251
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Basheer F, Huntly BJP. BET bromodomain inhibitors in leukemia. Exp Hematol 2015; 43:718-31. [PMID: 26163798 DOI: 10.1016/j.exphem.2015.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 01/01/2023]
Abstract
The last few years have seen the identification of bromodomain and extraterminal (BET) proteins as critical mediators of transcription with effects on its direct control and cisregulation. This discovery is important in furthering our understanding of the mechanisms of normal transcriptional control. Subsequent work has shed light on the multiple roles of BET proteins in various aberrant transcriptional pathways that have significant implications across many malignant cell types and other disease processes. Accordingly, considerable effort has been made to assess the utility of targeting BET proteins with specific small molecules in acute leukemia and across other types of cancer. In this review, we will discuss the most recent advances in our understanding of the mechanistic actions of BET proteins in normal transcriptional control, both at the gene body and cisregulatory elements; how this is subverted; and its aberrant downstream effects, specifically in the context of acute leukemia and other hematologic cancers. In particular, we will focus on altered epigenetic programs that have been shown to be central to the development and maintenance of acute myeloid leukemia in preclinical models. Finally, we will explore how the use of small-molecule BET inhibitors in leukemias has demonstrated significant promise in numerous single-agent and combination therapy preclinical models and will highlight efforts to translate this promise to the therapeutic arena through various clinical trials attempting to validate efficacy and safety. The considerable opportunities in epigenetically targeting leukemias through BET inhibition will undoubtedly play an important role in improving the management of these conditions in the future.
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Affiliation(s)
- Faisal Basheer
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Brian J P Huntly
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke's Hospital, University of Cambridge, Cambridge, UK; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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252
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Zhang X, Gao Y, Lu L, Zhang Z, Gan S, Xu L, Lei A, Cao Y. JmjC Domain-containing Protein 6 (Jmjd6) Derepresses the Transcriptional Repressor Transcription Factor 7-like 1 (Tcf7l1) and Is Required for Body Axis Patterning during Xenopus Embryogenesis. J Biol Chem 2015; 290:20273-83. [PMID: 26157142 DOI: 10.1074/jbc.m115.646554] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Indexed: 12/22/2022] Open
Abstract
Tcf7l1 (also known as Tcf3) is a bimodal transcription factor that plays essential roles in embryogenesis and embryonic and adult stem cells. On one hand, Tcf7l1 works as transcriptional repressor via the recruitment of Groucho-related transcriptional corepressors to repress the transcription of Wnt target genes, and, on the other hand, it activates Wnt target genes when Wnt-activated β-catenin interacts with it. However, how its activity is modulated is not well understood. Here we demonstrate that a JmjC-domain containing protein, Jmjd6, interacts with Tcf7l and derepresses Tcf7l. We show that Jmjd6 binds to a region of Tcf7l1 that is also responsible for Groucho interaction, therefore making it possible that Jmjd6 binding displaces the Groucho transcriptional corepressor from Tcf7l1. Moreover, we show that Jmjd6 antagonizes the repression effect of Tcf7l1 on target gene transcription and is able to enhance β-catenin-induced gene activation and that, vice versa, inhibition of Jmjd6 activity compromises gene activation in both cells and Xenopus early embryos. We also show that jmjd6 is both maternally and zygotically transcribed during Xenopus embryogenesis. Loss of Jmjd6 function causes defects in anterioposterior body axis formation and down-regulation of genes that are involved in anterioposterior axis patterning. The results elucidate a novel mechanism underlying the regulation of Tcf7l1 activity and the regulation of embryonic body axis formation.
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Affiliation(s)
- Xuena Zhang
- From the Model Animal Research Center of Nanjing University and the Ministry of Education Key Laboratory of Model Animals for Disease Study, Nanjing 210061, China
| | - Yan Gao
- From the Model Animal Research Center of Nanjing University and the Ministry of Education Key Laboratory of Model Animals for Disease Study, Nanjing 210061, China
| | - Lei Lu
- From the Model Animal Research Center of Nanjing University and the Ministry of Education Key Laboratory of Model Animals for Disease Study, Nanjing 210061, China
| | - Zan Zhang
- From the Model Animal Research Center of Nanjing University and the Ministry of Education Key Laboratory of Model Animals for Disease Study, Nanjing 210061, China
| | - Shengchun Gan
- From the Model Animal Research Center of Nanjing University and the Ministry of Education Key Laboratory of Model Animals for Disease Study, Nanjing 210061, China
| | - Liyang Xu
- From the Model Animal Research Center of Nanjing University and the Ministry of Education Key Laboratory of Model Animals for Disease Study, Nanjing 210061, China
| | - Anhua Lei
- From the Model Animal Research Center of Nanjing University and the Ministry of Education Key Laboratory of Model Animals for Disease Study, Nanjing 210061, China
| | - Ying Cao
- From the Model Animal Research Center of Nanjing University and the Ministry of Education Key Laboratory of Model Animals for Disease Study, Nanjing 210061, China
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253
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Wang CY, Filippakopoulos P. Beating the odds: BETs in disease. Trends Biochem Sci 2015; 40:468-79. [PMID: 26145250 DOI: 10.1016/j.tibs.2015.06.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 01/16/2023]
Abstract
Bromodomains (BRDs) are evolutionarily conserved protein interaction modules that specifically recognise acetyl-lysine on histones and other proteins, facilitating roles in regulating gene transcription. BRD-containing proteins bound to chromatin loci such as enhancers are often deregulated in disease leading to aberrant expression of proinflammatory cytokines and growth-promoting genes. Recent developments targeting the bromo and extraterminal (BET) subset of BRD proteins demonstrated remarkable efficacy in murine models providing a compelling rationale for drug development and translation to the clinic. Here we summarise recent advances in our understanding of the roles of BETs in regulating gene transcription in normal and diseased tissue as well as the current status of their clinical translation.
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Affiliation(s)
- Chen-Yi Wang
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK; Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
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254
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Hu YJ, Belaghzal H, Hsiao WY, Qi J, Bradner JE, Guertin DA, Sif S, Imbalzano AN. Transcriptional and post-transcriptional control of adipocyte differentiation by Jumonji domain-containing protein 6. Nucleic Acids Res 2015; 43:7790-804. [PMID: 26117538 PMCID: PMC4652747 DOI: 10.1093/nar/gkv645] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/12/2015] [Indexed: 12/17/2022] Open
Abstract
Jumonji domain-containing protein 6 (JMJD6) is a nuclear protein involved in histone modification, transcription and RNA processing. Although JMJD6 is crucial for tissue development, the link between its molecular functions and its roles in any given differentiation process is unknown. We report that JMJD6 is required for adipogenic gene expression and differentiation in a manner independent of Jumonji C domain catalytic activity. JMJD6 knockdown led to a reduction of C/EBPβ and C/EBPδ protein expression without affecting mRNA levels in the early phase of differentiation. However, ectopic expression of C/EBPβ and C/EBPδ did not rescue differentiation. Further analysis demonstrated that JMJD6 was associated with the Pparγ2 and Cebpα loci and putative enhancers. JMJD6 was previously found associated with bromodomain and extra-terminal domain (BET) proteins, which can be targeted by the bromodomain inhibitor JQ1. JQ1 treatment prevented chromatin binding of JMJD6, Pparγ2 and Cebpα expression, and adipogenic differentiation, yet had no effect on C/EBPβ and C/EBPδ expression or chromatin binding. These results indicate dual roles for JMJD6 in promoting adipogenic gene expression program by post-transcriptional regulation of C/EBPβ and C/EBPδ and direct transcriptional activation of Pparγ2 and Cebpα during adipocyte differentiation.
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Affiliation(s)
- Yu-Jie Hu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Houda Belaghzal
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Wen-Yu Hsiao
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - David A Guertin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Saïd Sif
- Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43210, USA Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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255
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Zeier Z, Esanov R, Belle KC, Volmar CH, Johnstone AL, Halley P, DeRosa BA, Khoury N, van Blitterswijk M, Rademakers R, Albert J, Brothers SP, Wuu J, Dykxhoorn DM, Benatar M, Wahlestedt C. Bromodomain inhibitors regulate the C9ORF72 locus in ALS. Exp Neurol 2015; 271:241-50. [PMID: 26099177 DOI: 10.1016/j.expneurol.2015.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/05/2015] [Accepted: 06/16/2015] [Indexed: 12/13/2022]
Abstract
A hexanucleotide repeat expansion residing within the C9ORF72 gene represents the most common known cause of amyotrophic lateral sclerosis (ALS) and places the disease among a growing family of repeat expansion disorders. The presence of RNA foci, repeat-associated translation products, and sequestration of RNA binding proteins suggests that toxic RNA gain-of-function contributes to pathology while C9ORF72 haploinsufficiency may be an additional pathological factor. One viable therapeutic strategy for treating expansion diseases is the use of small molecule inhibitors of epigenetic modifier proteins to reactivate expanded genetic loci. Indeed, previous studies have established proof of this principle by increasing the drug-induced expression of expanded (and abnormally heterochromatinized) FMR1, FXN and C9ORF72 genes in respective patient cells. While epigenetic modifier proteins are increasingly recognized as druggable targets, there have been few screening strategies to address this avenue of drug discovery in the context of expansion diseases. Here we utilize a semi-high-throughput gene expression based screen to identify siRNAs and small molecule inhibitors of epigenetic modifier proteins that regulate C9ORF72 RNA in patient fibroblasts, lymphocytes and reprogrammed motor neurons. We found that several bromodomain small molecule inhibitors increase the expression of C9ORF72 mRNA and pre-mRNA without affecting repressive epigenetic signatures of expanded C9ORF72 alleles. These data suggest that bromodomain inhibition increases the expression of unexpanded C9ORF72 alleles and may therefore compensate for haploinsufficiency without increasing the production of toxic RNA and protein products, thereby conferring therapeutic value.
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Affiliation(s)
- Zane Zeier
- Center for Therapeutic Innovation and Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Rustam Esanov
- Center for Therapeutic Innovation and Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Kinsley C Belle
- John P. Hussman Institute for Human Genomics and The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation and Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrea L Johnstone
- Center for Therapeutic Innovation and Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Paul Halley
- Center for Therapeutic Innovation and Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Brooke A DeRosa
- John P. Hussman Institute for Human Genomics and The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | - Nathalie Khoury
- Center for Therapeutic Innovation and Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | | | | | | - Shaun P Brothers
- Center for Therapeutic Innovation and Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami Miller School of Medicine, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics and The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | - Michael Benatar
- Department of Neurology, University of Miami Miller School of Medicine, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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256
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Lu H, Xue Y, Xue Y, Yu GK, Arias C, Lin J, Fong S, Faure M, Weisburd B, Ji X, Mercier A, Sutton J, Luo K, Gao Z, Zhou Q. Compensatory induction of MYC expression by sustained CDK9 inhibition via a BRD4-dependent mechanism. eLife 2015; 4:e06535. [PMID: 26083714 PMCID: PMC4490784 DOI: 10.7554/elife.06535] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 06/16/2015] [Indexed: 12/22/2022] Open
Abstract
CDK9 is the kinase subunit of positive transcription elongation factor b (P-TEFb) that enables RNA polymerase (Pol) II's transition from promoter-proximal pausing to productive elongation. Although considerable interest exists in CDK9 as a therapeutic target, little progress has been made due to lack of highly selective inhibitors. Here, we describe the development of i-CDK9 as such an inhibitor that potently suppresses CDK9 phosphorylation of substrates and causes genome-wide Pol II pausing. While most genes experience reduced expression, MYC and other primary response genes increase expression upon sustained i-CDK9 treatment. Essential for this increase, the bromodomain protein BRD4 captures P-TEFb from 7SK snRNP to deliver to target genes and also enhances CDK9's activity and resistance to inhibition. Because the i-CDK9-induced MYC expression and binding to P-TEFb compensate for P-TEFb's loss of activity, only simultaneously inhibiting CDK9 and MYC/BRD4 can efficiently induce growth arrest and apoptosis of cancer cells, suggesting the potential of a combinatorial treatment strategy.
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Affiliation(s)
- Huasong Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | | | - Yuahua Xue
- Innovation Center of Cell Signaling Network, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Guoying K Yu
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - Carolina Arias
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - Julie Lin
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - Susan Fong
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - Michel Faure
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - Ben Weisburd
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - Xiaodan Ji
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Alexandre Mercier
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - James Sutton
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - Kunxin Luo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Zhenhai Gao
- Novartis Institute for BioMedical Research, Emeryville, United States
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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257
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Arginine methylation of HSP70 regulates retinoid acid-mediated RARβ2 gene activation. Proc Natl Acad Sci U S A 2015; 112:E3327-36. [PMID: 26080448 DOI: 10.1073/pnas.1509658112] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although "histone" methyltransferases and demethylases are well established to regulate transcriptional programs and to use nonhistone proteins as substrates, their possible roles in regulation of heat-shock proteins in the nucleus have not been investigated. Here, we report that a highly conserved arginine residue, R469, in HSP70 (heat-shock protein of 70 kDa) proteins, an evolutionarily conserved protein family of ATP-dependent molecular chaperone, was monomethylated (me1), at least partially, by coactivator-associated arginine methyltransferase 1/protein arginine methyltransferase 4 (CARM1/PRMT4) and demethylated by jumonji-domain-containing 6 (JMJD6), both in vitro and in cultured cells. Functional studies revealed that HSP70 could directly regulate retinoid acid (RA)-induced retinoid acid receptor β2 (RARβ2) gene transcription through its binding to chromatin, with R469me1 being essential in this process. HSP70's function in gene transcriptional regulation appears to be distinct from its protein chaperon activity. R469me1 was shown to mediate the interaction between HSP70 and TFIIH, which involves in RNA polymerase II phosphorylation and thus transcriptional initiation. Our findings expand the repertoire of nonhistone substrates targeted by PRMT4 and JMJD6, and reveal a new function of HSP70 proteins in gene transcription at the chromatin level aside from its classic role in protein folding and quality control.
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258
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Andersson R, Sandelin A, Danko CG. A unified architecture of transcriptional regulatory elements. Trends Genet 2015; 31:426-33. [PMID: 26073855 DOI: 10.1016/j.tig.2015.05.007] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 11/19/2022]
Abstract
Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However, recent studies have revealed broad similarities between enhancers and promoters, blurring the distinction: active enhancers often initiate transcription, and some gene promoters have the potential to enhance transcriptional output of other promoters. Here, we propose a model in which promoters and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements and the surrounding sequences determine local transcriptional output as well as the enhancer and promoter activities of individual elements.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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259
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Stratikopoulos EE, Dendy M, Szabolcs M, Khaykin AJ, Lefebvre C, Zhou MM, Parsons R. Kinase and BET Inhibitors Together Clamp Inhibition of PI3K Signaling and Overcome Resistance to Therapy. Cancer Cell 2015; 27:837-51. [PMID: 26058079 PMCID: PMC4918409 DOI: 10.1016/j.ccell.2015.05.006] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 04/14/2015] [Accepted: 05/07/2015] [Indexed: 12/14/2022]
Abstract
Unsustained enzyme inhibition is a barrier to targeted therapy for cancer. Here, resistance to a class I PI3K inhibitor in a model of metastatic breast cancer driven by PI3K and MYC was associated with feedback activation of tyrosine kinase receptors (RTKs), AKT, mTOR, and MYC. Inhibitors of bromodomain and extra terminal domain (BET) proteins also failed to affect tumor growth. Interestingly, BET inhibitors lowered PI3K signaling and dissociated BRD4 from chromatin at regulatory regions of insulin receptor and EGFR family RTKs to reduce their expression. Combined PI3K and BET inhibition induced cell death, tumor regression, and clamped inhibition of PI3K signaling in a broad range of tumor cell lines to provide a strategy to overcome resistance to kinase inhibitor therapy.
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Affiliation(s)
- Elias E Stratikopoulos
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Meaghan Dendy
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Matthias Szabolcs
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA
| | - Alan J Khaykin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Celine Lefebvre
- Inserm U981, Institut Gustave Roussy, 94805 Villejuif, France
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Ramon Parsons
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA.
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260
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Böttger A, Islam MS, Chowdhury R, Schofield CJ, Wolf A. The oxygenase Jmjd6--a case study in conflicting assignments. Biochem J 2015; 468:191-202. [PMID: 25997831 DOI: 10.1042/bj20150278] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Jumonji domain-containing protein 6 (Jmjd6) is a member of the superfamily of non-haem iron(II) and 2-oxoglutarate (2OG)-dependent oxygenases; it plays an important developmental role in higher animals. Jmjd6 was initially assigned a role as the phosphatidylserine receptor responsible for engulfment of apoptotic cells but this now seems unlikely. Jmjd6 has been shown to be a nuclear localized protein with a JmjC domain comprising a distorted double-stranded β-helical structure characteristic of the 2OG-dependent oxygenases. Jmjd6 was subsequently assigned a role in catalysing N-methyl-arginine residue demethylation on the N-terminus of the human histones H3 and H4; however, this function is also subject to conflicting reports. Jmjd6 does catalyse 2OG-dependent C-5 hydroxylation of lysine residues in mRNA splicing-regulatory proteins and histones; there is also accumulating evidence that Jmjd6 plays a role in splicing (potentially in an iron- and oxygen-dependent manner) as well as in other processes regulating gene expression, including transcriptional pause release. Moreover, a link with tumour progression has been suggested. In the present review we look at biochemical, structural and cellular work on Jmjd6, highlighting areas of controversy and consensus.
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Affiliation(s)
- Angelika Böttger
- *Department of Biology II, Ludwig Maximillians University, Munich, Germany
| | - Md Saiful Islam
- †Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
| | - Rasheduzzaman Chowdhury
- †Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
| | - Christopher J Schofield
- †Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
| | - Alexander Wolf
- ‡Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
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261
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Poulard C, Rambaud J, Lavergne E, Jacquemetton J, Renoir JM, Trédan O, Chabaud S, Treilleux I, Corbo L, Romancer ML. Role of JMJD6 in Breast Tumourigenesis. PLoS One 2015; 10:e0126181. [PMID: 25951181 PMCID: PMC4423888 DOI: 10.1371/journal.pone.0126181] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/30/2015] [Indexed: 01/02/2023] Open
Abstract
Background Protein arginine methylation is a common post translational modification that regulates protein properties. This modification is carried out by a family of nine arginine methyltransferases (PRMTs). Arginine methylation has already been linked to tumourigenesis as overexpression of these enzymes was associated with various cancers, notably in breast cancers. Since the Jumonji Domain Containing 6 protein (JMJD6) possesses an arginine demethylase activity able to remove the methyl mark, we wanted to assess its potential role in breast tumourigenesis. Methods The expression of the protein by tissue microarray immunohistochemical staining was performed on a cohort of 133 breast tumours. Using cell lines stably overexpressing or knocked down for JMJD6, we evaluated its role on cell proliferation, cell migration, colony formation and mice tumour xenografts. Results The analysis of JMJD6 expression in a cohort of breast tumour samples indicates that JMJD6 was highly expressed in aggressive breast tumours. Moreover, high expression of JMJD6 was associated with poor disease-free survival of patients in this cohort. JMJD6 silencing in breast tumoural cells promotes certain characteristics of tumourigenesis including proliferation, migration in vitro, and tumour growth in vivo. These effects are dependent on its demethylase activity as an enzymatic dead mutant lost these properties. Conclusions Although JMJD6 displays anti-tumoral properties in cell lines, its expression in breast tumours may be a marker of poor prognosis, suggesting that its function could be altered in breast cancer.
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Affiliation(s)
- Coralie Poulard
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, F-69000 Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Equipe Labellisée "La Ligue
| | - Juliette Rambaud
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, F-69000 Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Equipe Labellisée "La Ligue
| | - Emilie Lavergne
- Centre Léon Bérard, Biostatistics Unit, F-69000 Lyon, France
| | - Julien Jacquemetton
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, F-69000 Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Equipe Labellisée "La Ligue
| | - Jack-Michel Renoir
- UMR CNRS 8203 Vectorology and anti-cancer therapeutics, Institut Gustave Roussy, 114, Rue E. Vaillant, 94805 Villejuif Cedex, France
| | - Olivier Trédan
- Centre Léon Bérard, Department of Medical Oncology, F-69000 Lyon, France
| | - Sylvie Chabaud
- Centre Léon Bérard, Biostatistics Unit, F-69000 Lyon, France
| | | | - Laura Corbo
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, F-69000 Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Equipe Labellisée "La Ligue
| | - Muriel Le Romancer
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, F-69000 Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Equipe Labellisée "La Ligue
- * E-mail:
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262
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Achour M, Le Gras S, Keime C, Parmentier F, Lejeune FX, Boutillier AL, Neri C, Davidson I, Merienne K. Neuronal identity genes regulated by super-enhancers are preferentially down-regulated in the striatum of Huntington's disease mice. Hum Mol Genet 2015; 24:3481-96. [DOI: 10.1093/hmg/ddv099] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/13/2015] [Indexed: 12/20/2022] Open
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263
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Myosin VI regulates gene pairing and transcriptional pause release in T cells. Proc Natl Acad Sci U S A 2015; 112:E1587-93. [PMID: 25770220 DOI: 10.1073/pnas.1502461112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Naive CD4 T cells differentiate into several effector lineages, which generate a stronger and more rapid response to previously encountered immunological challenges. Although effector function is a key feature of adaptive immunity, the molecular basis of this process is poorly understood. Here, we investigated the spatiotemporal regulation of cytokine gene expression in resting and restimulated effector T helper 1 (Th1) cells. We found that the Lymphotoxin (LT)/TNF alleles, which encode TNF-α, were closely juxtaposed shortly after T-cell receptor (TCR) engagement, when transcription factors are limiting. Allelic pairing required a nuclear myosin, myosin VI, which is rapidly recruited to the LT/TNF locus upon restimulation. Furthermore, transcription was paused at the TNF locus and other related genes in resting Th1 cells and released in a myosin VI-dependent manner following activation. We propose that homologous pairing and myosin VI-mediated transcriptional pause release account for the rapid and efficient expression of genes induced by an external stimulus.
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264
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Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 2015; 16:144-54. [PMID: 25650801 PMCID: PMC4517609 DOI: 10.1038/nrm3949] [Citation(s) in RCA: 670] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human body contains several hundred cell types, all of which share the same genome. In metazoans, much of the regulatory code that drives cell type-specific gene expression is located in distal elements called enhancers. Although mammalian genomes contain millions of potential enhancers, only a small subset of them is active in a given cell type. Cell type-specific enhancer selection involves the binding of lineage-determining transcription factors that prime enhancers. Signal-dependent transcription factors bind to primed enhancers, which enables these broadly expressed factors to regulate gene expression in a cell type-specific manner. The expression of genes that specify cell type identity and function is associated with densely spaced clusters of active enhancers known as super-enhancers. The functions of enhancers and super-enhancers are influenced by, and affect, higher-order genomic organization.
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Affiliation(s)
| | | | | | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, UC San Diego
- Department of Medicine, UC San Diego
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265
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Functions of BET proteins in erythroid gene expression. Blood 2015; 125:2825-34. [PMID: 25696920 DOI: 10.1182/blood-2014-10-607309] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/09/2015] [Indexed: 01/16/2023] Open
Abstract
Inhibitors of bromodomain and extraterminal motif proteins (BETs) are being evaluated for the treatment of cancer and other diseases, yet much remains to be learned about how BET proteins function during normal physiology. We used genomic and genetic approaches to examine BET function in a hematopoietic maturation system driven by GATA1, an acetylated transcription factor previously shown to interact with BETs. We found that BRD2, BRD3, and BRD4 were variably recruited to GATA1-regulated genes, with BRD3 binding the greatest number of GATA1-occupied sites. Pharmacologic BET inhibition impaired GATA1-mediated transcriptional activation, but not repression, genome-wide. Mechanistically, BETs promoted chromatin occupancy of GATA1 and subsequently supported transcriptional activation. Using a combination of CRISPR-Cas9-mediated genomic engineering and shRNA approaches, we observed that depletion of either BRD2 or BRD4 alone blunted erythroid gene activation. Surprisingly, depletion of BRD3 only affected erythroid transcription in the context of BRD2 deficiency. Consistent with functional overlap among BET proteins, forced BRD3 expression substantially rescued defects caused by BRD2 deficiency. These results suggest that pharmacologic BET inhibition should be interpreted in the context of distinct steps in transcriptional activation and overlapping functions among BET family members.
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266
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Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol 2015; 22:29-35. [DOI: 10.1038/nsmb.2921] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/22/2014] [Indexed: 12/20/2022]
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267
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Thinnes CC, England KS, Kawamura A, Chowdhury R, Schofield CJ, Hopkinson RJ. Targeting histone lysine demethylases - progress, challenges, and the future. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:1416-32. [PMID: 24859458 PMCID: PMC4316176 DOI: 10.1016/j.bbagrm.2014.05.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 05/06/2014] [Accepted: 05/13/2014] [Indexed: 12/20/2022]
Abstract
N-Methylation of lysine and arginine residues has emerged as a major mechanism of transcriptional regulation in eukaryotes. In humans, N(ε)-methyllysine residue demethylation is catalysed by two distinct subfamilies of demethylases (KDMs), the flavin-dependent KDM1 subfamily and the 2-oxoglutarate- (2OG) dependent JmjC subfamily, which both employ oxidative mechanisms. Modulation of histone methylation status is proposed to be important in epigenetic regulation and has substantial medicinal potential for the treatment of diseases including cancer and genetic disorders. This article provides an introduction to the enzymology of the KDMs and the therapeutic possibilities and challenges associated with targeting them, followed by a review of reported KDM inhibitors and their mechanisms of action from kinetic and structural perspectives.
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Affiliation(s)
- Cyrille C Thinnes
- The Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Akane Kawamura
- The Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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268
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Kanno T, Kanno Y, LeRoy G, Campos E, Sun HW, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D, Siebenlist U, O’Shea JJ, Ozato K. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat Struct Mol Biol 2014; 21:1047-57. [PMID: 25383670 PMCID: PMC4720983 DOI: 10.1038/nsmb.2912] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/06/2014] [Indexed: 02/07/2023]
Abstract
Small-molecule BET inhibitors interfere with the epigenetic interactions between acetylated histones and the bromodomains of the BET family proteins, including BRD4, and they potently inhibit growth of malignant cells by targeting cancer-promoting genes. BRD4 interacts with the pause-release factor P-TEFb and has been proposed to release RNA polymerase II (Pol II) from promoter-proximal pausing. We show that BRD4 occupies widespread genomic regions in mouse cells and directly stimulates elongation of both protein-coding transcripts and noncoding enhancer RNAs (eRNAs), in a manner dependent on bromodomain function. BRD4 interacts with elongating Pol II complexes and assists Pol II in progression through hyperacetylated nucleosomes by interacting with acetylated histones via bromodomains. On active enhancers, the BET inhibitor JQ1 antagonizes BRD4-associated eRNA synthesis. Thus, BRD4 is involved in multiple steps of the transcription hierarchy, primarily by facilitating transcript elongation both at enhancers and on gene bodies independently of P-TEFb.
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Affiliation(s)
- Tomohiko Kanno
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
- Program in Genomics of Differentiation, National Institutes of Child Health and Human Development, Bethesda, MD, USA
| | - Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Gary LeRoy
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Eric Campos
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Golnaz Vahedi
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Tom D Heightman
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, UK
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Ulrich Siebenlist
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - John J O’Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Keiko Ozato
- Program in Genomics of Differentiation, National Institutes of Child Health and Human Development, Bethesda, MD, USA
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269
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Chan CH, Fang C, Yarilina A, Prinjha RK, Qiao Y, Ivashkiv LB. BET bromodomain inhibition suppresses transcriptional responses to cytokine-Jak-STAT signaling in a gene-specific manner in human monocytes. Eur J Immunol 2014; 45:287-297. [PMID: 25345375 DOI: 10.1002/eji.201444862] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/17/2014] [Accepted: 10/21/2014] [Indexed: 11/12/2022]
Abstract
Disruption of the interaction of bromo and extraterminal (BET) proteins with acetylated histones using small molecule inhibitors suppresses Myc-driven cancers and TLR-induced inflammation in mouse models. The predominant mechanism of BET inhibitor action is to suppress BET-mediated recruitment of positive transcription elongation factor b and, thus, transcription elongation. We investigated the effects of BET inhibitor I-BET151 on transcriptional responses to TLR4 and TNF in primary human monocytes and also on responses to cytokines IFN-β, IFN-γ, IL-4, and IL-10, which activate the JAK-STAT signaling pathway and are important for monocyte polarization and inflammatory diseases. I-BET151 suppressed TLR4- and TNF-induced IFN responses by diminishing both autocrine IFN-β expression and transcriptional responses to IFN-β. I-BET151 inhibited cytokine-induced transcription of STAT targets in a gene-specific manner without affecting STAT activation or recruitment. This inhibition was independent of Myc or other upstream activators. IFN-stimulated gene transcription is regulated primarily at the level of transcription initiation. Accordingly, we found that I-BET151 suppressed the recruitment of transcriptional machinery to the CXCL10 promoter and an upstream enhancer. Our findings suggest that BET inhibition reduces inflammation partially through suppressing cytokine activity and expands the understanding of the inhibitory and potentially selective immunosuppressive effects of inhibiting BET proteins.
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Affiliation(s)
- Chun Hin Chan
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA
| | - Celestia Fang
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA
| | - Anna Yarilina
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA
| | - Rab K Prinjha
- GlaxoSmithKline, Epinova DPU, Stevenage, United Kingdom
| | - Yu Qiao
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA
| | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
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270
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Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature 2014; 518:249-53. [PMID: 25470060 DOI: 10.1038/nature13923] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 10/06/2014] [Indexed: 12/19/2022]
Abstract
DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helicase DDX21 can sense the transcriptional status of both RNA polymerase (Pol) I and II to control multiple steps of ribosome biogenesis in human cells. We demonstrate that DDX21 widely associates with Pol I- and Pol II-transcribed genes and with diverse species of RNA, most prominently with non-coding RNAs involved in the formation of ribonucleoprotein complexes, including ribosomal RNA, small nucleolar RNAs (snoRNAs) and 7SK RNA. Although broad, these molecular interactions, both at the chromatin and RNA level, exhibit remarkable specificity for the regulation of ribosomal genes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. In the nucleoplasm, DDX21 binds 7SK RNA and, as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, is recruited to the promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control.
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Affiliation(s)
- Eliezer Calo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lance Martin
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Robert C Spitale
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Joanna Wysocka
- 1] Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2] Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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271
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Kaikkonen MU, Niskanen H, Romanoski CE, Kansanen E, Kivelä AM, Laitalainen J, Heinz S, Benner C, Glass CK, Ylä-Herttuala S. Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. Nucleic Acids Res 2014; 42:12570-84. [PMID: 25352550 PMCID: PMC4227755 DOI: 10.1093/nar/gku1036] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Vascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using genome-wide global run-on sequencing (GRO-Seq). We demonstrate that half of VEGF-A-regulated gene promoters are characterized by a transcriptionally competent paused RNA polymerase II (Pol II). We show that transition into productive elongation is a major mechanism of gene activation of virtually all VEGF-regulated genes, whereas only ∼40% of the genes are induced at the level of initiation. In addition, we report a comprehensive chromatin interaction map generated in HUVECs using tethered conformation capture (TCC) and characterize chromatin interactions in relation to transcriptional activity. We demonstrate that sites of active transcription are more likely to engage in chromatin looping and cell type-specific transcriptional activity reflects the boundaries of chromatin interactions. Furthermore, we identify large chromatin compartments with a tendency to be coordinately transcribed upon VEGF-A stimulation. We provide evidence that these compartments are enriched for clusters of regulatory regions such as super-enhancers and for disease-associated single nucleotide polymorphisms (SNPs). Collectively, these findings provide new insights into mechanisms behind VEGF-A-regulated transcriptional programs in endothelial cells.
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Affiliation(s)
- Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Henri Niskanen
- A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Emilia Kansanen
- A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Annukka M Kivelä
- A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Jarkko Laitalainen
- A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Sven Heinz
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Finland
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272
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Abstract
Enhancers establish spatial or temporal patterns of gene expression that are critical for development, yet our understanding of how these DNA cis-regulatory elements function from a distance to increase transcription of their target genes and shape the cellular transcriptome has been gleaned primarily from studies of individual genes or gene families. High-throughput sequencing studies place enhancer-gene interactions within the 3D context of chromosome folding, inviting a new look at enhancer function and stimulating provocative new questions. Here, we integrate these whole-genome studies with recent mechanistic studies to illuminate how enhancers physically interact with target genes, how enhancer activity is regulated during development, and the role of noncoding RNAs transcribed from enhancers in their function.
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Affiliation(s)
- Jennifer L Plank
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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273
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Jahan S, Davie JR. Protein arginine methyltransferases (PRMTs): role in chromatin organization. Adv Biol Regul 2014; 57:173-84. [PMID: 25263650 DOI: 10.1016/j.jbior.2014.09.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/06/2014] [Indexed: 01/19/2023]
Abstract
The mammalian genome encodes eleven protein arginine methyltransferases (PRMTs) that are involved in the transfer of a methyl group from S-adenosylmethionine (AdoMet) to the guanidino nitrogen of arginine. The substrates for these enzymes range from histones to several nuclear and cytoplasmic proteins. Methylation of histones by PRMTs can block the docking site for other reader/effector molecules and thus this modification can interfere with histone code orchestration. Several members of the PRMTs have roles in chromatin organization and function. Although PRMT aberrant expression is correlated with several diseases including cancer, the underlying mechanisms are still obscure in most cases.
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Affiliation(s)
- Sanzida Jahan
- Manitoba Institute of Child Health, University of Manitoba, Winnipeg, Manitoba R3E 3P4 Canada
| | - James R Davie
- Manitoba Institute of Child Health, University of Manitoba, Winnipeg, Manitoba R3E 3P4 Canada.
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274
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Chen CF, Feng X, Liao HY, Jin WJ, Zhang J, Wang Y, Gong LL, Liu JJ, Yuan XH, Zhao BB, Zhang D, Chen GF, Wan Y, Guo J, Yan HP, He YW. Regulation of T cell proliferation by JMJD6 and PDGF-BB during chronic hepatitis B infection. Sci Rep 2014; 4:6359. [PMID: 25219359 PMCID: PMC4163673 DOI: 10.1038/srep06359] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/24/2014] [Indexed: 01/31/2023] Open
Abstract
T cell functional exhaustion during chronic hepatitis B virus (HBV) infection may contribute to the failed viral clearance; however, the underlying molecular mechanisms remain largely unknown. Here we demonstrate that jumonji domain-containing protein 6 (JMJD6) is a potential regulator of T cell proliferation during chronic HBV infection. The expression of JMJD6 was reduced in T lymphocytes in chronic hepatitis B (CHB) patients, and this reduction in JMJD6 expression was associated with impaired T cell proliferation. Moreover, silencing JMJD6 expression in primary human T cells impaired T cell proliferation. We found that JMJD6 promotes T cell proliferation by suppressing the mRNA expression of CDKN3. Furthermore, we have identified platelet derived growth factor-BB (PDGF-BB) as a regulator of JMJD6 expression. PDGF-BB downregulates JMJD6 expression and inhibits the proliferation of human primary T cells. Importantly, the expression levels of JMJD6 and PDGF-BB in lymphocytes from CHB patients were correlated with the degree of liver damage and the outcome of chronic HBV infection treatment. Our results demonstrate that PDGF-BB and JMJD6 regulate T cell function during chronic HBV infection and may provide insights for the treatment strategies for CHB patients.
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Affiliation(s)
- Cai-Feng Chen
- 1] MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, People's Republic of China [2]
| | - Xia Feng
- 1] Center for Infection and Immunity, YouAn Hospital, The Beijing Capital Medical University, Beijing, China [2]
| | - Hui-Yu Liao
- 1] Center for Infection and Immunity, YouAn Hospital, The Beijing Capital Medical University, Beijing, China [2]
| | - Wen-Jing Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, People's Republic of China
| | - Jian Zhang
- Diagnosis and Treatment Center of Liver Fibrosis, 302 Hospital, Beijing, China
| | - Yu Wang
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Lu-Lu Gong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, People's Republic of China
| | - Jing-Jun Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, People's Republic of China
| | - Xiao-Hui Yuan
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, People's Republic of China
| | - Bin-Bin Zhao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, People's Republic of China
| | - Ding Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, People's Republic of China
| | - Guo-Feng Chen
- Diagnosis and Treatment Center of Liver Fibrosis, 302 Hospital, Beijing, China
| | - Ying Wan
- Biomedical Analysis Center, The Third Military Medical University, Chongqing, China
| | - Jian Guo
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Hui-Ping Yan
- Center for Infection and Immunity, YouAn Hospital, The Beijing Capital Medical University, Beijing, China
| | - You-Wen He
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
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275
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Gayatri S, Bedford MT. Readers of histone methylarginine marks. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:702-10. [PMID: 24583552 PMCID: PMC4099268 DOI: 10.1016/j.bbagrm.2014.02.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/31/2014] [Accepted: 02/14/2014] [Indexed: 11/15/2022]
Abstract
Arginine methylation is a common posttranslational modification (PTM) that alters roughly 0.5% of all arginine residues in the cells. There are three types of arginine methylation: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA). These three PTMs are enriched on RNA-binding proteins and on histones, and also impact signal transduction cascades. To date, over thirty arginine methylation sites have been cataloged on the different core histones. These modifications alter protein structure, impact interactions with DNA, and also generate docking sites for effector molecules. The primary "readers" of methylarginine marks are Tudor domain-containing proteins. The complete family of thirty-six Tudor domain-containing proteins has yet to be fully characterized, but at least ten bind methyllysine motifs and eight bind methylarginine motifs. In this review, we will highlight the biological roles of the Tudor domains that interact with arginine methylated motifs, and also address other types of interactions that are regulated by these particular PTMs. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Sitaram Gayatri
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mark T Bedford
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
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276
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Nagarajan S, Hossan T, Alawi M, Najafova Z, Indenbirken D, Bedi U, Taipaleenmäki H, Ben-Batalla I, Scheller M, Loges S, Knapp S, Hesse E, Chiang CM, Grundhoff A, Johnsen SA. Bromodomain protein BRD4 is required for estrogen receptor-dependent enhancer activation and gene transcription. Cell Rep 2014; 8:460-9. [PMID: 25017071 PMCID: PMC4747248 DOI: 10.1016/j.celrep.2014.06.016] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/13/2014] [Accepted: 06/11/2014] [Indexed: 12/24/2022] Open
Abstract
The estrogen receptor α (ERα) controls cell proliferation and tumorigenesis by recruiting various cofactors to estrogen response elements (EREs) to control gene transcription. A deeper understanding of these transcriptional mechanisms may uncover therapeutic targets for ERα-dependent cancers. We show that BRD4 regulates ERα-induced gene expression by affecting elongation-associated phosphorylation of RNA polymerase II (RNAPII) and histone H2B monoubiquitination. Consistently, BRD4 activity is required for proliferation of ER(+) breast and endometrial cancer cells and uterine growth in mice. Genome-wide studies revealed an enrichment of BRD4 on transcriptional start sites of active genes and a requirement of BRD4 for H2B monoubiquitination in the transcribed region of estrogen-responsive genes. Importantly, we demonstrate that BRD4 occupancy on distal EREs enriched for H3K27ac is required for recruitment and elongation of RNAPII on EREs and the production of ERα-dependent enhancer RNAs. These results uncover BRD4 as a central regulator of ERα function and potential therapeutic target.
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Affiliation(s)
- Sankari Nagarajan
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany; Institute for Molecular Oncology, University Medical Center Göttingen, 37077 Göttingen, Germany; Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tareq Hossan
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany; Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Zeynab Najafova
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany; Institute for Molecular Oncology, University Medical Center Göttingen, 37077 Göttingen, Germany; Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Upasana Bedi
- Institute for Molecular Oncology, University Medical Center Göttingen, 37077 Göttingen, Germany; Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hanna Taipaleenmäki
- Heisenberg-Group for Molecular Skeletal Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Isabel Ben-Batalla
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Marina Scheller
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sonja Loges
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Target Discovery Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Eric Hesse
- Heisenberg-Group for Molecular Skeletal Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Cheng-Ming Chiang
- University of Texas Southwestern Medical Center, Dallas, TX 75390-8807, USA
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany; Institute for Molecular Oncology, University Medical Center Göttingen, 37077 Göttingen, Germany; Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
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277
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Bonora G, Plath K, Denholtz M. A mechanistic link between gene regulation and genome architecture in mammalian development. Curr Opin Genet Dev 2014; 27:92-101. [PMID: 24998386 DOI: 10.1016/j.gde.2014.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/15/2014] [Accepted: 05/10/2014] [Indexed: 11/19/2022]
Abstract
The organization of chromatin within the nucleus and the regulation of transcription are tightly linked. Recently, mechanisms underlying this relationship have been uncovered. By defining the organizational hierarchy of the genome, determining changes in chromatin organization associated with changes in cell identity, and describing chromatin organization within the context of linear genomic features (such as chromatin modifications and transcription factor binding) and architectural proteins (including Cohesin, CTCF, and Mediator), a new paradigm in genome biology was established wherein genomes are organized around gene regulatory factors that govern cell identity. As such, chromatin organization plays a central role in establishing and maintaining cell state during development, with gene regulation and genome organization being mutually dependent effectors of cell identity.
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Affiliation(s)
- Giancarlo Bonora
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, CA 90095, USA
| | - Kathrin Plath
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, CA 90095, USA.
| | - Matthew Denholtz
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, CA 90095, USA.
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278
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Verstraete N, Kuzmina A, Diribarne G, Nguyen VT, Kobbi L, Ludanyi M, Taube R, Bensaude O. A Cyclin T1 point mutation that abolishes positive transcription elongation factor (P-TEFb) binding to Hexim1 and HIV tat. Retrovirology 2014; 11:50. [PMID: 24985203 PMCID: PMC4227133 DOI: 10.1186/1742-4690-11-50] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background The positive transcription elongation factor b (P-TEFb) plays an essential role in activating HIV genome transcription. It is recruited to the HIV LTR promoter through an interaction between the Tat viral protein and its Cyclin T1 subunit. P-TEFb activity is inhibited by direct binding of its subunit Cyclin T (1 or 2) with Hexim (1 or 2), a cellular protein, bound to the 7SK small nuclear RNA. Hexim1 competes with Tat for P-TEFb binding. Results Mutations that impair human Cyclin T1/Hexim1 interaction were searched using systematic mutagenesis of these proteins coupled with a yeast two-hybrid screen for loss of protein interaction. Evolutionary conserved Hexim1 residues belonging to an unstructured peptide located N-terminal of the dimerization domain, were found to be critical for P-TEFb binding. Random mutagenesis of the N-terminal region of Cyclin T1 provided identification of single amino-acid mutations that impair Hexim1 binding in human cells. Furthermore, conservation of critical residues supported the existence of a functional Hexim1 homologue in nematodes. Conclusions Single Cyclin T1 amino-acid mutations that impair Hexim1 binding are located on a groove between the two cyclin folds and define a surface overlapping the HIV-1 Tat protein binding surface. One residue, Y175, in the centre of this groove was identified as essential for both Hexim1 and Tat binding to P-TEFb as well as for HIV transcription.
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Affiliation(s)
| | | | | | | | | | | | | | - Olivier Bensaude
- Institut de Biologie de l'Ecole Normale Supérieure, Paris F-75005, France.
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279
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Heim A, Grimm C, Müller U, Häußler S, Mackeen MM, Merl J, Hauck SM, Kessler BM, Schofield CJ, Wolf A, Böttger A. Jumonji domain containing protein 6 (Jmjd6) modulates splicing and specifically interacts with arginine-serine-rich (RS) domains of SR- and SR-like proteins. Nucleic Acids Res 2014; 42:7833-50. [PMID: 24914048 PMCID: PMC4081092 DOI: 10.1093/nar/gku488] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Fe(II) and 2-oxoglutarate dependent oxygenase Jmjd6 has been shown to hydroxylate lysine residues in the essential splice factor U2 auxiliary factor 65 kDa subunit (U2AF65) and to act as a modulator of alternative splicing. We describe further evidence for the role of Jmjd6 in the regulation of pre-mRNA processing including interactions of Jmjd6 with multiple arginine–serine-rich (RS)-domains of SR- and SR-related proteins including U2AF65, Luc7-like protein 3 (Luc7L3), SRSF11 and Acinus S′, but not with the bona fide RS-domain of SRSF1. The identified Jmjd6 target proteins are involved in different mRNA processing steps and play roles in exon dependent alternative splicing and exon definition. Moreover, we show that Jmjd6 modifies splicing of a constitutive splice reporter, binds RNA derived from the reporter plasmid and punctually co-localises with nascent RNA. We propose that Jmjd6 exerts its splice modulatory function by interacting with specific SR-related proteins during splicing in a RNA dependent manner.
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Affiliation(s)
- Astrid Heim
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Christina Grimm
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Udo Müller
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Simon Häußler
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Mukram M Mackeen
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK Research Unit Protein Science, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Juliane Merl
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Stefanie M Hauck
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Benedikt M Kessler
- School of Chemical Science, Faculty of Science and Technology, and Institute of Systems Biology (INBIOSIS) Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
| | - Christopher J Schofield
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Alexander Wolf
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Angelika Böttger
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
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280
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Abstract
The bromodomain and extraterminal (BET) protein Brd4 recruits transcriptional regulatory complexes to acetylated chromatin. While Brd4 is considered to be a general transcriptional regulator, pharmacological inhibition of BET proteins shows therapeutic activity in a variety of different pathologies, particularly in models of cancer and inflammation. Such effects have been attributed to a specific set of downstream target genes whose expression is disproportionately sensitive to pharmacological targeting of BET proteins. Emerging evidence links the transcriptional consequences of BET inhibition to the association of Brd4 with enhancer elements, which tend to be involved in lineage-specific gene regulation. Furthermore, Brd4 engages in direct regulatory interactions with several DNA-binding transcription factors to influence their disease-relevant functions. Here we review the current understanding of molecular mechanisms that underlie the promising therapeutic effects of BET bromodomain inhibition.
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Affiliation(s)
- Junwei Shi
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA
| | - Christopher R Vakoc
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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281
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Insights from Genetic Models of Melanoma in Fish. CURRENT PATHOBIOLOGY REPORTS 2014. [DOI: 10.1007/s40139-014-0043-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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282
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Affiliation(s)
- Kamaleldin E Elagib
- Department of Pathology; University of Virginia School of Medicine; Charlottesville, VA USA
| | - Adam N Goldfarb
- Department of Pathology; University of Virginia School of Medicine; Charlottesville, VA USA
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283
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JUNB promotes the survival of Flavopiridol treated human breast cancer cells. Biochem Biophys Res Commun 2014; 450:19-24. [PMID: 24858691 DOI: 10.1016/j.bbrc.2014.05.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/23/2022]
Abstract
Chemotherapy resistance is a major obstacle to achieving durable progression-free-survival in breast cancer patients. Identifying resistance mechanisms is crucial to the development of effective breast cancer therapies. Immediate early genes (IEGs) function in the initial cellular reprogramming response to alterations in the extracellular environment and IEGs have been implicated in cancer cell development and progression. The purpose of this study was to investigate the influence of kinase inhibitors on IEG expression in breast cancer cells. The results demonstrated that Flavopiridol (FP), a CDK9 inhibitor, effectively reduced gene expression. FP treatment, however, consistently produced a delayed induction of JUNB gene expression in multiple breast cancer cell lines. Similar results were obtained with Sorafenib, a multi-kinase inhibitor and U0126, a MEK1 inhibitor. Functional studies revealed that JUNB plays a pro-survival role in kinase inhibitor treated breast cancer cells. These results demonstrate a unique induction of JUNB in response to kinase inhibitor therapies that may be among the earliest events in the progression to treatment resistance.
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284
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Lyons DB, Lomvardas S. Repressive histone methylation: a case study in deterministic versus stochastic gene regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1373-84. [PMID: 24859457 DOI: 10.1016/j.bbagrm.2014.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 05/13/2014] [Indexed: 01/21/2023]
Abstract
Transcriptionally repressive histone lysine methylation is used by eukaryotes to tightly control cell fate. Here we explore the importance of this form of regulation in the control of clustered genes in the genome. Two distinctly regulated gene families with important roles in vertebrates are discussed, namely the Hox genes and olfactory receptor genes. Major recent advances in these two fields are compared and contrasted, with an emphasis on the roles of the two different forms of histone trimethylation. We discuss how this repression may impact both the transcriptional output of these loci and the way higher-order chromatin organization is related to their unique control.
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Affiliation(s)
- David B Lyons
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stavros Lomvardas
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Anatomy, University of California San Francisco, CA 94920, USA.
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285
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Abstract
A striking finding in the past decade is the production of numerous non-coding RNAs (ncRNAs) from mammalian genomes. While it is entirely possible that many of those ncRNAs are transcription noises or by-products of RNA processing, increasing evidence suggests that a large fraction of them are functional and provide various regulatory activities in the cell. Thus, functional genomics and proteomics are incomplete without understanding functional ribonomics. As has been long suggested by the 'RNA world' hypothesis, many ncRNAs have the capacity to act like proteins in diverse biochemical processes. The enormous amount of information residing in the primary sequences and secondary structures of ncRNAs makes them particularly suited to function as scaffolds for molecular interactions. In addition, their functions appear to be stringently controlled by default via abundant nucleases when not engaged in specific interactions. This review focuses on the functional properties of regulatory ncRNAs in comparison with proteins and emphasizes both the opportunities and challenges in future ncRNA research.
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Affiliation(s)
- Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
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286
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Schaefer U, Ho JSY, Prinjha RK, Tarakhovsky A. The "histone mimicry" by pathogens. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2014; 78:81-90. [PMID: 24733380 DOI: 10.1101/sqb.2013.78.020339] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One of the defining characteristics of human and animal viruses is their ability to suppress host antiviral responses. Viruses express proteins that impair the detection of viral nucleic acids by host pattern-recognition receptors, block signaling pathways that lead to the synthesis of type I interferons and other cytokines, or prevent the activation of virus-induced genes. We have identified a novel mechanism of virus-mediated suppression of antiviral gene expression that relies on the presence of histone-like sequences (histone mimics) in viral proteins. We describe how viral histone mimics can interfere with key regulators of gene expression and contribute to the suppression of antiviral responses. We also describe how viral histone mimics can facilitate the identification of novel mechanisms of antiviral gene regulation and lead to the development of drugs that use histone mimicry for interference with gene expression during diseases.
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Affiliation(s)
- Uwe Schaefer
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, New York 10065
| | - Jessica S Y Ho
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, New York 10065 Laboratory of Methyltransferases in Development and Disease, Institute of Molecular and Cell Biology (IMCB), Singapore 138673
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline, Medicines Research Centre, Stevenage SG1 2NY, United Kingdom
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, New York 10065
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287
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Lokody I. BRD4 and JMJD6 regulate antipause enhancers. Nat Rev Genet 2014. [DOI: 10.1038/nrg3671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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288
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Abstract
In the past several decades, intensive research in this field has uncovered a surprising number of regulatory factors and their associated enzymatic properties to reveal the network of complexes that function in activation and repression of the transcriptional programs mediated by nuclear receptors (NR). These factors and their associated complexes have been extensively characterized both biochemically and functionally [34, 87, 94]. Several principles have emerged: (1) It is widely recognized that ligand-dependent cofactor complexes mediating repression and activation exhibit ligand-dependent exchange. (2) These complexes mediate modifications of chromatin structure consequent to their binding at regulatory elements, particularly at promoter and enhancer Enhancer sites. (3) The concept about the rapid exchange of coregulatory complexes at regulatory sites has been suggested [88]. Key questions in the NR field have included: (a) What are the cofactors and exchange complexes used to mediate the ligand and signaling network-dependent switches in gene regulation programs; (b) Do long non-coding RNAs (lncRNAs) serve as regulatory "factors" for ligand-dependent gene programs, and do enhancers actually regulate transcription units encoding enhancer Enhancer non-coding RNAs (eRNAs) Enhancer RNA that might have functional significance; (c) What is the relationship between DNA damage repair machinery and transcriptional machinery? (d) Do Retinoic Acid Receptors (RAR) also regulate Pol III-dependent, non-coding repeat transcriptional units in stem cells? and (e) How have new technologies such as deep sequencing altered our ability to investigate transcriptional regulatory mechanisms utilized by NRs?
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Affiliation(s)
- Zhijie Liu
- Howard Hughes Medical Institute, Department of Medicine, University of California, La Jolla, San Diego, CA, USA,
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