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Li J, Shi J, Pan Y, Zhao Y, Yan F, Li H, Lei L. Transcription modulation by CDK9 regulates inflammatory genes and RIPK3-MLKL-mediated necroptosis in periodontitis progression. Sci Rep 2019; 9:17369. [PMID: 31758083 PMCID: PMC6874675 DOI: 10.1038/s41598-019-53910-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 02/07/2023] Open
Abstract
Cyclin-dependent kinase 9 (CDK9), one crucial molecule in promoting the transition from transcription pausing to elongation, is a critical modulator of cell survival and death. However, the pathological function of CDK9 in bacterial inflammatory diseases has never been explored. CDK9 inhibition or knock-down attenuated Porphyromonas gingivalis-triggered inflammatory gene expression. Gene-expression microarray analysis of monocytes revealed that knock-down of CDK9 not only affected inflammatory responses, but also impacted cell death network, especially the receptor-interacting protein kinase 3 (RIPK3)-mixed lineage kinase domain-like (MLKL)-mediated necroptosis after P. gingivalis infection. Inhibition of CDK9 significantly decreased necroptosis with downregulation of both MLKL and phosphorylated MLKL. By regulating caspase-8 and cellular FLICE inhibitory protein (cFLIP), key molecules in regulating cell survival and death, CDK9 affected not only the classic RIPK1-RIPK3-mediated necroptosis, but also the alternate TIR-domain-containing adapter-inducing interferon-β-RIPK3-mediated necroptosis. CDK9 inhibition dampened pro-inflammatory gene production in the acute infection process in the subcutaneous chamber model in vivo. Moreover, CDK9 inhibition contributed to the decreased periodontal bone loss and inflammatory response induced by P. gingivalis in the periodontal micro-environment. In conclusion, by modulating the RIPK3-MLKL-mediated necroptosis, CDK9 inhibition provided a novel mechanism to impact the progress of bacterial infection in the periodontal milieu.
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Affiliation(s)
- Jiao Li
- Department of Orthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jiahong Shi
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
- Department of Periodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yue Pan
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yunhe Zhao
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Fuhua Yan
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
- Department of Periodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Houxuan Li
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
- Department of Periodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Lang Lei
- Department of Orthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.
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2
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Gallagher SJ, Shklovskaya E, Hersey P. Epigenetic modulation in cancer immunotherapy. Curr Opin Pharmacol 2017; 35:48-56. [PMID: 28609681 DOI: 10.1016/j.coph.2017.05.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 02/07/2023]
Abstract
The success of immune checkpoint inhibitors in cancer immunotherapy has been widely heralded. However many cancer patients do not respond to immune checkpoint therapy and some relapse due to acquired tumor resistance. Epigenetic targeting may be beneficial in cancer immunotherapy by reversing immune avoidance and escape mechanisms employed by cancer cells, as well as by modulating immune cell differentiation and function. In this manuscript we review recent findings suggesting how epigenetics may be used to improve cancer immunotherapy. We focus on the inhibitors of the CTLA4 and PD1 immune checkpoints and epigenetic modifiers of histone acetylation and methylation and DNA methylation.
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Affiliation(s)
- Stuart J Gallagher
- Melanoma Immunology and Oncology Group, The Centenary Institute, University of Sydney, Camperdown, NSW, Australia; Melanoma Institute Australia, Crow's Nest 2065, Sydney, Australia.
| | - Elena Shklovskaya
- Melanoma Immunology and Oncology Group, The Centenary Institute, University of Sydney, Camperdown, NSW, Australia; Melanoma Institute Australia, Crow's Nest 2065, Sydney, Australia
| | - Peter Hersey
- Melanoma Immunology and Oncology Group, The Centenary Institute, University of Sydney, Camperdown, NSW, Australia; Melanoma Institute Australia, Crow's Nest 2065, Sydney, Australia
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3
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Hertweck A, Evans CM, Eskandarpour M, Lau JCH, Oleinika K, Jackson I, Kelly A, Ambrose J, Adamson P, Cousins DJ, Lavender P, Calder VL, Lord GM, Jenner RG. T-bet Activates Th1 Genes through Mediator and the Super Elongation Complex. Cell Rep 2016; 15:2756-70. [PMID: 27292648 PMCID: PMC4920892 DOI: 10.1016/j.celrep.2016.05.054] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 04/21/2016] [Accepted: 05/09/2016] [Indexed: 12/21/2022] Open
Abstract
The transcription factor T-bet directs Th1 cell differentiation, but the molecular mechanisms that underlie this lineage-specific gene regulation are not completely understood. Here, we show that T-bet acts through enhancers to allow the recruitment of Mediator and P-TEFb in the form of the super elongation complex (SEC). Th1 genes are occupied by H3K4me3 and RNA polymerase II in Th2 cells, while T-bet-mediated recruitment of P-TEFb in Th1 cells activates transcriptional elongation. P-TEFb is recruited to both genes and enhancers, where it activates enhancer RNA transcription. P-TEFb inhibition and Mediator and SEC knockdown selectively block activation of T-bet target genes, and P-TEFb inhibition abrogates Th1-associated experimental autoimmune uveitis. T-bet activity is independent of changes in NF-κB RelA and Brd4 binding, with T-bet- and NF-κB-mediated pathways instead converging to allow P-TEFb recruitment. These data provide insight into the mechanism through which lineage-specifying factors promote differentiation of alternative T cell fates.
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Affiliation(s)
- Arnulf Hertweck
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK; Department of Experimental Immunobiology and NIHR Comprehensive Biomedical Research Centre, Guy's and St. Thomas' Hospital and King's College London, SE1 9RT London, UK
| | - Catherine M Evans
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK
| | - Malihe Eskandarpour
- UCL Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - Jonathan C H Lau
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK
| | - Kristine Oleinika
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK
| | - Ian Jackson
- Department of Experimental Immunobiology and NIHR Comprehensive Biomedical Research Centre, Guy's and St. Thomas' Hospital and King's College London, SE1 9RT London, UK
| | - Audrey Kelly
- Department of Asthma, Allergy, and Respiratory Science, King's College London, SE1 9RT London, UK
| | - John Ambrose
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK
| | - Peter Adamson
- UCL Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - David J Cousins
- Department of Asthma, Allergy, and Respiratory Science, King's College London, SE1 9RT London, UK; Leicester Institute for Lung Health and Department of Infection, Immunity, and Inflammation, NIHR Leicester Respiratory Biomedical Research Unit, University of Leicester, LE3 9QP Leicester, UK
| | - Paul Lavender
- Department of Asthma, Allergy, and Respiratory Science, King's College London, SE1 9RT London, UK
| | - Virginia L Calder
- UCL Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - Graham M Lord
- Department of Experimental Immunobiology and NIHR Comprehensive Biomedical Research Centre, Guy's and St. Thomas' Hospital and King's College London, SE1 9RT London, UK.
| | - Richard G Jenner
- UCL Cancer Institute, University College London, 72 Huntley Street, W1T 4JF London, UK.
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Analysis of Subcellular RNA Fractions Revealed a Transcription-Independent Effect of Tumor Necrosis Factor Alpha on Splicing, Mediated by Spt5. Mol Cell Biol 2016; 36:1342-53. [PMID: 26903558 DOI: 10.1128/mcb.01117-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/16/2016] [Indexed: 12/21/2022] Open
Abstract
The proinflammatory cytokine tumor necrosis factor alpha (TNF-α) modulates the expression of many genes, primarily through activation of NF-κB. Here, we examined the global effects of the elongation factor Spt5 on nascent and mature mRNAs of TNF-α-induced cells using chromatin and cytosolic subcellular fractions. We identified several classes of TNF-α-induced genes controlled at the level of transcription, splicing, and chromatin retention. Spt5 was found to facilitate splicing and chromatin release in genes displaying high induction rates. Further analysis revealed striking effects of TNF-α on the splicing of 25% of expressed genes; the vast majority were not transcriptionally induced. Splicing enhancement of noninduced genes by TNF-α was transient and independent of NF-κB. Investigating the underlying basis, we found that Spt5 is required for the splicing facilitation of the noninduced genes. In line with this, Spt5 interacts with Sm core protein splicing factors. Furthermore, following TNF-α treatment, levels of RNA polymerase II (Pol II) but not Spt5 are reduced from the splicing-induced genes, suggesting that these genes become enriched with a Pol II-Spt5 form. Our findings revealed the Pol II-Spt5 complex as a highly competent coordinator of cotranscriptional splicing.
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5
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Zhang Z, Shi L, Dawany N, Kelsen J, Petri MA, Sullivan KE. H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus. Clin Epigenetics 2016; 8:14. [PMID: 26839600 PMCID: PMC4736279 DOI: 10.1186/s13148-016-0179-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/19/2016] [Indexed: 12/13/2022] Open
Abstract
Background The autoimmune disease systemic lupus erythematosus (SLE) has a modified epigenome with modified tri-methylation of histone H3 lysine 4 (H3K4me3) at specific loci across the genome. H3K4me3 is a canonical chromatin mark of active transcription. Recent studies have suggested that H3K4me3 breadth has an important regulatory role in cell identity. This project examined H3K4me3 breadth at transcription start sites (TSS) in primary monocytes and its association with differential gene transcription in SLE. Results Integrative analysis was applied to chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) data generated from primary monocytes as well as genomic data available in public repositories. Four distinctive H3K4me3 patterns of ChIP-seq peaks were identified at 8399 TSSs. Narrow peaks were highly enriched with genes related to housekeeping functions. The broader peaks with extended H3K4me3 immediately upstream and/or downstream of TSS were associated with immune response genes. Many TSSs had downstream H3K4me3 extended to ~650 bp, where the transition of H3K4me3 to H3K36me3, a transcriptional elongation mark, is often found. The H3K4me3 pattern was strongly associated with transcription in SLE. Genes with narrow peaks were less likely (OR = 0.14, p = 2 × 10−4) while genes with extended downstream H3K4me3 were more likely (OR = 2.37, p = 1 × 10−11) to be overexpressed in SLE. Of the genes significantly overexpressed in SLE, 78.8 % had increased downstream H3K4me3 while only 47.1 % had increased upstream H3K4me3. Gene transcription sensitively and consistently responded to H3K4me3 change downstream of TSSs. Every 1 % increase of H3K4me3 in this region leads to ~1.5 % average increase of transcription. Conclusions We identified the immediate TSS downstream nucleosome as a crucial regulator responsible for transcription changes in SLE. This study applied a unique method to study the effect of H3K4me3 breadth on diseases and revealed new insights about epigenetic modifications in SLE, which could lead to novel treatments. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0179-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Lihua Shi
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Noor Dawany
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Judith Kelsen
- Division of Gastroenterology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Michelle A Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA
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6
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Kaypee S, Sudarshan D, Shanmugam MK, Mukherjee D, Sethi G, Kundu TK. Aberrant lysine acetylation in tumorigenesis: Implications in the development of therapeutics. Pharmacol Ther 2016; 162:98-119. [PMID: 26808162 DOI: 10.1016/j.pharmthera.2016.01.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 'language' of covalent histone modifications translates environmental and cellular cues into gene expression. This vast array of post-translational modifications on histones are more than just covalent moieties added onto a protein, as they also form a platform on which crucial cellular signals are relayed. The reversible lysine acetylation has emerged as an important post-translational modification of both histone and non-histone proteins, dictating numerous epigenetic programs within a cell. Thus, understanding the complex biology of lysine acetylation and its regulators is essential for the development of epigenetic therapeutics. In this review, we will attempt to address the complexities of lysine acetylation in the context of tumorigenesis, their role in cancer progression and emphasize on the modalities developed to target lysine acetyltransferases towards cancer treatment.
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Affiliation(s)
- Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Deepthi Sudarshan
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
| | - Debanjan Mukherjee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India.
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7
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Yoshida H, Bansal K, Schaefer U, Chapman T, Rioja I, Proekt I, Anderson MS, Prinjha RK, Tarakhovsky A, Benoist C, Mathis D. Brd4 bridges the transcriptional regulators, Aire and P-TEFb, to promote elongation of peripheral-tissue antigen transcripts in thymic stromal cells. Proc Natl Acad Sci U S A 2015; 112:E4448-57. [PMID: 26216992 PMCID: PMC4538633 DOI: 10.1073/pnas.1512081112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aire controls immunologic tolerance by inducing a battery of thymic transcripts encoding proteins characteristic of peripheral tissues. Its unusually broad effect is achieved by releasing RNA polymerase II paused just downstream of transcriptional start sites. We explored Aire's collaboration with the bromodomain-containing protein, Brd4, uncovering an astonishing correspondence between those genes induced by Aire and those inhibited by a small-molecule bromodomain blocker. Aire:Brd4 binding depended on an orchestrated series of posttranslational modifications within Aire's caspase activation and recruitment domain. This interaction attracted P-TEFb, thereby mobilizing downstream transcriptional elongation and splicing machineries. Aire:Brd4 association was critical for tolerance induction, and its disruption could account for certain point mutations that provoke human autoimmune disease. Our findings evoke the possibility of unanticipated immunologic mechanisms subtending the potent antitumor effects of bromodomain blockers.
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Affiliation(s)
- Hideyuki Yoshida
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Kushagra Bansal
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Uwe Schaefer
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065
| | - Trevor Chapman
- Epinova Discovery Performance Unit, Immuno-Inflammation Therapy Area, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - Inmaculada Rioja
- Epinova Discovery Performance Unit, Immuno-Inflammation Therapy Area, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - Irina Proekt
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, CA 94143
| | - Rab K Prinjha
- Epinova Discovery Performance Unit, Immuno-Inflammation Therapy Area, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
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8
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Human Immunodeficiency Virus Type 1 Tat and Rev as Potential Targets for Drug Development. Antiviral Res 2014. [DOI: 10.1128/9781555815493.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Diamant G, Dikstein R. Transcriptional control by NF-κB: elongation in focus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:937-45. [PMID: 23624258 DOI: 10.1016/j.bbagrm.2013.04.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/15/2013] [Accepted: 04/17/2013] [Indexed: 01/01/2023]
Abstract
The NF-κB family of transcription factors governs the cellular reaction to a variety of extracellular signals. Following stimulation, NF-κB activates genes involved in inflammation, cell survival, cell cycle, immune cell homeostasis and more. This review focuses on studies of the past decade that uncover the transcription elongation process as a key regulatory stage in the activation pathway of NF-κB. Of interest are studies that point to the elongation phase as central to the selectivity of target gene activation by NF-κB. Particularly, the cascade leading to phosphorylation and acetylation of the NF-κB subunit p65 on serine 276 and lysine 310, respectively, was shown to mediate the recruitment of Brd4 and P-TEFb to many pro-inflammatory target genes, which in turn facilitate elongation and mRNA processing. On the other hand, some anti-inflammatory genes are refractory to this pathway and are dependent on the elongation factor DSIF for efficient elongation and mRNA processing. While these studies have advanced our knowledge of NF-κB transcriptional activity, they have also raised unresolved issues regarding the specific genomic and physiological contexts by which NF-κB utilizes different mechanisms for activation.
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Affiliation(s)
- Gil Diamant
- Dept. of Biological Chemistry, The Weizmann Institute of Science, Rehovot , Israel
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10
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Zhu J, Gaiha GD, John SP, Pertel T, Chin CR, Gao G, Qu H, Walker BD, Elledge SJ, Brass AL. Reactivation of latent HIV-1 by inhibition of BRD4. Cell Rep 2012; 2:807-16. [PMID: 23041316 DOI: 10.1016/j.celrep.2012.09.008] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/10/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022] Open
Abstract
HIV-1 depends on many host factors for propagation. Other host factors, however, antagonize HIV-1 and may have profound effects on viral activation. Curing HIV-1 requires the reduction of latent viral reservoirs that remain in the face of antiretroviral therapy. Using orthologous genetic screens, we identified bromodomain containing 4 (BRD4) as a negative regulator of HIV-1 replication. Antagonism of BRD4, via RNA interference or with a small molecule inhibitor, JQ1, both increased proviral transcriptional elongation and alleviated HIV-1 latency in cell-line models. In multiple instances, JQ1, when used in combination with the NF-κB activators Prostratin or PHA, enhanced the in vitro reactivation of latent HIV-1 in primary T cells. These data are consistent with a model wherein BRD4 competes with the virus for HIV-1 dependency factors (HDFs) and suggests that combinatorial therapies that activate HDFs and antagonize HIV-1 competitive factors may be useful for curing HIV-1 infection.
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Affiliation(s)
- Jian Zhu
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
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11
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Protein kinase A regulates molecular chaperone transcription and protein aggregation. PLoS One 2011; 6:e28950. [PMID: 22216146 PMCID: PMC3245242 DOI: 10.1371/journal.pone.0028950] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 11/17/2011] [Indexed: 12/25/2022] Open
Abstract
Heat shock factor 1 (HSF1) regulates one of the major pathways of protein quality control and is essential for deterrence of protein-folding disorders, particularly in neuronal cells. However, HSF1 activity declines with age, a change that may open the door to progression of neurodegenerative disorders such as Huntington's disease. We have investigated mechanisms of HSF1 regulation that may become compromised with age. HSF1 binds stably to the catalytic domain of protein kinase A (PKAcα) and becomes phosphorylated on at least one regulatory serine residue (S320). We show here that PKA is essential for effective transcription of HSP genes by HSF1. PKA triggers a cascade involving HSF1 binding to the histone acetylase p300 and positive translation elongation factor 1 (p-TEFb) and phosphorylation of the c-terminal domain of RNA polymerase II, a key mechanism in the downstream steps of HSF1-mediated transcription. This cascade appears to play a key role in protein quality control in neuronal cells expressing aggregation-prone proteins with long poly-glutamine (poly-Q) tracts. Such proteins formed inclusion bodies that could be resolved by HSF1 activation during heat shock. Resolution of the inclusions was inhibited by knockdown of HSF1, PKAcα, or the pTEFb component CDK9, indicating a key role for the HSF1-PKA cascade in protein quality control.
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12
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Ammosova T, Obukhov Y, Kotelkin A, Breuer D, Beullens M, Gordeuk VR, Bollen M, Nekhai S. Protein phosphatase-1 activates CDK9 by dephosphorylating Ser175. PLoS One 2011; 6:e18985. [PMID: 21533037 PMCID: PMC3080879 DOI: 10.1371/journal.pone.0018985] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 03/24/2011] [Indexed: 11/19/2022] Open
Abstract
The cyclin-dependent kinase CDK9/cyclin T1 induces HIV-1 transcription by phosphorylating the carboxyterminal domain (CTD) of RNA polymerase II (RNAPII). CDK9 activity is regulated by protein phosphatase-1 (PP1) which was previously shown to dephosphorylate CDK9 Thr186. Here, we analyzed the effect of PP1 on RNAPII phosphorylation and CDK9 activity. The selective inhibition of PP1 by okadaic acid and by NIPP1 inhibited phosphorylation of RNAPII CTD in vitro and in vivo. Expression of the central domain of NIPP1 in cultured cells inhibited the enzymatic activity of CDK9 suggesting its activation by PP1. Comparison of dephosphorylation of CDK9 phosphorylated by (32P) in vivo and dephosphorylation of CDK9's Thr186 analyzed by Thr186 phospho-specific antibodies, indicated that a residue other than Thr186 might be dephosphorylated by PP1. Analysis of dephosphorylation of phosphorylated peptides derived from CDK9's T-loop suggested that PP1 dephosphorylates CDK9 Ser175. In cultured cells, CDK9 was found to be phosphorylated on Ser175 as determined by combination of Hunter 2D peptide mapping and LC-MS analysis. CDK9 S175A mutant was active and S175D – inactive, and dephosphorylation of CDK9's Ser175 upregulated HIV-1 transcription in PP1-dependent manner. Collectively, our results point to CDK9 Ser175 as novel PP1-regulatory site which dephosphorylation upregulates CDK9 activity and contribute to the activation of HIV-1 transcription.
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Affiliation(s)
- Tatiana Ammosova
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
- RCMI Proteomics Core Facility, Howard University, Washington, D.C., United States of America
| | - Yuri Obukhov
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
- RCMI Proteomics Core Facility, Howard University, Washington, D.C., United States of America
| | - Alexander Kotelkin
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
| | - Denitra Breuer
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
- Department of Microbiology, Howard University, Washington, D.C., United States of America
| | - Monique Beullens
- Department of Molecular Cell Biology, Catholic University of Leuven, Leuven, Belgium
| | - Victor R. Gordeuk
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
| | - Mathieu Bollen
- Department of Molecular Cell Biology, Catholic University of Leuven, Leuven, Belgium
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
- RCMI Proteomics Core Facility, Howard University, Washington, D.C., United States of America
- Department of Microbiology, Howard University, Washington, D.C., United States of America
- * E-mail:
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13
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Abstract
Regulation of gene expression is essential to all aspects of physiological processes in single-cell as well as multicellular organisms. It gives ultimately cells the ability to efficiently respond to extra- and intracellular stimuli participating in cell cycle, growth, differentiation and survival. Regulation of gene expression is executed primarily at the level of transcription of specific mRNAs by RNA polymerase II (RNAPII), typically in several distinct phases. Among them, transcription elongation is positively regulated by the positive transcription elongation factor b (P-TEFb), consisting of CDK9 and cyclin T1, T2 or K. P-TEFb enables transition from abortive to productive transcription elongation by phosphorylating carboxyl-terminal domain (CTD) in RNAPII and negative transcription elongation factors. Over the years, we have learned a great deal about molecular composition of P-TEFb complexes, their assembly and their role in transcription of specific genes, but function of P-TEFb in other physiological processes was not apparent until just recently. In light of emerging discoveries connecting P-TEFb to regulation of cell cycle, development and several diseases, I would like to discuss these observations as well as future perspectives.
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Affiliation(s)
- Jiri Kohoutek
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic.
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Hargreaves DC, Horng T, Medzhitov R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 2009; 138:129-45. [PMID: 19596240 DOI: 10.1016/j.cell.2009.05.047] [Citation(s) in RCA: 517] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 03/13/2009] [Accepted: 05/19/2009] [Indexed: 11/25/2022]
Abstract
Most inducible transcriptional programs consist of primary and secondary response genes (PRGs and SRGs) that differ in their kinetics of expression and in their requirements for new protein synthesis and chromatin remodeling. Here we show that many PRGs, in contrast to SRGs, have preassembled RNA polymerase II (Pol II) and positive histone modifications at their promoters in the basal state. Pol II at PRGs generates low levels of full-length unspliced transcripts but fails to make mature, protein-coding transcripts in the absence of stimulation. Induction of PRGs is controlled at the level of transcriptional elongation and mRNA processing, through the signal-dependent recruitment of P-TEFb. P-TEFb is in turn recruited by the bromodomain-containing protein Brd4, which detects H4K5/8/12Ac inducibly acquired at PRG promoters. Our findings suggest that the permissive structure of PRGs both stipulates their unique regulation in the basal state by corepressor complexes and enables their rapid induction in multiple cell types.
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Affiliation(s)
- Diana C Hargreaves
- Howard Hughes Medical Institute and Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
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He F, Balling R, Zeng AP. Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives. J Biotechnol 2009; 144:190-203. [PMID: 19631244 DOI: 10.1016/j.jbiotec.2009.07.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 07/13/2009] [Accepted: 07/16/2009] [Indexed: 12/21/2022]
Abstract
Reverse engineering of gene networks aims at revealing the structure of the gene regulation network in a biological system by reasoning backward directly from experimental data. Many methods have recently been proposed for reverse engineering of gene networks by using gene transcript expression data measured by microarray. Whereas the potentials of the methods have been well demonstrated, the assumptions and limitations behind them are often not clearly stated or not well understood. In this review, we first briefly explain the principles of the major methods, identify the assumptions behind them and pinpoint the limitations and possible pitfalls in applying them to real biological questions. With regard to applications, we then discuss challenges in the experimental verification of gene networks generated from reverse engineering methods. We further propose an optimal experimental design for allocating sampling schedule and possible strategies for reducing the limitations of some of the current reverse engineering methods. Finally, we examine the perspectives for the development of reverse engineering and urge the need to move from revealing network structure to the dynamics of biological systems.
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Affiliation(s)
- Feng He
- Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
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