1
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Dokaneheifard S, Gomes Dos Santos H, Guiselle Valencia M, Arigela H, Edupuganti RR, Shiekhattar R. Neuronal differentiation requires BRAT1 complex to remove REST from chromatin. Proc Natl Acad Sci U S A 2024; 121:e2318740121. [PMID: 38805275 PMCID: PMC11161795 DOI: 10.1073/pnas.2318740121] [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: 10/26/2023] [Accepted: 04/17/2024] [Indexed: 05/30/2024] Open
Abstract
Repressor element-1 silencing transcription factor (REST) is required for the formation of mature neurons. REST dysregulation underlies a key mechanism of neurodegeneration associated with neurological disorders. However, the mechanisms leading to alterations of REST-mediated silencing of key neurogenesis genes are not known. Here, we show that BRCA1 Associated ATM Activator 1 (BRAT1), a gene linked to neurodegenerative diseases, is required for the activation of REST-responsive genes during neuronal differentiation. We find that INTS11 and INTS9 subunits of Integrator complex interact with BRAT1 as a distinct trimeric complex to activate critical neuronal genes during differentiation. BRAT1 depletion results in persistence of REST residence on critical neuronal genes disrupting the differentiation of NT2 cells into astrocytes and neuronal cells. We identified BRAT1 and INTS11 co-occupying the promoter region of these genes and pinpoint a role for BRAT1 in recruiting INTS11 to their promoters. Disease-causing mutations in BRAT1 diminish its association with INTS11/INTS9, linking the manifestation of disease phenotypes with a defect in transcriptional activation of key neuronal genes by BRAT1/INTS11/INTS9 complex. Finally, loss of Brat1 in mouse embryonic stem cells leads to a defect in neuronal differentiation assay. Importantly, while reconstitution with wild-type BRAT1 restores neuronal differentiation, the addition of a BRAT1 mutant is unable to associate with INTS11/INTS9 and fails to rescue the neuronal phenotype. Taken together, our study highlights the importance of BRAT1 association with INTS11 and INTS9 in the development of the nervous system.
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Affiliation(s)
- Sadat Dokaneheifard
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Helena Gomes Dos Santos
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Monica Guiselle Valencia
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Harikumar Arigela
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Raghu Ram Edupuganti
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Ramin Shiekhattar
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
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2
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Razew M, Fraudeau A, Pfleiderer MM, Linares R, Galej WP. Structural basis of the Integrator complex assembly and association with transcription factors. Mol Cell 2024:S1097-2765(24)00431-3. [PMID: 38823386 DOI: 10.1016/j.molcel.2024.05.009] [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: 09/01/2023] [Revised: 03/18/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Integrator is a multi-subunit protein complex responsible for premature transcription termination of coding and non-coding RNAs. This is achieved via two enzymatic activities, RNA endonuclease and protein phosphatase, acting on the promoter-proximally paused RNA polymerase Ⅱ (RNAPⅡ). Yet, it remains unclear how Integrator assembly and recruitment are regulated and what the functions of many of its core subunits are. Here, we report the structures of two human Integrator sub-complexes: INTS10/13/14/15 and INTS5/8/10/15, and an integrative model of the fully assembled Integrator bound to the RNAPⅡ paused elongating complex (PEC). An in silico protein-protein interaction screen of over 1,500 human transcription factors (TFs) identified ZNF655 as a direct interacting partner of INTS13 within the fully assembled Integrator. We propose a model wherein INTS13 acts as a platform for the recruitment of TFs that could modulate the stability of the Integrator's association at specific loci and regulate transcription attenuation of the target genes.
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Affiliation(s)
- Michal Razew
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Angelique Fraudeau
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Moritz M Pfleiderer
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Romain Linares
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France.
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3
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Heath JR, Fromuth DP, Dembowski JA. Integrator Complex Subunit 3 Knockdown Has Minimal Effect on Lytic Herpes Simplex Virus Type-1 Infection in Fibroblast Cells. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001171. [PMID: 38817634 PMCID: PMC11137619 DOI: 10.17912/micropub.biology.001171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/09/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024]
Abstract
Proteomic analysis of viral and cellular proteins that copurify with the herpes simplex virus type-1 (HSV-1) genome revealed that the cellular Integrator complex associates with viral DNA throughout infection. The Integrator complex plays a key role in the regulation of transcription of cellular coding and non-coding RNAs. We therefore predicted that it may regulate transcription of viral genes. Here, we demonstrate that knockdown of the Integrator complex subunit, Ints3, has minimal effect on HSV-1 infection. Despite reducing viral yield during low multiplicity infection, Ints3 knockdown had no effect on viral DNA replication, mRNA expression, or yield during high multiplicity infection.
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Affiliation(s)
- Joseph R Heath
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States
| | - Daniel P Fromuth
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States
| | - Jill A Dembowski
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States
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4
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Yang J, Li J, Miao L, Gao X, Sun W, Linghu S, Ren G, Peng B, Chen S, Liu Z, Wang B, Dong A, Huang D, Yuan J, Dang Y, Lai F. Transcription directionality is licensed by Integrator at active human promoters. Nat Struct Mol Biol 2024:10.1038/s41594-024-01272-z. [PMID: 38649617 DOI: 10.1038/s41594-024-01272-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 03/12/2024] [Indexed: 04/25/2024]
Abstract
A universal characteristic of eukaryotic transcription is that the promoter recruits RNA polymerase II (RNAPII) to produce both precursor mRNAs (pre-mRNAs) and short unstable promoter upstream transcripts (PROMPTs) toward the opposite direction. However, how the transcription machinery selects the correct direction to produce pre-mRNAs is largely unknown. Here, through multiple acute auxin-inducible degradation systems, we show that rapid depletion of an RNAPII-binding protein complex, Integrator, results in robust PROMPT accumulation throughout the genome. Interestingly, the accumulation of PROMPTs is compensated by the reduction of pre-mRNA transcripts in actively transcribed genes. Consistently, Integrator depletion alters the distribution of polymerase between the sense and antisense directions, which is marked by increased RNAPII-carboxy-terminal domain Tyr1 phosphorylation at PROMPT regions and a reduced Ser2 phosphorylation level at transcription start sites. Mechanistically, the endonuclease activity of Integrator is critical to suppress PROMPT production. Furthermore, our data indicate that the presence of U1 binding sites on nascent transcripts could counteract the cleavage activity of Integrator. In this process, the absence of robust U1 signal at most PROMPTs allows Integrator to suppress the antisense transcription and shift the transcriptional balance in favor of the sense direction.
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Affiliation(s)
- Jiao Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
- Southwest United Graduate School, Kunming, China
| | - Jingyang Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Langxi Miao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Xu Gao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Wenhao Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Shuo Linghu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Guiping Ren
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Bangya Peng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Shunkai Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Zhongqi Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Bo Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Ao Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Duo Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Jinrong Yuan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China.
| | - Fan Lai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China.
- Southwest United Graduate School, Kunming, China.
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5
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Azhar S, Shen WJ, Hu Z, Kraemer FB. MicroRNA regulation of adrenal glucocorticoid and androgen biosynthesis. VITAMINS AND HORMONES 2023; 124:1-37. [PMID: 38408797 DOI: 10.1016/bs.vh.2023.06.006] [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] [Indexed: 02/28/2024]
Abstract
Steroid hormones are derived from a common precursor molecule, cholesterol, and regulate a wide range of physiologic function including reproduction, salt balance, maintenance of secondary sexual characteristics, response to stress, neuronal function, and various metabolic processes. Among the steroids synthesized by the adrenal and gonadal tissues, adrenal mineralocorticoids, and glucocorticoids are essential for life. The process of steroidogenesis is regulated at multiple levels largely by transcriptional, posttranscriptional, translational, and posttranslational regulation of the steroidogenic enzymes (i.e., cytochrome P450s and hydroxysteroid dehydrogenases), cellular compartmentalization of the steroidogenic enzymes, and cholesterol processing and transport proteins. In recent years, small noncoding RNAs, termed microRNAs (miRNAs) have been recognized as major post-transcriptional regulators of gene expression with essential roles in numerous biological processes and disease pathologies. Although their role in the regulation of steroidogenesis is still emerging, several recent studies have contributed significantly to our understanding of the role miRNAs play in the regulation of the steroidogenic process. This chapter focuses on the recent developments in miRNA regulation of adrenal glucocorticoid and androgen production in humans and rodents.
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Affiliation(s)
- Salman Azhar
- Geriatric Research, Education and Clinical Center, VA Palo Alto Health Care System, Palo Alto, CA, United States; Division of Endocrinology, Gerontology and Metabolism, Stanford University School of Medicine, Stanford, CA, United States; Stanford Diabetes Research Center, Stanford, CA, United States.
| | - Wen-Jun Shen
- Geriatric Research, Education and Clinical Center, VA Palo Alto Health Care System, Palo Alto, CA, United States; Division of Endocrinology, Gerontology and Metabolism, Stanford University School of Medicine, Stanford, CA, United States
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology and College of Life Sciences, Nanjing Normal University, Nanjing, P.R. China
| | - Fredric B Kraemer
- Geriatric Research, Education and Clinical Center, VA Palo Alto Health Care System, Palo Alto, CA, United States; Division of Endocrinology, Gerontology and Metabolism, Stanford University School of Medicine, Stanford, CA, United States; Stanford Diabetes Research Center, Stanford, CA, United States
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6
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Gorbea C, Elhakiem A, Cazalla D. Shaping the host cell environment with viral noncoding RNAs. Semin Cell Dev Biol 2023; 146:20-30. [PMID: 36581481 PMCID: PMC10101873 DOI: 10.1016/j.semcdb.2022.12.008] [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: 08/29/2022] [Revised: 12/24/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022]
Abstract
Just like the cells they infect viruses express different classes of noncoding RNAs (ncRNAs). Viral ncRNAs come in all shapes and forms, and they usually associate with cellular proteins that are important for their functions. Viral ncRNAs have diverse functions, but they all contribute to the viral control of the cellular environment. Viruses utilize ncRNAs to regulate viral replication, to decide whether they should remain latent or reactivate, to evade the host immune responses, or to promote cellular transformation. In this review we describe the diverse functions played by different classes of ncRNAs expressed by adenoviruses and herpesviruses, how they contribute to the viral infection, and how their study led to insights into RNA-based mechanisms at play in host cells.
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Affiliation(s)
- Carlos Gorbea
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Abdalla Elhakiem
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Demián Cazalla
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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7
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Dokaneheifard S, Gomes Dos Santos H, Valencia MG, Arigela H, Shiekhattar R. BRAT1 associates with INTS11/INTS9 heterodimer to regulate key neurodevelopmental genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552743. [PMID: 37609215 PMCID: PMC10441392 DOI: 10.1101/2023.08.10.552743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Integrator is a multi-subunits protein complex involved in regulation of gene expression. Several Integrator subunits have been found to be mutated in human neurodevelopmental disorders, suggesting a key role for the complex in the development of nervous system. BRAT1 is similarly linked with neurodegenerative diseases and neurodevelopmental disorders such as rigidity and multifocal-seizure syndrome. Here, we show that INTS11 and INTS9 subunits of Integrator complex interact with BRAT1 and form a trimeric complex in human HEK293T cells as well as in pluripotent human embryonal carcinoma cell line (NT2). We find that BRAT1 depletion disrupts the differentiation of NT2 cells into astrocytes and neural cells. Loss of BRAT1 results in inability to activate many neuronal genes that are targets of REST, a neuronal silencer. We identified BRAT1 and INTS11 co-occupying the promoter region of these genes and pinpoint a role for BRAT1 in recruiting INTS11 to their promoters. Disease-causing mutations in BRAT1 diminish its association with INTS11/INTS9, linking the manifestation of disease phenotypes with a defect in transcriptional activation of key neuronal genes by BRAT1/INTS11/INTS9 complex. Highlights Integrator subunits INTS9 and INTS11 tightly interact with BRAT1 Depletion of BRAT1 causes a dramatic delay in human neural differentiation BRAT1 and INTS11 module targets the promoters of neural marker genes and co-regulates their expression. The recruitment of INTS11 to these sites is BRAT1-dependent. Pathogenic E522K mutation in BRAT1 disrupts its interaction with INTS11/INTS9 heterodimer.
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8
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Tepe B, Macke EL, Niceta M, Weisz Hubshman M, Kanca O, Schultz-Rogers L, Zarate YA, Schaefer GB, Granadillo De Luque JL, Wegner DJ, Cogne B, Gilbert-Dussardier B, Le Guillou X, Wagner EJ, Pais LS, Neil JE, Mochida GH, Walsh CA, Magal N, Drasinover V, Shohat M, Schwab T, Schmitz C, Clark K, Fine A, Lanpher B, Gavrilova R, Blanc P, Burglen L, Afenjar A, Steel D, Kurian MA, Prabhakar P, Gößwein S, Di Donato N, Bertini ES, Wangler MF, Yamamoto S, Tartaglia M, Klee EW, Bellen HJ. Bi-allelic variants in INTS11 are associated with a complex neurological disorder. Am J Hum Genet 2023; 110:774-789. [PMID: 37054711 PMCID: PMC10183469 DOI: 10.1016/j.ajhg.2023.03.012] [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: 01/05/2023] [Accepted: 03/18/2023] [Indexed: 04/15/2023] Open
Abstract
The Integrator complex is a multi-subunit protein complex that regulates the processing of nascent RNAs transcribed by RNA polymerase II (RNAPII), including small nuclear RNAs, enhancer RNAs, telomeric RNAs, viral RNAs, and protein-coding mRNAs. Integrator subunit 11 (INTS11) is the catalytic subunit that cleaves nascent RNAs, but, to date, mutations in this subunit have not been linked to human disease. Here, we describe 15 individuals from 10 unrelated families with bi-allelic variants in INTS11 who present with global developmental and language delay, intellectual disability, impaired motor development, and brain atrophy. Consistent with human observations, we find that the fly ortholog of INTS11, dIntS11, is essential and expressed in the central nervous systems in a subset of neurons and most glia in larval and adult stages. Using Drosophila as a model, we investigated the effect of seven variants. We found that two (p.Arg17Leu and p.His414Tyr) fail to rescue the lethality of null mutants, indicating that they are strong loss-of-function variants. Furthermore, we found that five variants (p.Gly55Ser, p.Leu138Phe, p.Lys396Glu, p.Val517Met, and p.Ile553Glu) rescue lethality but cause a shortened lifespan and bang sensitivity and affect locomotor activity, indicating that they are partial loss-of-function variants. Altogether, our results provide compelling evidence that integrity of the Integrator RNA endonuclease is critical for brain development.
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Affiliation(s)
- Burak Tepe
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Monika Weisz Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Yuri A Zarate
- Division of Genetics and Metabolism, University of Kentucky, Lexington, KY, USA
| | - G Bradley Schaefer
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jorge Luis Granadillo De Luque
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel J Wegner
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children's Hospital, St. Louis, Missouri, USA
| | - Benjamin Cogne
- Laboratory of Molecular Genetics, CHU de Nantes, Nantes, France
| | | | | | - Eric J Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Lynn S Pais
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Nurit Magal
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Valerie Drasinover
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Mordechai Shohat
- Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel; Medical Genetics Institute of Maccabi HMO, Rechovot, Israel
| | - Tanya Schwab
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Chris Schmitz
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl Clark
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Anthony Fine
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Brendan Lanpher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ralitza Gavrilova
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Pierre Blanc
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, 75012 Paris, France
| | - Lydie Burglen
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, 75012 Paris, France
| | - Alexandra Afenjar
- APHP. SU, Centre de Référence Malformations et maladies congénitales du cervelet, département de génétique et embryologie médicale, Hôpital Trousseau, 75012 Paris, France
| | - Dora Steel
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Prab Prabhakar
- Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Sophie Gößwein
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Enrico S Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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9
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Offley SR, Pfleiderer MM, Zucco A, Fraudeau A, Welsh SA, Razew M, Galej WP, Gardini A. A combinatorial approach to uncover an additional Integrator subunit. Cell Rep 2023; 42:112244. [PMID: 36920904 DOI: 10.1016/j.celrep.2023.112244] [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: 07/05/2022] [Revised: 11/15/2022] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
RNA polymerase II (RNAPII) controls expression of all protein-coding genes and most noncoding loci in higher eukaryotes. Calibrating RNAPII activity requires an assortment of polymerase-associated factors that are recruited at sites of active transcription. The Integrator complex is one of the most elusive transcriptional regulators in metazoans, deemed to be recruited after initiation to help establish and modulate paused RNAPII. Integrator is known to be composed of 14 subunits that assemble and operate in a modular fashion. We employed proteomics and machine-learning structure prediction (AlphaFold2) to identify an additional Integrator subunit, INTS15. We report that INTS15 assembles primarily with the INTS13/14/10 module and interfaces with the Int-PP2A module. Functional genomics analysis further reveals a role for INTS15 in modulating RNAPII pausing at a subset of genes. Our study shows that omics approaches combined with AlphaFold2-based predictions provide additional insights into the molecular architecture of large and dynamic multiprotein complexes.
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Affiliation(s)
- Sarah R Offley
- The Wistar Institute, Philadelphia, PA 19103, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Avery Zucco
- The Wistar Institute, Philadelphia, PA 19103, USA
| | - Angelique Fraudeau
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | | | - Michal Razew
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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10
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Welsh SA, Gardini A. Genomic regulation of transcription and RNA processing by the multitasking Integrator complex. Nat Rev Mol Cell Biol 2023; 24:204-220. [PMID: 36180603 PMCID: PMC9974566 DOI: 10.1038/s41580-022-00534-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 11/09/2022]
Abstract
In higher eukaryotes, fine-tuned activation of protein-coding genes and many non-coding RNAs pivots around the regulated activity of RNA polymerase II (Pol II). The Integrator complex is the only Pol II-associated large multiprotein complex that is metazoan specific, and has therefore been understudied for years. Integrator comprises at least 14 subunits, which are grouped into distinct functional modules. The phosphodiesterase activity of the core catalytic module is co-transcriptionally directed against several RNA species, including long non-coding RNAs (lncRNAs), U small nuclear RNAs (U snRNAs), PIWI-interacting RNAs (piRNAs), enhancer RNAs and nascent pre-mRNAs. Processing of non-coding RNAs by Integrator is essential for their biogenesis, and at protein-coding genes, Integrator is a key modulator of Pol II promoter-proximal pausing and transcript elongation. Recent studies have identified an Integrator-specific serine/threonine-protein phosphatase 2A (PP2A) module, which targets Pol II and other components of the basal transcription machinery. In this Review, we discuss how the activity of Integrator regulates transcription, RNA processing, chromatin landscape and DNA repair. We also discuss the diverse roles of Integrator in development and tumorigenesis.
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11
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Kirstein N, Dokaneheifard S, Cingaram PR, Valencia MG, Beckedorff F, Gomes Dos Santos H, Blumenthal E, Tayari MM, Gaidosh GS, Shiekhattar R. The Integrator complex regulates microRNA abundance through RISC loading. SCIENCE ADVANCES 2023; 9:eadf0597. [PMID: 36763664 PMCID: PMC9916992 DOI: 10.1126/sciadv.adf0597] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
MicroRNA (miRNA) homeostasis is crucial for the posttranscriptional regulation of their target genes during development and in disease states. miRNAs are derived from primary transcripts and are processed from a hairpin precursor intermediary to a mature 22-nucleotide duplex RNA. Loading of the duplex into the Argonaute (AGO) protein family is pivotal to miRNA abundance and its posttranscriptional function. The Integrator complex plays a key role in protein coding and noncoding RNA maturation, RNA polymerase II pause-release, and premature transcriptional termination. Here, we report that loss of Integrator results in global destabilization of mature miRNAs. Enhanced ultraviolet cross-linking and immunoprecipitation of Integrator uncovered an association with duplex miRNAs before their loading onto AGOs. Tracing miRNA fate from biogenesis to stabilization by incorporating 4-thiouridine in nascent transcripts pinpointed a critical role for Integrator in miRNA assembly into AGOs.
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Affiliation(s)
- Nina Kirstein
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Sadat Dokaneheifard
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Pradeep Reddy Cingaram
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Monica Guiselle Valencia
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Felipe Beckedorff
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Helena Gomes Dos Santos
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ezra Blumenthal
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
- Medical Scientist Training Program and Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mina Masoumeh Tayari
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Gabriel Stephen Gaidosh
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, 1501 NW 10th Avenue, Miami, FL 33136, USA
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12
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Sabath K, Jonas S. Take a break: Transcription regulation and RNA processing by the Integrator complex. Curr Opin Struct Biol 2022; 77:102443. [PMID: 36088798 DOI: 10.1016/j.sbi.2022.102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022]
Abstract
The metazoan-specific Integrator complex is a >1.5 MDa machinery that interacts with RNA polymerase II (RNAP2) to attenuate coding gene transcription by early termination close to transcription start sites. Using a highly related mechanism, Integrator also performs the initial 3'-end processing step for many non-coding RNAs. Its transcription regulation functions are essential for cell differentiation and response to external stimuli. Recent studies revealed that the complex incorporates phosphatase PP2A to counteract phosphorylation reactions that are required for transcription elongation. Structures of Integrator bound to RNAP2 explain the basis for its recruitment to promoter proximal RNAP2 by recognition of its paused state. Furthermore, several studies indicate that Integrator's cleavage activity is regulated at multiple levels through activators, modifications, and small molecules.
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Affiliation(s)
- Kevin Sabath
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Switzerland.
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13
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Bragado L, Magalnik M, Mammi P, Romero A, Gaioli N, Pozzi B, Srebrow A. SUMO conjugation regulates the activity of the Integrator complex. Nucleic Acids Res 2022; 50:12444-12461. [PMID: 36454007 PMCID: PMC9757034 DOI: 10.1093/nar/gkac1055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/13/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
RNA polymerase II (RNAPII) transcribes small nuclear RNA (snRNA) genes in close proximity to Cajal bodies, subnuclear compartments that depend on the SUMO isopeptidase USPL1 for their assembly. We show here that overexpression of USPL1 as well as of another nuclear SUMO isopeptidase, SENP6, alters snRNA 3'-end cleavage, a process carried out by the Integrator complex. Beyond its role in snRNA biogenesis, this complex is responsible for regulating the expression of different RNAPII transcripts. While several subunits of the complex are SUMO conjugation substrates, we found that the SUMOylation of the INTS11 subunit is regulated by USPL1 and SENP6. We defined Lys381, Lys462 and Lys475 as bona fide SUMO attachment sites on INTS11 and observed that SUMOylation of this protein modulates its subcellular localization and is required for Integrator activity. Moreover, while an INTS11 SUMOylation-deficient mutant is still capable of interacting with INTS4 and INTS9, its interaction with other subunits of the complex is affected. These findings point to a regulatory role for SUMO conjugation on Integrator activity and suggest the involvement of INTS11 SUMOylation in the assembly of the complex. Furthermore, this work adds Integrator-dependent RNA processing to the growing list of cellular processes regulated by SUMO conjugation.
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Affiliation(s)
- Laureano Bragado
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Melina Magalnik
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Pablo Mammi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Agustín Romero
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Nicolás Gaioli
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Berta Pozzi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
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14
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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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15
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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16
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Pawlica P, Yario TA, White S, Wang J, Moss WN, Hui P, Vinetz JM, Steitz JA. SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes. Proc Natl Acad Sci U S A 2021; 118:e2116668118. [PMID: 34903581 PMCID: PMC8719879 DOI: 10.1073/pnas.2116668118] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2-infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. However, we unexpectedly discovered a viral miRNA-like small RNA, named CoV2-miR-O7a (for SARS-CoV-2 miRNA-like ORF7a-derived small RNA). Its abundance ranges from low to moderate as compared to host miRNAs and it associates with Argonaute proteins-core components of the RNA interference pathway. We identify putative targets for CoV2-miR-O7a, including Basic Leucine Zipper ATF-Like Transcription Factor 2 (BATF2), which participates in interferon signaling. We demonstrate that CoV2-miR-O7a production relies on cellular machinery, yet is independent of Drosha protein, and is enhanced by the presence of a strong and evolutionarily conserved hairpin formed within the ORF7a sequence.
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Affiliation(s)
- Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536;
| | - Therese A Yario
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536
- HHMI, Yale University School of Medicine, New Haven, CT 06536
| | - Sylvia White
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Joseph M Vinetz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536;
- HHMI, Yale University School of Medicine, New Haven, CT 06536
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17
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Pfleiderer MM, Galej WP. Emerging insights into the function and structure of the Integrator complex. Transcription 2021; 12:251-265. [PMID: 35311473 PMCID: PMC9006982 DOI: 10.1080/21541264.2022.2047583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
The Integrator was originally discovered as a specialized 3'-end processing endonuclease complex required for maturation of RNA polymerase II (RNAPII)-dependent small nuclear RNAs (snRNAs). Since its discovery, Integrator's spectrum of substrates was significantly expanded to include non-polyadenylated long noncoding RNAs (lncRNA), enhancer RNAs (eRNAs), telomerase RNA (tertRNA), several Herpesvirus transcripts, and messenger RNAs (mRNAs). Recently emerging transcriptome-wide studies reveled an important role of the Integrator in protein-coding genes, where it contributes to gene expression regulation through promoter-proximal transcription attenuation. These new functional data are complemented by several structures of Integrator modules and higher-order complexes, providing mechanistic insights into Integrator-mediated processing events. In this work, we summarize recent progress in our understanding of the structure and function of the Integrator complex.
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18
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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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19
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Luo Y, Yu L, Feng Z, Chen Q, Lu L, Zhang Q, Xu D. Integrated analysis of viral miRNAs, mRNA and protein in the caudal fin cells of C. auratus gibelio with cyprinid herpesvirus 2 infection. JOURNAL OF FISH DISEASES 2021; 44:441-460. [PMID: 33577719 DOI: 10.1111/jfd.13289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 06/12/2023]
Abstract
Cyprinid herpesvirus 2 (CyHV-2), a member of the genus Cyprinivirus in the family Alloherpesviridae, has attracted worldwide attention because it causes severe disease and high mortality in crucian carp and goldfish. In this study, we focus on mRNA, protein and viral miRNA expression profiles in C. auratus gibelio caudal fin (GiCF) cells infected with CyHV-2, using high-throughput sequence techniques and TMT-labelled analyses. The results revealed that 156 virus genes were differentially expressed during the infection. Among these differentially expressed genes, 7 viral genes were significantly up-regulated and 28 were significantly down-regulated at 96 hpi (hours post-infection) vs 48 hpi. Besides, a total of 78 viral proteins, including a large number of membrane proteins and capsid proteins associated with the viral assembly, were successfully detected by using proteome analysis. Furthermore, a total of 225,143,474 raw reads were generated from cDNA library of CyHV-2-infected GiCF cells using high-throughput sequencing technology. Following annotation and secondary structure prediction, 10 viral miRNAs were found as significantly modulated in CyHV-2-infected GiCF cells (2 down-regulated and 8 up-regulated). Finally, the CyHV-2 genes (orf19, orf23, orf118, orf121, orf127) targeted by the viral miRNA CyHV-2-KT-635 identified in this study, were predicted and validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR), and the regulation of CyHV-2-KT-635 on orf121 protein expression was verified by western blotting assay. Taken together, this study provides a valuable basis for further research on the expression of virus genes during CyHV-2 replication and the molecular mechanisms by which miRNA may regulate CyHV-2 virus.
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Affiliation(s)
- Yang Luo
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Lu Yu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Zizhao Feng
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Qikang Chen
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, China
| | - Qiya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Wuhan, China
| | - Dan Xu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, China
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
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20
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Pfleiderer MM, Galej WP. Structure of the catalytic core of the Integrator complex. Mol Cell 2021; 81:1246-1259.e8. [PMID: 33548203 PMCID: PMC7980224 DOI: 10.1016/j.molcel.2021.01.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/29/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022]
Abstract
The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator's catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3' end-processing machineries points to distinct features and a unique architecture of the Integrator's catalytic module.
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Affiliation(s)
- Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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21
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Zheng H, Qi Y, Hu S, Cao X, Xu C, Yin Z, Chen X, Li Y, Liu W, Li J, Wang J, Wei G, Liang K, Chen FX, Xu Y. Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase. Science 2020; 370:370/6520/eabb5872. [DOI: 10.1126/science.abb5872] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/09/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Hai Zheng
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yilun Qi
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Shibin Hu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xuan Cao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Congling Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zhinang Yin
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yan Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jie Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
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22
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Song Z, Jia R, Tang M, Xia F, Xu H, Li Z, Huang C. Antisense oligonucleotide technology can be used to investigate a circular but not linear RNA-mediated function for its encoded gene locus. SCIENCE CHINA-LIFE SCIENCES 2020; 64:784-794. [PMID: 32815066 DOI: 10.1007/s11427-020-1743-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023]
Abstract
As a class of powerful molecular tool, antisense oligonucleotides (ASOs) are not only broadly used in protein and RNA biology, but also a highly selective therapeutic strategy for many diseases. Although the concept that ASO reagents only reduce expression of the targeted gene in a post-transcriptional manner has long been established, the effect and mechanism of ASO reagents on RNA polymerase II (Pol II) transcription are largely unknown. This raised question is particularly important for the appropriate use of ASOs and the valid interpretation of ASO-mediated experiments. In this study, our results show that linear RNA ASO attenuates transcription of nascent transcripts by inducing premature transcription termination which is combinatorially controlled by Integrator, exosome, and Rat1 in Drosophila. However, circular RNA (circRNA) ASO transfection does not affect transcription activity of the encoded gene. These data suggest that the ASO technique can be applied to study a circRNA-mediated but not linear RNA-mediated function for its encoded gene locus.
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Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Mingfeng Tang
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Fei Xia
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Haiyang Xu
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 400044, China. .,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China.
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23
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Mendoza-Figueroa MS, Tatomer DC, Wilusz JE. The Integrator Complex in Transcription and Development. Trends Biochem Sci 2020; 45:923-934. [PMID: 32800671 DOI: 10.1016/j.tibs.2020.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/03/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
The Integrator complex is conserved across metazoans and controls the fate of many nascent RNAs transcribed by RNA polymerase II (RNAPII). Among the 14 subunits of Integrator is an RNA endonuclease that is crucial for the biogenesis of small nuclear RNAs and enhancer RNAs. Integrator is further employed to trigger premature transcription termination at many protein-coding genes, thereby attenuating gene expression. Integrator thus helps to shape the transcriptome and ensure that genes can be robustly induced when needed. The molecular functions of Integrator subunits beyond the RNA endonuclease remain poorly understood, but some can act independently of the multisubunit complex. We highlight recent molecular insights into Integrator and propose how misregulation of this complex may lead to developmental defects and disease.
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Affiliation(s)
- María Saraí Mendoza-Figueroa
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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24
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Sheng P, Flood KA, Xie M. Short Hairpin RNAs for Strand-Specific Small Interfering RNA Production. Front Bioeng Biotechnol 2020; 8:940. [PMID: 32850763 PMCID: PMC7427337 DOI: 10.3389/fbioe.2020.00940] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
RNA interference (RNAi) is an effective mechanism for inhibiting gene expression at the post-transcriptional level. Expression of a messenger RNA (mRNA) can be inhibited by a ∼22-nucleotide (nt) small interfering (si)RNA with the corresponding reverse complementary sequence. Typically, a duplex of siRNA, composed of the desired siRNA and a passenger strand, is processed from a short hairpin RNA (shRNA) precursor by Dicer. Subsequently, one strand of the siRNA duplex is associated with Argonaute (Ago) protein for RNAi. Although RNAi is widely used, the off-target effect induced by the passenger strand remains a potential problem. Here, based on current understanding of endogenous precursor microRNA (pre-miRNA) hairpins, called Ago-shRNA and m7G-capped pre-miRNA, we discuss the principles of shRNA designs that produce a single siRNA from one strand of the hairpin.
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Affiliation(s)
- Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States.,UF Health Cancer Center, University of Florida, Gainesville, FL, United States
| | - Krystal A Flood
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States.,UF Health Cancer Center, University of Florida, Gainesville, FL, United States
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States.,UF Health Cancer Center, University of Florida, Gainesville, FL, United States.,UF Genetics Institute, University of Florida, Gainesville, FL, United States
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25
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Sabath K, Stäubli ML, Marti S, Leitner A, Moes M, Jonas S. INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module. Nat Commun 2020; 11:3422. [PMID: 32647223 PMCID: PMC7347597 DOI: 10.1038/s41467-020-17232-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/18/2020] [Indexed: 11/18/2022] Open
Abstract
The Integrator complex processes 3′-ends of spliceosomal small nuclear RNAs (snRNAs). Furthermore, it regulates transcription of protein coding genes by terminating transcription after unstable pausing. The molecular basis for Integrator’s functions remains obscure. Here, we show that INTS10, Asunder/INTS13 and INTS14 form a separable, functional Integrator module. The structure of INTS13-INTS14 reveals a strongly entwined complex with a unique chain interlink. Unexpected structural homology to the Ku70-Ku80 DNA repair complex suggests nucleic acid affinity. Indeed, the module displays affinity for DNA and RNA but prefers RNA hairpins. While the module plays an accessory role in snRNA maturation, it has a stronger influence on transcription termination after pausing. Asunder/INTS13 directly binds Integrator’s cleavage module via a conserved C-terminal motif that is involved in snRNA processing and required for spermatogenesis. Collectively, our data establish INTS10-INTS13-INTS14 as a nucleic acid-binding module and suggest that it brings cleavage module and target transcripts into proximity. The Integrator complex (INT) is responsible for the 3′-end processing of several classes of non-coding RNAs. Here the authors show that the INTS10-INTS13-INTS14 complex forms a distinct submodule of INT and suggest it facilitates RNA substrate targeting.
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Affiliation(s)
- Kevin Sabath
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Melanie L Stäubli
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Sabrina Marti
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Murielle Moes
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093, Zurich, Switzerland.
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26
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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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27
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Kretov DA, Walawalkar IA, Mora-Martin A, Shafik AM, Moxon S, Cifuentes D. Ago2-Dependent Processing Allows miR-451 to Evade the Global MicroRNA Turnover Elicited during Erythropoiesis. Mol Cell 2020; 78:317-328.e6. [PMID: 32191872 DOI: 10.1016/j.molcel.2020.02.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/02/2019] [Accepted: 02/24/2020] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) are sequentially processed by two RNase III enzymes, Drosha and Dicer. miR-451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute-2 (Ago2). miR-451 is highly conserved in vertebrates and regulates erythrocyte maturation, where it becomes the most abundant miRNA. However, the basis for the non-canonical biogenesis of miR-451 is unclear. Here, we show that Ago2 is less efficient than Dicer in processing pre-miRNAs, but this deficit is overcome when miR-144 represses Dicer in a negative-feedback loop during erythropoiesis. Loss of miR-144-mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR-451 maturation. Overexpression of Ago2 rescues some of the defects of miR-451 processing. Thus, the evolution of Ago2-dependent processing allows miR-451 to circumvent the global repression of canonical miRNAs elicited, in part, by the miR-144 targeting of Dicer during erythropoiesis.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Isha A Walawalkar
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | - Andrew M Shafik
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
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28
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Ebola Virus Produces Discrete Small Noncoding RNAs Independently of the Host MicroRNA Pathway Which Lack RNA Interference Activity in Bat and Human Cells. J Virol 2020; 94:JVI.01441-19. [PMID: 31852785 DOI: 10.1128/jvi.01441-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
The question as to whether RNA viruses produce bona fide microRNAs (miRNAs) during infection has been the focus of intense research and debate. Recently, several groups using computational prediction methods have independently reported possible miRNA candidates produced by Ebola virus (EBOV). Additionally, efforts to detect these predicted RNA products in samples from infected animals and humans have produced positive results. However, these studies and their conclusions are predicated on the assumption that these RNA products are actually processed through, and function within, the miRNA pathway. In the present study, we performed the first rigorous assessment of the ability of filoviruses to produce miRNA products during infection of both human and bat cells. Using next-generation sequencing, we detected several candidate miRNAs from both EBOV and the closely related Marburg virus (MARV). Focusing our validation efforts on EBOV, we found evidence contrary to the idea that these small RNA products function as miRNAs. The results of our study are important because they highlight the potential pitfalls of relying on computational methods alone for virus miRNA discovery.IMPORTANCE Here, we report the discovery, via deep sequencing, of numerous noncoding RNAs (ncRNAs) derived from both EBOV and MARV during infection of both bat and human cell lines. In addition to identifying several novel ncRNAs from both viruses, we identified two EBOV ncRNAs in our sequencing data that were near-matches to computationally predicted viral miRNAs reported in the literature. Using molecular and immunological techniques, we assessed the potential of EBOV ncRNAs to function as viral miRNAs. Importantly, we found little evidence supporting this hypothesis. Our work is significant because it represents the first rigorous assessment of the potential for EBOV to encode viral miRNAs and provides evidence contrary to the existing paradigm regarding the biological role of computationally predicted EBOV ncRNAs. Moreover, our work highlights further avenues of research regarding the nature and function of EBOV ncRNAs.
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29
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Elrod ND, Henriques T, Huang KL, Tatomer DC, Wilusz JE, Wagner EJ, Adelman K. The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes. Mol Cell 2020; 76:738-752.e7. [PMID: 31809743 DOI: 10.1016/j.molcel.2019.10.034] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/15/2019] [Accepted: 10/25/2019] [Indexed: 12/11/2022]
Abstract
The transition of RNA polymerase II (Pol II) from initiation to productive elongation is a central, regulated step in metazoan gene expression. At many genes, Pol II pauses stably in early elongation, remaining engaged with the 25- to 60-nt-long nascent RNA for many minutes while awaiting signals for release into the gene body. However, 15%-20% of genes display highly unstable promoter Pol II, suggesting that paused polymerase might dissociate from template DNA at these promoters and release a short, non-productive mRNA. Here, we report that paused Pol II can be actively destabilized by the Integrator complex. Specifically, we present evidence that Integrator utilizes its RNA endonuclease activity to cleave nascent RNA and drive termination of paused Pol II. These findings uncover a previously unappreciated mechanism of metazoan gene repression, akin to bacterial transcription attenuation, wherein promoter-proximal Pol II is prevented from entering productive elongation through factor-regulated termination.
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Affiliation(s)
- Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA.
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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30
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Tatomer DC, Wilusz JE. Attenuation of Eukaryotic Protein-Coding Gene Expression via Premature Transcription Termination. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:83-93. [PMID: 32086332 DOI: 10.1101/sqb.2019.84.039644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A complex network of RNA transcripts is generated from eukaryotic genomes, many of which are processed in unexpected ways. Here, we highlight how premature transcription termination events at protein-coding gene loci can simultaneously lead to the generation of short RNAs and attenuate production of full-length mRNA transcripts. We recently showed that the Integrator (Int) complex can be selectively recruited to protein-coding gene loci, including Drosophila metallothionein A (MtnA), where the IntS11 RNA endonuclease cleaves nascent transcripts near their 5' ends. Such premature termination events catalyzed by Integrator can repress the expression of some full-length mRNAs by more than 100-fold. Transcription at small nuclear RNA (snRNA) loci is likewise terminated by Integrator cleavage, but protein-coding and snRNA gene loci have notably distinct dependencies on Integrator subunits. Additional mechanisms that attenuate eukaryotic gene outputs via premature termination have been discovered, including by the cleavage and polyadenylation machinery in a manner controlled by U1 snRNP. These mechanisms appear to function broadly across the transcriptome. This suggests that synthesis of full-length transcripts is not always the default option and that premature termination events can lead to a variety of transcripts, some of which may have important and unexpected biological functions.
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Affiliation(s)
- Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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31
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Sankaranarayanan R, Palani SN, Kumar A, Selvakumar A. S. P, Tennyson J. Prediction and experimental confirmation of banana bract mosaic virus encoding miRNAs and their targets. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s41544-019-0044-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Potyviridae is the largest plant infecting family under the monophyletic group Riboviria, infects many of the food, fodder and ornamental crops. Due to the higher mutation and recombination rate, potyvirids are evolving rapidly, adapting to the environmental chaos and expanding their hosts. Virus control measures are need to be updated as the economic importance of potyvirids is massive. microRNAs (miRNAs) are well known for their functional importance in eukaryotes and many viruses. Regardless of its biogenesis, whether canonical or noncanonical, microRNA centric antivirus approaches attract the researchers to the hopeful future of next-generation broad-spectrum antiviral measures.
Methods
In this study, we predicted and screened banana bract mosaic virus (BBrMV) encoding miRNAs by computation approaches and their targets on banana transcriptome using plant small RNA target analysis server (psRNAtarget). The target gene functions were annotated by Blast2GO. The predicted BBrMV miRNAs were experimentally screened by stem-loop RT-PCR.
Results
The results showed that, among the predicted BBrMV miRNAs, miRNA2 is conserved throughout BBrMV isolates and has multiple virus-specific target transcripts. In addition, primary experimental validation for the predicted miRNAs revealed that miRNA2 exists in the BBrMV infected banana leaf samples.
Conclusions
The existence of BBrMV miRNA2 is confirmed by stem-loop RT-PCR followed by cloning and sequencing. The presence of miRNA of Potyviridae is rarely addressed and would definitely spread the hope to understand the virus infectious cycle. Our report would also help to better understand and manipulate potyviral infections.
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32
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Elrod ND, Henriques T, Huang KL, Tatomer DC, Wilusz JE, Wagner EJ, Adelman K. The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes. Mol Cell 2019; 76:738-752.e7. [PMID: 31809743 DOI: 10.1101/725507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/15/2019] [Accepted: 10/25/2019] [Indexed: 05/27/2023]
Abstract
The transition of RNA polymerase II (Pol II) from initiation to productive elongation is a central, regulated step in metazoan gene expression. At many genes, Pol II pauses stably in early elongation, remaining engaged with the 25- to 60-nt-long nascent RNA for many minutes while awaiting signals for release into the gene body. However, 15%-20% of genes display highly unstable promoter Pol II, suggesting that paused polymerase might dissociate from template DNA at these promoters and release a short, non-productive mRNA. Here, we report that paused Pol II can be actively destabilized by the Integrator complex. Specifically, we present evidence that Integrator utilizes its RNA endonuclease activity to cleave nascent RNA and drive termination of paused Pol II. These findings uncover a previously unappreciated mechanism of metazoan gene repression, akin to bacterial transcription attenuation, wherein promoter-proximal Pol II is prevented from entering productive elongation through factor-regulated termination.
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Affiliation(s)
- Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA.
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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33
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Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, Torabi SF, Steitz JA. Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology. Annu Rev Virol 2019; 6:297-317. [PMID: 31039329 PMCID: PMC6768742 DOI: 10.1146/annurev-virology-092818-015811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Like their host cells, many viruses express noncoding RNAs (ncRNAs). Despite the technical challenge of ascribing function to ncRNAs, diverse biological roles for virally expressed ncRNAs have been described, including regulation of viral replication, modulation of host gene expression, host immune evasion, cellular survival, and cellular transformation. Insights into conserved interactions between viral ncRNAs and host cell machinery frequently lead to novel findings concerning host cell biology. In this review, we discuss the functions and biogenesis of ncRNAs produced by animal viruses. Specifically, we describe noncanonical pathways of microRNA (miRNA) biogenesis and novel mechanisms used by viruses to manipulate miRNA and messenger RNA stability. We also highlight recent advances in understanding the function of viral long ncRNAs and circular RNAs.
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Affiliation(s)
- Johanna B Withers
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Vanessa Mondol
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Salehe Ghasempur
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Seyed F Torabi
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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34
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Tatomer DC, Elrod ND, Liang D, Xiao MS, Jiang JZ, Jonathan M, Huang KL, Wagner EJ, Cherry S, Wilusz JE. The Integrator complex cleaves nascent mRNAs to attenuate transcription. Genes Dev 2019; 33:1525-1538. [PMID: 31530651 PMCID: PMC6824465 DOI: 10.1101/gad.330167.119] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
Abstract
In this study, Tatomer et al. systematically identify regulators of inducible gene expression; they performed high-throughput RNAi screening of the Drosophila Metallothionein A (MtnA) promoter, which showed that the Integrator complex attenuates MtnA transcription during copper stress. Their findings suggest that attenuation via Integrator cleavage limits production of many full-length mRNAs, allowing precise control of transcription outputs. Cellular homeostasis requires transcriptional outputs to be coordinated, and many events post-transcription initiation can dictate the levels and functions of mature transcripts. To systematically identify regulators of inducible gene expression, we performed high-throughput RNAi screening of the Drosophila Metallothionein A (MtnA) promoter. This revealed that the Integrator complex, which has a well-established role in 3′ end processing of small nuclear RNAs (snRNAs), attenuates MtnA transcription during copper stress. Integrator complex subunit 11 (IntS11) endonucleolytically cleaves MtnA transcripts, resulting in premature transcription termination and degradation of the nascent RNAs by the RNA exosome, a complex also identified in the screen. Using RNA-seq, we then identified >400 additional Drosophila protein-coding genes whose expression increases upon Integrator depletion. We focused on a subset of these genes and confirmed that Integrator is bound to their 5′ ends and negatively regulates their transcription via IntS11 endonuclease activity. Many noncatalytic Integrator subunits, which are largely dispensable for snRNA processing, also have regulatory roles at these protein-coding genes, possibly by controlling Integrator recruitment or RNA polymerase II dynamics. Altogether, our results suggest that attenuation via Integrator cleavage limits production of many full-length mRNAs, allowing precise control of transcription outputs.
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Affiliation(s)
- Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77550, USA
| | - Dongming Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Mei-Sheng Xiao
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jeffrey Z Jiang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Michael Jonathan
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77550, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77550, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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35
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Bradley MW, Aiello KA, Ponnapalli SP, Hanson HA, Alter O. GSVD- and tensor GSVD-uncovered patterns of DNA copy-number alterations predict adenocarcinomas survival in general and in response to platinum. APL Bioeng 2019; 3:036104. [PMID: 31463421 PMCID: PMC6701977 DOI: 10.1063/1.5099268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022] Open
Abstract
More than a quarter of lung, uterine, and ovarian adenocarcinoma (LUAD, USEC, and OV) tumors are resistant to platinum drugs. Only recently and only in OV, patterns of copy-number alterations that predict survival in response to platinum were discovered, and only by using the tensor GSVD to compare Agilent microarray platform-matched profiles of patient-matched normal and primary tumor DNA. Here, we use the GSVD to compare whole-genome sequencing (WGS) and Affymetrix microarray profiles of patient-matched normal and primary LUAD, USEC, and OV tumor DNA. First, the GSVD uncovers patterns similar to one Agilent OV pattern, where a loss of most of the chromosome arm 6p combined with a gain of 12p encode for transformation. Like the Agilent OV pattern, the WGS LUAD and Affymetrix LUAD, USEC, and OV patterns are correlated with shorter survival, in general and in response to platinum. Like the tensor GSVD, the GSVD separates these tumor-exclusive genotypes from experimental inconsistencies. Second, by identifying the shorter survival phenotypes among the WGS- and Affymetrix-profiled tumors, the Agilent pattern proves to be a technology-independent predictor of survival, independent also of the best other indicator at diagnosis, i.e., stage. Third, like no other indicator, the pattern predicts the overall survival of OV patients experiencing progression-free survival, in general and in response to platinum. We conclude that comparative spectral decompositions, such as the GSVD and tensor GSVD, underlie a mathematically universal description of the relationships between a primary tumor's genotype and a patient's overall survival phenotype, which other methods miss.
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Affiliation(s)
| | | | - Sri Priya Ponnapalli
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah 84112, USA
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36
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Albrecht TR, Shevtsov SP, Wu Y, Mascibroda LG, Peart NJ, Huang KL, Sawyer IA, Tong L, Dundr M, Wagner EJ. Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module. Nucleic Acids Res 2019; 46:4241-4255. [PMID: 29471365 PMCID: PMC5934644 DOI: 10.1093/nar/gky100] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 02/17/2018] [Indexed: 12/14/2022] Open
Abstract
Integrator (INT) is a transcriptional regulatory complex associated with RNA polymerase II that is required for the 3′-end processing of both UsnRNAs and enhancer RNAs. Integrator subunits 9 (INTS9) and INTS11 constitute the catalytic core of INT and are paralogues of the cleavage and polyadenylation specificity factors CPSF100 and CPSF73. While CPSF73/100 are known to associate with a third protein called Symplekin, there is no paralog of Symplekin within INT raising the question of how INTS9/11 associate with the other INT subunits. Here, we have identified that INTS4 is a specific and conserved interaction partner of INTS9/11 that does not interact with either subunit individually. Although INTS4 has no significant homology with Symplekin, it possesses N-terminal HEAT repeats similar to Symplekin but also contains a β-sheet rich C-terminal region, both of which are important to bind INTS9/11. We assess three functions of INT including UsnRNA 3′-end processing, maintenance of Cajal body structural integrity, and formation of histone locus bodies to conclude that INTS4/9/11 are the most critical of the INT subunits for UsnRNA biogenesis. Altogether, these results indicate that INTS4/9/11 compose a heterotrimeric complex that likely represents the Integrator ‘cleavage module’ responsible for its endonucleolytic activity.
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Affiliation(s)
- Todd R Albrecht
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Sergey P Shevtsov
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA
| | - Yixuan Wu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Lauren G Mascibroda
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Natoya J Peart
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Iain A Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA.,Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
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37
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Watson SF, Knol LI, Witteveldt J, Macias S. Crosstalk Between Mammalian Antiviral Pathways. Noncoding RNA 2019; 5:E29. [PMID: 30909383 PMCID: PMC6468734 DOI: 10.3390/ncrna5010029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/15/2022] Open
Abstract
As part of their innate immune response against viral infections, mammals activate the expression of type I interferons to prevent viral replication and dissemination. An antiviral RNAi-based response can be also activated in mammals, suggesting that several mechanisms can co-occur in the same cell and that these pathways must interact to enable the best antiviral response. Here, we will review how the classical type I interferon response and the recently described antiviral RNAi pathways interact in mammalian cells. Specifically, we will uncover how the small RNA biogenesis pathway, composed by the nucleases Drosha and Dicer can act as direct antiviral factors, and how the type-I interferon response regulates the function of these. We will also describe how the factors involved in small RNA biogenesis and specific small RNAs impact the activation of the type I interferon response and antiviral activity. With this, we aim to expose the complex and intricate network of interactions between the different antiviral pathways in mammals.
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Affiliation(s)
- Samir F Watson
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Lisanne I Knol
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Jeroen Witteveldt
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
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38
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Temporal Viral Genome-Protein Interactions Define Distinct Stages of Productive Herpesviral Infection. mBio 2018; 9:mBio.01182-18. [PMID: 30018111 PMCID: PMC6050965 DOI: 10.1128/mbio.01182-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Herpesviruses utilize multiple mechanisms to redirect host proteins for use in viral processes and to avoid recognition and repression by the host. To investigate dynamic interactions between herpes simplex virus type 1 (HSV-1) DNA and viral and host proteins throughout infection, we developed an approach to identify proteins that associate with the infecting viral genome from nuclear entry through packaging. To accomplish this, virus stocks were prepared in the presence of ethynyl-modified nucleotides to enable covalent tagging of viral genomes after infection for analysis of viral genome-protein interactions by imaging or affinity purification. Affinity purification was combined with stable isotope labeling of amino acids in cell culture (SILAC) mass spectrometry to enable the distinction between proteins that were brought into the cell by the virus or expressed within the infected cell before or during infection. We found that input viral DNA progressed within 6 h through four temporal stages where the genomes sequentially (i) interacted with intrinsic antiviral and DNA damage response proteins, (ii) underwent a robust transcriptional switch mediated largely by ICP4, (iii) engaged in replication, repair, and continued transcription, and then (iv) transitioned to a more transcriptionally inert state engaging de novo-synthesized viral structural components while maintaining interactions with replication proteins. Using a combination of genetic, imaging, and proteomic approaches, we provide a new and temporally compressed view of the HSV-1 life cycle based on input genome-proteome dynamics. Herpesviruses are highly prevalent and ubiquitous human pathogens. Studies of herpesviruses and other viruses have previously been limited by the ability to directly study events that occur on the viral DNA throughout infection. We present a new powerful approach, which allows for the temporal investigation of viral genome-protein interactions at all phases of infection. This work has integrated many results from previous studies with the discovery of novel factors potentially involved in viral infection that may represent new antiviral targets. In addition, the study provides a new view of the HSV-1 life cycle based on genome-proteome dynamics.
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39
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Sheng P, Fields C, Aadland K, Wei T, Kolaczkowski O, Gu T, Kolaczkowski B, Xie M. Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites. Nucleic Acids Res 2018; 46:5737-5752. [PMID: 29746670 PMCID: PMC6009592 DOI: 10.1093/nar/gky306] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/01/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs into the cytoplasm for Dicer processing. Alternatively, pre-miRNAs containing a 5' 7-methylguanine (m7G-) cap can be generated independently of Drosha and XPO5. Here we identify a class of m7G-capped pre-miRNAs with 5' extensions up to 39 nt long. The 5'-extended pre-miRNAs are transported by Exportin-1 (XPO1). Unexpectedly, a long 5' extension does not block Dicer processing. Rather, Dicer directly cleaves 5'-extended pre-miRNAs by recognizing its 3' end to produce mature 3p miRNA and extended 5p miRNA both in vivo and in vitro. The recognition of 5'-extended pre-miRNAs by the Dicer Platform-PAZ-Connector (PPC) domain can be traced back to ancestral animal Dicers, suggesting that this previously unrecognized Dicer reaction mode is evolutionarily conserved. Our work reveals additional genetic sources for small regulatory RNAs and substantiates Dicer's essential role in RNAi-based gene regulation.
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Affiliation(s)
- Peike Sheng
- Department of Biochemistry and Molecular Biology
- UF Health Cancer Center
| | | | - Kelsey Aadland
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
| | - Tianqi Wei
- Department of Biochemistry and Molecular Biology
| | - Oralia Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
| | - Tongjun Gu
- Interdisciplinary Center for Biotechnology Research
| | - Bryan Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology
- UF Health Cancer Center
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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40
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Abstract
Viruses masterfully regulate host gene expression during infection. Many do so, in part, by expressing non-coding RNAs. Recent work has shown that HSUR 2, a viral non-coding RNA expressed by the oncogenic Herpesvirus saimiri, regulates mRNA expression through a novel mechanism. HSUR 2 base pairs with both target mRNAs and host miRNAs in infected cells. This results in HSUR 2-dependent recruitment of host miRNAs and associated Ago proteins to target mRNAs, and the subsequent destabilization of target mRNAs. Using this mechanism, this virus regulates key cellular pathways during viral infection. Here I discuss the evolution of our thinking about HSUR function and explore the implications of recent findings in relation to the current views on the functions of interactions between miRNAs and other classes of non-coding RNAs, the potential advantages of this mechanism of regulation of gene expression, and the evolutionary origin of HSUR 2.
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Affiliation(s)
- Demián Cazalla
- a Department of Biochemistry , University of Utah School of Medicine , Salt Lake City , UT , USA
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41
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The Involvement of MicroRNAs in Modulation of Innate and Adaptive Immunity in Systemic Lupus Erythematosus and Lupus Nephritis. J Immunol Res 2018; 2018:4126106. [PMID: 29854836 PMCID: PMC5964414 DOI: 10.1155/2018/4126106] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
Noncoding RNAs (ncRNAs), including microRNAs (miRNAs), represent a family of RNA molecules that do not translate into protein. Nevertheless, they have the ability to regulate gene expression and play an essential role in immune cell differentiation and function. MicroRNAs were found to be differentially expressed in various tissues, and changes in their expression have been associated with several pathological processes. Yet, their roles in systemic lupus erythematosus (SLE) and lupus nephritis (LN) remain to be elucidated. Both SLE and LN are characterized by a complex dysfunction of the innate and adaptive immunity. Recently, significant findings have been made in understanding SLE through the use of genetic variant identification and expression pattern analysis and mouse models, as well as epigenetic analyses. Abnormalities in immune cell responses, cytokine and chemokine production, cell activation, and apoptosis have been linked to a unique expression pattern of a number of miRNAs that have been implicated in the immune pathogenesis of this autoimmune disease. The recent evidence that significantly increased the understanding of the pathogenesis of SLE drives a renewed interest in efficient therapy targets. This review aims at providing an overview of the current state of research on the expression and role of miRNAs in the immune pathogenesis of SLE and LN.
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42
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Abstract
MicroRNAs (miRNAs) are ∼22 nt RNAs that direct posttranscriptional repression of mRNA targets in diverse eukaryotic lineages. In humans and other mammals, these small RNAs help sculpt the expression of most mRNAs. This article reviews advances in our understanding of the defining features of metazoan miRNAs and their biogenesis, genomics, and evolution. It then reviews how metazoan miRNAs are regulated, how they recognize and cause repression of their targets, and the biological functions of this repression, with a compilation of knockout phenotypes that shows that important biological functions have been identified for most of the broadly conserved miRNAs of mammals.
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Affiliation(s)
- David P Bartel
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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43
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Xia J, Li L, Li T, Fang Z, Zhang K, Zhou J, Peng H, Zhang W. Detecting and characterizing microRNAs of diverse genomic origins via miRvial. Nucleic Acids Res 2017; 45:e176. [PMID: 29036674 PMCID: PMC5716067 DOI: 10.1093/nar/gkx834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 09/12/2017] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs form an essential class of post-transcriptional gene regulator of eukaryotic species, and play critical parts in development and disease and stress responses. MicroRNAs may originate from various genomic loci, have structural characteristics, and appear in canonical or modified forms, making them subtle to detect and analyze. We present miRvial, a robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs. Extensive results comparing miRvial and six existing microRNA finding methods on six model organisms, Mus musculus, Drosophila melanogaste, Arabidopsis thaliana, Oryza sativa, Physcomitrella patens and Chlamydomonas reinhardtii, demonstrated the utility and rigor of miRvial in detecting novel microRNAs and characterizing features of microRNAs. Experimental validation of several novel microRNAs in C. reinhardtii that were predicted by miRvial but missed by the other methods illustrated the superior performance of miRvial over the existing methods. miRvial is open source and available at https://github.com/SystemsBiologyOfJianghanUniversity/miRvial.
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Affiliation(s)
- Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Kevin Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO 63130, USA
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44
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Kamel W, Akusjärvi G. An Ago2-associated capped transcriptional start site small RNA suppresses adenovirus DNA replication. RNA (NEW YORK, N.Y.) 2017; 23:1700-1711. [PMID: 28839112 PMCID: PMC5648037 DOI: 10.1261/rna.061291.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Here we show that the adenovirus major late promoter produces a 31-nucleotide transcriptional start site small RNA (MLP-TSS-sRNA) that retains the 7-methylguanosine (m7G)-cap and is incorporated onto Ago2-containing RNA-induced silencing complexes (RISC) in human adenovirus-37 infected cells. RNA polymerase II CLIP (UV-cross linking immunoprecipitation) experiments suggest that the MLP-TSS-sRNA is produced by promoter proximal stalling/termination of RNA polymerase II transcription at the site of the small RNA 3' end. The MLP-TSS-sRNA is highly stable in cells and functionally active, down-regulating complementary targets in a sequence and dose-dependent manner. The MLP-TSS-sRNA is transcribed from the opposite strand to the adenoviral DNA polymerase and preterminal protein mRNAs, two essential viral replication proteins. We show that the MLP-TSS-sRNA act in trans to reduce DNA polymerase and preterminal protein mRNA expression. As a consequence of this, the MLP-TSS-sRNA has an inhibitory effect on the efficiency of viral DNA replication. Collectively, our results suggest that this novel sRNA may serve a regulatory function controlling viral genome replication during a lytic and/or persistent adenovirus infection in its natural host.
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Affiliation(s)
- Wael Kamel
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, SE-751 23 Uppsala, Sweden
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45
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Lu J, Xu D, Jiang Y, Kong S, Shen Z, Xia S, Lu L. Integrated analysis of mRNA and viral miRNAs in the kidney of Carassius auratus gibelio response to cyprinid herpesvirus 2. Sci Rep 2017; 7:13787. [PMID: 29062054 PMCID: PMC5653811 DOI: 10.1038/s41598-017-14217-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 10/06/2017] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding single stranded RNAs that play crucial roles in numerous biological processes. Vertebrate herpesviruses encode multiple viral miRNAs that modulate host and viral genes. However, the roles of viral miRNAs in lower vertebrates have not been fully determined. Here, we used high-throughput sequencing to analyse the miRNA and mRNA expression profiles of Carassius auratus gibelio in response to infection by cyprinid herpesvirus 2 (CyHV-2). RNA sequencing obtained 26,664 assembled transcripts, including 2,912 differentially expressed genes. Based on small RNA sequencing and secondary structure predictions, we identified 17 CyHV-2 encoded miRNAs, among which 14 were validated by stem-loop quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) and eight were validated by northern blotting. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of miRNAs-mRNA pairs revealed diverse affected immune signalling pathways, including the RIG-I-like receptor and JAK-STAT pathways. Finally, we presented four genes involved in RIG-I-like pathways, including host gene IRF3, RBMX, PIN1, viral gene ORF4, which are negatively regulated by CyHV-2 encoded miRNA miR-C4. The present study is the first to provide a comprehensive overview of viral miRNA-mRNA co-regulation, which might have a key role in controlling post-transcriptomic regulation during CyHV-2 infection.
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Affiliation(s)
- Jianfei Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
| | - Dan Xu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
- Key Laboratory of Agriculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, P. R. China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, P. R. China
| | - Yousheng Jiang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
- Key Laboratory of Agriculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, P. R. China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, P. R. China
| | - Shanyun Kong
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
| | - Zhaoyuan Shen
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
| | - Siyao Xia
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China.
- Key Laboratory of Agriculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, P. R. China.
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, P. R. China.
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46
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A viral Sm-class RNA base-pairs with mRNAs and recruits microRNAs to inhibit apoptosis. Nature 2017; 550:275-279. [PMID: 28976967 DOI: 10.1038/nature24034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/22/2017] [Indexed: 01/17/2023]
Abstract
Viruses express several classes of non-coding RNAs; the functions and mechanisms by which most of these act are unknown. Herpesvirus saimiri, a γ-herpesvirus that establishes latency in the T cells of New World primates and has the ability to cause aggressive leukaemias and lymphomas in non-natural hosts, expresses seven small nuclear uracil-rich non-coding RNAs (called HSURs) in latently infected cells. These HSURs associate with Sm proteins, and share biogenesis and structural features with cellular Sm-class small nuclear RNAs. One of these HSURs (HSUR2) base-pairs with two host cellular microRNAs (miR-142-3p and miR-16) but does not affect their abundance or activity, which suggests that its interactions with them perform alternative functions. Here we show that HSUR2 also base-pairs with mRNAs in infected cells. We combined in vivo psoralen-mediated RNA-RNA crosslinking and high-throughput sequencing to identify the mRNAs targeted by HSUR2, which include mRNAs that encode retinoblastoma and factors involved in p53 signalling and apoptosis. We show that HSUR2 represses the expression of target mRNAs and that base-pairing between HSUR2 and miR-142-3p and miR-16 is essential for this repression, suggesting that HSUR2 recruits these two cellular microRNAs to its target mRNAs. Furthermore, we show that HSUR2 uses this mechanism to inhibit apoptosis. Our results uncover a role for this viral Sm-class RNA as a microRNA adaptor in the regulation of gene expression that follows precursor mRNA processing.
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47
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Martinez I, Hayes KE, Barr JA, Harold AD, Xie M, Bukhari SIA, Vasudevan S, Steitz JA, DiMaio D. An Exportin-1-dependent microRNA biogenesis pathway during human cell quiescence. Proc Natl Acad Sci U S A 2017; 114:E4961-E4970. [PMID: 28584122 PMCID: PMC5488920 DOI: 10.1073/pnas.1618732114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The reversible state of proliferative arrest known as "cellular quiescence" plays an important role in tissue homeostasis and stem cell biology. By analyzing the expression of miRNAs and miRNA-processing factors during quiescence in primary human fibroblasts, we identified a group of miRNAs that are induced during quiescence despite markedly reduced expression of Exportin-5, a protein required for canonical miRNA biogenesis. The biogenesis of these quiescence-induced miRNAs is independent of Exportin-5 and depends instead on Exportin-1. Moreover, these quiescence-induced primary miRNAs (pri-miRNAs) are modified with a 2,2,7-trimethylguanosine (TMG)-cap, which is known to bind Exportin-1, and knockdown of Exportin-1 or trimethylguanosine synthase 1, responsible for (TMG)-capping, inhibits their biogenesis. Surprisingly, in quiescent cells Exportin-1-dependent pri-miR-34a is present in the cytoplasm together with a small isoform of Drosha, implying the existence of a different miRNA processing pathway in these cells. Our findings suggest that during quiescence the canonical miRNA biogenesis pathway is down-regulated and specific miRNAs are generated by an alternative pathway to regulate genes involved in cellular growth arrest.
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Affiliation(s)
- Ivan Martinez
- Department of Microbiology, West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506;
| | - Karen E Hayes
- Department of Microbiology, West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506
| | - Jamie A Barr
- Department of Microbiology, West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506
| | - Abby D Harold
- Department of Microbiology, West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32610
| | - Syed I A Bukhari
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Shobha Vasudevan
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536;
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06536
- Yale Cancer Center, New Haven, CT 06520
| | - Daniel DiMaio
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536
- Yale Cancer Center, New Haven, CT 06520
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06510
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Burke JM, Kincaid RP, Nottingham RM, Lambowitz AM, Sullivan CS. DUSP11 activity on triphosphorylated transcripts promotes Argonaute association with noncanonical viral microRNAs and regulates steady-state levels of cellular noncoding RNAs. Genes Dev 2017; 30:2076-2092. [PMID: 27798849 PMCID: PMC5066614 DOI: 10.1101/gad.282616.116] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/02/2016] [Indexed: 12/22/2022]
Abstract
Here, Burke et al. delineate a new pathway for mammalian small RNAs to enter the RNAi gene silencing machinery. They show that DUSP11 directly dephosphorylates viral triphosphate ncRNA transcripts and that this is required for efficient silencing by RISC, suggesting that mammalian viral pathogens can use DUSP11 to generate atypical microRNAs. RNA silencing is a conserved eukaryotic gene expression regulatory mechanism mediated by small RNAs. In Caenorhabditis elegans, the accumulation of a distinct class of siRNAs synthesized by an RNA-dependent RNA polymerase (RdRP) requires the PIR-1 phosphatase. However, the function of PIR-1 in RNAi has remained unclear. Since mammals lack an analogous siRNA biogenesis pathway, an RNA silencing role for the mammalian PIR-1 homolog (dual specificity phosphatase 11 [DUSP11]) was unexpected. Here, we show that the RNA triphosphatase activity of DUSP11 promotes the RNA silencing activity of viral microRNAs (miRNAs) derived from RNA polymerase III (RNAP III) transcribed precursors. Our results demonstrate that DUSP11 converts the 5′ triphosphate of miRNA precursors to a 5′ monophosphate, promoting loading of derivative 5p miRNAs into Argonaute proteins via a Dicer-coupled 5′ monophosphate-dependent strand selection mechanism. This mechanistic insight supports a likely shared function for PIR-1 in C. elegans. Furthermore, we show that DUSP11 modulates the 5′ end phosphate group and/or steady-state level of several host RNAP III transcripts, including vault RNAs and Alu transcripts. This study shows that steady-state levels of select noncoding RNAs are regulated by DUSP11 and defines a previously unknown portal for small RNA-mediated silencing in mammals, revealing that DUSP11-dependent RNA silencing activities are shared among diverse metazoans.
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Affiliation(s)
- James M Burke
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,John Ring LaMontagne Center for Infectious Disease, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Rodney P Kincaid
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,John Ring LaMontagne Center for Infectious Disease, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Christopher S Sullivan
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA.,John Ring LaMontagne Center for Infectious Disease, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
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49
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Bruscella P, Bottini S, Baudesson C, Pawlotsky JM, Feray C, Trabucchi M. Viruses and miRNAs: More Friends than Foes. Front Microbiol 2017; 8:824. [PMID: 28555130 PMCID: PMC5430039 DOI: 10.3389/fmicb.2017.00824] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/21/2017] [Indexed: 02/06/2023] Open
Abstract
There is evidence that eukaryotic miRNAs (hereafter called host miRNAs) play a role in the replication and propagation of viruses. Expression or targeting of host miRNAs can be involved in cellular antiviral responses. Most times host miRNAs play a role in viral life-cycles and promote infection through complex regulatory pathways. miRNAs can also be encoded by a viral genome and be expressed in the host cell. Viral miRNAs can share common sequences with host miRNAs or have totally different sequences. They can regulate a variety of biological processes involved in viral infection, including apoptosis, evasion of the immune response, or modulation of viral life-cycle phases. Overall, virus/miRNA pathway interaction is defined by a plethora of complex mechanisms, though not yet fully understood. This article review summarizes recent advances and novel biological concepts related to the understanding of miRNA expression, control and function during viral infections. The article also discusses potential therapeutic applications of this particular host–pathogen interaction.
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Affiliation(s)
- Patrice Bruscella
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis", Université Paris-EstCréteil, France
| | | | - Camille Baudesson
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis", Université Paris-EstCréteil, France
| | - Jean-Michel Pawlotsky
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis", Université Paris-EstCréteil, France
| | - Cyrille Feray
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis", Université Paris-EstCréteil, France
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Hawley ZCE, Campos-Melo D, Droppelmann CA, Strong MJ. MotomiRs: miRNAs in Motor Neuron Function and Disease. Front Mol Neurosci 2017; 10:127. [PMID: 28522960 PMCID: PMC5415563 DOI: 10.3389/fnmol.2017.00127] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/18/2017] [Indexed: 12/12/2022] Open
Abstract
MiRNAs are key regulators of the mammalian transcriptome that have been increasingly linked to degenerative diseases of the motor neurons. Although many of the miRNAs currently incriminated as participants in the pathogenesis of these diseases are also important to the normal development and function of motor neurons, at present there is no knowledge of the complete miRNA profile of motor neurons. In this review, we examine the current understanding with respect to miRNAs that are specifically required for motor neuron development, function and viability, and provide evidence that these should be considered as a functional network of miRNAs which we have collectively termed MotomiRs. We will also summarize those MotomiRs currently known to be associated with both amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), and discuss their potential use as biomarkers.
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Affiliation(s)
- Zachary C E Hawley
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada.,Department of Pathology, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada.,Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada
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