progress in understanding RISC formation, action, and degradation, and discuss new, intriguing questions in the field.
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Affiliation(s)
- Hiro-Oki Iwakawa
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
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Gainetdinov I, Colpan C, Cecchini K, Arif A, Jouravleva K, Albosta P, Vega-Badillo J, Lee Y, Özata DM, Zamore PD. Terminal modification, sequence, length, and PIWI-protein identity determine piRNA stability. Mol Cell 2021; 81:4826-4842.e8. [PMID: 34626567 DOI: 10.1016/j.molcel.2021.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) silence transposons, fight viral infections, and regulate gene expression. piRNA biogenesis concludes with 3' terminal trimming and 2'-O-methylation. Both trimming and methylation influence piRNA stability. Our biochemical data show that multiple mechanisms destabilize unmethylated mouse piRNAs, depending on whether the piRNA 5' or 3' sequence is complementary to a trigger RNA. Unlike target-directed degradation of microRNAs, complementarity-dependent destabilization of piRNAs in mice and flies is blocked by 3' terminal 2'-O-methylation and does not require base pairing to both the piRNA seed and the 3' sequence. In flies, 2'-O-methylation also protects small interfering RNAs (siRNAs) from complementarity-dependent destruction. By contrast, pre-piRNA trimming protects mouse piRNAs from a degradation pathway unaffected by trigger complementarity. In testis lysate and in vivo, internal or 3' terminal uridine- or guanine-rich tracts accelerate pre-piRNA decay. Loss of both trimming and 2'-O-methylation causes the mouse piRNA pathway to collapse, demonstrating that these modifications collaborate to stabilize piRNAs.
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Affiliation(s)
- Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Cansu Colpan
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Katharine Cecchini
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Amena Arif
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Karina Jouravleva
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Paul Albosta
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Joel Vega-Badillo
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Yongjin Lee
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Deniz M Özata
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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Li L, Sheng P, Li T, Fields CJ, Hiers NM, Wang Y, Li J, Guardia CM, Licht JD, Xie M. Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins. Genes Dev 2021; 35:1595-1609. [PMID: 34819352 PMCID: PMC8653786 DOI: 10.1101/gad.348874.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022]
Abstract
Binding of microRNAs (miRNAs) to mRNAs normally results in post-transcriptional repression of gene expression. However, extensive base-pairing between miRNAs and target RNAs can trigger miRNA degradation, a phenomenon called target RNA-directed miRNA degradation (TDMD). Here, we systematically analyzed Argonaute-CLASH (cross-linking, ligation, and sequencing of miRNA-target RNA hybrids) data and identified numerous candidate TDMD triggers, focusing on their ability to induce nontemplated nucleotide addition at the miRNA 3' end. When exogenously expressed in various cell lines, eight triggers induce degradation of corresponding miRNAs. Both the TDMD base-pairing and surrounding sequences are essential for TDMD. CRISPR knockout of endogenous trigger or ZSWIM8, a ubiquitin ligase essential for TDMD, reduced miRNA degradation. Furthermore, degradation of miR-221 and miR-222 by a trigger in BCL2L11, which encodes a proapoptotic protein, enhances apoptosis. Therefore, we uncovered widespread TDMD triggers in target RNAs and demonstrated an example that could functionally cooperate with the encoded protein.
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Affiliation(s)
- Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Christopher J Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Yuzhi Wang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Jianping Li
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Division of Hematology/Oncology, University of Florida, Gainesville, Florida 32610, USA
| | - Casey M Guardia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Jonathan D Licht
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Division of Hematology/Oncology, University of Florida, Gainesville, Florida 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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Vieux KF, Prothro KP, Kelley LH, Palmer C, Maine EM, Veksler-Lublinsky I, McJunkin K. Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans. Nucleic Acids Res 2021; 49:11167-11180. [PMID: 34586415 DOI: 10.1093/nar/gkab840] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022] Open
Abstract
microRNAs are frequently modified by addition of untemplated nucleotides to the 3' end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using Caenorhabditis elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2-here named GLD-2-related 2 (GLDR-2)-is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median = 20.7 h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay in C. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.
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Affiliation(s)
- Karl-Frédéric Vieux
- National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20815, USA
| | - Katherine P Prothro
- National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20815, USA.,Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leanne H Kelley
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Cameron Palmer
- National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20815, USA
| | - Eleanor M Maine
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | | | - Katherine McJunkin
- National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20815, USA
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Frédérick PM, Simard MJ. Regulation and different functions of the animal microRNA-induced silencing complex. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1701. [PMID: 34725940 DOI: 10.1002/wrna.1701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 01/03/2023]
Abstract
Among the different types of small RNAs, microRNAs (miRNAs) are key players in controlling gene expression at the mRNA level. To be active, they must associate with an Argonaute protein to form the miRNA induced silencing complex (miRISC) and binds to specific mRNA through complementarity sequences. The miRISC binding to an mRNA can lead to multiple outcomes, the most frequent being inhibition of the translation and/or deadenylation followed by decapping and mRNA decay. In the last years, several studies described different mechanisms modulating miRISC functions in animals. For instance, the regulation of the Argonaute protein through post-translational modifications can change the miRISC gene regulatory activity as well as modulate its binding to proteins, mRNA targets and miRISC stability. Furthermore, the presence of RNA binding proteins and multiple miRISCs at the targeted mRNA 3' untranslated region (3'UTR) can also affect its function through cooperation or competition mechanisms, underlying the importance of the 3'UTR environment in miRNA-mediated repression. Another way to regulate the miRISC function is by modulation of its interactors, forming different types of miRNA silencing complexes that affect gene regulation differently. It is also reported that the subcellular localization of several components of the miRNA pathway can modulate miRISC function, suggesting an important role for vesicular trafficking in the regulation of this essential silencing complex. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Pierre-Marc Frédérick
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada.,Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Martin J Simard
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada.,Université Laval Cancer Research Centre, Québec, QC, Canada
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Learning noncoding RNA biology from viruses. Mamm Genome 2021; 33:412-420. [PMID: 34491378 DOI: 10.1007/s00335-021-09915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Insights into interactions between viral factors and the cellular machinery usually lead to discoveries concerning host cell biology. Thus, the gene expression field has historically relied on viral model systems to discover mechanisms underlying different cellular processes. In recent years, the functional characterization of the small nuclear noncoding RNAs expressed by the oncogenic Herpesvirus saimiri, called HSURs, resulted in the discovery of two mechanisms for the regulation of gene expression. HSUR1 and HSUR2 associate with host microRNAs, which are small noncoding RNAs that broadly regulate gene expression by binding to messenger RNAs. HSUR1 provided the first example of a process known as target-directed miRNA degradation that operates in cells to regulate miRNA populations. HSUR2 functions as a miRNA adaptor, uncovering an entirely new, indirect mechanism by which miRNAs can inhibit mRNA function. Here, I review the path that led to these discoveries and their implications and postulate new exciting questions about the functions of these fascinating viral noncoding RNAs.
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40
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Kingston ER, Bartel DP. Ago2 protects Drosophila siRNAs and microRNAs from target-directed degradation, even in the absence of 2'- O-methylation. RNA (NEW YORK, N.Y.) 2021; 27:710-724. [PMID: 33853897 PMCID: PMC8127995 DOI: 10.1261/rna.078746.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/07/2021] [Indexed: 05/07/2023]
Abstract
Target-directed microRNA (miRNA) degradation (TDMD), which is mediated by the protein ZSWIM8, plays a widespread role in shaping miRNA abundances across bilateria. Some endogenous small interfering RNAs (siRNAs) of Drosophila cells have target sites resembling those that trigger TDMD, raising the question as to whether they too might undergo such regulation by Dora, the Drosophila ZSWIM8 homolog. Here, we find that some of these siRNAs are indeed sensitive to Dora when loaded into Ago1, the Argonaute paralog that preferentially associates with miRNAs. Despite this sensitivity when loaded into Ago1, these siRNAs are not detectably regulated by target-directed degradation because most molecules are loaded into Ago2, the Argonaute paralog that preferentially associates with siRNAs, and we find that siRNAs and miRNAs loaded into Ago2 are insensitive to Dora. One explanation for the protection of these small RNAs loaded into Ago2 is that these small RNAs are 2'-O-methylated at their 3' termini. However, 2'-O-methylation does not protect these RNAs from Dora-mediated target-directed degradation, which indicates that their protection is instead conferred by features of the Ago2 protein itself. Together, these observations clarify the requirements for regulation by target-directed degradation and expand our understanding of the role of 2'-O-methylation in small-RNA biology.
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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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Wang H, Shi Y, Chen CH, Wen Y, Zhou Z, Yang C, Sun J, Du G, Wu J, Mao X, Liu R, Chen C. KLF5-induced lncRNA IGFL2-AS1 promotes basal-like breast cancer cell growth and survival by upregulating the expression of IGFL1. Cancer Lett 2021; 515:49-62. [PMID: 34052325 DOI: 10.1016/j.canlet.2021.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Basal-like breast cancer (BLBC) is the most malignant subtype of breast cancer and has a poor prognosis. Kruppel-like factor 5 (KLF5) is an oncogenic transcription factor in BLBCs. The mechanism by which KLF5 promotes BLBC by regulating the transcription of lncRNAs has not been fully elucidated. In this study, we discovered that lncRNA IGFL2-AS1 is a downstream target gene of KLF5 and that IGFL2-AS1 mediates the pro-proliferation and pro-survival functions of KLF5. Additionally, we demonstrated that IGFL2-AS1 functions by upregulating the transcription of its neighboring gene IGFL1 via two independent mechanisms. On the one hand, nuclear IGFL2-AS1 promotes the formation of a KLF5/TEAD4 transcriptional complex at the IGFL1 gene enhancer. On the other hand, cytoplasmic IGFL2-AS1 inhibits the expression of miR4795-3p, which targets the IGFL1 gene. TNFα induces the expression of IGFL2-AS1 and IGFL1 through KLF5. Taken together, the results of this study indicate that IGFL2-AS1 and IGFL1 may serve as new therapeutic targets for BLBCs.
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Affiliation(s)
- Haixia Wang
- School of Life Science, University of Science & Technology of China, Hefei, 230027, Anhui, China; Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yujie Shi
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, 450003, China
| | - Chuan-Huizi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yi Wen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Chuanyu Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jian Sun
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guangshi Du
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jiao Wu
- Department of the Second Medical Oncology, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, 650118, China
| | - Xiaoyun Mao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China; Translational Cancer Research Center, Peking University First Hospital, Beijing, 100034, China.
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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Pereira-da-Silva T, Napoleão P, Costa MC, Gabriel AF, Selas M, Silva F, Enguita FJ, Ferreira RC, Carmo MM. Cigarette Smoking, miR-27b Downregulation, and Peripheral Artery Disease: Insights into the Mechanisms of Smoking Toxicity. J Clin Med 2021; 10:jcm10040890. [PMID: 33671744 PMCID: PMC7926909 DOI: 10.3390/jcm10040890] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/14/2021] [Accepted: 02/17/2021] [Indexed: 12/26/2022] Open
Abstract
Cigarette smoking is a risk factor for the development of peripheral artery disease (PAD), although the proatherosclerotic mediators of cigarette smoking are not entirely known. We explored whether circulating microRNAs (miRNAs) are dysregulated in cigarette smokers and associated with the presence of PAD. Ninety-four participants were recruited, including 58 individuals without and 36 with PAD, 51 never smokers, 28 prior smokers, and 15 active smokers. The relative expression of six circulating miRNAs with distinct biological roles (miR-21, miR-27b, miR-29a, miR-126, miR-146, and miR-218) was assessed. Cigarette smoking was associated with the presence of PAD in multivariate analysis. Active smokers, but not prior smokers, presented miR-27b downregulation and higher leukocyte, neutrophil, and lymphocyte counts; miR-27b expression levels were independently associated with active smoking. Considering the metabolic and/or inflammatory abnormalities induced by cigarette smoking, miR-27b was independently associated with the presence of PAD and downregulated in patients with more extensive PAD. In conclusion, the atheroprotective miR-27b was downregulated in active smokers, but not in prior smokers, and miR-27b expression was independently associated with the presence of PAD. These unreported data suggest that the proatherogenic properties of cigarette smoking are mediated by a downregulation of miR-27b, which may be attenuated by smoking cessation.
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Affiliation(s)
- Tiago Pereira-da-Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
- NOVA Doctoral School, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Correspondence: ; Tel.: +351-919908505
| | - Patrícia Napoleão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
| | - Marina C. Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - André F. Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Mafalda Selas
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Filipa Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Rui Cruz Ferreira
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Miguel Mota Carmo
- Chronic Diseases Research Center (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
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Constanty F, Shkumatava A. lncRNAs in development and differentiation: from sequence motifs to functional characterization. Development 2021; 148:148/1/dev182741. [PMID: 33441380 DOI: 10.1242/dev.182741] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of long noncoding RNAs (lncRNAs) with characterized developmental and cellular functions continues to increase, but our understanding of the molecular mechanisms underlying lncRNA functions, and how they are dictated by RNA sequences, remains limited. Relatively short, conserved sequence motifs embedded in lncRNA transcripts are often important determinants of lncRNA localization, stability and interactions. Identifying such RNA motifs remains challenging due to the substantial length of lncRNA transcripts and the rapid evolutionary turnover of lncRNA sequences. Nevertheless, the recent discovery of specific RNA elements, together with their experimental interrogation, has enabled the first step in classifying heterogeneous lncRNAs into sub-groups with similar molecular mechanisms and functions. In this Review, we focus on lncRNAs with roles in development, cell differentiation and normal physiology in vertebrates, and we discuss the sequence elements defining their functions. We also summarize progress on the discovery of regulatory RNA sequence elements, as well as their molecular functions and interaction partners.
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Affiliation(s)
- Florian Constanty
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Alena Shkumatava
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
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44
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Liu Z, Wang J, Ge Y, Xu Y, Guo M, Mi K, Xu R, Pei Y, Zhang Q, Luan X, Hu Z, Chi Y, Liu X. SARS-CoV-2 encoded microRNAs are involved in the process of virus infection and host immune response. J Biomed Res 2021; 35:216-227. [PMID: 33963094 PMCID: PMC8193712 DOI: 10.7555/jbr.35.20200154] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The outbreak of COVID-19 caused by SARS-CoV-2 is spreading worldwide, with the pathogenesis mostly unclear. Both virus and host-derived microRNA (miRNA) play essential roles in the pathology of virus infection. This study aims to uncover the mechanism for SARS-CoV-2 pathogenicity from the perspective of miRNA. We scanned the SARS-CoV-2 genome for putative miRNA genes and miRNA targets and conducted in vivo experiments to validate the virus-encoded miRNAs and their regulatory role on the putative targets. One of such virus-encoded miRNAs, MR147-3p, was overexpressed that resulted in significantly decreased transcript levels of all of the predicted targets in human,i.e., EXOC7, RAD9A, and TFE3 in the virus-infected cells. The analysis showed that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Additionally, the genomic mutation of SARS-CoV-2 contributed to the changed miRNA repository and targets, suggesting a possible role of miRNAs in the attenuated phenotype of SARS-CoV-2 during its evolution. This study provided a comprehensive view of the miRNA-involved regulatory system during SARS-CoV-2 infection, indicating possible antiviral therapeutics against SARS-CoV-2 through intervening miRNA regulation.
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Affiliation(s)
- Zhi Liu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jianwei Wang
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yiyue Ge
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu 210009, China
| | - Yuyu Xu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Mengchen Guo
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Kai Mi
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Rui Xu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yang Pei
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qiankun Zhang
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaoting Luan
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ying Chi
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu 210009, China
| | - Xingyin Liu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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45
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Han J, LaVigne CA, Jones BT, Zhang H, Gillett F, Mendell JT. A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming. Science 2020; 370:eabc9546. [PMID: 33184234 PMCID: PMC8177725 DOI: 10.1126/science.abc9546] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/14/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) act in concert with Argonaute (AGO) proteins to repress target messenger RNAs. After AGO loading, miRNAs generally exhibit slow turnover. An important exception occurs when miRNAs encounter highly complementary targets, which can trigger a process called target-directed miRNA degradation (TDMD). During TDMD, miRNAs undergo tailing and trimming, suggesting that this is an important step in the decay mechanism. We identified a cullin-RING ubiquitin ligase (CRL), containing the substrate adaptor ZSWIM8, that mediates TDMD. The ZSWIM8 CRL interacts with AGO proteins, promotes TDMD in a tailing and trimming-independent manner, and regulates miRNA expression in multiple cell types. These findings suggest a model in which the ZSWIM8 ubiquitin ligase mediates TDMD by directing proteasomal decay of miRNA-containing complexes engaged with highly complementary targets.
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Affiliation(s)
- Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Collette A LaVigne
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin T Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Frank Gillett
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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46
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Shi CY, Kingston ER, Kleaveland B, Lin DH, Stubna MW, Bartel DP. The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation. Science 2020; 370:science.abc9359. [PMID: 33184237 DOI: 10.1126/science.abc9359] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/07/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to direct widespread posttranscriptional gene repression. Although association with AGO typically protects miRNAs from nucleases, extensive pairing to some unusual target RNAs can trigger miRNA degradation. We found that this target-directed miRNA degradation (TDMD) required the ZSWIM8 Cullin-RING E3 ubiquitin ligase. This and other findings support a mechanistic model of TDMD in which target-directed proteolysis of AGO by the ubiquitin-proteasome pathway exposes the miRNA for degradation. Moreover, loss-of-function studies indicated that the ZSWIM8 Cullin-RING ligase accelerates degradation of numerous miRNAs in cells of mammals, flies, and nematodes, thereby specifying the half-lives of most short-lived miRNAs. These results elucidate the mechanism of TDMD and expand its inferred role in shaping miRNA levels in bilaterian animals.
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Affiliation(s)
- Charlie Y Shi
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elena R Kingston
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin Kleaveland
- Department of Pathology and Lab Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Daniel H Lin
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael W Stubna
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. .,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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47
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Dunn LEM, Ivens A, Netherton CL, Chapman DAG, Beard PM. Identification of a Functional Small Noncoding RNA of African Swine Fever Virus. J Virol 2020; 94:e01515-20. [PMID: 32796064 PMCID: PMC7565616 DOI: 10.1128/jvi.01515-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 01/08/2023] Open
Abstract
African swine fever virus (ASFV) causes a lethal hemorrhagic disease of domestic pigs, against which no vaccine is available. ASFV has a large, double-stranded DNA genome that encodes over 150 proteins. Replication takes place predominantly in the cytoplasm of the cell and involves complex interactions with host cellular components, including small noncoding RNAs (sncRNAs). A number of DNA viruses are known to manipulate sncRNA either by encoding their own or disrupting host sncRNA. To investigate the interplay between ASFV and sncRNAs, a study of host and viral small RNAs extracted from ASFV-infected primary porcine macrophages (PAMs) was undertaken. We discovered that ASFV infection had only a modest effect on host miRNAs, with only 6 miRNAs differentially expressed during infection. The data also revealed 3 potential novel small RNAs encoded by ASFV, ASFVsRNA1-3. Further investigation of ASFVsRNA2 detected it in lymphoid tissue from pigs with ASF. Overexpression of ASFVsRNA2 led to an up to 1-log reduction in ASFV growth, indicating that ASFV utilizes a virus-encoded small RNA to disrupt its own replication.IMPORTANCE African swine fever (ASF) poses a major threat to pig populations and food security worldwide. The disease is endemic to Africa and Eastern Europe and is rapidly emerging into Asia, where it has led to the deaths of millions of pigs in the last 12 months. The development of safe and effective vaccines to protect pigs against ASF has been hindered by lack of understanding of the complex interactions between ASFV and the host cell. We focused our work on characterizing the interactions between ASFV and sncRNAs. Although comparatively modest changes to host sncRNA abundances were observed upon ASFV infection, we discovered and characterized a novel functional ASFV-encoded sncRNA. The results from this study add important insights into ASFV host-pathogen interactions. This knowledge may be exploited to develop more effective ASFV vaccines that take advantage of the sncRNA system.
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Affiliation(s)
- Laura E M Dunn
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom
| | - Alasdair Ivens
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Philippa M Beard
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom
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48
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Gasparini S, Licursi V, Presutti C, Mannironi C. The Secret Garden of Neuronal circRNAs. Cells 2020; 9:E1815. [PMID: 32751850 PMCID: PMC7463782 DOI: 10.3390/cells9081815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
High-throughput transcriptomic profiling approaches have revealed that circular RNAs (circRNAs) are important transcriptional gene products, identified across a broad range of organisms throughout the eukaryotic tree of life. In the nervous system, they are particularly abundant, developmentally regulated, region-specific, and enriched in genes for neuronal proteins and synaptic factors. These features suggested that circRNAs are key components of an important layer of neuronal gene expression regulation, with known and anticipated functions. Here, we review major recognized aspects of circRNA biogenesis, metabolism and biological activities, examining potential new functions in the context of the nervous system.
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Affiliation(s)
- Silvia Gasparini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Carlo Presutti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy
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49
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Degradation of MicroRNA miR-466d-3p by Japanese Encephalitis Virus NS3 Facilitates Viral Replication and Interleukin-1β Expression. J Virol 2020; 94:JVI.00294-20. [PMID: 32461319 DOI: 10.1128/jvi.00294-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/13/2020] [Indexed: 11/20/2022] Open
Abstract
Japanese encephalitis virus (JEV) infection alters microRNA (miRNA) expression in the central nervous system (CNS). However, the mechanism contributing to miRNA regulation in the CNS is not known. We discovered global degradation of mature miRNA in mouse brains and neuroblastoma (NA) cells after JEV infection. Integrative analysis of miRNAs and mRNAs suggested that several significantly downregulated miRNAs and their targeted mRNAs were clustered into an inflammation pathway. Transfection with miRNA 466d-3p (miR-466d-3p) decreased interleukin-1β (IL-1β) expression and inhibited JEV replication in NA cells. However, miR-466d-3p expression increased after JEV infection in the presence of cycloheximide, indicating that viral protein expression reduced miR-466d-3p expression. We generated all the JEV coding proteins and demonstrated NS3 helicase protein to be a potent miRNA suppressor. The NS3 proteins of Zika virus, West Nile virus, and dengue virus serotype 1 (DENV-1) and DENV-2 also decreased miR-466d-3p expression. Results from helicase-blocking assays and in vitro unwinding assays demonstrated that NS3 could unwind pre-miR-466d and induce miRNA dysfunction. Computational models and an RNA immunoprecipitation assay revealed arginine-rich domains of NS3 to be crucial for pre-miRNA binding and degradation of host miRNAs. Importantly, site-directed mutagenesis of conserved residues in NS3 revealed that R226G and R202W reduced the binding affinity and degradation of pre-miR-466d. These results expand the function of flavivirus helicases beyond unwinding duplex RNA to degrade pre-miRNAs. Hence, we revealed a new mechanism for NS3 in regulating miRNA pathways and promoting neuroinflammation.IMPORTANCE Host miRNAs have been reported to regulate JEV-induced inflammation in the CNS. We found that JEV infection could reduce expression of host miRNA. The helicase region of the NS3 protein bound specifically to miRNA precursors and could lead to incorrect unwinding of miRNA precursors, thereby reducing the expression of mature miRNAs. This observation led to two major findings. First, our results suggested that JEV NS3 protein induced miR-466d-3p degradation, which promoted IL-1β expression and JEV replication. Second, arginine molecules on NS3 were the main miRNA-binding sites, because we demonstrated that miRNA degradation was abolished if arginines at R226 and R202 were mutated. Our study provides new insights into the molecular mechanism of JEV and reveals several amino acid sites that could be mutated for a JEV vaccine.
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50
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Tagawa T, Serquiña A, Kook I, Ziegelbauer J. Viral non-coding RNAs: Stealth strategies in the tug-of-war between humans and herpesviruses. Semin Cell Dev Biol 2020; 111:135-147. [PMID: 32631785 DOI: 10.1016/j.semcdb.2020.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 12/23/2022]
Abstract
Oncogenic DNA viruses establish lifelong infections in humans, and they cause cancers, often in immunocompromised patients, despite anti-viral immune surveillance targeted against viral antigens. High-throughput sequencing techniques allowed the field to identify novel viral non-coding RNAs (ncRNAs). ncRNAs are ideal factors for DNA viruses to exploit; they are non-immunogenic to T cells, thus viral ncRNAs can manipulate host cells without evoking adaptive immune responses. Viral ncRNAs may still trigger the host innate immune response, but many viruses encode decoys/inhibitors to counter-act and evade recognition. In addition, ncRNAs can be secreted to the extracellular space and influence adjacent cells to create a pro-viral microenvironment. In this review, we present recent progress in understanding interactions between oncoviruses and ncRNAs including small and long ncRNAs, microRNAs, and recently identified viral circular RNAs. In addition, potential clinical applications for ncRNA will be discussed. Extracellular ncRNAs are suggested to be diagnostic and prognostic biomarkers and, with the realization of the importance of viral ncRNAs in tumorigenesis, approaches to target critical viral ncRNAs are emerging. Further understanding of viral utilization of ncRNAs will advance anti-viral therapeutics beyond conventional medication and vaccination.
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Affiliation(s)
- Takanobu Tagawa
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Anna Serquiña
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Insun Kook
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Joseph Ziegelbauer
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland 20892, United States.
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