151
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Rice AP. The HIV-1 Tat Protein: Mechanism of Action and Target for HIV-1 Cure Strategies. Curr Pharm Des 2018; 23:4098-4102. [PMID: 28677507 DOI: 10.2174/1381612823666170704130635] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 02/07/2023]
Abstract
The general mechanism involved in Tat activation of RNA Polymerase II (RNAP II) elongation of the integrated HIV-1 was elucidated over 20 years ago. This mechanism involves Tat binding to the TAR RNA element that forms at the 5' end of viral transcripts and recruiting a general RNAP II elongation factor termed as PTEFb. This elongation factor consists of CDK9 and Cyclin T1, and when recruited by Tat to TAR RNA, CDK9 was proposed to phosphorylate the carboxyl terminal domain of RNAP II and thereby activate elongation. Research in the past two decades has shown that the mechanism of Tat action is considerably more complicated than this simple model. In metabolically active cells, CDK9 and Cyclin T1 are now known to be largely sequestered in a RNA-protein complex termed the 7SK RNP. CDK9 and Cyclin T1 are released from the 7SK RNP by mechanisms not yet fully elucidated and along with Tat, bind to TAR RNA and orchestrate the assembly of a Super Elongation Complex (SEC) containing several additional proteins. CDK9 in the SEC then phosphorylates multiple substrates in the RNAP II complex to activate elongation. Importantly for therapeutic strategies, CDK9 and Cyclin T1 functions are down-regulated in resting CD4+ T cells that harbor latent HIV-1, and their up-regulation is required for reactivation of latent virus. Current strategies for a functional cure of HIV-1 infection therefore are likely to require development of latency reversal agents that up-regulate CDK9 and Cyclin T1 function in resting CD4+ T cells.
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Affiliation(s)
- Andrew P Rice
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030. United States
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152
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Abstract
BACKGROUND The viral transactivator Tat protein is a key modulator of HIV-1 replication, as it regulates transcriptional elongation from the integrated proviral genome. Tat recruits the human transcription elongation factor b, and other host proteins, such as the super elongation complex, to activate the cellular RNA polymerase II, normally stalled shortly after transcription initiation at the HIV promoter. By means of a complex set of interactions with host cellular factors, Tat determines the fate of viral activity within the infected cell. The virus will either actively replicate to promote dissemination in blood and tissues, or become dormant mostly in memory CD4+ T cells, as part of a small but long-living latent reservoir, the main obstacle for HIV eradication. OBJECTIVE In this review, we summarize recent advances in the understanding of the multi-step mechanism that regulates Tat-mediated HIV-1 transcription and RNA polymerase II release, to promote viral transcription elongation. Early events of the human transcription elongation factor b release from the inhibitory 7SK small nuclear ribonucleoprotein complex and its recruitment to the HIV promoter will be discussed. Specific roles of the super elongation complex subunits during transcription elongation, and insight on recently identified cellular factors and mechanisms regulating HIV latency will be detailed. CONCLUSION Understanding the complexity of HIV transcriptional regulation by host factors may open the door for development of novel strategies to eradicate the resilient latent reservoir.
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Affiliation(s)
- Guillaume Mousseau
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
| | - Susana T Valente
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
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153
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Connelly KE, Hedrick V, Paschoal Sobreira TJ, Dykhuizen EC, Aryal UK. Analysis of Human Nuclear Protein Complexes by Quantitative Mass Spectrometry Profiling. Proteomics 2018; 18:e1700427. [PMID: 29655301 DOI: 10.1002/pmic.201700427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/07/2018] [Indexed: 12/23/2022]
Abstract
Analysis of protein complexes provides insights into how the ensemble of expressed proteome is organized into functional units. While there have been advances in techniques for proteome-wide profiling of cytoplasmic protein complexes, information about human nuclear protein complexes are very limited. To close this gap, we combined native size exclusion chromatography (SEC) with label-free quantitative MS profiling to characterize hundreds of nuclear protein complexes isolated from human glioblastoma multiforme T98G cells. We identified 1794 proteins that overlapped between two biological replicates of which 1244 proteins were characterized as existing within stably associated putative complexes. co-IP experiments confirmed the interaction of PARP1 with Ku70/Ku80 proteins and HDAC1 (histone deacetylase complex 1) and CHD4. HDAC1/2 also co-migrated with various SIN3A and nucleosome remodeling and deacetylase components in SEC fractionation including SIN3A, SAP30, RBBP4, RBBP7, and NCOR1. Co-elution of HDAC1/2/3 with both the KDM1A and RCOR1 further confirmed that these proteins are integral components of human deacetylase complexes. Our approach also demonstrated the ability to identify potential moonlighting complexes and novel complexes containing uncharacterized proteins. Overall, the results demonstrated the utility of SEC fractionation and LC-MS analysis for system-wide profiling of proteins to predict the existence of distinct forms of nuclear protein complexes.
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Affiliation(s)
- Katelyn E Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University Street, 47907, West Lafayette, IN, USA
| | - Victoria Hedrick
- Purdue Proteomics Facility, Bindley Biosciences Center, Discovery Park, Purdue University, 1203 W. State Street, 47907, West Lafayette, IN, USA
| | - Tiago Jose Paschoal Sobreira
- Purdue Proteomics Facility, Bindley Biosciences Center, Discovery Park, Purdue University, 1203 W. State Street, 47907, West Lafayette, IN, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University Street, 47907, West Lafayette, IN, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Biosciences Center, Discovery Park, Purdue University, 1203 W. State Street, 47907, West Lafayette, IN, USA
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154
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Abstract
As obligate intracellular parasites, viruses are dependent on their infected hosts for survival. Consequently, viruses are under enormous selective pressure to utilize available cellular components and processes to their own advantage. As most, if not all, cellular activities are regulated at some level via protein interactions, host protein interaction networks are particularly vulnerable to viral exploitation. Indeed, viral proteins frequently target highly connected “hub” proteins to “hack” the cellular network, defining the molecular basis for viral control over the host. This widespread and successful strategy of network intrusion and exploitation has evolved convergently among numerous genetically distinct viruses as a result of the endless evolutionary arms race between pathogens and hosts. Here we examine the means by which a particularly well-connected viral hub protein, human adenovirus E1A, compromises and exploits the vulnerabilities of eukaryotic protein interaction networks. Importantly, these interactions identify critical regulatory hubs in the human proteome and help define the molecular basis of their function.
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155
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Chen Y, Zhang B, Bao L, Jin L, Yang M, Peng Y, Kumar A, Wang JE, Wang C, Zou X, Xing C, Wang Y, Luo W. ZMYND8 acetylation mediates HIF-dependent breast cancer progression and metastasis. J Clin Invest 2018; 128:1937-1955. [PMID: 29629903 PMCID: PMC5919820 DOI: 10.1172/jci95089] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 02/27/2018] [Indexed: 12/21/2022] Open
Abstract
Altered epigenetic reprogramming contributes to breast cancer progression and metastasis. How the epigenetic reader mediates breast cancer progression remains poorly understood. Here, we showed that the epigenetic reader zinc finger MYND-type containing 8 (ZMYND8) is induced by HIF-1 and HIF-2 in breast cancer cells and also upregulated in human breast tumors, and is correlated with poor survival of patients with breast cancer. Genetic deletion of ZMYND8 decreases breast cancer cell colony formation, migration, and invasion in vitro, and inhibits breast tumor growth and metastasis to the lungs in mice. The ZMYND8's oncogenic effect in breast cancer requires HIF-1 and HIF-2. We further showed that ZMYND8 interacts with HIF-1α and HIF-2α and enhances elongation of the global HIF-induced oncogenic genes by increasing recruitment of BRD4 and subsequent release of paused RNA polymerase II in breast cancer cells. ZMYND8 acetylation at lysines 1007 and 1034 by p300 is required for HIF activation and breast cancer progression and metastasis. These findings uncover a primary epigenetic mechanism of HIF activation and HIF-mediated breast cancer progression, and discover a possible molecular target for the diagnosis and treatment of breast cancer.
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Affiliation(s)
| | | | | | | | | | | | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development
| | | | | | | | - Chao Xing
- Eugene McDermott Center for Human Growth and Development
- Department of Bioinformatics
- Department of Clinical Sciences
| | - Yingfei Wang
- Department of Pathology
- Department of Neurology and Neurotherapeutics, and
| | - Weibo Luo
- Department of Pathology
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
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156
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Ali M, Ajore R, Wihlborg AK, Niroula A, Swaminathan B, Johnsson E, Stephens OW, Morgan G, Meissner T, Turesson I, Goldschmidt H, Mellqvist UH, Gullberg U, Hansson M, Hemminki K, Nahi H, Waage A, Weinhold N, Nilsson B. The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression. Nat Commun 2018; 9:1649. [PMID: 29695719 PMCID: PMC5917026 DOI: 10.1038/s41467-018-04082-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 03/26/2018] [Indexed: 02/06/2023] Open
Abstract
Recently, we identified ELL2 as a susceptibility gene for multiple myeloma (MM). To understand its mechanism of action, we performed expression quantitative trait locus analysis in CD138+ plasma cells from 1630 MM patients from four populations. We show that the MM risk allele lowers ELL2 expression in these cells (Pcombined = 2.5 × 10−27; βcombined = −0.24 SD), but not in peripheral blood or other tissues. Consistent with this, several variants representing the MM risk allele map to regulatory genomic regions, and three yield reduced transcriptional activity in plasmocytoma cell lines. One of these (rs3777189-C) co-locates with the best-supported lead variants for ELL2 expression and MM risk, and reduces binding of MAFF/G/K family transcription factors. Moreover, further analysis reveals that the MM risk allele associates with upregulation of gene sets related to ribosome biogenesis, and knockout/knockdown and rescue experiments in plasmocytoma cell lines support a cause–effect relationship. Our results provide mechanistic insight into MM predisposition. ELL2 was recently discovered as a susceptibility gene for multiple myeloma (MM). Here, they show that the MM risk allele lowers ELL2 expression in plasma cells, that it also upregulates gene sets related to ribosome biogenesis, and that one of the linked variants reduces binding of MAFF/G/K family transcription factors.
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Affiliation(s)
- Mina Ali
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Ram Ajore
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Anna-Karin Wihlborg
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Abhishek Niroula
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Bhairavi Swaminathan
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Ellinor Johnsson
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Owen W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Gareth Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Tobias Meissner
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD, 57105, USA
| | - Ingemar Turesson
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany.,National Center for Tumor Diseases, Ulm, 69120, Heidelberg, Germany
| | | | - Urban Gullberg
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Markus Hansson
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden.,Hematology Clinic, Skåne University Hospital, SE 221 85, Lund, Sweden
| | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, SE 205 02, Malmö, Sweden
| | - Hareth Nahi
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, SE 171 77, Stockholm, Sweden
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Björn Nilsson
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden. .,Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA.
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157
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Yu F, Shi G, Cheng S, Chen J, Wu SY, Wang Z, Xia N, Zhai Y, Wang Z, Peng Y, Wang D, Du JX, Liao L, Duan SZ, Shi T, Cheng J, Chiang CM, Li J, Wong J. SUMO suppresses and MYC amplifies transcription globally by regulating CDK9 sumoylation. Cell Res 2018; 28:670-685. [PMID: 29588524 DOI: 10.1038/s41422-018-0023-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/28/2018] [Accepted: 02/11/2018] [Indexed: 01/21/2023] Open
Abstract
Regulation of transcription is fundamental to the control of cellular gene expression and function. Although recent studies have revealed a role for the oncoprotein MYC in amplifying global transcription, little is known as to how the global transcription is suppressed. Here we report that SUMO and MYC mediate opposite effects upon global transcription by controlling the level of CDK9 sumoylation. On one hand, SUMO suppresses global transcription via sumoylation of CDK9, the catalytic subunit of P-TEFb kinase essential for productive transcriptional elongation. On the other hand, MYC amplifies global transcription by antagonizing CDK9 sumoylation. Sumoylation of CDK9 blocks its interaction with Cyclin T1 and thus the formation of active P-TEFb complex. Transcription profiling analyses reveal that SUMO represses global transcription, particularly of moderately to highly expressed genes and by generating a sumoylation-resistant CDK9 mutant, we confirm that sumoylation of CDK9 inhibits global transcription. Together, our data reveal that SUMO and MYC oppositely control global gene expression by regulating the dynamic sumoylation and desumoylation of CDK9.
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Affiliation(s)
- Fang Yu
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Guang Shi
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Gene Engineering of the Ministry of Education and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shimeng Cheng
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiwei Chen
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Shwu-Yuan Wu
- Simmons Comprehensive Cancer Center, Department of Biochemistry, and Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Zhiqiang Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Nansong Xia
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yunhao Zhai
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Zhenxing Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yu Peng
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dong Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - James X Du
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Sheng-Zhong Duan
- Laboratory of Oral Microbiology, Shanghai Research Institute of Stomatology, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital, School of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Tieliu Shi
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jinke Cheng
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Biochemistry, and Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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158
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Fitz J, Neumann T, Pavri R. Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation. EMBO J 2018. [PMID: 29514850 PMCID: PMC5897773 DOI: 10.15252/embj.201797965] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Spt5 is a highly conserved RNA polymerase II (Pol II)‐associated pausing and elongation factor. However, its impact on global elongation and Pol II processivity in mammalian cells has not been clarified. Here, we show that depleting Spt5 in mouse embryonic fibroblasts (MEFs) does not cause global elongation defects or decreased elongation rates. Instead, in Spt5‐depleted cells, a fraction of Pol II molecules are dislodged during elongation, thus decreasing the number of Pol II complexes that complete the transcription cycle. Most strikingly, this decrease is restricted to a narrow window between 15 and 20 kb from the promoter, a distance which coincides with the stage where accelerating Pol II attains maximum elongation speed. Consequently, long genes show a greater dependency on Spt5 for optimal elongation efficiency and overall gene expression than short genes. We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning toward maximum elongation speed 15–20 kb from the promoter.
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Affiliation(s)
- Johanna Fitz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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159
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018; 7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation.
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160
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Huang M, Garcia JS, Thomas D, Zhu L, Nguyen LXT, Chan SM, Majeti R, Medeiros BC, Mitchell BS. Autophagy mediates proteolysis of NPM1 and HEXIM1 and sensitivity to BET inhibition in AML cells. Oncotarget 2018; 7:74917-74930. [PMID: 27732946 PMCID: PMC5342712 DOI: 10.18632/oncotarget.12493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022] Open
Abstract
The mechanisms underlying activation of the BET pathway in AML cells remain poorly understood. We have discovered that autophagy is activated in acute leukemia cells expressing mutant nucleophosmin 1 (NPMc+) or MLL-fusion proteins. Autophagy activation results in the degradation of NPM1 and HEXIM1, two negative regulators of BET pathway activation. Inhibition of autophagy with pharmacologic inhibitors or through knocking down autophagy-related gene 5 (Atg5) expression increases the expression of both NPM1 and HEXIM1. The Brd4 inhibitors JQ1 and I-BET-151 also inhibit autophagy and increase NPM1 and HEXIM1 expression. We conclude that the degradation of NPM1 and HEXIM1 through autophagy in certain AML subsets contributes to the activation of the BET pathway in these cells.
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Affiliation(s)
- Min Huang
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Jacqueline S Garcia
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Daniel Thomas
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
| | - Li Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Steven M Chan
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
| | - Ravindra Majeti
- Stanford Cancer Institute, Stanford University, Stanford, California, USA.,Division of Hematology, Department of Medicine, Stanford University, Stanford, California, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
| | - Bruno C Medeiros
- Stanford Cancer Institute, Stanford University, Stanford, California, USA.,Division of Hematology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Beverly S Mitchell
- Stanford Cancer Institute, Stanford University, Stanford, California, USA.,Division of Hematology, Department of Medicine, Stanford University, Stanford, California, USA
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161
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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162
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Phuyal S, Kasem M, Knittelfelder O, Sharma A, Fonseca DDM, Vebraite V, Shaposhnikov S, Slupphaug G, Skaug V, Zienolddiny S. Characterization of the proteome and lipidome profiles of human lung cells after low dose and chronic exposure to multiwalled carbon nanotubes. Nanotoxicology 2018; 12:138-152. [PMID: 29350075 DOI: 10.1080/17435390.2018.1425500] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The effects of long-term chronic exposure of human lung cells to multi-walled carbon nanotubes (MWCNT) and their impact upon cellular proteins and lipids were investigated. Since the lung is the major target organ, an in vitro normal bronchial epithelial cell line model was used. Additionally, to better mimic exposure to manufactured nanomaterials at occupational settings, cells were continuously exposed to two non-toxic and low doses of a MWCNT for 13-weeks. MWCNT-treatment increased ROS levels in cells without increasing oxidative DNA damage and resulted in differential expression of multiple anti- and pro-apoptotic proteins. The proteomic analysis of the MWCNT-exposed cells showed that among more than 5000 identified proteins; more than 200 were differentially expressed in the treated cells. Functional analyses revealed association of these differentially regulated proteins to cellular processes such as cell death and survival, cellular assembly, and organization. Similarly, shotgun lipidomic profiling revealed accumulation of multiple lipid classes. Our results indicate that long-term MWCNT-exposure of human normal lung cells at occupationally relevant low-doses may alter both the proteome and the lipidome profiles of the target epithelial cells in the lung.
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Affiliation(s)
- Santosh Phuyal
- a Department of Chemical and Biological Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Mayes Kasem
- a Department of Chemical and Biological Work Environment , National Institute of Occupational Health , Oslo , Norway
| | | | - Animesh Sharma
- c Department of Clinical and Molecular Medicine , Norwegian University of Science and Technology , Trondheim , Norway.,d Proteomics and Metabolomics Core Facility (PROMEC) , NTNU and the Central Norway Regional Health Authority , Trondheim , Norway
| | - Davi de Miranda Fonseca
- c Department of Clinical and Molecular Medicine , Norwegian University of Science and Technology , Trondheim , Norway.,d Proteomics and Metabolomics Core Facility (PROMEC) , NTNU and the Central Norway Regional Health Authority , Trondheim , Norway
| | | | | | - Geir Slupphaug
- c Department of Clinical and Molecular Medicine , Norwegian University of Science and Technology , Trondheim , Norway.,d Proteomics and Metabolomics Core Facility (PROMEC) , NTNU and the Central Norway Regional Health Authority , Trondheim , Norway
| | - Vidar Skaug
- a Department of Chemical and Biological Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Shanbeh Zienolddiny
- a Department of Chemical and Biological Work Environment , National Institute of Occupational Health , Oslo , Norway
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163
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Scruggs BS, Adelman K. The Importance of Controlling Transcription Elongation at Coding and Noncoding RNA Loci. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 80:33-44. [PMID: 27325707 DOI: 10.1101/sqb.2015.80.027235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Here we discuss current paradigms for how transcription initiation and elongation control are achieved in mammalian cells, and how they differ at protein-coding mRNA genes versus noncoding RNA (ncRNA) loci. We present a model for the function of ncRNAs wherein the act of transcription is regulatory, rather than the ncRNA products themselves. We further describe how the establishment of transcriptionally engaged, but paused, RNA polymerase II impacts chromatin structure around divergent transcription start sites, and how this can influence transcription factor binding and mRNA gene activity in the region.
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Affiliation(s)
- Benjamin S Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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164
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Li Y, Liu M, Chen LF, Chen R. P-TEFb: Finding its ways to release promoter-proximally paused RNA polymerase II. Transcription 2018; 9:88-94. [PMID: 28102758 PMCID: PMC5834220 DOI: 10.1080/21541264.2017.1281864] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/09/2017] [Accepted: 01/09/2017] [Indexed: 12/26/2022] Open
Abstract
The release of a paused Pol II depends on the recruitment of P-TEFb. Recent studies showed that both active P-TEFb and inactive P-TEFb (7SK snRNP) can be recruited to the promoter regions of global genes by different mechanisms. Here, we summarize the recent advances on these distinct recruitment mechanisms.
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Affiliation(s)
- You Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lin-Feng Chen
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ruichuan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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165
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Wu YH, Graff RE, Passarelli MN, Hoffman JD, Ziv E, Hoffmann TJ, Witte JS. Identification of Pleiotropic Cancer Susceptibility Variants from Genome-Wide Association Studies Reveals Functional Characteristics. Cancer Epidemiol Biomarkers Prev 2018; 27:75-85. [PMID: 29150481 PMCID: PMC5760292 DOI: 10.1158/1055-9965.epi-17-0516] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/05/2017] [Accepted: 10/17/2017] [Indexed: 12/17/2022] Open
Abstract
Background: There exists compelling evidence that some genetic variants are associated with the risk of multiple cancer sites (i.e., pleiotropy). However, the biological mechanisms through which the pleiotropic variants operate are unclear.Methods: We obtained all cancer risk associations from the National Human Genome Research Institute-European Bioinformatics Institute GWAS Catalog, and correlated cancer risk variants were clustered into groups. Pleiotropic variant groups and genes were functionally annotated. Associations of pleiotropic cancer risk variants with noncancer traits were also obtained.Results: We identified 1,431 associations between variants and cancer risk, comprised of 989 unique variants associated with 27 unique cancer sites. We found 20 pleiotropic variant groups (2.1%) composed of 33 variants (3.3%), including novel pleiotropic variants rs3777204 and rs56219066 located in the ELL2 gene. Relative to single-cancer risk variants, pleiotropic variants were more likely to be in genes (89.0% vs. 65.3%, P = 2.2 × 10-16), and to have somewhat larger risk allele frequencies (median RAF = 0.49 versus 0.39, P = 0.046). The 27 genes to which the pleiotropic variants mapped were suggestive for enrichment in response to radiation and hypoxia, alpha-linolenic acid metabolism, cell cycle, and extension of telomeres. In addition, we observed that 8 of 33 pleiotropic cancer risk variants were associated with 16 traits other than cancer.Conclusions: This study identified and functionally characterized genetic variants showing pleiotropy for cancer risk.Impact: Our findings suggest biological pathways common to different cancers and other diseases, and provide a basis for the study of genetic testing for multiple cancers and repurposing cancer treatments. Cancer Epidemiol Biomarkers Prev; 27(1); 75-85. ©2017 AACR.
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Affiliation(s)
- Yi-Hsuan Wu
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Michael N Passarelli
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Elad Ziv
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Division of General Internal Medicine, Department of Medicine, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
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166
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Erwin GS, Grieshop MP, Ali A, Qi J, Lawlor M, Kumar D, Ahmad I, McNally A, Teider N, Worringer K, Sivasankaran R, Syed DN, Eguchi A, Ashraf M, Jeffery J, Xu M, Park PMC, Mukhtar H, Srivastava AK, Faruq M, Bradner JE, Ansari AZ. Synthetic transcription elongation factors license transcription across repressive chromatin. Science 2017; 358:1617-1622. [PMID: 29192133 PMCID: PMC6037176 DOI: 10.1126/science.aan6414] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022]
Abstract
The release of paused RNA polymerase II into productive elongation is highly regulated, especially at genes that affect human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators. Here we present Syn-TEF1, a molecule that actively enables transcription across repressive GAA repeats that silence frataxin expression in Friedreich's ataxia, a terminal neurodegenerative disease with no effective therapy. The modular design of Syn-TEF1 defines a general framework for developing a class of molecules that license transcription elongation at targeted genomic loci.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew P Grieshop
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asfa Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepak Kumar
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Istaq Ahmad
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Anna McNally
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Natalia Teider
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Katie Worringer
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Deeba N Syed
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asuka Eguchi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Md Ashraf
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Justin Jeffery
- Small Animal Imaging Facility, University of Wisconsin Carbone Cancer Center, Madison, WI 53792, USA
| | - Mousheng Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hasan Mukhtar
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
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167
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Ljungman M, Parks L, Hulbatte R, Bedi K. The role of H3K79 methylation in transcription and the DNA damage response. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 780:48-54. [PMID: 31395348 DOI: 10.1016/j.mrrev.2017.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/19/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022]
Abstract
Chromatin plays a critical role in organizing and protecting DNA. However, chromatin acts as an impediment for transcription and DNA repair. Histone modifications, such as H3K79 methylation, promote transcription and genomic stability by enhancing transcription elongation and by serving as landing sites for proteins involved in the DNA damage response. This review summarizes the current understanding of the role of H3K79 methylation in transcription, how it affects genome stability and opportunities to develop impactful therapeutic interventions for cancer.
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Affiliation(s)
- Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States.
| | - Luke Parks
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States; Department of Cell and Molecular Biology, Uppsala University, Box 256, 75105 Uppsala, Sweden
| | - Radhika Hulbatte
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
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168
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Helmlinger D, Tora L. Sharing the SAGA. Trends Biochem Sci 2017; 42:850-861. [PMID: 28964624 PMCID: PMC5660625 DOI: 10.1016/j.tibs.2017.09.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
Transcription initiation is a major regulatory step in eukaryotic gene expression. Co-activators establish transcriptionally competent promoter architectures and chromatin signatures to allow the formation of the pre-initiation complex (PIC), comprising RNA polymerase II (Pol II) and general transcription factors (GTFs). Many GTFs and co-activators are multisubunit complexes, in which individual components are organized into functional modules carrying specific activities. Recent advances in affinity purification and mass spectrometry analyses have revealed that these complexes often share functional modules, rather than containing unique components. This observation appears remarkably prevalent for chromatin-modifying and remodeling complexes. Here, we use the modular organization of the evolutionary conserved Spt-Ada-Gcn5 acetyltransferase (SAGA) complex as a paradigm to illustrate how co-activators share and combine a relatively limited set of functional tools.
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Affiliation(s)
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
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169
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Mi W, Guan H, Lyu J, Zhao D, Xi Y, Jiang S, Andrews FH, Wang X, Gagea M, Wen H, Tora L, Dent SYR, Kutateladze TG, Li W, Li H, Shi X. YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. Nat Commun 2017; 8:1088. [PMID: 29057918 PMCID: PMC5651844 DOI: 10.1038/s41467-017-01173-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 08/24/2017] [Indexed: 12/17/2022] Open
Abstract
Recognition of modified histones by “reader” proteins constitutes a key mechanism regulating diverse chromatin-associated processes important for normal and neoplastic development. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. Here, we show that the YEATS2 gene is highly amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell growth and survival. YEATS2 binds to acetylated histone H3 via its YEATS domain. The YEATS2-containing ATAC complex co-localizes with H3K27 acetylation (H3K27ac) on the promoters of actively transcribed genes. Depletion of YEATS2 or disruption of the interaction between its YEATS domain and acetylated histones reduces the ATAC complex-dependent promoter H3K9ac levels and deactivates the expression of essential genes. Taken together, our study identifies YEATS2 as a histone H3K27ac reader that regulates a transcriptional program essential for NSCLC tumorigenesis. Histone modification recognition is an important mechanism for gene expression regulation in cancer. Here, the authors identify YEATS2 as a histone H3K27ac reader, regulating a transcriptional program essential for tumorigenesis in human non-small cell lung cancer.
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Affiliation(s)
- Wenyi Mi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Haipeng Guan
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jie Lyu
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dan Zhao
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuanxin Xi
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shiming Jiang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Xiaolu Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mihai Gagea
- Department of Veterinary Medicine & Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hong Wen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Genes and Development and Epigenetics & Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Wei Li
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,Genes and Development and Epigenetics & Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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170
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Abstract
PURPOSE OF REVIEW HOXA9 is a homeodomain transcription factor that plays an essential role in normal hematopoiesis and acute leukemia, in which its overexpression is strongly correlated with poor prognosis. The present review highlights recent advances in the understanding of genetic alterations leading to deregulation of HOXA9 and the downstream mechanisms of HOXA9-mediated transformation. RECENT FINDINGS A variety of genetic alterations including MLL translocations, NUP98-fusions, NPM1 mutations, CDX deregulation, and MOZ-fusions lead to high-level HOXA9 expression in acute leukemias. The mechanisms resulting in HOXA9 overexpression are beginning to be defined and represent attractive therapeutic targets. Small molecules targeting MLL-fusion protein complex members, such as DOT1L and menin, have shown promising results in animal models, and a DOT1L inhibitor is currently being tested in clinical trials. Essential HOXA9 cofactors and collaborators are also being identified, including transcription factors PU.1 and C/EBPα, which are required for HOXA9-driven leukemia. HOXA9 targets including IGF1, CDX4, INK4A/INK4B/ARF, mir-21, and mir-196b and many others provide another avenue for potential drug development. SUMMARY HOXA9 deregulation underlies a large subset of aggressive acute leukemias. Understanding the mechanisms regulating the expression and activity of HOXA9, along with its critical downstream targets, shows promise for the development of more selective and effective leukemia therapies.
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171
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Wang AH, Juan AH, Ko KD, Tsai PF, Zare H, Dell'Orso S, Sartorelli V. The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins. Mol Cell 2017; 68:398-413.e6. [PMID: 29033324 DOI: 10.1016/j.molcel.2017.09.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/23/2017] [Accepted: 09/12/2017] [Indexed: 01/07/2023]
Abstract
Spt6 coordinates nucleosome dis- and re-assembly, transcriptional elongation, and mRNA processing. Here, we report that depleting Spt6 in embryonic stem cells (ESCs) reduced expression of pluripotency factors, increased expression of cell-lineage-affiliated developmental regulators, and induced cell morphological and biochemical changes indicative of ESC differentiation. Selective downregulation of pluripotency factors upon Spt6 depletion may be mechanistically explained by its enrichment at ESC super-enhancers, where Spt6 controls histone H3K27 acetylation and methylation and super-enhancer RNA transcription. In ESCs, Spt6 interacted with the PRC2 core subunit Suz12 and prevented H3K27me3 accumulation at ESC super-enhancers and associated promoters. Biochemical as well as functional experiments revealed that Spt6 could compete for binding of the PRC2 methyltransferase Ezh2 to Suz12 and reduce PRC2 chromatin engagement. Thus, in addition to serving as a histone chaperone and transcription elongation factor, Spt6 counteracts repression by opposing H3K27me3 deposition at critical genomic regulatory regions.
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Affiliation(s)
- A Hongjun Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Aster H Juan
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Pei-Fang Tsai
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Hossein Zare
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Stefania Dell'Orso
- High-Throughput Sequencing Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA.
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172
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Franco LC, Morales F, Boffo S, Giordano A. CDK9: A key player in cancer and other diseases. J Cell Biochem 2017; 119:1273-1284. [PMID: 28722178 DOI: 10.1002/jcb.26293] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023]
Abstract
Cyclin-Dependent Kinase 9 (CDK9) is part of a functional diverse group of enzymes responsible for cell cycle control and progression. It associates mainly with Cyclin T1 and forms the Positive Transcription Elongation Factor b (p-TEFb) complex responsible for regulation of transcription elongation and mRNA maturation. Recent studies have highlighted the importance of CDK9 in many relevant pathologic processes, like cancer, cardiovascular diseases, and viral replication. Herein we provide an overview of the different pathways in which CDK9 is directly and indirectly involved.
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Affiliation(s)
- Lia Carolina Franco
- Escuela de Medicina, Universidad de las Americas (UDLA), Quito, Ecuador.,Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, College of Science and Technology, Temple University, PA, Pennsylvania
| | - Fátima Morales
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, College of Science and Technology, Temple University, PA, Pennsylvania.,Departamento de Química Orgánica, Universidad de Murcia, Murcia, Spain
| | - Silvia Boffo
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, College of Science and Technology, Temple University, PA, Pennsylvania
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, College of Science and Technology, Temple University, PA, Pennsylvania.,Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
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173
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Wang Y, Shen Y, Dai Q, Yang Q, Zhang Y, Wang X, Xie W, Luo Z, Lin C. A permissive chromatin state regulated by ZFP281-AFF3 in controlling the imprinted Meg3 polycistron. Nucleic Acids Res 2017; 45:1177-1185. [PMID: 28180295 PMCID: PMC5388394 DOI: 10.1093/nar/gkw1051] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 12/15/2022] Open
Abstract
Genomic imprinting is an epigenetic regulation that leads to gene expression in a parent-of-origin specific manner. AFF3, the central component of the Super Elongation Complex-like 3 (SEC-L3), is enriched at both the intergenic-differentially methylated region (IG-DMR) and the Meg3 enhancer within the imprinted Dlk1-Dio3 locus to regulate the allele-specific gene expression in this locus. The localization of AFF3 to IG-DMR requires ZFP57. However, how AFF3 functions at the Meg3 enhancer in maintaining allele-specific gene expression remains unclear. Here, we demonstrate that AFF3 is associated with the Krüppel-like zinc finger protein ZFP281 in mouse embryonic stem (ES) cells. ZFP281 recruits AFF3 to the Meg3 enhancer within the imprinted Dlk1-Dio3 locus, thus regulating the allele-specific expression of the Meg3 polycistron. Our genome-wide analyses further identify ZFP281 as a critical factor generally associating with AFF3 at enhancers and functioning together with AFF3 in regulating the expression of a subset of genes. Our study suggests that different zinc finger proteins can recruit AFF3 to different regulatory elements and differentially regulate the function of AFF3 in a context-dependent manner.
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Affiliation(s)
- Yan Wang
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Yang Shen
- Bioinformatics Core, A*STAR Genome Institute of Singapore, 60 Biopolis Street, Singapore
| | - Qian Dai
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Qian Yang
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Yue Zhang
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Xin Wang
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Wei Xie
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Zhuojuan Luo
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Chengqi Lin
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
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174
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Transcriptional Elongation Control of Hepatitis B Virus Covalently Closed Circular DNA Transcription by Super Elongation Complex and BRD4. Mol Cell Biol 2017; 37:MCB.00040-17. [PMID: 28694331 DOI: 10.1128/mcb.00040-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/28/2017] [Indexed: 12/13/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection can lead to liver cirrhosis and hepatocellular carcinoma. HBV reactivation during or after chemotherapy is a potentially fatal complication for cancer patients with chronic HBV infection. Transcription of HBV is a critical intermediate step of the HBV life cycle. However, factors controlling HBV transcription remain largely unknown. Here, we found that different P-TEFb complexes are involved in the transcription of the HBV viral genome. Both BRD4 and the super elongation complex (SEC) bind to the HBV genome. The treatment of bromodomain inhibitor JQ1 stimulates HBV transcription and increases the occupancy of BRD4 on the HBV genome, suggesting the bromodomain-independent recruitment of BRD4 to the HBV genome. JQ1 also leads to the increased binding of SEC to the HBV genome, and SEC is required for JQ1-induced HBV transcription. These findings reveal a novel mechanism by which the HBV genome hijacks the host P-TEFb-containing complexes to promote its own transcription. Our findings also point out an important clinical implication, that is, the potential risk of HBV reactivation during therapy with a BRD4 inhibitor, such as JQ1 or its analogues, which are a potential treatment for acute myeloid leukemia.
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175
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VEGF amplifies transcription through ETS1 acetylation to enable angiogenesis. Nat Commun 2017; 8:383. [PMID: 28851877 PMCID: PMC5575285 DOI: 10.1038/s41467-017-00405-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 06/22/2017] [Indexed: 12/21/2022] Open
Abstract
Release of promoter-proximally paused RNA polymerase II (RNAPII) is a recently recognized transcriptional regulatory checkpoint. The biological roles of RNAPII pause release and the mechanisms by which extracellular signals control it are incompletely understood. Here we show that VEGF stimulates RNAPII pause release by stimulating acetylation of ETS1, a master endothelial cell transcriptional regulator. In endothelial cells, ETS1 binds transcribed gene promoters and stimulates their expression by broadly increasing RNAPII pause release. 34VEGF enhances ETS1 chromatin occupancy and increases ETS1 acetylation, enhancing its binding to BRD4, which recruits the pause release machinery and increases RNAPII pause release. Endothelial cell angiogenic responses in vitro and in vivo require ETS1-mediated transduction of VEGF signaling to release paused RNAPII. Our results define an angiogenic pathway in which VEGF enhances ETS1–BRD4 interaction to broadly promote RNAPII pause release and drive angiogenesis. Promoter proximal RNAPII pausing is a rate-limiting transcriptional mechanism. Chen et al. show that this process is essential in angiogenesis by demonstrating that the endothelial master transcription factor ETS1 promotes global RNAPII pause release, and that this process is governed by VEGF.
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176
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Abstract
Stem cells self-renew and produce progenitors with limited proliferative potential. Reporting in Developmental Cell, Liu et al. (2017) demonstrate that in some neural stem cells, Notch activity is asymmetrically amplified by a positive feedback loop with the super elongation complex (SEC) to quickly differentiate between stem cells and progenitors.
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Affiliation(s)
- Anthony M Rossi
- Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003, USA
| | - Claude Desplan
- Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003, USA.
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177
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Liu K, Shen D, Shen J, Gao SM, Li B, Wong C, Feng W, Song Y. The Super Elongation Complex Drives Neural Stem Cell Fate Commitment. Dev Cell 2017; 40:537-551.e6. [PMID: 28350987 DOI: 10.1016/j.devcel.2017.02.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/13/2017] [Accepted: 02/26/2017] [Indexed: 10/19/2022]
Abstract
Asymmetric stem cell division establishes an initial difference between a stem cell and its differentiating sibling, critical for maintaining homeostasis and preventing carcinogenesis. Yet the mechanisms that consolidate and lock in such initial fate bias remain obscure. Here, we use Drosophila neuroblasts to demonstrate that the super elongation complex (SEC) acts as an intrinsic amplifier to drive cell fate commitment. SEC is highly expressed in neuroblasts, where it promotes self-renewal by physically associating with Notch transcription activation complex and enhancing HES (hairy and E(spl)) transcription. HES in turn upregulates SEC activity, forming an unexpected self-reinforcing feedback loop with SEC. SEC inactivation leads to neuroblast loss, whereas its forced activation results in neural progenitor dedifferentiation and tumorigenesis. Our studies unveil an SEC-mediated intracellular amplifier mechanism in ensuring robustness and precision in stem cell fate commitment and provide mechanistic explanation for the highly frequent association of SEC overactivation with human cancers.
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Affiliation(s)
- Kun Liu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Dan Shen
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jingwen Shen
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shihong M Gao
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Bo Li
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chouin Wong
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weidong Feng
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Song
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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178
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Yang H, Basquin D, Pauli D, Oliver B. Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults. BMC Genomics 2017; 18:384. [PMID: 28521739 PMCID: PMC5436443 DOI: 10.1186/s12864-017-3755-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/03/2017] [Indexed: 11/22/2022] Open
Abstract
Background Transcriptional elongation is a generic function, but is also regulated to allow rapid transcription responses. Following relatively long initiation and promoter clearance, RNA polymerase II can pause and then rapidly elongate following recruitment of positive elongation factors. Multiple elongation complexes exist, but the role of specific components in adult Drosophila is underexplored. Results We conducted RNA-seq experiments to analyze the effect of RNAi knockdown of Suppressor of Triplolethal and lilliputian. We similarly analyzed the effect of expressing a dominant negative Cyclin-dependent kinase 9 allele. We observed that almost half of the genes expressed in adults showed reduced expression, supporting a broad role for the three tested genes in steady-state transcript abundance. Expression profiles following lilliputian and Suppressor of Triplolethal RNAi were nearly identical raising the possibility that they are obligatory co-factors. Genes showing reduced expression due to these RNAi treatments were short and enriched for genes encoding metabolic or enzymatic functions. The dominant-negative Cyclin-dependent kinase 9 profiles showed both overlapping and specific differential expression, suggesting involvement in multiple complexes. We also observed hundreds of genes with sex-biased differential expression following treatment. Conclusion Transcriptional profiles suggest that Lilliputian and Suppressor of Triplolethal are obligatory cofactors in the adult and that they can also function with Cyclin-dependent kinase 9 at a subset of loci. Our results suggest that transcriptional elongation control is especially important for rapidly expressed genes to support digestion and metabolism, many of which have sex-biased function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3755-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haiwang Yang
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA.
| | - Denis Basquin
- Department of Genetics & Evolution, Sciences III, University of Geneva, Boulevard d'Yvoy 4, CH 1205, Geneva, Switzerland
| | - Daniel Pauli
- Department of Genetics & Evolution, Sciences III, University of Geneva, Boulevard d'Yvoy 4, CH 1205, Geneva, Switzerland
| | - Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA
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179
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Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma. Proc Natl Acad Sci U S A 2017; 114:E4184-E4192. [PMID: 28484033 DOI: 10.1073/pnas.1702086114] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT midline carcinoma (NMC), we have identified protein interactions unique to the BRD4-NUT fusion oncoprotein compared with wild-type BRD4. Using cross-linking, affinity purification, and mass spectrometry, we identified the EP300 acetyltransferase as uniquely associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. We also discovered ZNF532 associated with BRD4-NUT in NMC patient cells but not detectable in 293T cells. EP300 and ZNF532 are both implicated in feed-forward regulatory loops leading to propagation of the oncogenic chromatin complex in BRD4-NUT patient cells. Adding key functional significance to our biochemical findings, we independently discovered a ZNF532-NUT translocation fusion in a newly diagnosed NMC patient. ChIP sequencing of the major players NUT, ZNF532, BRD4, EP300, and H3K27ac revealed the formation of ZNF532-NUT-associated hyperacetylated megadomains, distinctly localized but otherwise analogous to those found in BRD4-NUT patient cells. Our results support a model in which NMC is dependent on ectopic NUT-mediated interactions between EP300 and components of BRD4 regulatory complexes, leading to a cascade of misregulation.
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180
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Alfonso-Dunn R, Turner AMW, Jean Beltran PM, Arbuckle JH, Budayeva HG, Cristea IM, Kristie TM. Transcriptional Elongation of HSV Immediate Early Genes by the Super Elongation Complex Drives Lytic Infection and Reactivation from Latency. Cell Host Microbe 2017; 21:507-517.e5. [PMID: 28407486 DOI: 10.1016/j.chom.2017.03.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/06/2017] [Accepted: 03/13/2017] [Indexed: 12/23/2022]
Abstract
The cellular transcriptional coactivator HCF-1 is required for initiation of herpes simplex virus (HSV) lytic infection and for reactivation from latency in sensory neurons. HCF-1 stabilizes the viral Immediate Early (IE) gene enhancer complex and mediates chromatin transitions to promote IE transcription initiation. In infected cells, HCF-1 was also found to be associated with a network of transcription elongation components including the super elongation complex (SEC). IE genes exhibit characteristics of genes controlled by transcriptional elongation, and the SEC-P-TEFb complex is specifically required to drive the levels of productive IE mRNAs. Significantly, compounds that enhance the levels of SEC-P-TEFb also potently stimulated HSV reactivation from latency both in a sensory ganglia model system and in vivo. Thus, transcriptional elongation of HSV IE genes is a key limiting parameter governing both the initiation of HSV infection and reactivation of latent genomes.
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Affiliation(s)
- Roberto Alfonso-Dunn
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20814, USA
| | - Anne-Marie W Turner
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20814, USA
| | | | - Jesse H Arbuckle
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20814, USA
| | - Hanna G Budayeva
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Thomas M Kristie
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20814, USA.
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181
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Egloff S, Vitali P, Tellier M, Raffel R, Murphy S, Kiss T. The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression. EMBO J 2017; 36:934-948. [PMID: 28254838 DOI: 10.15252/embj.201695740] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/26/2017] [Accepted: 01/27/2017] [Indexed: 11/09/2022] Open
Abstract
The 7SK small nuclear RNP (snRNP), composed of the 7SK small nuclear RNA (snRNA), MePCE, and Larp7, regulates the mRNA elongation capacity of RNA polymerase II (RNAPII) through controlling the nuclear activity of positive transcription elongation factor b (P-TEFb). Here, we demonstrate that the human 7SK snRNP also functions as a canonical transcription factor that, in collaboration with the little elongation complex (LEC) comprising ELL, Ice1, Ice2, and ZC3H8, promotes transcription of RNAPII-specific spliceosomal snRNA and small nucleolar RNA (snoRNA) genes. The 7SK snRNA specifically associates with a fraction of RNAPII hyperphosphorylated at Ser5 and Ser7, which is a hallmark of RNAPII engaged in snRNA synthesis. Chromatin immunoprecipitation (ChIP) and chromatin isolation by RNA purification (ChIRP) experiments revealed enrichments for all components of the 7SK snRNP on RNAPII-specific sn/snoRNA genes. Depletion of 7SK snRNA or Larp7 disrupts LEC integrity, inhibits RNAPII recruitment to RNAPII-specific sn/snoRNA genes, and reduces nascent snRNA and snoRNA synthesis. Thus, through controlling both mRNA elongation and sn/snoRNA synthesis, the 7SK snRNP is a key regulator of nuclear RNA production by RNAPII.
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Affiliation(s)
- Sylvain Egloff
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Patrice Vitali
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Raoul Raffel
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Tamás Kiss
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France .,Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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182
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Kuzmina A, Krasnopolsky S, Taube R. Super elongation complex promotes early HIV transcription and its function is modulated by P-TEFb. Transcription 2017; 8:133-149. [PMID: 28340332 DOI: 10.1080/21541264.2017.1295831] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Early work on the control of transcription of the human immunodeficiency virus (HIV) laid the foundation for our current knowledge of how RNA Polymerase II is released from promoter-proximal pausing sites and transcription elongation is enhanced. The viral Tat activator recruits Positive Transcription Elongation Factor b (P-TEFb) and Super Elongation Complex (SEC) that jointly drive transcription elongation. While substantial progress in understanding the role of SEC in HIV gene transcription elongation has been obtained, defining of the mechanisms that govern SEC functions is still limited, and the role of SEC in controlling HIV transcription in the absence of Tat is less clear. Here we revisit the contribution of SEC in early steps of HIV gene transcription. In the absence of Tat, the AF4/FMR2 Family member 4 (AFF4) of SEC efficiently activates HIV transcription, while gene activation by its homolog AFF1 is substantially lower. Differential recruitment to the HIV promoter and association with Human Polymerase-Associated Factor complex (PAFc) play key role in this functional distinction between AFF4 and AFF1. Moreover, while depletion of cyclin T1 expression has subtle effects on HIV gene transcription in the absence of Tat, knockout (KO) of AFF1, AFF4, or both proteins slightly repress this early step of viral transcription. Upon Tat expression, HIV transcription reaches optimal levels despite KO of AFF1 or AFF4 expression. However, double AFF1/AFF4 KO completely diminishes Tat trans-activation. Significantly, our results show that P-TEFb phosphorylates AFF4 and modulates SEC assembly, AFF1/4 dimerization and recruitment to the viral promoter. We conclude that SEC promotes both early steps of HIV transcription in the absence of Tat, as well as elongation of transcription, when Tat is expressed. Significantly, SEC functions are modulated by P-TEFb.
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Affiliation(s)
- Alona Kuzmina
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| | - Simona Krasnopolsky
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| | - Ran Taube
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
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183
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Qiu X, Pascal LE, Song Q, Zang Y, Ai J, O'Malley KJ, Nelson JB, Wang Z. Physical and Functional Interactions between ELL2 and RB in the Suppression of Prostate Cancer Cell Proliferation, Migration, and Invasion. Neoplasia 2017; 19:207-215. [PMID: 28167296 PMCID: PMC5293724 DOI: 10.1016/j.neo.2017.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/22/2016] [Accepted: 01/02/2017] [Indexed: 12/24/2022] Open
Abstract
Elongation factor, RNA polymerase II, 2 (ELL2) is expressed and regulated by androgens in the prostate. ELL2 and ELL-associated factor 2 (EAF2) form a stable complex, and their orthologs in Caenorhabditis elegans appear to be functionally similar. In C. elegans, the EAF2 ortholog eaf-1 was reported to interact with the retinoblastoma (RB) pathway to control development and fertility in worms. Because RB loss is frequent in prostate cancer, ELL2 interaction with RB might be important for prostate homeostasis. The present study explored physical and functional interaction of ELL2 with RB in prostate cancer. ELL2 expression in human prostate cancer specimens was detected using quantitative polymerase chain reaction coupled with laser capture microdissection. Co-immunoprecipitation coupled with deletion mutagenesis was used to determine ELL2 association with RB. Functional interaction between ELL2 and RB was tested using siRNA knockdown, BrdU incorporation, Transwell, and/or invasion assays in LNCaP, C4-2, and 22Rv1 prostate cancer cells. ELL2 expression was downregulated in high-Gleason score prostate cancer specimens. ELL2 could be bound and stabilized by RB, and this interaction was mediated through the N-terminus of ELL2 and the C-terminus of RB. Concurrent siRNA knockdown of ELL2 and RB enhanced cell proliferation, migration, and invasion as compared to knockdown of ELL2 or RB alone in prostate cancer cells. ELL2 and RB can interact physically and functionally to suppress prostate cancer progression.
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Affiliation(s)
- Xiaonan Qiu
- Tsinghua MD Program, School of Medicine, Tsinghua University, Beijing, China; Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Laura E Pascal
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Qiong Song
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Center for Translational Medicine, Guangxi Medical University, Nanning, Guangxi, China.
| | - Yachen Zang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Urology, The Second Affiliate Hospital of Soochow University, Suzhou, China.
| | - Junkui Ai
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Katherine J O'Malley
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Joel B Nelson
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Zhou Wang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Center for Translational Medicine, Guangxi Medical University, Nanning, Guangxi, China; University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, and University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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184
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Reiter F, Wienerroither S, Stark A. Combinatorial function of transcription factors and cofactors. Curr Opin Genet Dev 2017; 43:73-81. [PMID: 28110180 DOI: 10.1016/j.gde.2016.12.007] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 12/31/2022]
Abstract
Differential gene expression gives rise to the many cell types of complex organisms. Enhancers regulate transcription by binding transcription factors (TFs), which in turn recruit cofactors to activate RNA Polymerase II at core promoters. Transcriptional regulation is typically mediated by distinct combinations of TFs, enabling a relatively small number of TFs to generate a large diversity of cell types. However, how TFs achieve combinatorial enhancer control and how enhancers, enhancer-bound TFs, and the cofactors they recruit regulate RNA Polymerase II activity is not entirely clear. Here, we review how TF synergy is mediated at the level of DNA binding and after binding, the role of cofactors and the post-translational modifications they catalyze, and discuss different models of enhancer-core-promoter communication.
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Affiliation(s)
- Franziska Reiter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Sebastian Wienerroither
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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185
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Marschalek R. Systematic Classification of Mixed-Lineage Leukemia Fusion Partners Predicts Additional Cancer Pathways. Ann Lab Med 2017; 36:85-100. [PMID: 26709255 PMCID: PMC4713862 DOI: 10.3343/alm.2016.36.2.85] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 11/26/2015] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
Chromosomal translocations of the human mixed-lineage leukemia (MLL) gene have been analyzed for more than 20 yr at the molecular level. So far, we have collected about 80 direct MLL fusions (MLL-X alleles) and about 120 reciprocal MLL fusions (X-MLL alleles). The reason for the higher amount of reciprocal MLL fusions is that the excess is caused by 3-way translocations with known direct fusion partners. This review is aiming to propose a solution for an obvious problem, namely why so many and completely different MLL fusion alleles are always leading to the same leukemia phenotypes (ALL, AML, or MLL). This review is aiming to explain the molecular consequences of MLL translocations, and secondly, the contribution of the different fusion partners. A new hypothesis will be posed that can be used for future research, aiming to find new avenues for the treatment of this particular leukemia entity.
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Affiliation(s)
- Rolf Marschalek
- Institute of Pharmaceutical Biology/DCAL, Goethe-University of Frankfurt, Biocenter, Frankfurt/Main, Germany.
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186
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Abstract
Transcription by RNA polymerase (RNAP) II is regulated at multiple steps by phosphorylation, catalyzed mainly by members of the cyclin-dependent kinase (CDK) family. The CDKs involved in transcription have overlapping substrate specificities, but play largely non-redundant roles in coordinating gene expression. Novel functions and targets of CDKs have recently emerged at the end of the transcription cycle, when the primary transcript is cleaved, and in most cases polyadenylated, and transcription is terminated by the action of the "torpedo" exonuclease Xrn2, which is a CDK substrate. Collectively, various functions have been ascribed to CDKs or CDK-mediated phosphorylation: recruiting cleavage and polyadenylation factors, preventing premature termination within gene bodies while promoting efficient termination of full-length transcripts, and preventing extensive readthrough transcription into intergenic regions or neighboring genes. The assignment of precise functions to specific CDKs is still in progress, but recent advances suggest ways in which the CDK network and RNAP II machinery might cooperate to ensure timely exit from the transcription cycle.
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Affiliation(s)
- Robert P Fisher
- a Department of Oncological Sciences , Icahn School of Medicine at Mount Sinai , New York , NY , USA
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187
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Targeting Chromatin Remodeling in Inflammation and Fibrosis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 107:1-36. [PMID: 28215221 DOI: 10.1016/bs.apcsb.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mucosal surfaces of the human body are lined by a contiguous epithelial cell surface that forms a barrier to aerosolized pathogens. Specialized pattern recognition receptors detect the presence of viral pathogens and initiate protective host responses by triggering activation of the nuclear factor κB (NFκB)/RelA transcription factor and formation of a complex with the positive transcription elongation factor (P-TEFb)/cyclin-dependent kinase (CDK)9 and Bromodomain-containing protein 4 (BRD4) epigenetic reader. The RelA·BRD4·P-TEFb complex produces acute inflammation by regulating transcriptional elongation, which produces a rapid genomic response by inactive genes maintained in an open chromatin configuration engaged with hypophosphorylated RNA polymerase II. We describe recent studies that have linked prolonged activation of the RelA-BRD4 pathway with the epithelial-mesenchymal transition (EMT) by inducing a core of EMT corepressors, stimulating secretion of growth factors promoting airway fibrosis. The mesenchymal state produces rewiring of the kinome and reprogramming of innate responses toward inflammation. In addition, the core regulator Zinc finger E-box homeodomain 1 (ZEB1) silences the expression of the interferon response factor 1 (IRF1), required for type III IFN expression. This epigenetic silencing is mediated by the Enhancer of Zeste 2 (EZH2) histone methyltransferase. Because of their potential applications in cancer and inflammation, small-molecule inhibitors of NFκB/RelA, CDK9, BRD4, and EZH2 have been the targets of medicinal chemistry efforts. We suggest that disruption of the RelA·BRD4·P-TEFb pathway and EZH2 methyltransferase has important implications for reversing fibrosis and restoring normal mucosal immunity in chronic inflammatory diseases.
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188
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Andrews FH, Shanle EK, Strahl BD, Kutateladze TG. The essential role of acetyllysine binding by the YEATS domain in transcriptional regulation. Transcription 2016; 7:14-20. [PMID: 26934307 DOI: 10.1080/21541264.2015.1125987] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The YEATS domains of AF9 and Taf14 have recently been found to recognize the histone H3K9ac modification. In this commentary, we discuss the mechanistic and biological implications of this interaction. We compare structures of the YEATS-H3K9ac complexes the highlighting a novel mechanism for the acetyllysine recognition through the aromatic cage. We also summarize the latest findings underscoring a critical role of the acetyllysine binding function of AF9 and Taf14 in transcriptional regulation and DNA repair.
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Affiliation(s)
- Forest H Andrews
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
| | - Erin K Shanle
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
| | - Brian D Strahl
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
| | - Tatiana G Kutateladze
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
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189
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DeLaney E, Luse DS. Gdown1 Associates Efficiently with RNA Polymerase II after Promoter Clearance and Displaces TFIIF during Transcript Elongation. PLoS One 2016; 11:e0163649. [PMID: 27716820 PMCID: PMC5055313 DOI: 10.1371/journal.pone.0163649] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022] Open
Abstract
Pausing during the earliest stage of transcript elongation by RNA polymerase II (Pol II) is a nearly universal control point in metazoan gene expression. The substoichiometric Pol II subunit Gdown1 facilitates promoter proximal pausing in vitro in extract-based transcription reactions, out-competes the initiation/elongation factor TFIIF for binding to free Pol II and co-localizes with paused Pol II in vivo. However, we have shown that Gdown1 cannot functionally associate with the Pol II preinitiation complex (PIC), which contains TFIIF. In the present study, we determined at what point after initiation Gdown1 can associate with Pol II and how rapidly this competition with TFIIF occurs. We show that, as with the PIC, Gdown1 cannot functionally load into open complexes or complexes engaged in abortive synthesis of very short RNAs. Gdown1 can load into early elongation complexes (EECs) with 5–9 nt RNAs, but efficient association with EECs does not take place until the point at which the upstream segment of the long initial transcription bubble reanneals. Tests of EECs assembled on a series of promoter variants confirm that this bubble collapse transition, and not transcript length, modulates Gdown1 functional affinity. Gdown1 displaces TFIIF effectively from all complexes downstream of the collapse transition, but this displacement is surprisingly slow: complete loss of TFIIF stimulation of elongation requires 5 min of incubation with Gdown1. The relatively slow functional loading of Gdown1 in the presence of TFIIF suggests that Gdown1 works in promoter-proximal pausing by locking in the paused state after elongation is already antagonized by other factors, including DSIF, NELF and possibly the first downstream nucleosome.
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Affiliation(s)
- Elizabeth DeLaney
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Donal S. Luse
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- * E-mail:
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190
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The Multifaceted Contributions of Chromatin to HIV-1 Integration, Transcription, and Latency. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 328:197-252. [PMID: 28069134 DOI: 10.1016/bs.ircmb.2016.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood. Transcription from the HIV-1 genome occurs in the context of chromatin and is subjected to the same regulatory mechanisms that drive cellular gene expression. Much like in eukaryotic genes, the nucleosomal landscape of the HIV-1 promoter and its position within genomic chromatin are determinants of its transcriptional activity. Understanding the multilayered chromatin-mediated mechanisms that underpin HIV-1 integration and expression is of utmost importance for the development of therapeutic strategies aimed at reducing the pool of latently infected cells. In this review, we discuss the impact of chromatin structure on viral integration, transcriptional regulation and latency, and the host factors that influence HIV-1 replication by regulating chromatin organization. Finally, we describe therapeutic strategies under development to target the chromatin-HIV-1 interplay.
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191
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Resto M, Kim BH, Fernandez AG, Abraham BJ, Zhao K, Lewis BA. O-GlcNAcase Is an RNA Polymerase II Elongation Factor Coupled to Pausing Factors SPT5 and TIF1β. J Biol Chem 2016; 291:22703-22713. [PMID: 27601472 DOI: 10.1074/jbc.m116.751420] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/29/2016] [Indexed: 12/24/2022] Open
Abstract
We describe here the identification and functional characterization of the enzyme O-GlcNAcase (OGA) as an RNA polymerase II elongation factor. Using in vitro transcription elongation assays, we show that OGA activity is required for elongation in a crude nuclear extract system, whereas in a purified system devoid of OGA the addition of rOGA inhibited elongation. Furthermore, OGA is physically associated with the known RNA polymerase II (pol II) pausing/elongation factors SPT5 and TRIM28-KAP1-TIF1β, and a purified OGA-SPT5-TIF1β complex has elongation properties. Lastly, ChIP-seq experiments show that OGA maps to the transcriptional start site/5' ends of genes, showing considerable overlap with RNA pol II, SPT5, TRIM28-KAP1-TIF1β, and O-GlcNAc itself. These data all point to OGA as a component of the RNA pol II elongation machinery regulating elongation genome-wide. Our results add a novel and unexpected dimension to the regulation of elongation by the insertion of O-GlcNAc cycling into the pol II elongation regulatory dynamics.
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Affiliation(s)
- Melissa Resto
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893
| | - Bong-Hyun Kim
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Alfonso G Fernandez
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893
| | - Brian J Abraham
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, and.,Laboratory of Epigenome Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Keji Zhao
- Laboratory of Epigenome Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Brian A Lewis
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893,
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192
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CRISPR-Cas9 mediated genetic engineering for the purification of the endogenous integrator complex from mammalian cells. Protein Expr Purif 2016; 128:101-8. [PMID: 27546450 DOI: 10.1016/j.pep.2016.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 01/14/2023]
Abstract
The Integrator Complex (INT) is a large multi-subunit protein complex, containing at least 14 subunits and a host of associated factors. These protein components have been established through pulldowns of overexpressed epitope tagged subunits or by using antibodies raised against specific subunits. Here, we utilize CRISPR/Cas9 gene editing technology to introduce N-terminal FLAG epitope tags into the endogenous genes that encode Integrator subunit 4 and 11 within HEK293T cells. We provide specific details regarding design, approaches for facile screening, and our observed frequency of successful recombination. Finally, using silver staining, Western blotting and LC-MS/MS we compare the components of INT of purifications from CRISPR derived lines to 293T cells overexpressing FLAG-INTS11 to define a highly resolved constituency of mammalian INT.
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193
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Sharma N. Regulation of RNA polymerase II-mediated transcriptional elongation: Implications in human disease. IUBMB Life 2016; 68:709-16. [DOI: 10.1002/iub.1538] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/14/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Nimisha Sharma
- University School of Biotechnology, G.G.S. Indraprastha University; Dwarka New Delhi 110078 India
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194
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Ahmad K, Scholz B, Capelo R, Schweighöfer I, Kahnt AS, Marschalek R, Steinhilber D. AF4 and AF4-MLL mediate transcriptional elongation of 5-lipoxygenase mRNA by 1, 25-dihydroxyvitamin D3. Oncotarget 2016; 6:25784-800. [PMID: 26329759 PMCID: PMC4694866 DOI: 10.18632/oncotarget.4703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/10/2015] [Indexed: 12/22/2022] Open
Abstract
The human 5-lipoxygenase (5-LO), encoded by the ALOX5 gene, is the key enzyme in the formation of pro-inflammatory leukotrienes. ALOX5 gene transcription is strongly stimulated by calcitriol (1α, 25-dihydroxyvitamin D3) and TGFβ (transforming growth factor-β). Here, we investigated the influence of MLL (activator of transcript initiation), AF4 (activator of transcriptional elongation) as well as of the leukemogenic fusion proteins MLL-AF4 (ectopic activator of transcript initiation) and AF4-MLL (ectopic activator of transcriptional elongation) on calcitriol/TGFβ-dependent 5-LO transcript elongation. We present evidence that the AF4 complex directly interacts with the vitamin D receptor (VDR) and promotes calcitriol-dependent ALOX5 transcript elongation. Activation of transcript elongation was strongly enhanced by the AF4-MLL fusion protein but was sensitive to Flavopiridol. By contrast, MLL-AF4 displayed no effect on transcriptional elongation. Furthermore, HDAC class I inhibitors inhibited the ectopic effects caused by AF4-MLL on transcriptional elongation, suggesting that HDAC class I inhibitors are potential therapeutics for the treatment of t(4;11)(q21;q23) leukemia.
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Affiliation(s)
- Khalil Ahmad
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Bastian Scholz
- Institute of Pharmaceutical Biology / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Ricardo Capelo
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Ilona Schweighöfer
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Astrid Stefanie Kahnt
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry / ZAFES, Goethe University Frankfurt, Frankfurt, Germany
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195
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Vernimmen D, Bickmore WA. The Hierarchy of Transcriptional Activation: From Enhancer to Promoter. Trends Genet 2016; 31:696-708. [PMID: 26599498 DOI: 10.1016/j.tig.2015.10.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/18/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Regulatory elements (enhancers) that are remote from promoters play a critical role in the spatial, temporal, and physiological control of gene expression. Studies on specific loci, together with genome-wide approaches, suggest that there may be many common mechanisms involved in enhancer-promoter communication. Here, we discuss the multiprotein complexes that are recruited to enhancers and the hierarchy of events taking place between regulatory elements and promoters.
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Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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196
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Lu X, Zhu X, Li Y, Liu M, Yu B, Wang Y, Rao M, Yang H, Zhou K, Wang Y, Chen Y, Chen M, Zhuang S, Chen LF, Liu R, Chen R. Multiple P-TEFbs cooperatively regulate the release of promoter-proximally paused RNA polymerase II. Nucleic Acids Res 2016; 44:6853-67. [PMID: 27353326 PMCID: PMC5001612 DOI: 10.1093/nar/gkw571] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/06/2016] [Indexed: 01/09/2023] Open
Abstract
The association of DSIF and NELF with initiated RNA Polymerase II (Pol II) is the general mechanism for inducing promoter-proximal pausing of Pol II. However, it remains largely unclear how the paused Pol II is released in response to stimulation. Here, we show that the release of the paused Pol II is cooperatively regulated by multiple P-TEFbs which are recruited by bromodomain-containing protein Brd4 and super elongation complex (SEC) via different recruitment mechanisms. Upon stimulation, Brd4 recruits P-TEFb to Spt5/DSIF via a recruitment pathway consisting of Med1, Med23 and Tat-SF1, whereas SEC recruits P-TEFb to NELF-A and NELF-E via Paf1c and Med26, respectively. P-TEFb-mediated phosphorylation of Spt5, NELF-A and NELF-E results in the dissociation of NELF from Pol II, thereby transiting transcription from pausing to elongation. Additionally, we demonstrate that P-TEFb-mediated Ser2 phosphorylation of Pol II is dispensable for pause release. Therefore, our studies reveal a co-regulatory mechanism of Brd4 and SEC in modulating the transcriptional pause release by recruiting multiple P-TEFbs via a Mediator- and Paf1c-coordinated recruitment network.
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Affiliation(s)
- Xiaodong Lu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Xinxing Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - You Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Bin Yu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yu Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Muhua Rao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Haiyang Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Kai Zhou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yanheng Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Meihua Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Songkuan Zhuang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Lin-Feng Chen
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Runzhong Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Ruichuan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
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197
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Hatch VL, Marin-Barba M, Moxon S, Ford CT, Ward NJ, Tomlinson ML, Desanlis I, Hendry AE, Hontelez S, van Kruijsbergen I, Veenstra GJC, Münsterberg AE, Wheeler GN. The positive transcriptional elongation factor (P-TEFb) is required for neural crest specification. Dev Biol 2016; 416:361-72. [PMID: 27343897 DOI: 10.1016/j.ydbio.2016.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 05/06/2016] [Accepted: 06/08/2016] [Indexed: 12/31/2022]
Abstract
Regulation of gene expression at the level of transcriptional elongation has been shown to be important in stem cells and tumour cells, but its role in the whole animal is only now being fully explored. Neural crest cells (NCCs) are a multipotent population of cells that migrate during early development from the dorsal neural tube throughout the embryo where they differentiate into a variety of cell types including pigment cells, cranio-facial skeleton and sensory neurons. Specification of NCCs is both spatially and temporally regulated during embryonic development. Here we show that components of the transcriptional elongation regulatory machinery, CDK9 and CYCLINT1 of the P-TEFb complex, are required to regulate neural crest specification. In particular, we show that expression of the proto-oncogene c-Myc and c-Myc responsive genes are affected. Our data suggest that P-TEFb is crucial to drive expression of c-Myc, which acts as a 'gate-keeper' for the correct temporal and spatial development of the neural crest.
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Affiliation(s)
- Victoria L Hatch
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Marta Marin-Barba
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Christopher T Ford
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Nicole J Ward
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew L Tomlinson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Ines Desanlis
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Adam E Hendry
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Saartje Hontelez
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Ila van Kruijsbergen
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Andrea E Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Grant N Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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198
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Anwar D, Takahashi H, Watanabe M, Suzuki M, Fukuda S, Hatakeyama S. p53 represses the transcription of snRNA genes by preventing the formation of little elongation complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:975-82. [PMID: 27268141 DOI: 10.1016/j.bbagrm.2016.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/12/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022]
Abstract
The regulation of transcription by RNA polymerase II (Pol II) is important for a variety of cellular functions. ELL/EAF-containing little elongation complex (LEC) was found to be required for transcription of Pol II-dependent small nuclear RNA (snRNA) genes. It was shown that the tumor suppressor p53 interacts with ELL and inhibits transcription elongation activity of ELL. Here, we show that p53 inhibits interaction between ELL/EAF and ICE1 in LEC and thereby p53 represses transcription of Pol II-dependent snRNA genes through inhibiting LEC function. Furthermore, induction of p53 expression by ultraviolet (UV) irradiation decreases the occupancy of ICE1 at Pol II-dependent snRNA genes. Consistent with the results, knockdown of p53 increased both the expression of snRNA genes and the occupancy of Pol II and components of LEC at snRNA genes. Our results indicate that p53 interferes with the interaction between ELL/EAF and ICE1 and represses transcription of snRNA genes by Pol II.
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Affiliation(s)
- Delnur Anwar
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan; Department of Otolaryngology, Head & Neck Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Hidehisa Takahashi
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Masashi Watanabe
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Masanobu Suzuki
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan; Department of Otolaryngology, Head & Neck Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Satoshi Fukuda
- Department of Otolaryngology, Head & Neck Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan.
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199
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Knutson BA, Smith ML, Walker-Kopp N, Xu X. Super elongation complex contains a TFIIF-related subcomplex. Transcription 2016; 7:133-40. [PMID: 27223670 DOI: 10.1080/21541264.2016.1194027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Super elongation complex (SEC) belongs to a family of RNA polymerase II (Pol II) elongation factors that has similar properties as TFIIF, a general transcription factor that increases the transcription elongation rate by reducing pausing. Although SEC has TFIIF-like functional properties, it apparently lacks sequence and structural homology. Using HHpred, we find that SEC contains an evolutionarily related TFIIF-like subcomplex. We show that the SEC subunit ELL interacts with the Pol II Rbp2 subunit, as expected for a TFIIF-like factor. These findings suggest a new model for how SEC functions as a Pol II elongation factor and how it suppresses Pol II pausing.
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Affiliation(s)
- Bruce A Knutson
- a Department of Biochemistry and Molecular Biology , SUNY Upstate Medical University , Syracuse , NY , USA
| | - Marissa L Smith
- a Department of Biochemistry and Molecular Biology , SUNY Upstate Medical University , Syracuse , NY , USA
| | - Nancy Walker-Kopp
- a Department of Biochemistry and Molecular Biology , SUNY Upstate Medical University , Syracuse , NY , USA
| | - Xia Xu
- a Department of Biochemistry and Molecular Biology , SUNY Upstate Medical University , Syracuse , NY , USA
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200
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Asamitsu K, Omagari K, Okuda T, Hibi Y, Okamoto T. Quantification of the HIV transcriptional activator complex in live cells by image-based protein-protein interaction analysis. Genes Cells 2016; 21:706-16. [PMID: 27193293 DOI: 10.1111/gtc.12375] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/17/2016] [Indexed: 01/16/2023]
Abstract
The virus-encoded Tat protein is essential for HIV transcription in infected cells. The interaction of Tat with the cellular transcription elongation factor P-TEFb (positive transcriptional elongation factor b) containing cyclin T1 (CycT1) and cyclin-dependent kinase 9 (CDK9) is critical for its activity. In this study, we use the Fluoppi (fluorescent-based technology detecting protein-protein interaction) system, which enables the quantification of interactions between biomolecules, such as proteins, in live cells. Quantitative measurement of the molecular interactions among Tat, CycT1 and CDK9 has showed that any third molecule enhances the binding between the other two molecules. These findings suggest that each component of the Tat:P-TEFb complex stabilizes the overall complex, thereby supporting the efficient transcriptional elongation during viral RNA synthesis. These interactions may serve as appropriate targets for novel anti-HIV therapy.
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Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Katsumi Omagari
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Tomoya Okuda
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Yurina Hibi
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
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