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Pessoa J, Carvalho C. Human RNA Polymerase II Segregates from Genes and Nascent RNA and Transcribes in the Presence of DNA-Bound dCas9. Int J Mol Sci 2024; 25:8411. [PMID: 39125980 PMCID: PMC11312690 DOI: 10.3390/ijms25158411] [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: 06/13/2024] [Revised: 07/21/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
RNA polymerase II (Pol II) dysfunction is frequently implied in human disease. Understanding its functional mechanism is essential for designing innovative therapeutic strategies. To visualize its supra-molecular interactions with genes and nascent RNA, we generated a human cell line carrying ~335 consecutive copies of a recombinant β-globin gene. Confocal microscopy showed that Pol II was not homogeneously concentrated around these identical gene copies. Moreover, Pol II signals partially overlapped with the genes and their nascent RNA, revealing extensive compartmentalization. Using a cell line carrying a single copy of the β-globin gene, we also tested if the binding of catalytically dead CRISPR-associated system 9 (dCas9) to different gene regions affected Pol II transcriptional activity. We assessed Pol II localization and nascent RNA levels using chromatin immunoprecipitation and droplet digital reverse transcription PCR, respectively. Some enrichment of transcriptionally paused Pol II accumulated in the promoter region was detected in a strand-specific way of gRNA binding, and there was no decrease in nascent RNA levels. Pol II preserved its transcriptional activity in the presence of DNA-bound dCas9. Our findings contribute further insight into the complex mechanism of mRNA transcription in human cells.
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Affiliation(s)
- João Pessoa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal;
- Department of Medical Sciences and Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Célia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal;
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2
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Jin L, Zhang S, Song Z, Heng X, Chen SJ. Kinetic pathway of HIV-1 TAR cotranscriptional folding. Nucleic Acids Res 2024; 52:6066-6078. [PMID: 38738640 PMCID: PMC11162800 DOI: 10.1093/nar/gkae362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
The Trans-Activator Receptor (TAR) RNA, located at the 5'-end untranslated region (5' UTR) of the human immunodeficiency virus type 1 (HIV-1), is pivotal in the virus's life cycle. As the initial functional domain, it folds during the transcription of viral mRNA. Although TAR's role in recruiting the Tat protein for trans-activation is established, the detailed kinetic mechanisms at play during early transcription, especially at points of temporary transcriptional pausing, remain elusive. Moreover, the precise physical processes of transcriptional pause and subsequent escape are not fully elucidated. This study focuses on the folding kinetics of TAR and the biological implications by integrating computer simulations of RNA folding during transcription with nuclear magnetic resonance (NMR) spectroscopy data. The findings reveal insights into the folding mechanism of a non-native intermediate that triggers transcriptional pause, along with different folding pathways leading to transcriptional pause and readthrough. The profiling of the cotranscriptional folding pathway and identification of kinetic structural intermediates reveal a novel mechanism for viral transcriptional regulation, which could pave the way for new antiviral drug designs targeting kinetic cotranscriptional folding pathways in viral RNAs.
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Affiliation(s)
- Lei Jin
- Department of Physics and Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sicheng Zhang
- Department of Physics and Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Zhenwei Song
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Shi-Jie Chen
- Department of Physics and Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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3
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LaPorte A, Pathak R, Eliscovich C, Martins L, Nell R, Spivak A, Suzuki M, Planelles V, Singer R, Kalpana G. Single-molecule RNA-FISH analysis reveals stochasticity in reactivation of latent HIV-1 regulated by Nuclear Orphan Receptors NR4A and cMYC. RESEARCH SQUARE 2024:rs.3.rs-4166090. [PMID: 38699331 PMCID: PMC11065080 DOI: 10.21203/rs.3.rs-4166090/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
HIV-1 eradication strategies require complete reactivation of HIV-1 latent cells by Latency Reversing Agents (LRA). Current methods lack effectiveness due to incomplete proviral reactivation. We employed a single-molecule RNA-FISH (smRNA-FISH) and FISH-Quant analysis and found that proviral reactivation is highly variable from cell-to-cell, stochastic, and occurs in bursts and waves, with different kinetics in response to diverse LRAs. Approximately 1-5% of latent cells exhibited stochastic reactivation without LRAs. Through single-cell RNA-seq analysis, we identified NR4A3 and cMYC as extrinsic factors associated with stochastic HIV-1 reactivation. Concomitant with HIV-1 reactivation cMYC was downregulated and NR4A3 was upregulated in both latent cell lines and primary CD4 + T-cells from aviremic patients. By inhibiting cMYC using SN-38, an active metabolite of irinotecan, we induced NR4A3 and HIV-1 expression. Our results suggest that inherent stochasticity in proviral reactivation contributes to cell-to-cell variability, which could potentially be modulated by drugs targeting cMYC and NR4A3.
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Gambut S, Hope TJ, Mamede JI. Infectious Virus Tracking by Fluorescent Live Cell Imaging in Primary Cells. Methods Mol Biol 2024; 2807:3-14. [PMID: 38743217 DOI: 10.1007/978-1-0716-3862-0_1] [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] [Indexed: 05/16/2024]
Abstract
To successfully infect a cell, HIV-1 has to overcome several host barriers while exploiting cellular cofactors. HIV-1 infection is highly inefficient with the great majority of viral particles not being able to successfully integrate into the target cell genome. Nonproductive HIV-1 particles are degraded or accumulated in cellular compartments. Thus, it becomes hard to distinguish between viral behaviors that lead to effectively infecting the cell from the ones that do not by using traditional methods. Here, we describe the infectious virus tracking method that detects and quantifies individual fluorescent viral particles over time and links viral particle behavior to its infectivity. This method employs live-cell imaging at ultra-low MOIs to detect the outcome of infection for every HIV-1 particle.
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Affiliation(s)
- Stephanie Gambut
- Department of Microbial Pathogens & Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Thomas J Hope
- Department of Biomedical Engineering, Northwestern University, Chicago, IL, USA
- Department of Cell & Developmental Biology, Northwestern University, Chicago, IL, USA
- Department of Obstetrics & Gynecology, Northwestern University, Chicago, IL, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Chicago, IL, USA
| | - João I Mamede
- Department of Microbial Pathogens & Immunity, Rush University Medical Center, Chicago, IL, USA.
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5
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Damour A, Slaninova V, Radulescu O, Bertrand E, Basyuk E. Transcriptional Stochasticity as a Key Aspect of HIV-1 Latency. Viruses 2023; 15:1969. [PMID: 37766375 PMCID: PMC10535884 DOI: 10.3390/v15091969] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
This review summarizes current advances in the role of transcriptional stochasticity in HIV-1 latency, which were possible in a large part due to the development of single-cell approaches. HIV-1 transcription proceeds in bursts of RNA production, which stem from the stochastic switching of the viral promoter between ON and OFF states. This switching is caused by random binding dynamics of transcription factors and nucleosomes to the viral promoter and occurs at several time scales from minutes to hours. Transcriptional bursts are mainly controlled by the core transcription factors TBP, SP1 and NF-κb, the chromatin status of the viral promoter and RNA polymerase II pausing. In particular, spontaneous variability in the promoter chromatin creates heterogeneity in the response to activators such as TNF-α, which is then amplified by the Tat feedback loop to generate high and low viral transcriptional states. This phenomenon is likely at the basis of the partial and stochastic response of latent T cells from HIV-1 patients to latency-reversing agents, which is a barrier for the development of shock-and-kill strategies of viral eradication. A detailed understanding of the transcriptional stochasticity of HIV-1 and the possibility to precisely model this phenomenon will be important assets to develop more effective therapeutic strategies.
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Affiliation(s)
- Alexia Damour
- MFP UMR 5234 CNRS, Université de Bordeaux, 33076 Bordeaux, France;
| | - Vera Slaninova
- IGH UMR 9002 CNRS, Université de Montpellier, 34094 Montpellier, France;
| | - Ovidiu Radulescu
- LPHI, UMR 5294 CNRS, University of Montpellier, 34095 Montpellier, France;
| | - Edouard Bertrand
- IGH UMR 9002 CNRS, Université de Montpellier, 34094 Montpellier, France;
| | - Eugenia Basyuk
- MFP UMR 5234 CNRS, Université de Bordeaux, 33076 Bordeaux, France;
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Owusu LB, Ababio C, Boahene S, Zakaria AFS, Emikpe AO, Dwumfour CK, Appiagyei KA, Apiribu F. The predictors of unsuppressed viremia among PLHIV: a cross-sectional study in Ghana. BMC Public Health 2023; 23:1113. [PMID: 37296400 PMCID: PMC10257285 DOI: 10.1186/s12889-023-16032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Unsuppressed viremia in HIV infected patients is generally associated with increased rates of disease transmission and poor patient survival. This study assessed the socio-demographic determinants of People Living with HIV/AIDS, having viral load non-suppression and who are receiving antiretroviral therapy in a District Hospital in Ghana. METHODS The study utilized the cross-sectional research design with both primary and secondary data conducted from September to October 2021 in Ghana. Data were collected from 331 PLHIV who were placed on Anti-Retroviral Therapy (ART) for more than 12 months at the ART centre at a District Hospital in Ghana. Unsuppressed viremia was defined as plasma viral load of ≥ 1000 copies/mL after 12 months on an ART with effective adherent support. A structured questionnaire was used to collect primary data on participants and a Secondary data was also collected from patients' folders, hospital registers and the computerized health information systems at the study site. SPSS was used to analyse descriptive and inferential data. Pearson's chi-square and Fisher's exact test were used to assess the independent determinants of viral load non-suppression. Pearson's chi-square test was used for tests giving ≤ 20% of expected cell counts less than five while Fisher's exact test was used for tests giving > 20% of expected cell counts less than five. A p value of < 0.05 was considered statistically significant. RESULTS Out of the 331 PLHIV who participated in the study, 174 (53%) were female and 157 (47%) were Male. The study found viral load non-suppression of 19% with age (p = 0.03), income (p = 0.02), employment (p = 0.04), means of transportation (p = 0.02), cost of transportation to the ART centre (p = 0.03) and level of medication adherence (p = 0.02) as determinants of viral load non-suppression. CONCLUSION There was a low level of viral load non-suppression among PLHIV after 12 months of active antiretroviral therapy with age, income, employment, means of transportation, cost of transportation and level of medication adherence influencing viral non-suppression. Thus, ART drugs and services should be decentralized to the community health workers' level within the various localities of patients to decrease the economic consequences involved in accessing health care for PLHIV/AIDS. This will minimize defaulting, improve adherence and promote viral load suppression.
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Affiliation(s)
| | - Christiana Ababio
- New Edubiase Government Hospital, Adansi South District, Ashanti Region, Ghana
| | - Selina Boahene
- New Edubiase Government Hospital, Adansi South District, Ashanti Region, Ghana
| | | | | | | | | | - Felix Apiribu
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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7
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Marasco LE, Dujardin G, Sousa-Luís R, Liu YH, Stigliano JN, Nomakuchi T, Proudfoot NJ, Krainer AR, Kornblihtt AR. Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy. Cell 2022; 185:2057-2070.e15. [PMID: 35688133 DOI: 10.1016/j.cell.2022.04.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/17/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022]
Abstract
Spinal muscular atrophy (SMA) is a motor-neuron disease caused by mutations of the SMN1 gene. The human paralog SMN2, whose exon 7 (E7) is predominantly skipped, cannot compensate for the lack of SMN1. Nusinersen is an antisense oligonucleotide (ASO) that upregulates E7 inclusion and SMN protein levels by displacing the splicing repressors hnRNPA1/A2 from their target site in intron 7. We show that by promoting transcriptional elongation, the histone deacetylase inhibitor VPA cooperates with a nusinersen-like ASO to promote E7 inclusion. Surprisingly, the ASO promotes the deployment of the silencing histone mark H3K9me2 on the SMN2 gene, creating a roadblock to RNA polymerase II elongation that inhibits E7 inclusion. By removing the roadblock, VPA counteracts the chromatin effects of the ASO, resulting in higher E7 inclusion without large pleiotropic effects. Combined administration of the nusinersen-like ASO and VPA in SMA mice strongly synergizes SMN expression, growth, survival, and neuromuscular function.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina
| | - Gwendal Dujardin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Rui Sousa-Luís
- Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon, 1649-028 Lisboa, Portugal
| | - Ying Hsiu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jose N Stigliano
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina.
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8
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Pathak DV, Sagar SR, Bhatt HG, Patel PK. A search for potential anti-HIV phytoconstituents from the natural product repository. ADVANCES IN TRADITIONAL MEDICINE 2022. [DOI: 10.1007/s13596-022-00646-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Evans EL, Pocock GM, Einsdorf G, Behrens RT, Dobson ETA, Wiedenmann M, Birkhold C, Ahlquist P, Eliceiri KW, Sherer NM. HIV RGB: Automated Single-Cell Analysis of HIV-1 Rev-Dependent RNA Nuclear Export and Translation Using Image Processing in KNIME. Viruses 2022; 14:903. [PMID: 35632645 PMCID: PMC9145009 DOI: 10.3390/v14050903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Single-cell imaging has emerged as a powerful means to study viral replication dynamics and identify sites of virus−host interactions. Multivariate aspects of viral replication cycles yield challenges inherent to handling large, complex imaging datasets. Herein, we describe the design and implementation of an automated, imaging-based strategy, “Human Immunodeficiency Virus Red-Green-Blue” (HIV RGB), for deriving comprehensive single-cell measurements of HIV-1 unspliced (US) RNA nuclear export, translation, and bulk changes to viral RNA and protein (HIV-1 Rev and Gag) subcellular distribution over time. Differentially tagged fluorescent viral RNA and protein species are recorded using multicolor long-term (>24 h) time-lapse video microscopy, followed by image processing using a new open-source computational imaging workflow dubbed “Nuclear Ring Segmentation Analysis and Tracking” (NR-SAT) based on ImageJ plugins that have been integrated into the Konstanz Information Miner (KNIME) analytics platform. We describe a typical HIV RGB experimental setup, detail the image acquisition and NR-SAT workflow accompanied by a step-by-step tutorial, and demonstrate a use case wherein we test the effects of perturbing subcellular localization of the Rev protein, which is essential for viral US RNA nuclear export, on the kinetics of HIV-1 late-stage gene regulation. Collectively, HIV RGB represents a powerful platform for single-cell studies of HIV-1 post-transcriptional RNA regulation. Moreover, we discuss how similar NR-SAT-based design principles and open-source tools might be readily adapted to study a broad range of dynamic viral or cellular processes.
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Affiliation(s)
- Edward L. Evans
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ginger M. Pocock
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Gabriel Einsdorf
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | - Ryan T. Behrens
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
| | - Ellen T. A. Dobson
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
| | - Marcel Wiedenmann
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | | | - Paul Ahlquist
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Morgridge Institute for Research, Madison, WI 53715, USA
- John and Jeanne Rowe Center for Research in Virology, Madison, WI 53715, USA
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
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Biswas J, Li W, Singer RH, Coleman RA. Imaging Organization of RNA Processing within the Nucleus. Cold Spring Harb Perspect Biol 2021; 13:a039453. [PMID: 34127450 PMCID: PMC8635003 DOI: 10.1101/cshperspect.a039453] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Within the nucleus, messenger RNA is generated and processed in a highly organized and regulated manner. Messenger RNA processing begins during transcription initiation and continues until the RNA is translated and degraded. Processes such as 5' capping, alternative splicing, and 3' end processing have been studied extensively with biochemical methods and more recently with single-molecule imaging approaches. In this review, we highlight how imaging has helped understand the highly dynamic process of RNA processing. We conclude with open questions and new technological developments that may further our understanding of RNA processing.
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Affiliation(s)
- Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Weihan Li
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robert A Coleman
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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11
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Basyuk E, Rage F, Bertrand E. RNA transport from transcription to localized translation: a single molecule perspective. RNA Biol 2021; 18:1221-1237. [PMID: 33111627 PMCID: PMC8354613 DOI: 10.1080/15476286.2020.1842631] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transport of mRNAs is an important step of gene expression, which brings the genetic message from the DNA in the nucleus to a precise cytoplasmic location in a regulated fashion. Perturbation of this process can lead to pathologies such as developmental and neurological disorders. In this review, we discuss recent advances in the field of mRNA transport made using single molecule fluorescent imaging approaches. We present an overview of these approaches in fixed and live cells and their input in understanding the key steps of mRNA journey: transport across the nucleoplasm, export through the nuclear pores and delivery to its final cytoplasmic location. This review puts a particular emphasis on the coupling of mRNA transport with translation, such as localization-dependent translational regulation and translation-dependent mRNA localization. We also highlight the recently discovered translation factories, and how cellular and viral RNAs can hijack membrane transport systems to travel in the cytoplasm.
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Affiliation(s)
- Eugenia Basyuk
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS-UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Florence Rage
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
- Equipe Labélisée Ligue Nationale Contre Le Cancer, Montpellier, France
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12
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Muniz L, Nicolas E, Trouche D. RNA polymerase II speed: a key player in controlling and adapting transcriptome composition. EMBO J 2021; 40:e105740. [PMID: 34254686 PMCID: PMC8327950 DOI: 10.15252/embj.2020105740] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit of time, is a major determinant of transcriptome composition. It controls co-transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating the production of alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, or read-through transcripts. RNA Pol II speed itself is regulated in response to intra- and extra-cellular stimuli and can in turn affect the transcriptome composition in response to these stimuli. Evidence points to a potentially important role of transcriptome composition modification through RNA Pol II speed regulation for adaptation of cells to a changing environment, thus pointing to a function of RNA Pol II speed regulation in cellular physiology. Analyzing RNA Pol II speed dynamics may therefore be central to fully understand the regulation of physiological processes, such as the development of multicellular organisms. Recent findings also raise the possibility that RNA Pol II speed deregulation can be detrimental and participate in disease progression. Here, we review initial and current approaches to measure RNA Pol II speed, as well as providing an overview of the factors controlling speed and the co-transcriptional processes which are affected. Finally, we discuss the role of RNA Pol II speed regulation in cell physiology.
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Affiliation(s)
- Lisa Muniz
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Estelle Nicolas
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Didier Trouche
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
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13
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Hani S, Cuyas L, David P, Secco D, Whelan J, Thibaud MC, Merret R, Mueller F, Pochon N, Javot H, Faklaris O, Maréchal E, Bertrand E, Nussaume L. Live single-cell transcriptional dynamics via RNA labelling during the phosphate response in plants. NATURE PLANTS 2021; 7:1050-1064. [PMID: 34373603 DOI: 10.1038/s41477-021-00981-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Plants are constantly adapting to ambient fluctuations through spatial and temporal transcriptional responses. Here, we implemented the latest-generation RNA imaging system and combined it with microfluidics to visualize transcriptional regulation in living Arabidopsis plants. This enabled quantitative measurements of the transcriptional activity of single loci in single cells, in real time and under changing environmental conditions. Using phosphate-responsive genes as a model, we found that active genes displayed high transcription initiation rates (one initiation event every ~3 s) and frequently clustered together in endoreplicated cells. We observed gene bursting and large allelic differences in single cells, revealing that at steady state, intrinsic noise dominated extrinsic variations. Moreover, we established that transcriptional repression triggered in roots by phosphate, a crucial macronutrient limiting plant development, occurred with unexpectedly fast kinetics (on the order of minutes) and striking heterogeneity between neighbouring cells. Access to single-cell RNA polymerase II dynamics in live plants will benefit future studies of signalling processes.
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Affiliation(s)
- Sahar Hani
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, SAVE (Signalisation pour l'Adaptation des Végétaux à leur Environnement), Saint-Paul lez Durance, France
| | - Laura Cuyas
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, SAVE (Signalisation pour l'Adaptation des Végétaux à leur Environnement), Saint-Paul lez Durance, France
- Agroinnovation International-TIMAC AGRO, Groupe Roullier, Saint-Malo, France
| | - Pascale David
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, SAVE (Signalisation pour l'Adaptation des Végétaux à leur Environnement), Saint-Paul lez Durance, France
| | - David Secco
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Marie-Christine Thibaud
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, SAVE (Signalisation pour l'Adaptation des Végétaux à leur Environnement), Saint-Paul lez Durance, France
| | - Rémy Merret
- UMR5096 CNRS/Université de Perpignan, Laboratoire Génome et Développement des Plantes, Perpignan, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, Paris, France
| | - Nathalie Pochon
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, SAVE (Signalisation pour l'Adaptation des Végétaux à leur Environnement), Saint-Paul lez Durance, France
| | - Hélène Javot
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, SAVE (Signalisation pour l'Adaptation des Végétaux à leur Environnement), Saint-Paul lez Durance, France
| | - Orestis Faklaris
- MRI, BioCampus Montpellier, CRBM, Univ. Montpellier, CNRS, Montpellier, France
| | - Eric Maréchal
- UMR 5168 CNRS-CEA-INRA-Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire et Végétale, iRIG, CEA-Grenoble, Grenoble, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Univ. Montpellier, CNRS, Montpellier, France.
- Institut de Génétique Humaine, Univ. Montpellier, CNRS, Montpellier, France.
- Equipe labélisée Ligue Nationale Contre le Cancer, Montpellier, France.
| | - Laurent Nussaume
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, SAVE (Signalisation pour l'Adaptation des Végétaux à leur Environnement), Saint-Paul lez Durance, France.
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14
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Tantale K, Garcia-Oliver E, Robert MC, L'Hostis A, Yang Y, Tsanov N, Topno R, Gostan T, Kozulic-Pirher A, Basu-Shrivastava M, Mukherjee K, Slaninova V, Andrau JC, Mueller F, Basyuk E, Radulescu O, Bertrand E. Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting. Nat Commun 2021; 12:4503. [PMID: 34301927 PMCID: PMC8302722 DOI: 10.1038/s41467-021-24462-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
Promoter-proximal pausing of RNA polymerase II is a key process regulating gene expression. In latent HIV-1 cells, it prevents viral transcription and is essential for latency maintenance, while in acutely infected cells the viral factor Tat releases paused polymerase to induce viral expression. Pausing is fundamental for HIV-1, but how it contributes to bursting and stochastic viral reactivation is unclear. Here, we performed single molecule imaging of HIV-1 transcription. We developed a quantitative analysis method that manages multiple time scales from seconds to days and that rapidly fits many models of promoter dynamics. We found that RNA polymerases enter a long-lived pause at latent HIV-1 promoters (>20 minutes), thereby effectively limiting viral transcription. Surprisingly and in contrast to current models, pausing appears stochastic and not obligatory, with only a small fraction of the polymerases undergoing long-lived pausing in absence of Tat. One consequence of stochastic pausing is that HIV-1 transcription occurs in bursts in latent cells, thereby facilitating latency exit and providing a rationale for the stochasticity of viral rebounds.
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Affiliation(s)
- Katjana Tantale
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Encar Garcia-Oliver
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marie-Cécile Robert
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
| | - Adèle L'Hostis
- LPHI, UMR CNRS 5235, University of Montpellier, Montpellier, France
| | - Yueyuxiao Yang
- LPHI, UMR CNRS 5235, University of Montpellier, Montpellier, France
| | - Nikolay Tsanov
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Rachel Topno
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
- LPHI, UMR CNRS 5235, University of Montpellier, Montpellier, France
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Alja Kozulic-Pirher
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Meenakshi Basu-Shrivastava
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Kamalika Mukherjee
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Vera Slaninova
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, Paris, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France.
- Microbiology Fundamental and Pathogenicity CNRS UMR 5234, University of Bordeaux, Bordeaux, France.
| | - Ovidiu Radulescu
- LPHI, UMR CNRS 5235, University of Montpellier, Montpellier, France.
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France.
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France.
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15
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Popp AP, Hettich J, Gebhardt J. Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene. Nucleic Acids Res 2021; 49:6249-6266. [PMID: 34060631 PMCID: PMC8216454 DOI: 10.1093/nar/gkab443] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022] Open
Abstract
Transcription is a vital process activated by transcription factor (TF) binding. The active gene releases a burst of transcripts before turning inactive again. While the basic course of transcription is well understood, it is unclear how binding of a TF affects the frequency, duration and size of a transcriptional burst. We systematically varied the residence time and concentration of a synthetic TF and characterized the transcription of a synthetic reporter gene by combining single molecule imaging, single molecule RNA-FISH, live transcript visualisation and analysis with a novel algorithm, Burst Inference from mRNA Distributions (BIRD). For this well-defined system, we found that TF binding solely affected burst frequency and variations in TF residence time had a stronger influence than variations in concentration. This enabled us to device a model of gene transcription, in which TF binding triggers multiple successive steps before the gene transits to the active state and actual mRNA synthesis is decoupled from TF presence. We quantified all transition times of the TF and the gene, including the TF search time and the delay between TF binding and the onset of transcription. Our quantitative measurements and analysis revealed detailed kinetic insight, which may serve as basis for a bottom-up understanding of gene regulation.
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Affiliation(s)
- Achim P Popp
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johannes Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - J Christof M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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16
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Salifou K, Burnard C, Basavarajaiah P, Grasso G, Helsmoortel M, Mac V, Depierre D, Franckhauser C, Beyne E, Contreras X, Dejardin J, Rouquier S, Cuvier O, Kiernan R. Chromatin-associated MRN complex protects highly transcribing genes from genomic instability. SCIENCE ADVANCES 2021; 7:7/21/eabb2947. [PMID: 34020942 PMCID: PMC8139584 DOI: 10.1126/sciadv.abb2947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/31/2021] [Indexed: 05/05/2023]
Abstract
MRN-MDC1 plays a central role in the DNA damage response (DDR) and repair. Using proteomics of isolated chromatin fragments, we identified DDR factors, such as MDC1, among those highly associating with a genomic locus upon transcriptional activation. Purification of MDC1 in the absence of exogenous DNA damage revealed interactions with factors involved in gene expression and RNA processing, in addition to DDR factors. ChIP-seq showed that MRN subunits, MRE11 and NBS1, colocalized throughout the genome, notably at TSSs and bodies of actively transcribing genes, which was dependent on the RNAPII transcriptional complex rather than transcription per se. Depletion of MRN increased RNAPII abundance at MRE11/NBS1-bound genes. Prolonged MRE11 or NBS1 depletion induced single-nucleotide polymorphisms across actively transcribing MRN target genes. These data suggest that association of MRN with the transcriptional machinery constitutively scans active genes for transcription-induced DNA damage to preserve the integrity of the coding genome.
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Affiliation(s)
- Kader Salifou
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Callum Burnard
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Poornima Basavarajaiah
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Giuseppa Grasso
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Marion Helsmoortel
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Victor Mac
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - David Depierre
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Céline Franckhauser
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Emmanuelle Beyne
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Xavier Contreras
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Jérôme Dejardin
- CNRS-UMR 9002, IGH/University of Montpellier, Biology of Repeated Sequences Lab, 34396, France
| | - Sylvie Rouquier
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Olivier Cuvier
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Rosemary Kiernan
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France.
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17
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Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG. Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Comput Biol 2021; 17:e1008999. [PMID: 34003867 PMCID: PMC8162642 DOI: 10.1371/journal.pcbi.1008999] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/28/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022] Open
Abstract
The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.
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Affiliation(s)
- Jonathan Liu
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
| | - Donald Hansen
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Elizabeth Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Meghan Turner
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, United States of America
| | - Hernan G. Garcia
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, United States of America
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California, United States of America
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18
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Bruce JW, Bracken M, Evans E, Sherer N, Ahlquist P. ZBTB2 represses HIV-1 transcription and is regulated by HIV-1 Vpr and cellular DNA damage responses. PLoS Pathog 2021; 17:e1009364. [PMID: 33635925 PMCID: PMC7946322 DOI: 10.1371/journal.ppat.1009364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 03/10/2021] [Accepted: 02/08/2021] [Indexed: 11/19/2022] Open
Abstract
Previously, we reported that cellular transcription factor ZASC1 facilitates DNA-dependent/RNA-independent recruitment of HIV-1 TAT and the cellular elongation factor P-TEFb to the HIV-1 promoter and is a critical factor in regulating HIV-1 transcriptional elongation (PLoS Path e1003712). Here we report that cellular transcription factor ZBTB2 is a novel repressor of HIV-1 gene expression. ZBTB2 strongly co-immunoprecipitated with ZASC1 and was dramatically relocalized by ZASC1 from the cytoplasm to the nucleus. Mutations abolishing ZASC1/ZBTB2 interaction prevented ZBTB2 nuclear relocalization. We show that ZBTB2-induced repression depends on interaction of cellular histone deacetylases (HDACs) with the ZBTB2 POZ domain. Further, ZASC1 interaction specifically recruited ZBTB2 to the HIV-1 promoter, resulting in histone deacetylation and transcription repression. Depleting ZBTB2 by siRNA knockdown or CRISPR/CAS9 knockout in T cell lines enhanced transcription from HIV-1 vectors lacking Vpr, but not from these vectors expressing Vpr. Since HIV-1 Vpr activates the viral LTR by inducing the ATR kinase/DNA damage response pathway, we investigated ZBTB2 response to Vpr and DNA damaging agents. Expressing Vpr or stimulating the ATR pathway with DNA damaging agents impaired ZASC1’s ability to localize ZBTB2 to the nucleus. Moreover, the effects of DNA damaging agents and Vpr on ZBTB2 localization could be blocked by ATR kinase inhibitors. Critically, Vpr and DNA damaging agents decreased ZBTB2 binding to the HIV-1 promoter and increased promoter histone acetylation. Thus, ZBTB2 is recruited to the HIV-1 promoter by ZASC1 and represses transcription, but ATR pathway activation leads to ZBTB2 removal from the promoter, cytoplasmic sequestration and activation of viral transcription. Together, our data show that ZASC1/ZBTB2 integrate the functions of TAT and Vpr to maximize HIV-1 gene expression. The Human immunodeficiency virus 1 (HIV-1) TAT and VPR proteins, in combination with cellular transcription factors, regulate the switch between transcriptionally active productive infection and the transcriptionally inactive latent state. Previously we reported that ZASC1, a cellular transcription factor linked to multiple squamous cell carcinomas and inherited ataxias, contributes to an RNA-independent, DNA-dependent step in recruiting the TAT/P-TEFb complex that is critical for HIV-1 transcription elongation to the HIV-1 promoter. Here we show ZASC1 interacts with ZBTB2, another cellular transcription factor with strong links to cancer. ZASC1 interaction relocalizes ZBTB2 from the cytoplasm to the HIV-1 promoter in the nucleus where ZBTB2 interacts with cellular HDACs, increases HIV-1 promoter histone deacetylation and represses viral transcription. We show that Vpr-mediated activation of the ATR/DNA damage pathway regulates ZBTB2 relocalization by ZASC1. Thus, the cellular transcription factors ZASC1 and ZBTB2 regulate the transcription elongation activities of HIV-1 TAT and the Vpr activation of the cellular DNA damage response pathway to determine the transcriptional fate of the HIV-1 provirus. These results also have strong implications for the role of ZASC1/ZBTB2 and the DNA damage response in cancer and inherited ataxias.
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Affiliation(s)
- James W. Bruce
- Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Megan Bracken
- Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Edward Evans
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Nathan Sherer
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Paul Ahlquist
- Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
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19
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Sego TJ, Aponte-Serrano JO, Ferrari Gianlupi J, Heaps SR, Breithaupt K, Brusch L, Crawshaw J, Osborne JM, Quardokus EM, Plemper RK, Glazier JA. A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness. PLoS Comput Biol 2020; 16:e1008451. [PMID: 33347439 PMCID: PMC7785254 DOI: 10.1371/journal.pcbi.1008451] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/05/2021] [Accepted: 10/20/2020] [Indexed: 12/23/2022] Open
Abstract
Simulations of tissue-specific effects of primary acute viral infections like COVID-19 are essential for understanding disease outcomes and optimizing therapies. Such simulations need to support continuous updating in response to rapid advances in understanding of infection mechanisms, and parallel development of components by multiple groups. We present an open-source platform for multiscale spatiotemporal simulation of an epithelial tissue, viral infection, cellular immune response and tissue damage, specifically designed to be modular and extensible to support continuous updating and parallel development. The base simulation of a simplified patch of epithelial tissue and immune response exhibits distinct patterns of infection dynamics from widespread infection, to recurrence, to clearance. Slower viral internalization and faster immune-cell recruitment slow infection and promote containment. Because antiviral drugs can have side effects and show reduced clinical effectiveness when given later during infection, we studied the effects on progression of treatment potency and time-of-first treatment after infection. In simulations, even a low potency therapy with a drug which reduces the replication rate of viral RNA greatly decreases the total tissue damage and virus burden when given near the beginning of infection. Many combinations of dosage and treatment time lead to stochastic outcomes, with some simulation replicas showing clearance or control (treatment success), while others show rapid infection of all epithelial cells (treatment failure). Thus, while a high potency therapy usually is less effective when given later, treatments at late times are occasionally effective. We illustrate how to extend the platform to model specific virus types (e.g., hepatitis C) and add additional cellular mechanisms (tissue recovery and variable cell susceptibility to infection), using our software modules and publicly-available software repository.
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Affiliation(s)
- T. J. Sego
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
| | - Josua O. Aponte-Serrano
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
| | - Juliano Ferrari Gianlupi
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
| | - Samuel R. Heaps
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
| | - Kira Breithaupt
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
- Cognitive Science Program, Indiana University, Bloomington, Indiana, United States of America
| | - Lutz Brusch
- Center for Information Services and High Performance Computing (ZIH), Technische Universität, Dresden, Germany
| | - Jessica Crawshaw
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - James M. Osborne
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Ellen M. Quardokus
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
| | - Richard K. Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
| | - James A. Glazier
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
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20
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Sego TJ, Aponte-Serrano JO, Gianlupi JF, Heaps SR, Breithaupt K, Brusch L, Crawshaw J, Osborne JM, Quardokus EM, Plemper RK, Glazier JA. A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness: A multiscale model of viral infection in epithelial tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.27.064139. [PMID: 32511367 PMCID: PMC7263495 DOI: 10.1101/2020.04.27.064139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Simulations of tissue-specific effects of primary acute viral infections like COVID-19 are essential for understanding disease outcomes and optimizing therapies. Such simulations need to support continuous updating in response to rapid advances in understanding of infection mechanisms, and parallel development of components by multiple groups. We present an open-source platform for multiscale spatiotemporal simulation of an epithelial tissue, viral infection, cellular immune response and tissue damage, specifically designed to be modular and extensible to support continuous updating and parallel development. The base simulation of a simplified patch of epithelial tissue and immune response exhibits distinct patterns of infection dynamics from widespread infection, to recurrence, to clearance. Slower viral internalization and faster immune-cell recruitment slow infection and promote containment. Because antiviral drugs can have side effects and show reduced clinical effectiveness when given later during infection, we studied the effects on progression of treatment potency and time-of-first treatment after infection. In simulations, even a low potency therapy with a drug which reduces the replication rate of viral RNA greatly decreases the total tissue damage and virus burden when given near the beginning of infection. Many combinations of dosage and treatment time lead to stochastic outcomes, with some simulation replicas showing clearance or control (treatment success), while others show rapid infection of all epithelial cells (treatment failure). Thus, while a high potency therapy usually is less effective when given later, treatments at late times are occasionally effective. We illustrate how to extend the platform to model specific virus types (e.g., hepatitis C) and add additional cellular mechanisms (tissue recovery and variable cell susceptibility to infection), using our software modules and publicly-available software repository.
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Affiliation(s)
- T J Sego
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
- Biocomplexity Institute, Indiana University, Bloomington, IN, USA
| | - Josua O Aponte-Serrano
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
- Biocomplexity Institute, Indiana University, Bloomington, IN, USA
| | - Juliano Ferrari Gianlupi
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
- Biocomplexity Institute, Indiana University, Bloomington, IN, USA
| | - Samuel R Heaps
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Kira Breithaupt
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
- Cognitive Science Program, Indiana University, Bloomington, IN, USA
| | - Lutz Brusch
- Center for Information Services and High Performance Computing (ZIH), Technische Universität Dresden, Germany
| | - Jessica Crawshaw
- School of Mathematics and Statistics, University of Melbourne, Melbourne, 3010, Australia
| | - James M Osborne
- School of Mathematics and Statistics, University of Melbourne, Melbourne, 3010, Australia
| | - Ellen M Quardokus
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - James A Glazier
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
- Biocomplexity Institute, Indiana University, Bloomington, IN, USA
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21
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Smith M, Querido E, Chartrand P, Sfeir A. Quantitative Imaging of MS2-Tagged hTR in Cajal Bodies: Photobleaching and Photoactivation. STAR Protoc 2020; 1:100112. [PMID: 33377008 PMCID: PMC7756913 DOI: 10.1016/j.xpro.2020.100112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Advances in imaging technologies, gene editing, and fluorescent molecule development have made real-time imaging of nucleic acids practical. Here, we detail methods for imaging the human telomerase RNA template, hTR via the use of three inserted MS2 stem loops and cognate MS2 coat protein (MCP) tagged with superfolder GFP or photoactivatable GFP. These technologies enable tracking of the dynamics of RNA species through Cajal bodies and offer insight into their residence time in Cajal bodies through photobleaching and photoactivation experiments. For complete details on the use and execution of this protocol, please refer to Laprade et al. (2020).
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Affiliation(s)
- Michael Smith
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Emmanuelle Querido
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Canada
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
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22
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Markey FB, Parashar V, Batish M. Methods for spatial and temporal imaging of the different steps involved in RNA processing at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1608. [PMID: 32543077 DOI: 10.1002/wrna.1608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/26/2022]
Abstract
RNA plays a quintessential role as a messenger of information from genotype (DNA) to phenotype (proteins), as well as acts as a regulatory molecule (noncoding RNAs). All steps in the journey of RNA from synthesis (transcription), splicing, transport, localization, translation, to its eventual degradation, comprise important steps in gene expression, thereby controlling the fate of the cell. This lifecycle refers to the majority of RNAs (primarily mRNAs), but not other RNAs such as tRNAs. Imaging these processes in fixed cells and in live cells has been an important tool in developing an understanding of the regulatory steps in RNAs journey. Single-cell and single-molecule imaging techniques enable a much deeper understanding of cellular biology, which is not possible with bulk studies involving RNA isolated from a large pool of cells. Classic techniques, such as fluorescence in situ hybridization (FISH), as well as more recent aptamer-based approaches, have provided detailed insights into RNA localization, and have helped to predict the functions carried out by many RNA species. However, there are still certain processing steps that await high-resolution imaging, which is an exciting and upcoming area of research. In this review, we will discuss the methods that have revolutionized single-molecule resolution imaging in general, the steps of RNA processing in which these methods have been used, and new emerging technologies. This article is categorized under: RNA Export and Localization > RNA Localization RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions.
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Affiliation(s)
- Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.,Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
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23
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Mori L, Valente ST. Key Players in HIV-1 Transcriptional Regulation: Targets for a Functional Cure. Viruses 2020; 12:E529. [PMID: 32403278 PMCID: PMC7291152 DOI: 10.3390/v12050529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 establishes a life-long infection when proviral DNA integrates into the host genome. The provirus can then either actively transcribe RNA or enter a latent state, without viral production. The switch between these two states is governed in great part by the viral protein, Tat, which promotes RNA transcript elongation. Latency is also influenced by the availability of host transcription factors, integration site, and the surrounding chromatin environment. The latent reservoir is established in the first few days of infection and serves as the source of viral rebound upon treatment interruption. Despite effective suppression of HIV-1 replication by antiretroviral therapy (ART), to below the detection limit, ART is ineffective at reducing the latent reservoir size. Elimination of this reservoir has become a major goal of the HIV-1 cure field. However, aside from the ideal total HIV-1 eradication from the host genome, an HIV-1 remission or functional cure is probably more realistic. The "block-and-lock" approach aims at the transcriptional silencing of the viral reservoir, to render suppressed HIV-1 promoters extremely difficult to reactivate from latency. There are unfortunately no clinically available HIV-1 specific transcriptional inhibitors. Understanding the mechanisms that regulate latency is expected to provide novel targets to be explored in cure approaches.
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Affiliation(s)
| | - Susana T. Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA;
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24
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Maldonado RJK, Rice B, Chen EC, Tuffy KM, Chiari EF, Fahrbach KM, Hope TJ, Parent LJ. Visualizing Association of the Retroviral Gag Protein with Unspliced Viral RNA in the Nucleus. mBio 2020; 11:e00524-20. [PMID: 32265329 PMCID: PMC7157774 DOI: 10.1128/mbio.00524-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
Packaging of genomic RNA (gRNA) by retroviruses is essential for infectivity, yet the subcellular site of the initial interaction between the Gag polyprotein and gRNA remains poorly defined. Because retroviral particles are released from the plasma membrane, it was previously thought that Gag proteins initially bound to gRNA in the cytoplasm or at the plasma membrane. However, the Gag protein of the avian retrovirus Rous sarcoma virus (RSV) undergoes active nuclear trafficking, which is required for efficient gRNA encapsidation (L. Z. Scheifele, R. A. Garbitt, J. D. Rhoads, and L. J. Parent, Proc Natl Acad Sci U S A 99:3944-3949, 2002, https://doi.org/10.1073/pnas.062652199; R. Garbitt-Hirst, S. P. Kenney, and L. J. Parent, J Virol 83:6790-6797, 2009, https://doi.org/10.1128/JVI.00101-09). These results raise the intriguing possibility that the primary contact between Gag and gRNA might occur in the nucleus. To examine this possibility, we created a RSV proviral construct that includes 24 tandem repeats of MS2 RNA stem-loops, making it possible to track RSV viral RNA (vRNA) in live cells in which a fluorophore-conjugated MS2 coat protein is coexpressed. Using confocal microscopy, we observed that both wild-type Gag and a nuclear export mutant (Gag.L219A) colocalized with vRNA in the nucleus. In live-cell time-lapse images, the wild-type Gag protein trafficked together with vRNA as a single ribonucleoprotein (RNP) complex in the nucleoplasm near the nuclear periphery, appearing to traverse the nuclear envelope into the cytoplasm. Furthermore, biophysical imaging methods suggest that Gag and the unspliced vRNA physically interact in the nucleus. Taken together, these data suggest that RSV Gag binds unspliced vRNA to export it from the nucleus, possibly for packaging into virions as the viral genome.IMPORTANCE Retroviruses cause severe diseases in animals and humans, including cancer and acquired immunodeficiency syndromes. To propagate infection, retroviruses assemble new virus particles that contain viral proteins and unspliced vRNA to use as gRNA. Despite the critical requirement for gRNA packaging, the molecular mechanisms governing the identification and selection of gRNA by the Gag protein remain poorly understood. In this report, we demonstrate that the Rous sarcoma virus (RSV) Gag protein colocalizes with unspliced vRNA in the nucleus in the interchromatin space. Using live-cell confocal imaging, RSV Gag and unspliced vRNA were observed to move together from inside the nucleus across the nuclear envelope, suggesting that the Gag-gRNA complex initially forms in the nucleus and undergoes nuclear export into the cytoplasm as a viral ribonucleoprotein (vRNP) complex.
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Affiliation(s)
| | - Breanna Rice
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Eunice C Chen
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Kevin M Tuffy
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Estelle F Chiari
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Kelly M Fahrbach
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois, USA
| | - Thomas J Hope
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois, USA
| | - Leslie J Parent
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
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25
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Mougel M, Akkawi C, Chamontin C, Feuillard J, Pessel-Vivares L, Socol M, Laine S. NXF1 and CRM1 nuclear export pathways orchestrate nuclear export, translation and packaging of murine leukaemia retrovirus unspliced RNA. RNA Biol 2020; 17:528-538. [PMID: 31918596 PMCID: PMC7237160 DOI: 10.1080/15476286.2020.1713539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022] Open
Abstract
Cellular mRNAs are exported from the nucleus as fully spliced RNAs. Proofreading mechanisms eliminate unprocessed and irregular pre-mRNAs to control the quality of gene expression. Retroviruses need to export partially spliced and unspliced full-length RNAs to the cytoplasm where they serve as templates for protein synthesis and/or as encapsidated RNA in progeny viruses. Genetically complex retroviruses such as HIV-1 use Rev-equivalent proteins to export intron-retaining RNA from the nucleus using the cellular CRM1-driven nuclear export machinery. By contrast, genetically simpler retroviruses such as murine leukaemia virus (MLV) recruit the NXF1 RNA export machinery. In this study, we reveal for the first time that MLV hijacks both NXF1 and CRM1-dependent pathways to achieve optimal replication capacity. The CRM1-pathway marks the MLV full-length RNA (FL RNA) for packaging, while NXF1-driven nuclear export is coupled to translation. Thus, the cytoplasmic function of the viral RNA is determined early in the nucleus. Depending on the nature of ribonucleoprotein complex formed on FL RNA cargo in the nucleus, the FL RNA will be addressed to the translation machinery sites or to the virus-assembly sites at the plasma membrane.
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Affiliation(s)
- M. Mougel
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, FranceG
| | - C. Akkawi
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, FranceG
| | - C. Chamontin
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, FranceG
| | - J. Feuillard
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, FranceG
| | - L. Pessel-Vivares
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, FranceG
| | - M. Socol
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, FranceG
| | - S. Laine
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, FranceG
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26
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Hochberg-Laufer H, Neufeld N, Brody Y, Nadav-Eliyahu S, Ben-Yishay R, Shav-Tal Y. Availability of splicing factors in the nucleoplasm can regulate the release of mRNA from the gene after transcription. PLoS Genet 2019; 15:e1008459. [PMID: 31765392 PMCID: PMC6901260 DOI: 10.1371/journal.pgen.1008459] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 12/09/2019] [Accepted: 10/04/2019] [Indexed: 11/18/2022] Open
Abstract
Gene expression dynamics can be measured in single living cells. Using a detectable transcriptionally active gene in living cells, we previously found that an mRNA undergoing several splicing events was retained at this gene after transcription until completion of mRNA processing. To determine the reason for this delay in release and whether mRNA retention on the gene might depend on splicing factor availability, we modulated the levels of splicing factors in the nucleus. Increasing the abundance of the diffusing fraction of splicing factors by their overexpression or by Clk1 kinase overexpression to disassemble nuclear speckles, led to a reduction in splicing factor residence times on the active gene, and the retained mRNA was rapidly released from the gene. Other treatments such as overexpression of a mutant inactive Clk1, the downregulation of MALAT1 lncRNA or of the Son protein, or the overexpression of the splicing factor import factor TNPO3, did not affect the dynamics of mRNA release from the gene. We found that the faster release of the mRNA from the gene mediated by increased availability of splicing factors, was dependent on the RS domain of the splicing factors and its phosphorylation state. We propose that the relative abundancies of splicing factors in the nucleoplasm can affect their availability for the splicing events taking place, and regulate the kinetics of mRNA release from the gene after processing. Genetic information is contained in the cell nucleus and encodes proteins. However, protein production takes place in the cytoplasm, and so a molecule is needed to connect between the nucleus and cytoplasm. This messenger molecule is called messenger RNA (mRNA). It is produced and copied from the DNA, and after some processing will travel to the cytoplasm to encode proteins. This study focuses on the timing of mRNA release from the gene after it is copied from the DNA. Processing of mRNA includes the removal of some of its pieces and the stitching back of the remaining parts. This is called splicing. We found that mRNAs undergoing many splicing events are retained on the gene until splicing has completed, and examined what is the cause for this delay. We found that the factors performing the splicing might be limiting the process if their levels are not high enough at the gene locus. By increasing splicing factor levels in the nucleus we show that their abundance increases the rate at which mRNA is released. This means that the cell can regulate gene expression rates by limiting the availability of splicing factors that are free to take part in the processing of mRNA.
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Affiliation(s)
- Hodaya Hochberg-Laufer
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Neufeld
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Yehuda Brody
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Shani Nadav-Eliyahu
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Rakefet Ben-Yishay
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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27
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Maslon MM, Braunschweig U, Aitken S, Mann AR, Kilanowski F, Hunter CJ, Blencowe BJ, Kornblihtt AR, Adams IR, Cáceres JF. A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes. EMBO J 2019; 38:embj.2018101244. [PMID: 30988016 PMCID: PMC6484407 DOI: 10.15252/embj.2018101244] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022] Open
Abstract
The rate of RNA polymerase II (RNAPII) elongation has an important role in the control of alternative splicing (AS); however, the in vivo consequences of an altered elongation rate are unknown. Here, we generated mouse embryonic stem cells (ESCs) knocked in for a slow elongating form of RNAPII We show that a reduced transcriptional elongation rate results in early embryonic lethality in mice. Focusing on neuronal differentiation as a model, we observed that slow elongation impairs development of the neural lineage from ESCs, which is accompanied by changes in AS and in gene expression along this pathway. In particular, we found a crucial role for RNAPII elongation rate in transcription and splicing of long neuronal genes involved in synapse signaling. The impact of the kinetic coupling of RNAPII elongation rate with AS is greater in ESC-differentiated neurons than in pluripotent cells. Our results demonstrate the requirement for an appropriate transcriptional elongation rate to ensure proper gene expression and to regulate AS during development.
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Affiliation(s)
- Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ulrich Braunschweig
- Donnelly Centre, Department of Molecular Genetics University of Toronto, Toronto, ON, Canada
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Abigail R Mann
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Fiona Kilanowski
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Chris J Hunter
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Benjamin J Blencowe
- Donnelly Centre, Department of Molecular Genetics University of Toronto, Toronto, ON, Canada
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ian R Adams
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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28
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Ben-Yishay R, Shav-Tal Y. The dynamic lifecycle of mRNA in the nucleus. Curr Opin Cell Biol 2019; 58:69-75. [PMID: 30889416 DOI: 10.1016/j.ceb.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/16/2019] [Accepted: 02/20/2019] [Indexed: 12/15/2022]
Abstract
The mRNA molecule roams through the nucleus on its way out to the cytoplasm. mRNA encounters and is bound by many protein factors, from the moment it begins to emerge from RNA polymerase II and during its travel in the nucleoplasm, where it will come upon chromatin and nuclear bodies. Some of the protein factors that engage with the mRNA can process it, until finally reaching a mature state fit for export through the nuclear pore complex (NPC). Examining the lifecycle of mRNAs in living cells using mRNA tagging techniques opens a window into our understanding of the rules that drive the dynamics of gene expression from transcription to mRNA export.
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Affiliation(s)
- Rakefet Ben-Yishay
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel.
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29
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Adivarahan S, Zenklusen D. Lessons from (pre-)mRNA Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:247-284. [DOI: 10.1007/978-3-030-31434-7_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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Hansen MMK, Desai RV, Simpson ML, Weinberger LS. Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability. Cell Syst 2018; 7:384-397.e6. [PMID: 30243562 PMCID: PMC6202163 DOI: 10.1016/j.cels.2018.08.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/14/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022]
Abstract
Transcription is an episodic process characterized by probabilistic bursts, but how the transcriptional noise from these bursts is modulated by cellular physiology remains unclear. Using simulations and single-molecule RNA counting, we examined how cellular processes influence cell-to-cell variability (noise). The results show that RNA noise is higher in the cytoplasm than the nucleus in ∼85% of genes across diverse promoters, genomic loci, and cell types (human and mouse). Measurements show further amplification of RNA noise in the cytoplasm, fitting a model of biphasic mRNA conversion between translation- and degradation-competent states. This multi-state translation-degradation of mRNA also causes substantial noise amplification in protein levels, ultimately accounting for ∼74% of intrinsic protein variability in cell populations. Overall, the results demonstrate how noise from transcriptional bursts is intrinsically amplified by mRNA processing, leading to a large super-Poissonian variability in protein levels.
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Affiliation(s)
- Maike M K Hansen
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ravi V Desai
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael L Simpson
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Leor S Weinberger
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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31
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Pichon X, Lagha M, Mueller F, Bertrand E. A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges. Mol Cell 2018; 71:468-480. [DOI: 10.1016/j.molcel.2018.07.022] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022]
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32
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Abstract
When a virus infects a host cell, it hijacks the biosynthetic capacity of the cell to produce virus progeny, a process that may take less than an hour or more than a week. The overall time required for a virus to reproduce depends collectively on the rates of multiple steps in the infection process, including initial binding of the virus particle to the surface of the cell, virus internalization and release of the viral genome within the cell, decoding of the genome to make viral proteins, replication of the genome, assembly of progeny virus particles, and release of these particles into the extracellular environment. For a large number of virus types, much has been learned about the molecular mechanisms and rates of the various steps. However, in only relatively few cases during the last 50 years has an attempt been made-using mathematical modeling-to account for how the different steps contribute to the overall timing and productivity of the infection cycle in a cell. Here we review the initial case studies, which include studies of the one-step growth behavior of viruses that infect bacteria (Qβ, T7, and M13), human immunodeficiency virus, influenza A virus, poliovirus, vesicular stomatitis virus, baculovirus, hepatitis B and C viruses, and herpes simplex virus. Further, we consider how such models enable one to explore how cellular resources are utilized and how antiviral strategies might be designed to resist escape. Finally, we highlight challenges and opportunities at the frontiers of cell-level modeling of virus infections.
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Affiliation(s)
- John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jacob Redovich
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
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33
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Live-Cell Imaging of Early Steps of Single HIV-1 Infection. Viruses 2018; 10:v10050275. [PMID: 29783762 PMCID: PMC5977268 DOI: 10.3390/v10050275] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 01/10/2023] Open
Abstract
Live-cell imaging of single HIV-1 entry offers a unique opportunity to delineate the spatio-temporal regulation of infection. Novel virus labeling and imaging approaches enable the visualization of key steps of HIV-1 entry leading to nuclear import, integration into the host genome, and viral protein expression. Here, we discuss single virus imaging strategies, focusing on live-cell imaging of single virus fusion and productive uncoating that culminates in HIV-1 infection.
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34
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Hansen MMK, Wen WY, Ingerman E, Razooky BS, Thompson CE, Dar RD, Chin CW, Simpson ML, Weinberger LS. A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization. Cell 2018; 173:1609-1621.e15. [PMID: 29754821 PMCID: PMC6044448 DOI: 10.1016/j.cell.2018.04.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/19/2018] [Accepted: 04/03/2018] [Indexed: 11/25/2022]
Abstract
Diverse biological systems utilize fluctuations ("noise") in gene expression to drive lineage-commitment decisions. However, once a commitment is made, noise becomes detrimental to reliable function, and the mechanisms enabling post-commitment noise suppression are unclear. Here, we find that architectural constraints on noise suppression are overcome to stabilize fate commitment. Using single-molecule and time-lapse imaging, we find that-after a noise-driven event-human immunodeficiency virus (HIV) strongly attenuates expression noise through a non-transcriptional negative-feedback circuit. Feedback is established through a serial cascade of post-transcriptional splicing, whereby proteins generated from spliced mRNAs auto-deplete their own precursor unspliced mRNAs. Strikingly, this auto-depletion circuitry minimizes noise to stabilize HIV's commitment decision, and a noise-suppression molecule promotes stabilization. This feedback mechanism for noise suppression suggests a functional role for delayed splicing in other systems and may represent a generalizable architecture of diverse homeostatic signaling circuits.
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Affiliation(s)
- Maike M K Hansen
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Winnie Y Wen
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elena Ingerman
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Brandon S Razooky
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Cassandra E Thompson
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Roy D Dar
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Charles W Chin
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA
| | - Michael L Simpson
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA
| | - Leor S Weinberger
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
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35
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Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate. Cell Rep 2017; 18:2635-2650. [PMID: 28297668 PMCID: PMC5368414 DOI: 10.1016/j.celrep.2017.02.046] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/13/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
The nuclear cap-binding complex (CBC) stimulates processing reactions of capped RNAs, including their splicing, 3′-end formation, degradation, and transport. CBC effects are particular for individual RNA families, but how such selectivity is achieved remains elusive. Here, we analyze three main CBC partners known to impact different RNA species. ARS2 stimulates 3′-end formation/transcription termination of several transcript types, ZC3H18 stimulates degradation of a diverse set of RNAs, and PHAX functions in pre-small nuclear RNA/small nucleolar RNA (pre-snRNA/snoRNA) transport. Surprisingly, these proteins all bind capped RNAs without strong preferences for given transcripts, and their steady-state binding correlates poorly with their function. Despite this, PHAX and ZC3H18 compete for CBC binding and we demonstrate that this competitive binding is functionally relevant. We further show that CBC-containing complexes are short lived in vivo, and we therefore suggest that RNA fate involves the transient formation of mutually exclusive CBC complexes, which may only be consequential at particular checkpoints during RNA biogenesis. PHAX and ZC3H18 compete for binding to the nuclear CBC PHAX and ZC3H18 have opposite effects on the fate of snRNA precursors and other RNAs PHAX, ARS2, and ZC3H18 bind capped RNAs without strong preference for given transcripts CBC-containing complexes are short lived in vivo, with a lifetime of a few seconds
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36
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Vosnakis N, Koch M, Scheer E, Kessler P, Mély Y, Didier P, Tora L. Coactivators and general transcription factors have two distinct dynamic populations dependent on transcription. EMBO J 2017; 36:2710-2725. [PMID: 28724529 PMCID: PMC5599802 DOI: 10.15252/embj.201696035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 06/08/2017] [Accepted: 06/15/2017] [Indexed: 12/29/2022] Open
Abstract
SAGA and ATAC are two distinct chromatin modifying co‐activator complexes with distinct enzymatic activities involved in RNA polymerase II (Pol II) transcription regulation. To investigate the mobility of co‐activator complexes and general transcription factors in live‐cell nuclei, we performed imaging experiments based on photobleaching. SAGA and ATAC, but also two general transcription factors (TFIID and TFIIB), were highly dynamic, exhibiting mainly transient associations with chromatin, contrary to Pol II, which formed more stable chromatin interactions. Fluorescence correlation spectroscopy analyses revealed that the mobile pool of the two co‐activators, as well as that of TFIID and TFIIB, can be subdivided into “fast” (free) and “slow” (chromatin‐interacting) populations. Inhibiting transcription elongation decreased H3K4 trimethylation and reduced the “slow” population of SAGA, ATAC, TFIIB and TFIID. In addition, inhibiting histone H3K4 trimethylation also reduced the “slow” populations of SAGA and ATAC. Thus, our results demonstrate that in the nuclei of live cells the equilibrium between fast and slow population of SAGA or ATAC complexes is regulated by active transcription via changes in the abundance of H3K4me3 on chromatin.
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Affiliation(s)
- Nikolaos Vosnakis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Marc Koch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pascal Kessler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Yves Mély
- Université de Strasbourg, Illkirch, France.,Laboratoire de Biophotonique et Pharmacologie, Illkirch, France
| | - Pascal Didier
- Université de Strasbourg, Illkirch, France.,Laboratoire de Biophotonique et Pharmacologie, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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37
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Vishnoi N, Yao J. Single-cell, single-mRNA analysis of Ccnb1 promoter regulation. Sci Rep 2017; 7:2065. [PMID: 28522800 PMCID: PMC5437063 DOI: 10.1038/s41598-017-02240-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/06/2017] [Indexed: 11/09/2022] Open
Abstract
Promoter activation drives gene transcriptional output. Here we report generating site-specifically integrated single-copy promoter transgenes and measuring their expression to indicate promoter activities at single-mRNA level. mRNA counts, Pol II density and Pol II firing rates of the Ccnb1 promoter transgene resembled those of the native Ccnb1 gene both among asynchronous cells and during the cell cycle. We observed distinct activation states of the Ccnb1 promoter among G1 and G2/M cells, suggesting cell cycle-independent origin of cell-to-cell variation in Ccnb1 promoter activation. Expressing a dominant-negative mutant of NF-YA, a key transcriptional activator of the Ccnb1 promoter, increased its “OFF”/“ON” time ratios but did not alter Pol II firing rates during the “ON” period. Furthermore, comparing H3K4me2 and H3K79me2 levels at the Ccnb1 promoter transgene and the native Ccnb1 gene indicated that the enrichment of these two active histone marks did not predispose higher transcriptional activities. In summary, this experimental system enables bridging transcription imaging with molecular analysis to provide novel insights into eukaryotic transcriptional regulation.
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Affiliation(s)
- Nidhi Vishnoi
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Jie Yao
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06510, USA.
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38
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Hochberg H, Brody Y, Shav-Tal Y. Measuring transcription dynamics in living cells using a photobleaching approach. Methods 2017; 120:58-64. [PMID: 28434903 DOI: 10.1016/j.ymeth.2017.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/02/2017] [Accepted: 04/14/2017] [Indexed: 11/28/2022] Open
Abstract
The transcriptional kinetics of RNA polymerase II, the enzyme responsible for mRNA transcription in the nucleoplasm, can be modulated by a variety of factors. It is therefore important to establish experimental systems that will enable the readout of transcription kinetics of specific genes as they occur in real time within individual cells. This can be performed by implementing fluorescent tagging of the mRNA under live-cell conditions. This chapter describes how to generate fluorescently tagged genes and mRNA, and how a photobleaching approach can produce information on mRNA transcription kinetics.
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Affiliation(s)
- Hodaya Hochberg
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yehuda Brody
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel.
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39
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Urbanek MO, Michalak M, Krzyzosiak WJ. 2D and 3D FISH of expanded repeat RNAs in human lymphoblasts. Methods 2017; 120:49-57. [PMID: 28404480 DOI: 10.1016/j.ymeth.2017.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/09/2017] [Accepted: 04/05/2017] [Indexed: 12/18/2022] Open
Abstract
The first methods for visualizing RNAs within cells were designed for simple imaging of specific transcripts in cells or tissues and since then significant technical advances have been made in this field. Today, high-resolution images can be obtained, enabling visualization of single transcript molecules, quantitative analyses of images, and precise localization of RNAs within cells as well as co-localization of transcripts with specific proteins or other molecules. In addition, tracking of RNA dynamics within single cell has become possible. RNA imaging techniques have been utilized for investigating the role of mutant RNAs in a number of human disorders caused by simple microsatellite expansions. These diseases include myotonic dystrophy type 1 and 2, amyotrophic lateral sclerosis/frontotemporal dementia, fragile X-associated tremor/ataxia syndrome, and Huntington's disease. Mutant RNAs with expanded repeats tend to aggregate predominantly within cell nuclei, forming structures called RNA foci. In this study, we demonstrate methods for fluorescent visualization of RNAs in both fixed and living cells using the example of RNAs containing various expanded repeat tracts (CUG, CCUG, GGGGCC, CGG, and CAG) from experiment design to image analysis. We describe in detail 2D and 3D fluorescence in situ hybridization (FISH) protocols for imaging expanded repeats RNAs, and we review briefly live imaging techniques used to characterize RNA foci formed by mutant RNAs. These methods could be used to image the entire cellular pathway of RNAs, from transcription to degradation.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Michal Michalak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
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40
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Yao J. Imaging Transcriptional Regulation of Eukaryotic mRNA Genes: Advances and Outlook. J Mol Biol 2017; 429:14-31. [DOI: 10.1016/j.jmb.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/03/2016] [Accepted: 11/10/2016] [Indexed: 01/07/2023]
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41
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Pichon X, Bastide A, Safieddine A, Chouaib R, Samacoits A, Basyuk E, Peter M, Mueller F, Bertrand E. Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells. J Cell Biol 2016; 214:769-81. [PMID: 27597760 PMCID: PMC5021097 DOI: 10.1083/jcb.201605024] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 08/16/2016] [Indexed: 12/13/2022] Open
Abstract
Pichon et al. describe a method to visualize translation of single endogenous mRNPs in live cells and provide evidence for specialized translation factories, as well as measurements of translation elongation rate, ribosome loading, and movements of single polysomes. Translation is an essential step in gene expression. In this study, we used an improved SunTag system to label nascent proteins and image translation of single messenger ribonucleoproteins (mRNPs) in human cells. Using a dedicated reporter RNA, we observe that translation of single mRNPs stochastically turns on and off while they diffuse through the cytoplasm. We further measure a ribosome density of 1.3 per kilobase and an elongation rate of 13–18 amino acids per second. Tagging the endogenous POLR2A gene revealed similar elongation rates and ribosomal densities and that nearly all messenger RNAs (mRNAs) are engaged in translation. Remarkably, tagging of the heavy chain of dynein 1 (DYNC1H1) shows this mRNA accumulates in foci containing three to seven RNA molecules. These foci are translation sites and thus represent specialized translation factories. We also observe that DYNC1H1 polysomes are actively transported by motors, which may deliver the mature protein at appropriate cellular locations. The SunTag should be broadly applicable to study translational regulation in live single cells.
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Affiliation(s)
- Xavier Pichon
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Amandine Bastide
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Adham Safieddine
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Racha Chouaib
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Aubin Samacoits
- Unité Imagerie et Modélisation, Institut Pasteur, UMR3691, Centre National de la Recherche Scientifique, 75015 Paris, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Marion Peter
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur, UMR3691, Centre National de la Recherche Scientifique, 75015 Paris, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
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42
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A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting. Nat Commun 2016; 7:12248. [PMID: 27461529 PMCID: PMC4974459 DOI: 10.1038/ncomms12248] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 06/15/2016] [Indexed: 12/15/2022] Open
Abstract
Live-cell imaging has revealed unexpected features of gene expression. Here using improved single-molecule RNA microscopy, we show that synthesis of HIV-1 RNA is achieved by groups of closely spaced polymerases, termed convoys, as opposed to single isolated enzymes. Convoys arise by a Mediator-dependent reinitiation mechanism, which generates a transient but rapid succession of polymerases initiating and escaping the promoter. During elongation, polymerases are spaced by few hundred nucleotides, and physical modelling suggests that DNA torsional stress may maintain polymerase spacing. We additionally observe that the HIV-1 promoter displays stochastic fluctuations on two time scales, which we refer to as multi-scale bursting. Each time scale is regulated independently: Mediator controls minute-scale fluctuation (convoys), while TBP-TATA-box interaction controls sub-hour fluctuations (long permissive/non-permissive periods). A cellular promoter also produces polymerase convoys and displays multi-scale bursting. We propose that slow, TBP-dependent fluctuations are important for phenotypic variability of single cells. HIV-1 viral gene expression stochastically switches between active and inactive states. Here, using improved single molecule RNA microscopy, the authors show that HIV-1 RNA stochastic transcription is achieved by groups of closely spaced polymerases, and is regulated by Mediator and TBP at different time scales.
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43
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Laprade H, Lalonde M, Guérit D, Chartrand P. Live-cell imaging of budding yeast telomerase RNA and TERRA. Methods 2016; 114:46-53. [PMID: 27474163 DOI: 10.1016/j.ymeth.2016.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/11/2016] [Accepted: 07/23/2016] [Indexed: 02/02/2023] Open
Abstract
In most eukaryotes, the ribonucleoprotein complex telomerase is responsible for maintaining telomere length. In recent years, single-cell microscopy techniques such as fluorescent in situ hybridization and live-cell imaging have been developed to image the RNA subunit of the telomerase holoenzyme. These techniques are now becoming important tools for the study of telomerase biogenesis, its association with telomeres and its regulation. Here, we present detailed protocols for live-cell imaging of the Saccharomyces cerevisiae telomerase RNA subunit, called TLC1, and also of the non-coding telomeric repeat-containing RNA TERRA. We describe the approach used for genomic integration of MS2 stem-loops in these transcripts, and provide information for optimal live-cell imaging of these non-coding RNAs.
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Affiliation(s)
- Hadrien Laprade
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3C 3J7, Canada
| | - Maxime Lalonde
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3C 3J7, Canada
| | - David Guérit
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3C 3J7, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3C 3J7, Canada.
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44
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Ferrer M, Clerté C, Chamontin C, Basyuk E, Lainé S, Hottin J, Bertrand E, Margeat E, Mougel M. Imaging HIV-1 RNA dimerization in cells by multicolor super-resolution and fluctuation microscopies. Nucleic Acids Res 2016; 44:7922-34. [PMID: 27280976 PMCID: PMC5027490 DOI: 10.1093/nar/gkw511] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/27/2016] [Indexed: 11/15/2022] Open
Abstract
Dimerization is a unique and vital characteristic of retroviral genomes. It is commonly accepted that genomic RNA (gRNA) must be dimeric at the plasma membrane of the infected cells to be packaged during virus assembly. However, where, when and how HIV-1 gRNA find each other and dimerize in the cell are long-standing questions that cannot be answered using conventional approaches. Here, we combine two state-of-the-art, multicolor RNA labeling strategies with two single-molecule microscopy technologies to address these questions. We used 3D-super-resolution structured illumination microscopy to analyze and quantify the spatial gRNA association throughout the cell and monitored the dynamics of RNA-RNA complexes in living-cells by cross-correlation fluctuation analysis. These sensitive and complementary approaches, combined with trans-complementation experiments, reveal for the first time the presence of interacting gRNA in the cytosol, a challenging observation due to the low frequency of these events and their dilution among the bulk of other RNAs, and allow the determination of the subcellular orchestration of the HIV-1 dimerization process.
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Affiliation(s)
- Mireia Ferrer
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Caroline Clerté
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 Montpellier, France
| | - Célia Chamontin
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Sébastien Lainé
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Jérome Hottin
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Emmanuel Margeat
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 Montpellier, France
| | - Marylène Mougel
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
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45
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Cho WK, Jayanth N, English BP, Inoue T, Andrews JO, Conway W, Grimm JB, Spille JH, Lavis LD, Lionnet T, Cisse II. RNA Polymerase II cluster dynamics predict mRNA output in living cells. eLife 2016; 5. [PMID: 27138339 PMCID: PMC4929003 DOI: 10.7554/elife.13617] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/02/2016] [Indexed: 12/11/2022] Open
Abstract
Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. We developed a live-cell super-resolution approach to uncover the correlation between mRNA synthesis and the dynamics of RNA Polymerase II (Pol II) clusters at a gene locus. For endogenous β-actin genes in mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol II clusters correlate with basal mRNA output. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a pre-transcriptional regulatory event that predictably modulates nascent mRNA output. DOI:http://dx.doi.org/10.7554/eLife.13617.001
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Affiliation(s)
- Won-Ki Cho
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - Namrata Jayanth
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - Brian P English
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Takuma Inoue
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - J Owen Andrews
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - William Conway
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jan-Hendrik Spille
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Timothée Lionnet
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Ibrahim I Cisse
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
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46
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Abstract
The transcription cycle can be roughly divided into three stages: initiation, elongation, and termination. Understanding the molecular events that regulate all these stages requires a dynamic view of the underlying processes. The development of techniques to visualize and quantify transcription in single living cells has been essential in revealing the transcription kinetics. They have revealed that (a) transcription is heterogeneous between cells and (b) transcription can be discontinuous within a cell. In this review, we discuss the progress in our quantitative understanding of transcription dynamics in living cells, focusing on all parts of the transcription cycle. We present the techniques allowing for single-cell transcription measurements, review evidence from different organisms, and discuss how these experiments have broadened our mechanistic understanding of transcription regulation.
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Affiliation(s)
- Tineke L Lenstra
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Joseph Rodriguez
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Huimin Chen
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
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47
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Sánchez-Hernández N, Boireau S, Schmidt U, Muñoz-Cobo JP, Hernández-Munain C, Bertrand E, Suñé C. The in vivo dynamics of TCERG1, a factor that couples transcriptional elongation with splicing. RNA (NEW YORK, N.Y.) 2016; 22:571-582. [PMID: 26873599 PMCID: PMC4793212 DOI: 10.1261/rna.052795.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/23/2015] [Indexed: 06/05/2023]
Abstract
Coupling between transcription and RNA processing is key for gene regulation. Using live-cell photobleaching techniques, we investigated the factor TCERG1, which coordinates transcriptional elongation with splicing. We demonstrate that TCERG1 is highly mobile in the nucleoplasm and that this mobility is slightly decreased when it is associated with speckles. Dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) but not α-amanitin treatment reduced the mobility of TCERG1, which suggests interaction with paused transcription elongation complexes. We found that TCERG1 mobility is rapid at the transcription site (TS) of a reporter that splices post-transcriptionally and that TCERG1 is recruited to the active TS independent of the CTD of RNAPII, thus excluding phosphorylated CTD as a requirement for recruiting this factor to the TS. Importantly, the mobility of TCERG1 is reduced when the reporter splices cotranscriptionally, which suggests that TCERG1 forms new macromolecular complexes when splicing occurs cotranscriptionally. In this condition, spliceostatin A has no effect, indicating that TCERG1 rapidly binds and dissociates from stalled spliceosomal complexes and that the mobility properties of TCERG1 do not depend on events occurring after the initial spliceosome formation. Taken together, these data suggest that TCERG1 binds independently to elongation and splicing complexes, thus performing their coupling by transient interactions rather than by stable association with one or the other complexes. This finding has conceptual implications for understanding the coupling between transcription and RNA processing.
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Affiliation(s)
- Noemí Sánchez-Hernández
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Stéphanie Boireau
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Ute Schmidt
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Juan Pablo Muñoz-Cobo
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
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48
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Miorin L, Maiuri P, Marcello A. Visual detection of Flavivirus RNA in living cells. Methods 2016; 98:82-90. [PMID: 26542763 PMCID: PMC7129942 DOI: 10.1016/j.ymeth.2015.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/29/2015] [Accepted: 11/01/2015] [Indexed: 12/24/2022] Open
Abstract
Flaviviruses include a wide range of important human pathogens delivered by insects or ticks. These viruses have a positive-stranded RNA genome that is replicated in the cytoplasm of the infected cell. The viral RNA genome is the template for transcription by the virally encoded RNA polymerase and for translation of the viral proteins. Furthermore, the double-stranded RNA intermediates of viral replication are believed to trigger the innate immune response through interaction with cytoplasmic cellular sensors. Therefore, understanding the subcellular distribution and dynamics of Flavivirus RNAs is of paramount importance to understand the interaction of the virus with its cellular host, which could be of insect, tick or mammalian, including human, origin. Recent advances on the visualization of Flavivirus RNA in living cells together with the development of methods to measure the dynamic properties of viral RNA are reviewed and discussed in this essay. In particular the application of bleaching techniques such as fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP) are analysed in the context of tick-borne encephalitis virus replication. Conclusions driven by this approached are discussed in the wider context Flavivirus infection.
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MESH Headings
- Animals
- Cell Line
- Cricetinae
- Encephalitis Viruses, Tick-Borne/genetics
- Encephalitis Viruses, Tick-Borne/metabolism
- Encephalitis Viruses, Tick-Borne/ultrastructure
- Fluorescence Recovery After Photobleaching
- Fluorescent Dyes/chemistry
- Gene Expression Regulation, Viral
- Host-Pathogen Interactions
- Humans
- Molecular Imaging/methods
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Staining and Labeling/methods
- Ticks/virology
- Transcription, Genetic
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Affiliation(s)
- Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paolo Maiuri
- IFOM - Istituto FIRC di Oncologia Molecolare, via Adamello 16, 20139 Milan, Italy
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.
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49
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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50
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Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-98. [PMID: 26034889 DOI: 10.1146/annurev-biochem-060614-034242] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays a pivotal role in the flow of genetic information from DNA to proteins by expanding the coding capacity of genomes. Regulation of alternative splicing is as important as regulation of transcription to determine cell- and tissue-specific features, normal cell functioning, and responses of eukaryotic cells to external cues. Its importance is confirmed by the evolutionary conservation and diversification of alternative splicing and the fact that its deregulation causes hereditary disease and cancer. This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in which chromatin structure, DNA methylation, histone marks, and nucleosome positioning play a fundamental role in providing a dynamic scaffold for interactions between the splicing and transcription machineries. We focus on evidence for how the kinetics of RNA polymerase II (RNAPII) elongation and the recruitment of splicing factors and adaptor proteins to chromatin components act in coordination to regulate alternative splicing.
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Affiliation(s)
- Shiran Naftelberg
- Sackler Medical School, Tel Aviv University, Tel Aviv 69978, Israel;
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