1
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Tang Y, Behrens RT, St Gelais C, Wu S, Vivekanandan S, Razin E, Fang P, Wu L, Sherer N, Musier-Forsyth K. Human lysyl-tRNA synthetase phosphorylation promotes HIV-1 proviral DNA transcription. Nucleic Acids Res 2023; 51:12111-12123. [PMID: 37933844 PMCID: PMC10711549 DOI: 10.1093/nar/gkad941] [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: 11/04/2022] [Revised: 09/18/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
Human lysyl-tRNA synthetase (LysRS) was previously shown to be re-localized from its normal cytoplasmic location in a multi-aminoacyl-tRNA synthetase complex (MSC) to the nucleus of HIV-1 infected cells. Nuclear localization depends on S207 phosphorylation but the nuclear function of pS207-LysRS in the HIV-1 lifecycle is unknown. Here, we show that HIV-1 replication was severely reduced in a S207A-LysRS knock-in cell line generated by CRISPR/Cas9; this effect was rescued by S207D-LysRS. LysRS phosphorylation up-regulated HIV-1 transcription, as did direct transfection of Ap4A, an upstream transcription factor 2 (USF2) activator that is synthesized by pS207-LysRS. Overexpressing an MSC-derived peptide known to stabilize LysRS MSC binding inhibited HIV-1 replication. Transcription of HIV-1 proviral DNA and other USF2 target genes was reduced in peptide-expressing cells. We propose that nuclear pS207-LysRS generates Ap4A, leading to activation of HIV-1 transcription. Our results suggest a new role for nuclear LysRS in facilitating HIV-1 replication and new avenues for antiviral therapy.
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Affiliation(s)
- Yingke Tang
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
| | - Ryan T Behrens
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Corine St Gelais
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Siqi Wu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, China
| | - Saravanan Vivekanandan
- Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore and The Hebrew University of Jerusalem (NUS–HUJ), Singapore
| | - Ehud Razin
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Israel
| | - Pengfei Fang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, China
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nathan Sherer
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
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2
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Borrmann H, Ulkar G, Kliszczak AE, Ismed D, Schilling M, Magri A, Harris JM, Balfe P, Vasudevan S, Borrow P, Zhuang X, McKeating JA. Molecular components of the circadian clock regulate HIV-1 replication. iScience 2023; 26:107007. [PMID: 37534138 PMCID: PMC10391662 DOI: 10.1016/j.isci.2023.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/24/2023] [Accepted: 05/26/2023] [Indexed: 08/04/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) causes major health burdens worldwide and still lacks curative therapies and vaccines. Circadian rhythms are endogenous daily oscillations that coordinate an organism's response to its environment and invading pathogens. Peripheral viral loads of HIV-1 infected patients show diurnal variation; however, the underlying mechanisms remain unknown. Here, we demonstrate a role for the cell-intrinsic clock to regulate rhythmic HIV-1 replication in circadian-synchronized systems. Silencing the circadian activator Bmal1 abolishes this phenotype, and we observe BMAL1 binding to the HIV-1 promoter. Importantly, we show differential binding of the nuclear receptors REV-ERB and ROR to the HIV-long terminal repeat at different circadian times, demonstrating a dynamic interplay in time-of-day regulation of HIV-1 transcription. Bioinformatic analysis shows circadian regulation of host factors that control HIV-1 replication, providing an additional mechanism for rhythmic viral replication. This study increases our understanding of the circadian regulation of HIV-1, which can ultimately inform new therapies.
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Affiliation(s)
- Helene Borrmann
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Görkem Ulkar
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Anna E. Kliszczak
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dini Ismed
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mirjam Schilling
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Andrea Magri
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - James M. Harris
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Peter Balfe
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Jane A. McKeating
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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3
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Schaefer M, Nabih A, Spies D, Hermes V, Bodak M, Wischnewski H, Stalder P, Ngondo RP, Liechti LA, Sajic T, Aebersold R, Gatfield D, Ciaudo C. Global and precise identification of functional
miRNA
targets in
mESCs
by integrative analysis. EMBO Rep 2022; 23:e54762. [PMID: 35899551 PMCID: PMC9442311 DOI: 10.15252/embr.202254762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
MicroRNA (miRNA) loaded Argonaute (AGO) complexes regulate gene expression via direct base pairing with their mRNA targets. Previous works suggest that up to 60% of mammalian transcripts might be subject to miRNA‐mediated regulation, but it remains largely unknown which fraction of these interactions are functional in a specific cellular context. Here, we integrate transcriptome data from a set of miRNA‐depleted mouse embryonic stem cell (mESC) lines with published miRNA interaction predictions and AGO‐binding profiles. Using this integrative approach, combined with molecular validation data, we present evidence that < 10% of expressed genes are functionally and directly regulated by miRNAs in mESCs. In addition, analyses of the stem cell‐specific miR‐290‐295 cluster target genes identify TFAP4 as an important transcription factor for early development. The extensive datasets developed in this study will support the development of improved predictive models for miRNA‐mRNA functional interactions.
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Affiliation(s)
- Moritz Schaefer
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Amena Nabih
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Daniel Spies
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Victoria Hermes
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Maxime Bodak
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Harry Wischnewski
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Patrick Stalder
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Richard Patryk Ngondo
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Luz Angelica Liechti
- Center for Integrative Genomics (CIG) University of Lausanne Lausanne Switzerland
| | - Tatjana Sajic
- Swiss Federal Institute of Technology Zurich, IMSB Zürich Switzerland
| | - Ruedi Aebersold
- Swiss Federal Institute of Technology Zurich, IMSB Zürich Switzerland
| | - David Gatfield
- Center for Integrative Genomics (CIG) University of Lausanne Lausanne Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
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4
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Ye F, Alvarez-Carbonell D, Nguyen K, Leskov K, Garcia-Mesa Y, Sreeram S, Valadkhan S, Karn J. Recruitment of the CoREST transcription repressor complexes by Nerve Growth factor IB-like receptor (Nurr1/NR4A2) mediates silencing of HIV in microglial cells. PLoS Pathog 2022; 18:e1010110. [PMID: 35797416 PMCID: PMC9295971 DOI: 10.1371/journal.ppat.1010110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 07/19/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Human immune deficiency virus (HIV) infection in the brain leads to chronic neuroinflammation due to the production of pro-inflammatory cytokines, which in turn promotes HIV transcription in infected microglial cells. However, powerful counteracting silencing mechanisms in microglial cells result in the rapid shutdown of HIV expression after viral reactivation to limit neuronal damage. Here we investigated whether the Nerve Growth Factor IB-like nuclear receptor Nurr1 (NR4A2), which is a repressor of inflammation in the brain, acts directly to restrict HIV expression. HIV silencing following activation by TNF-α, or a variety of toll-like receptor (TLR) agonists, in both immortalized human microglial cells (hμglia) and induced pluripotent stem cells (iPSC)-derived human microglial cells (iMG) was enhanced by Nurr1 agonists. Similarly, overexpression of Nurr1 led to viral suppression, while conversely, knock down (KD) of endogenous Nurr1 blocked HIV silencing. The effect of Nurr1 on HIV silencing is direct: Nurr1 binds directly to the specific consensus binding sites in the U3 region of the HIV LTR and mutation of the Nurr1 DNA binding domain blocked its ability to suppress HIV-1 transcription. Chromatin immunoprecipitation (ChIP) assays also showed that after Nurr1 binding to the LTR, the CoREST/HDAC1/G9a/EZH2 transcription repressor complex is recruited to the HIV provirus. Finally, transcriptomic studies demonstrated that in addition to repressing HIV transcription, Nurr1 also downregulated numerous cellular genes involved in inflammation, cell cycle, and metabolism, further promoting HIV latency and microglial homoeostasis. Nurr1 therefore plays a pivotal role in modulating the cycles of proviral reactivation by potentiating the subsequent proviral transcriptional shutdown. These data highlight the therapeutic potential of Nurr1 agonists for inducing HIV silencing and microglial homeostasis and ultimately for the amelioration of the neuroinflammation associated with HIV-associated neurocognitive disorders (HAND).
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Affiliation(s)
- Fengchun Ye
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - David Alvarez-Carbonell
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Kien Nguyen
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Konstantin Leskov
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Yoelvis Garcia-Mesa
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sheetal Sreeram
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
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5
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McKay LGA, Thomas J, Albalawi W, Fattaccioli A, Dieu M, Ruggiero A, McKeating JA, Ball JK, Tarr AW, Renard P, Pollakis G, Paxton WA. The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway. Front Immunol 2022; 13:831695. [PMID: 35371105 PMCID: PMC8964954 DOI: 10.3389/fimmu.2022.831695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Following acute HCV infection, the virus establishes a chronic disease in the majority of patients whilst few individuals clear the infection spontaneously. The precise mechanisms that determine chronic HCV infection or spontaneous clearance are not completely understood but are proposed to be driven by host and viral genetic factors as well as HCV encoded immunomodulatory proteins. Using the HIV-1 LTR as a tool to measure NF-κB activity, we identified that the HCV E1E2 glycoproteins and more so the E2 protein down-modulates HIV-1 LTR activation in 293T, TZM-bl and the more physiologically relevant Huh7 liver derived cell line. We demonstrate this effect is specifically mediated through inhibiting NF-κB binding to the LTR and show that this effect was conserved for all HCV genotypes tested. Transcriptomic analysis of 293T cells expressing the HCV glycoproteins identified E1E2 mediated stimulation of the endoplasmic reticulum (ER) stress response pathway and upregulation of stress response genes such as ATF3. Through shRNA mediated inhibition of ATF3, one of the components, we observed that E1E2 mediated inhibitory effects on HIV-1 LTR activity was alleviated. Our in vitro studies demonstrate that HCV Env glycoprotein activates host ER Stress Pathways known to inhibit NF-κB activity. This has potential implications for understanding HCV induced immune activation as well as oncogenesis.
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Affiliation(s)
- Lindsay G. A. McKay
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Wejdan Albalawi
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Antoine Fattaccioli
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Marc Dieu
- MaSUN, Mass Spectrometry Facility, University of Namur (UNamur), Namur, Belgium
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jonathan K. Ball
- Wolfson Centre for Global Virus Research and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- Wolfson Centre for Global Virus Research and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium,MaSUN, Mass Spectrometry Facility, University of Namur (UNamur), Namur, Belgium
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - William A. Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom,*Correspondence: William A. Paxton,
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6
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Suleman S, Payne A, Bowden J, Haque SA, Zahn M, Fawaz S, Khalifa MS, Jobling S, Hay D, Franco M, Fronza R, Wang W, Strobel-Freidekind O, Deichmann A, Takeuchi Y, Waddington SN, Gil-Farina I, Schmidt M, Themis M. HIV- 1 lentivirus tethering to the genome is associated with transcription factor binding sites found in genes that favour virus survival. Gene Ther 2022; 29:720-729. [PMID: 35513551 PMCID: PMC9750860 DOI: 10.1038/s41434-022-00335-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 01/09/2023]
Abstract
Lentiviral vectors (LV) are attractive for permanent and effective gene therapy. However, integration into the host genome can cause insertional mutagenesis highlighting the importance of understanding of LV integration. Insertion site (IS) tethering is believed to involve cellular proteins such as PSIP1/LEDGF/p75, which binds to the virus pre-integration complexes (PICs) helping to target the virus genome. Transcription factors (TF) that bind both the vector LTR and host genome are also suspected influential to this. To determine the role of TF in the tethering process, we mapped predicted transcription factor binding sites (pTFBS) near to IS chosen by HIV-1 LV using a narrow 20 bp window in infected human induced pluripotent stem cells (iPSCs) and their hepatocyte-like cell (HLC) derivatives. We then aligned the pTFBS with these sequences found in the LTRs of native and self-inactivated LTRs. We found significant enrichment of these sequences for pTFBS essential to HIV-1 life cycle and virus survival. These same sites also appear in HIV-1 patient IS and in mice infected with HIV-1 based LV. This in silco data analysis suggests pTFBS present in the virus LTR and IS sites selected by HIV-1 LV are important to virus survival and propagation.
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Affiliation(s)
- Saqlain Suleman
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK ,Testavec Ltd, Queensgate House, Maidenhead, UK
| | - Annette Payne
- Testavec Ltd, Queensgate House, Maidenhead, UK ,grid.7728.a0000 0001 0724 6933Department of Computer Science, College of Engineering Design and Physical Sciences, Brunel University London, Uxbridge, UK
| | - Johnathan Bowden
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Sharmin Al Haque
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Marco Zahn
- Genewerk GmbH, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373University Heidelberg, Medical Faculty, Heidelberg, Germany
| | - Serena Fawaz
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Mohammad S. Khalifa
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Susan Jobling
- Testavec Ltd, Queensgate House, Maidenhead, UK ,grid.7728.a0000 0001 0724 6933Institute of Environment, Health and Societies, College of Business, Arts and Social Sciences, Brunel University London, Uxbridge, UK
| | - David Hay
- grid.4305.20000 0004 1936 7988Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | | | | | - Wei Wang
- Genewerk GmbH, Heidelberg, Germany
| | | | | | - Yasuhiro Takeuchi
- grid.83440.3b0000000121901201Division of Infection and Immunity, University College London, London, UK ,grid.70909.370000 0001 2199 6511Division of Advanced Therapies, National Institute for Biological Standards and Control, Potters Bar, UK
| | - Simon N. Waddington
- grid.83440.3b0000000121901201Gene Transfer Technology, EGA Institute for Women’s Health, University College London, London, UK ,grid.11951.3d0000 0004 1937 1135MRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | | | - Manfred Schmidt
- Genewerk GmbH, Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Oncology, NCT and DKFZ, Heidelberg, Germany
| | - Michael Themis
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK ,grid.7445.20000 0001 2113 8111Division of Ecology and Evolution, Department of Life Sciences, Imperial College London, London, UK
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7
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Stern J, Solomon A, Dantanarayana A, Pascoe R, Reynaldi A, Davenport MP, Milush J, Deeks SG, Hartogensis W, Hecht FM, Cockerham L, Roche M, Lewin SR. Cell-associated HIV RNA has a Circadian Cycle in Males Living with HIV on Antiretroviral Therapy. J Infect Dis 2021; 225:1721-1730. [PMID: 34655216 DOI: 10.1093/infdis/jiab533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Circadian transcription factors that regulate cell-autonomous circadian clocks can also increase HIV transcription in vitro. We aimed to determine if circadian variation in HIV transcription exists in people living with HIV (PLHIV) on antiretroviral therapy (ART). METHODS We performed a prospective observational study of male PLHIV on ART, sampling blood every four hours for 24 hours. Using qPCR, we quantified expression of circadian associated genes, HIV DNA and cell-associated unspliced (CA-US) RNA in peripheral blood CD4+ T-cells. Plasma sex hormones were quantified alongside plasma and salivary cortisol. The primary outcome was to identify temporal variations in CA-US HIV RNA using a linear mixed effect regression framework and maximum likelihood estimation. RESULTS Salivary and plasma cortisol, and circadian genes including Clock, Bmal1, and Per3 varied with a circadian rhythm. CA-US HIV RNA and the ratio of CA-US HIV RNA-to-DNA in CD4+ T-cells also demonstrated circadian variations, with no variation in HIV DNA. Circulating oestradiol was highly predictive of CA-US HIV RNA variation in vivo. CONCLUSION CA-US HIV RNA in PLHIV on ART varies temporally with a circadian rhythm. These findings have implications for the design of clinical trials and biomarkers to assess HIV cure interventions.
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Affiliation(s)
- Jared Stern
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Ajantha Solomon
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Ashanti Dantanarayana
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Rachel Pascoe
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Arnold Reynaldi
- The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Miles P Davenport
- The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Jeffrey Milush
- Department of Medicine, University of California, San Francisco, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, USA
| | - Wendy Hartogensis
- Osher Center for Integrative Medicine, University of California San Francisco, San Francisco, USA
| | - Frederick M Hecht
- Osher Center for Integrative Medicine, University of California San Francisco, San Francisco, USA
| | - Leslie Cockerham
- Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, USA
| | - Michael Roche
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
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8
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Vecellio M, Chen L, Cohen CJ, Cortes A, Li Y, Bonham S, Selmi C, Brown MA, Fischer R, Knight JC, Wordsworth BP. Functional Genomic Analysis of a RUNX3 Polymorphism Associated With Ankylosing Spondylitis. Arthritis Rheumatol 2021; 73:980-990. [PMID: 33369221 PMCID: PMC8251554 DOI: 10.1002/art.41628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/28/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To investigate the functional consequences of the single-nucleotide polymorphism rs4648889 in a putative enhancer upstream of the RUNX3 promoter associated with susceptibility to ankylosing spondylitis (AS). METHODS Using nuclear extracts from Jurkat cells and primary human CD8+ T cells, the effects of rs4648889 on allele-specific transcription factor (TF) binding were investigated by DNA pull-down assay and quantitative mass spectrometry (qMS), with validation by electrophoretic mobility shift assay (EMSA), Western blotting of the pulled-down eluates, and chromatin immunoprecipitation (ChIP)-quantitative polymerase chain reaction (qPCR) analysis. Further functional effects were tested by small interfering RNA knockdown of the gene for interferon regulatory factor 5 (IRF5), followed by reverse transcription-qPCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA) to measure the levels of IFNγ messenger RNA (mRNA) and protein, respectively. RESULTS In nuclear extracts from CD8+ T cells, results of qMS showed that relative TF binding to the AS-risk A allele of rs4648889 was increased 3.7-fold (P < 0.03) for Ikaros family zinc-finger protein 3 (IKZF3; Aiolos) and components of the NuRD complex, including chromodomain helicase DNA binding protein 4 (CHD4) (3.6-fold increase; P < 0.05) and retinoblastoma binding protein 4 (RBBP4) (4.1-fold increase; P < 0.03). In contrast, IRF5 bound significantly more to the AS-protective G allele compared to the AS-risk A allele (fold change 8.2; P = 0.003). Validation with Western blotting, EMSA, and ChIP-qPCR confirmed the differential allelic binding of IKZF3, CHD4, RBBP4, and IRF5. Silencing of IRF5 in CD8+ T cells increased the levels of IFNγ mRNA as measured by RT-qPCR (P = 0.03) and IFNγ protein as measured by ELISA (P = 0.02). CONCLUSION These findings suggest that the association of rs4648889 with AS reflects allele-specific binding of this enhancer-like region to certain TFs, including IRF5, IKZF3, and members of the NuRD complex. IRF5 may have crucial influences on the functions of CD8+ lymphocytes, a finding that could reveal new therapeutic targets for the management of AS.
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Affiliation(s)
- Matteo Vecellio
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Botnar Research Centre, Nuffield Orthopaedic Centre, NIHR Oxford Comprehensive Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Liye Chen
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Botnar Research Centre, Nuffield Orthopaedic Centre, NIHR Oxford Comprehensive Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Carla J Cohen
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Botnar Research Centre, Nuffield Orthopaedic Centre, NIHR Oxford Comprehensive Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Adrian Cortes
- John Radcliffe Hospital, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yan Li
- The First Affiliated Hospital of Xiamen University and Xiamen University School of Medicine, Xiamen, China
| | - Sarah Bonham
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Carlo Selmi
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Matthew A Brown
- NIHR Guy's and St. Thomas' Biomedical Research Centre, London, UK, and University of Queensland, Brisbane, Queensland, Australia
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - B Paul Wordsworth
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Botnar Research Centre, Nuffield Orthopaedic Centre, NIHR Oxford Comprehensive Biomedical Research Centre, University of Oxford, Oxford, UK
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9
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Wlazło A, Święcicka M, Koter MD, Krępski T, Bolibok L, Stochmal A, Kowalczyk M, Rakoczy-Trojanowska M. Genes ScBx1 and ScIgl-Competitors or Cooperators? Genes (Basel) 2020; 11:genes11020223. [PMID: 32093268 PMCID: PMC7074272 DOI: 10.3390/genes11020223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Two genes, Bx1 and Igl, both encoding indole-3-glycerol phosphate lyase (IGL), are believed to control the conversion of indole-3-glycerol phosphate (IGP) to indole. The first of these has generally been supposed to be regulated developmentally, being expressed at early stages of plant development with the indole being used in the benzoxazinoid (BX) biosynthesis pathway. In contrast, it has been proposed that the second one is regulated by stresses and that the associated free indole is secreted as a volatile. However, our previous results contradicted this. In the present study, we show that the ScIgl gene takes over the role of ScBx1 at later developmental stages, between the 42nd and 70th days after germination. In the majority of plants with silenced ScBx1 expression, ScIgl was either expressed at a significantly higher level than ScBx1 or it was the only gene with detectable expression. Therefore, we postulate that the synthesis of indole used in BX biosynthesis in rye is controlled by both ScBx1 and ScIgl, which are both regulated developmentally and by stresses. In silico and in vivo analyses of the promoter sequences further confirmed our hypothesis that the roles and modes of regulation of the ScBx1 and ScIgl genes are similar.
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Affiliation(s)
- Anna Wlazło
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (A.W.); (M.Ś.); (M.D.K.); (T.K.)
| | - Magdalena Święcicka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (A.W.); (M.Ś.); (M.D.K.); (T.K.)
| | - Marek D. Koter
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (A.W.); (M.Ś.); (M.D.K.); (T.K.)
| | - Tomasz Krępski
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (A.W.); (M.Ś.); (M.D.K.); (T.K.)
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences, 02-787 Warsaw, Poland;
| | - Anna Stochmal
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation, State Research Institute, 24-100 Puławy, Poland; (A.S.); (M.K.)
| | - Mariusz Kowalczyk
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation, State Research Institute, 24-100 Puławy, Poland; (A.S.); (M.K.)
| | - Monika Rakoczy-Trojanowska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (A.W.); (M.Ś.); (M.D.K.); (T.K.)
- Correspondence: ; Tel.: +48-225932150
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10
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Schwarzer R, Gramatica A, Greene WC. Reduce and Control: A Combinatorial Strategy for Achieving Sustained HIV Remissions in the Absence of Antiretroviral Therapy. Viruses 2020; 12:v12020188. [PMID: 32046251 PMCID: PMC7077203 DOI: 10.3390/v12020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/05/2020] [Accepted: 02/05/2020] [Indexed: 12/23/2022] Open
Abstract
Human immunodeficiency virus (HIV-1) indefinitely persists, despite effective antiretroviral therapy (ART), within a small pool of latently infected cells. These cells often display markers of immunologic memory and harbor both replication-competent and -incompetent proviruses at approximately a 1:100 ratio. Although complete HIV eradication is a highly desirable goal, this likely represents a bridge too far for our current and foreseeable technologies. A more tractable goal involves engineering a sustained viral remission in the absence of ART––a “functional cure.” In this setting, HIV remains detectable during remission, but the size of the reservoir is small and the residual virus is effectively controlled by an engineered immune response or other intervention. Biological precedence for such an approach is found in the post-treatment controllers (PTCs), a rare group of HIV-infected individuals who, following ART withdrawal, do not experience viral rebound. PTCs are characterized by a small reservoir, greatly reduced inflammation, and the presence of a poorly understood immune response that limits viral rebound. Our goal is to devise a safe and effective means for replicating durable post-treatment control on a global scale. This requires devising methods to reduce the size of the reservoir and to control replication of this residual virus. In the following sections, we will review many of the approaches and tools that likely will be important for implementing such a “reduce and control” strategy and for achieving a PTC-like sustained HIV remission in the absence of ART.
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11
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He DD, Lu Y, Gittelman R, Jin Y, Ling F, Joshua A. Positive selection of the TRIM family regulatory region in primate genomes. Proc Biol Sci 2017; 283:rspb.2016.1602. [PMID: 27733547 DOI: 10.1098/rspb.2016.1602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022] Open
Abstract
Viral selection pressure has acted on restriction factors that play an important role in the innate immune system by inhibiting the replication of viruses during primate evolution. Tripartite motif-containing (TRIM) family members are some of these restriction factors. It is becoming increasingly clear that gene expression differences, rather than protein-coding regions changes, could play a vital role in the anti-retroviral immune mechanism. Increasingly, recent studies have created genome-scale catalogues of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To improve our understanding of the molecular evolution mechanism of antiviral differences between species, we leveraged 14 130 DHSs derived from 145 cell types to characterize the regulatory landscape of the TRIM region. Subsequently, we compared the alignments of the DHSs across six primates and found 375 DHSs that are conserved in non-human primates but exhibit significantly accelerated rates of evolution in the human lineage (haDHSs). Furthermore, we discovered 31 human-specific potential transcription factor motifs within haDHSs, including the KROX and SP1, that both interact with HIV-1 Importantly, the corresponding haDHS was correlated with antiviral factor TRIM23 Thus, our results suggested that some viruses may contribute, through regulatory DNA differences, to organismal evolution by mediating TRIM gene expression to escape immune surveillance.
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Affiliation(s)
- Dan-Dan He
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Yueer Lu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Rachel Gittelman
- Department of Genome Sciences, University of Washington, Seattle, WA 98125, USA
| | - Yabin Jin
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Fei Ling
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Akey Joshua
- Department of Genome Sciences, University of Washington, Seattle, WA 98125, USA
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12
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Gosselin P, Rando G, Fleury-Olela F, Schibler U. Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM). Genes Dev 2017; 30:1895-907. [PMID: 27601530 PMCID: PMC5024686 DOI: 10.1101/gad.284828.116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/02/2016] [Indexed: 12/23/2022]
Abstract
Gosselin et al. designed a widely applicable method, dubbed BC-STAR-PROM, to identify signal-activated TFs without any prior knowledge of their properties. To establish proof of concept for BC-STAR-PROM, they applied it to the identification of TFs induced by drugs affecting actin and tubulin cytoskeleton dynamics. The discovery of transcription factors (TFs) controlling pathways in health and disease is of paramount interest. We designed a widely applicable method, dubbed barcorded synthetic tandem repeat promoter screening (BC-STAR-PROM), to identify signal-activated TFs without any a priori knowledge about their properties. The BC-STAR-PROM library consists of ∼3000 luciferase expression vectors, each harboring a promoter (composed of six tandem repeats of synthetic random DNA) and an associated barcode of 20 base pairs (bp) within the 3′ untranslated mRNA region. Together, the promoter sequences encompass >400,000 bp of random DNA, a sequence complexity sufficient to capture most TFs. Cells transfected with the library are exposed to a signal, and the mRNAs that it encodes are counted by next-generation sequencing of the barcodes. This allows the simultaneous activity tracking of each of the ∼3000 synthetic promoters in a single experiment. Here we establish proof of concept for BC-STAR-PROM by applying it to the identification of TFs induced by drugs affecting actin and tubulin cytoskeleton dynamics. BC-STAR-PROM revealed that serum response factor (SRF) is the only immediate early TF induced by both actin polymerization and microtubule depolymerization. Such changes in cytoskeleton dynamics are known to occur during the cell division cycle, and real-time bioluminescence microscopy indeed revealed cell-autonomous SRF–myocardin-related TF (MRTF) activity bouts in proliferating cells.
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Affiliation(s)
- Pauline Gosselin
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Gianpaolo Rando
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | | | - Ueli Schibler
- Department of Molecular Biology, University of Geneva, CH-1211 Geneva, Switzerland
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13
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Identification of HIV-1 Tat-Associated Proteins Contributing to HIV-1 Transcription and Latency. Viruses 2017; 9:v9040067. [PMID: 28368303 PMCID: PMC5408673 DOI: 10.3390/v9040067] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/19/2017] [Accepted: 03/24/2017] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) Tat is a virus-encoded trans-activator that plays a central role in viral transcription. We used our recently developed parallel analysis of in vitro translated open reading frames (ORFs) (PLATO) approach to identify host proteins that associate with HIV-1 Tat. From this proteomic assay, we identify 89 Tat-associated proteins (TAPs). We combine our results with other datasets of Tat or long terminal repeat (LTR)-associated proteins. For some of these proteins (NAT10, TINP1, XRCC5, SIN3A), we confirm their strong association with Tat. These TAPs also suppress Tat-mediated HIV-1 transcription. Removing suppression of HIV-1 transcription benefits the reversal of post-integrated, latent HIV-1 proviruses. We demonstrate that these transcriptionally suppressing TAPs contribute to HIV-1 latency in Jurkat latency (J-LAT) cells. Therefore, our proteomic analysis highlights the previously unappreciated TAPs that play a role in maintaining HIV-1 latency and can be further studied as potential pharmacological targets for the “shock and kill” HIV-1 cure strategy.
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14
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Glorieux C, Sandoval JM, Fattaccioli A, Dejeans N, Garbe JC, Dieu M, Verrax J, Renard P, Huang P, Calderon PB. Chromatin remodeling regulates catalase expression during cancer cells adaptation to chronic oxidative stress. Free Radic Biol Med 2016; 99:436-450. [PMID: 27591797 DOI: 10.1016/j.freeradbiomed.2016.08.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/27/2016] [Accepted: 08/28/2016] [Indexed: 12/31/2022]
Abstract
Regulation of ROS metabolism plays a major role in cellular adaptation to oxidative stress in cancer cells, but the molecular mechanism that regulates catalase, a key antioxidant enzyme responsible for conversion of hydrogen peroxide to water and oxygen, remains to be elucidated. Therefore, we investigated the transcriptional regulatory mechanism controlling catalase expression in three human mammary cell lines: the normal mammary epithelial 250MK primary cells, the breast adenocarcinoma MCF-7 cells and an experimental model of MCF-7 cells resistant against oxidative stress resulting from chronic exposure to H2O2 (Resox), in which catalase was overexpressed. Here we identify a novel promoter region responsible for the regulation of catalase expression at -1518/-1226 locus and the key molecules that interact with this promoter and affect catalase transcription. We show that the AP-1 family member JunB and retinoic acid receptor alpha (RARα) mediate catalase transcriptional activation and repression, respectively, by controlling chromatin remodeling through a histone deacetylases-dependent mechanism. This regulatory mechanism plays an important role in redox adaptation to chronic exposure to H2O2 in breast cancer cells. Our study suggests that cancer adaptation to oxidative stress may be regulated by transcriptional factors through chromatin remodeling, and reveals a potential new mechanism to target cancer cells.
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Affiliation(s)
- Christophe Glorieux
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510275 Guangzhou, China.
| | - Juan Marcelo Sandoval
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Facultad de Ciencias de la Salud, Universidad Arturo Prat, 1100000 Iquique, Chile
| | - Antoine Fattaccioli
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Nicolas Dejeans
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium
| | - James C Garbe
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marc Dieu
- Mass Spectrometry University of Namur (MaSUN), University of Namur, 5000 Namur, Belgium
| | - Julien Verrax
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Peng Huang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510275 Guangzhou, China; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pedro Buc Calderon
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Facultad de Ciencias de la Salud, Universidad Arturo Prat, 1100000 Iquique, Chile.
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15
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Luo Y, Muesing MA. Mass spectrometry-based proteomic approaches for discovery of HIV-host interactions. Future Virol 2014; 9:979-992. [PMID: 25544858 DOI: 10.2217/fvl.14.86] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A molecular understanding of viral infection requires a multi-disciplinary approach. Mass spectrometry has emerged as an indispensable tool to investigate the complex and dynamic interactions between HIV-1 and its host. It has been employed to study protein associations, changes in protein abundance and post-translational modifications occurring after viral infection. Here, we review and provide examples of mass spectrometry-based proteomic approaches currently used to explore virus-host interaction. Efforts in this area are certain to accelerate the discovery of the unique molecular strategies utilized by the virus to commandeer the cell as well as mechanisms of host defense.
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Affiliation(s)
- Yang Luo
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, 455 First Avenue 7th Floor, New York, NY 10016, USA
| | - Mark A Muesing
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, 455 First Avenue 7th Floor, New York, NY 10016, USA
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16
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A DNA-centric protein interaction map of ultraconserved elements reveals contribution of transcription factor binding hubs to conservation. Cell Rep 2013; 5:531-45. [PMID: 24139795 DOI: 10.1016/j.celrep.2013.09.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/06/2013] [Accepted: 09/11/2013] [Indexed: 12/19/2022] Open
Abstract
Ultraconserved elements (UCEs) have been the subject of great interest because of their extreme sequence identity and their seemingly cryptic and largely uncharacterized functions. Although in vivo studies of UCE sequences have demonstrated regulatory activity, protein interactors at UCEs have not been systematically identified. Here, we combined high-throughput affinity purification, high-resolution mass spectrometry, and SILAC quantification to map intrinsic protein interactions for 193 UCE sequences. The interactome contains over 400 proteins, including transcription factors with known developmental roles. We demonstrate based on our data that UCEs consist of strongly conserved overlapping binding sites. We also generated a fine-resolution interactome of a UCE, confirming the hub-like nature of the element. The intrinsic interactions mapped here are reflected in open chromatin, as indicated by comparison with existing ChIP data. Our study argues for a strong contribution of protein-DNA interactions to UCE conservation and provides a basis for further functional characterization of UCEs.
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17
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Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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18
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Selective recognition of viral promoters by host cell transcription complexes: challenges and opportunities to control latency. Curr Opin Virol 2013; 3:380-6. [PMID: 23827503 DOI: 10.1016/j.coviro.2013.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 06/07/2013] [Accepted: 06/10/2013] [Indexed: 12/15/2022]
Abstract
The rate of transcription driven by the HIV promoter defines both the entry into and reactivation from viral latency. The HIV core promoter plays a pivotal role in HIV latency by recruiting host cell RNA polymerase II pre-initiation complexes essential for viral transcription. Pioneering studies on the HIV core promoter revealed that the architecture of the HIV core promoter is specifically required for the amplification of transcription in response to the viral trans-activator Tat, and provided the proof-of-concept that the HIV core promoter represents a tractable drug target. The recent discovery of host cell transcription complexes that selectively recognize the HIV core promoter provides new impetus to investigate their components as novel targets to therapeutically extinguish or eradicate latent HIV.
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