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Chang CY, Liu HM, Chang MF, Chang SC. Middle East Respiratory Syndrome Coronavirus Nucleocapsid Protein Suppresses Type I and Type III Interferon Induction by Targeting RIG-I Signaling. J Virol 2020; 94:e00099-20. [PMID: 32295922 PMCID: PMC7307178 DOI: 10.1128/jvi.00099-20] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Type I and type III interferons (IFNs) are the frontline of antiviral defense mechanisms that trigger hundreds of downstream antiviral genes. In this study, we observed that MERS-CoV nucleocapsid (N) protein suppresses type I and type III IFN gene expression. The N protein suppresses Sendai virus-induced IFN-β and IFN-λ1 by reducing their promoter activity and mRNA levels, as well as downstream IFN-stimulated genes (ISGs). Retinoic acid-inducible gene I (RIG-I) is known to recognize viral RNA and induce IFN expression through tripartite motif-containing protein 25 (TRIM25)-mediated ubiquitination of RIG-I caspase activation and recruitment domains (CARDs). We discovered that MERS-CoV N protein suppresses RIG-I-CARD-induced, but not MDA5-CARD-induced, IFN-β and IFN-λ1 promoter activity. By interacting with TRIM25, N protein impedes RIG-I ubiquitination and activation and inhibits the phosphorylation of transcription factors IFN-regulatory factor 3 (IRF3) and NF-κB that are known to be important for IFN gene activation. By employing a recombinant Sindbis virus-EGFP replication system, we showed that viral N protein downregulated the production of not only IFN mRNA but also bioactive IFN proteins. Taken together, MERS-CoV N protein functions as an IFN antagonist. It suppresses RIG-I-induced type I and type III IFN production by interfering with TRIM25-mediated RIG-I ubiquitination. Our study sheds light on the pathogenic mechanism of how MERS-CoV causes disease.IMPORTANCE MERS-CoV causes death of about 35% of patients. Published studies showed that some coronaviruses are capable of suppressing interferon (IFN) expression in the early phase of infection and MERS-CoV proteins can modulate host immune response. In this study, we demonstrated that MERS-CoV nucleocapsid (N) protein suppresses the production of both type I and type III IFNs via sequestering TRIM25, an E3 ubiquitin ligase that is essential for activating the RIG-I signaling pathway. Ectopic expression of TRIM25 rescues the suppressive effect of the N protein. In addition, the C-terminal domain of the viral N protein plays a pivotal role in the suppression of IFN-β promoter activity. Our findings reveal how MERS-CoV evades innate immunity and provide insights into the interplay between host immune response and viral pathogenicity.
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Affiliation(s)
- Chi-You Chang
- Institute of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Helene Minyi Liu
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ming-Fu Chang
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shin C Chang
- Institute of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
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2
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The High Mobility Group A1 (HMGA1) Chromatin Architectural Factor Modulates Nuclear Stiffness in Breast Cancer Cells. Int J Mol Sci 2019; 20:ijms20112733. [PMID: 31167352 PMCID: PMC6600462 DOI: 10.3390/ijms20112733] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022] Open
Abstract
Plasticity is an essential condition for cancer cells to invade surrounding tissues. The nucleus is the most rigid cellular organelle and it undergoes substantial deformations to get through environmental constrictions. Nuclear stiffness mostly depends on the nuclear lamina and chromatin, which in turn might be affected by nuclear architectural proteins. Among these is the HMGA1 (High Mobility Group A1) protein, a factor that plays a causal role in neoplastic transformation and that is able to disentangle heterochromatic domains by H1 displacement. Here we made use of atomic force microscopy to analyze the stiffness of breast cancer cellular models in which we modulated HMGA1 expression to investigate its role in regulating nuclear plasticity. Since histone H1 is the main modulator of chromatin structure and HMGA1 is a well-established histone H1 competitor, we correlated HMGA1 expression and cellular stiffness with histone H1 expression level, post-translational modifications, and nuclear distribution. Our results showed that HMGA1 expression level correlates with nuclear stiffness, is associated to histone H1 phosphorylation status, and alters both histone H1 chromatin distribution and expression. These data suggest that HMGA1 might promote chromatin relaxation through a histone H1-mediated mechanism strongly impacting on the invasiveness of cancer cells.
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3
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Cao L, Yang G, Gao S, Jing C, Montgomery RR, Yin Y, Wang P, Fikrig E, You F. HIPK2 is necessary for type I interferon-mediated antiviral immunity. Sci Signal 2019; 12:12/573/eaau4604. [PMID: 30890658 DOI: 10.1126/scisignal.aau4604] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Precise control of interferons (IFNs) is crucial to maintain immune homeostasis. Here, we demonstrated that homeodomain-interacting protein kinase 2 (HIPK2) was required for the production of type I IFNs in response to RNA virus infection. HIPK2 deficiency markedly impaired IFN production in macrophages after vesicular stomatitis virus (VSV) infection, and HIPK2-deficient mice were more susceptible to lethal VSV disease than were wild-type mice. After VSV infection, HIPK2 was cleaved by active caspases, which released a hyperactive, N-terminal fragment that translocated to the nucleus and further augmented antiviral responses. In part, HIPK2 interacted with ELF4 and promoted its phosphorylation at Ser369, which enabled Ifn-b transcription. In addition, HIPK2 production was stimulated by type I IFNs to further enhance antiviral immunity. These data suggest that the kinase activity and nuclear localization of HIPK2 are essential for the production of type I IFNs.
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Affiliation(s)
- Lili Cao
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China
| | - Guang Yang
- Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 208022, USA.,Department of Parasitology, Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, No. 601, Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Shandian Gao
- Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 208022, USA
| | - Chunxia Jing
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Ruth R Montgomery
- Section of Rheumatology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China
| | - Penghua Wang
- Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 208022, USA.,Department of Immunology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Erol Fikrig
- Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 208022, USA. .,Howard Hughes Medical Institute, Chevy Chase, MA 20815, USA
| | - Fuping You
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
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The murine cytomegalovirus M35 protein antagonizes type I IFN induction downstream of pattern recognition receptors by targeting NF-κB mediated transcription. PLoS Pathog 2017; 13:e1006382. [PMID: 28542326 PMCID: PMC5444856 DOI: 10.1371/journal.ppat.1006382] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/26/2017] [Indexed: 12/25/2022] Open
Abstract
The type I interferon (IFN) response is imperative for the establishment of the early antiviral immune response. Here we report the identification of the first type I IFN antagonist encoded by murine cytomegalovirus (MCMV) that shuts down signaling following pattern recognition receptor (PRR) sensing. Screening of an MCMV open reading frame (ORF) library identified M35 as a novel and strong negative modulator of IFNβ promoter induction following activation of both RNA and DNA cytoplasmic PRR. Additionally, M35 inhibits the proinflammatory cytokine response downstream of Toll-like receptors (TLR). Using a series of luciferase-based reporters with specific transcription factor binding sites, we determined that M35 targets NF-κB-, but not IRF-mediated, transcription. Expression of M35 upon retroviral transduction of immortalized bone marrow-derived macrophages (iBMDM) led to reduced IFNβ transcription and secretion upon activation of stimulator of IFN genes (STING)-dependent signaling. On the other hand, M35 does not antagonize interferon-stimulated gene (ISG) 56 promoter induction or ISG transcription upon exogenous stimulation of the type I IFN receptor (IFNAR). M35 is present in the viral particle and, upon MCMV infection of fibroblasts, is immediately shuttled to the nucleus where it exerts its immunomodulatory effects. Deletion of M35 from the MCMV genome and hence from the viral particle resulted in elevated type I IFN transcription and secretion in vitro and in vivo. In the absence of M35, lower viral titers are observed during acute infection of the host, and productive infection in the salivary glands was not detected. In conclusion, the M35 protein is released by MCMV immediately upon infection in order to deftly inhibit the antiviral type I IFN response by targeting NF-κB-mediated transcription. The identification of this novel viral protein reinforces the importance of timely countermeasures in the complex relationship between virus and host. The herpesvirus cytomegalovirus can cause severe morbidity in immunosuppressed people and poses a much greater global problem in the context of congenital infections than the Zika virus. To establish infection, cytomegalovirus needs to modulate the antiviral immune response of its host. One of the first lines of defense against viral infections is the type I interferon response which is activated by cellular sensors called pattern recognition receptors. These receptors sense viral entry and rapidly induce the transcription of type I interferons, which are instrumental for the induction of an antiviral state in infected and surrounding cells. We have identified the first viral protein encoded by murine cytomegalovirus, the M35 protein, that counteracts type I interferon transcription downstream of multiple pattern recognition receptors. We found that this viral countermeasure occurs shortly after viral entry into the host cell, as M35 is delivered with the viral particle. M35 then localizes to the nucleus where it modulates NF-κB-mediated transcription. In vivo, murine cytomegalovirus deficient of the M35 protein replicates to lower levels in spleen and liver and cannot establish a productive infection in the salivary glands, which is a key site of viral transmission, highlighting the important role of M35 for the establishment of infection. Our study provides novel insights into the complex interaction between cytomegalovirus and the innate immune response of its host.
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β-Catenin Upregulates the Constitutive and Virus-Induced Transcriptional Capacity of the Interferon Beta Promoter through T-Cell Factor Binding Sites. Mol Cell Biol 2015; 36:13-29. [PMID: 26459757 DOI: 10.1128/mcb.00641-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/02/2015] [Indexed: 12/12/2022] Open
Abstract
Rapid upregulation of interferon beta (IFN-β) expression following virus infection is essential to set up an efficient innate antiviral response. Biological roles related to the antiviral and immune response have also been associated with the constitutive production of IFN-β in naive cells. However, the mechanisms capable of modulating constitutive IFN-β expression in the absence of infection remain largely unknown. In this work, we demonstrate that inhibition of the kinase glycogen synthase kinase 3 (GSK-3) leads to the upregulation of the constitutive level of IFN-β expression in noninfected cells, provided that GSK-3 inhibition is correlated with the binding of β-catenin to the IFN-β promoter. Under these conditions, IFN-β expression occurred through the T-cell factor (TCF) binding sites present on the IFN-β promoter independently of interferon regulatory factor 3 (IRF3). Enhancement of the constitutive level of IFN-β per se was able to confer an efficient antiviral state to naive cells and acted in synergy with virus infection to stimulate virus-induced IFN-β expression. Further emphasizing the role of β-catenin in the innate antiviral response, we show here that highly pathogenic Rift Valley fever virus (RVFV) targets the Wnt/β-catenin pathway and the formation of active TCF/β-catenin complexes at the transcriptional and protein level in RVFV-infected cells and mice.
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Idelman G, Smith DLH, Zucker SD. Bilirubin inhibits the up-regulation of inducible nitric oxide synthase by scavenging reactive oxygen species generated by the toll-like receptor 4-dependent activation of NADPH oxidase. Redox Biol 2015; 5:398-408. [PMID: 26163808 PMCID: PMC4506991 DOI: 10.1016/j.redox.2015.06.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 06/15/2015] [Indexed: 12/15/2022] Open
Abstract
It has been previously shown that bilirubin prevents the up-regulation of inducible nitric oxide synthase (iNOS) in response to LPS. The present study examines whether this effect is exerted through modulation of Toll-Like Receptor-4 (TLR4) signaling. LPS-stimulated iNOS and NADPH oxidase (Nox) activity in RAW 264.7 murine macrophages was assessed by measuring cellular nitrate and superoxide ( [Formula: see text] ) production, respectively. The generation of both nitrate and [Formula: see text] in response to LPS was suppressed by TLR4 inhibitors, indicating that activation of iNOS and Nox is TLR4-dependent. While treatment with superoxide dismutase (SOD) and bilirubin effectively abolished LPS-mediated [Formula: see text] production, hydrogen peroxide and nitrate release were inhibited by bilirubin and PEG-catalase, but not SOD, supporting that iNOS activation is primarily dependent upon intracellular H2O2. LPS treatment increased nuclear translocation of the redox-sensitive transcription factor Hypoxia Inducible Factor-1α (HIF-1α), an effect that was abolished by bilirubin. Cells transfected with murine iNOS reporter constructs in which the HIF-1α-specific hypoxia response element was disrupted exhibited a blunted response to LPS, supporting that HIF-1α mediates Nox-dependent iNOS expression. Bilirubin, but not SOD, blocked the cellular production of interferon-β, while interleukin-6 production remained unaffected. These data support that bilirubin inhibits the TLR4-mediated up-regulation of iNOS by preventing activation of HIF-1α through scavenging of Nox-derived reactive oxygen species. Bilirubin also suppresses interferon-β release via a ROS-independent mechanism. These findings characterize potential mechanisms for the anti-inflammatory effects of bilirubin.
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Affiliation(s)
- Gila Idelman
- Division of Digestive Diseases, University of Cincinnati, Cincinnati, OH 45267-0595, USA
| | - Darcey L H Smith
- Division of Digestive Diseases, University of Cincinnati, Cincinnati, OH 45267-0595, USA
| | - Stephen D Zucker
- Division of Digestive Diseases, University of Cincinnati, Cincinnati, OH 45267-0595, USA.
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7
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ELF4 is critical for induction of type I interferon and the host antiviral response. Nat Immunol 2013; 14:1237-46. [PMID: 24185615 DOI: 10.1038/ni.2756] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/01/2013] [Indexed: 12/25/2022]
Abstract
Induction of type I interferon is a central event of innate immunity, essential for host defense. Here we report that the transcription factor ELF4 is induced by type I interferon and upregulates interferon expression in a feed-forward loop. ELF4 deficiency leads to reduced interferon production, resulting in enhanced susceptibility to West Nile virus encephalitis in mice. After viral infection, ELF4 is recruited by STING, interacts with and is activated by the MAVS-TBK1 complex, and translocates into the nucleus to bind interferon promoters. Cooperative binding with ELF4 increases the binding affinity of interferon regulatory factors IRF3 and IRF7, which is mediated by EICE elements. Thus, in addition to identifying a regulator of innate immune signaling, we uncovered a role for EICE elements in interferon transactivation.
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Han W, Shi M, Spivack SD. Site-specific methylated reporter constructs for functional analysis of DNA methylation. Epigenetics 2013; 8:1176-87. [PMID: 24004978 DOI: 10.4161/epi.26195] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Methods to experimentally alter and functionally evaluate cytosine methylation in a site-specific manner have proven elusive. We describe a site-specific DNA methylation method, using synthetically methylated primers and high fidelity PCR coupled with ligation of reporter constructs. We applied this method to introduce methylated cytosines into fragments of the respective DAPK and RASSF1A promoters that had been cloned into luciferase reporters. We found that methylation of 3-7 residue CpG clusters that were 5' adjacent to the transcription start site (TSS) of the DAPK gene produced up to a 54% decrease in promoter activity (p<0.01). Similarly, for RASSF1A promoter reporter constructs, the methylation of either of two clusters of four CpGs each, but not an intervening cluster, produced a 63% decrease in promoter activity (p<0.01), suggesting that precise mCpG position is crucial, and factors other than simple proximity to the TSS are at play. Chromatin immunoprecipitation analysis of these reporter constructs demonstrated that transcription factor Oct-1 and Sp1 preferentially bound the unmethylated vs. methylated DAPK or RASSF1A promoter reporter constructs at the functional CpG sites. Histone H1, hnRNP1, and MeCP2 showed preferential binding to methylated sequence at functional sites in these reporter constructs, as well as highly preferential (> 8-80-fold) binding to native methylated vs. unmethylated chromatin. These results suggest that: (1) site-specific, precision DNA methylation of a reporter construct can be used for functional analysis of commonly observed gene promoter methylation patterns; (2) the reporter system contains key elements of the endogenous chromatin machinery.
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Affiliation(s)
- Weiguo Han
- Pulmonary Medicine; Albert Einstein College of Medicine; Bronx, NY USA
| | - Miao Shi
- Pulmonary Medicine; Albert Einstein College of Medicine; Bronx, NY USA
| | - Simon D Spivack
- Pulmonary Medicine; Albert Einstein College of Medicine; Bronx, NY USA; Genetics; Albert Einstein College of Medicine; Bronx, NY USA
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9
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Watanabe M, Ni S, Lindenberger AL, Cho J, Tinch SL, Kennedy MA. Characterization of the Stoichiometry of HMGA1/DNA Complexes. Open Biochem J 2013; 7:73-81. [PMID: 24062859 PMCID: PMC3778555 DOI: 10.2174/1874091x01307010073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 12/09/2011] [Accepted: 12/20/2011] [Indexed: 11/22/2022] Open
Abstract
High-mobility group A1 (HMGA1) non-histone chromatin architectural transcription factors regulate gene expression, embryogenesis, cell differentiation, and adaptive immune responses by binding DNA and other transcription factors. HMGA1 has also been shown to be highly over-expressed in many human cancers and is considered to be a valuable cancer biomarker. Elevated HMGA1 expression levels also make cancer cells resistant to chemotherapy. Here, HMGA1/DNA complex formation was investigated using electrophoretic mobility shift assays (EMSA). Collectively, the EMSA results indicated that full length HMGA1 mixed with DNA containing three AT-hook binding sites formed four distinct HMGA1/DNA complexes ranging in stoichiometry from 1:2 to 3:1 in HMGA1:DNA ratio. The data indicated that the distribution of complexes with different HMGA1 to DNA stoichiometries depended on the molar ratio of HMGA1 to DNA in solution, which could have significant biological implications given that HMGA1 is highly over-expressed in human cancer cells. The two naturally occurring isoforms of HMGA1, HMGA1a and HMGA1b, the latter containing an 11 amino acid deletion between the first and second AT-hooks, were observed to have slightly different DNA binding profiles. Finally, HMGA1 binding affinity to DNA was found to be influenced by the DNA A:T segment sequence context, with higher specificity be observed in HMGA1 binding to TnAn segments, which have two local minor groove minima on either side of the TpA step, compared to An:Tn segments, which have a single minor groove minimum at the 3' end of the An run, implying AT-hook binding favors narrow minor groove structure.
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Affiliation(s)
- Miki Watanabe
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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10
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Cao K, Lailler N, Zhang Y, Kumar A, Uppal K, Liu Z, Lee EK, Wu H, Medrzycki M, Pan C, Ho PY, Cooper GP, Dong X, Bock C, Bouhassira EE, Fan Y. High-resolution mapping of h1 linker histone variants in embryonic stem cells. PLoS Genet 2013; 9:e1003417. [PMID: 23633960 PMCID: PMC3636266 DOI: 10.1371/journal.pgen.1003417] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 02/13/2013] [Indexed: 02/07/2023] Open
Abstract
H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H10 displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d, and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark. Embryonic stem cells (ESCs) possess unique chromatin and epigenetic signatures, which are important in defining the identity and genome plasticity of pluripotent stem cells. Although ESC epigenomes have been extensively characterized, the genome localization of histone H1 variants, the chromatin structural proteins facilitating higher-order chromatin folding, remains elusive. Linker histone H1 is essential for mammalian development and regulates the expression of specific genes in ESCs. Here, by using a knock-in system coupled with ChIP–seq, we first achieve the high resolution mapping of two H1 variants on a genome-wide scale in mouse ESCs. Our study reveals the correlations of this underexplored histone family with other epigenetic marks and genome attributes. Surprisingly, we identify a dramatic enrichment of H1d and H1c at major satellite sequences. H10, mapped using an overexpressing ESC line, shows similar features at active promoters but differential binding at repetitive sequences compared with H1d and H1c. Furthermore, using mutant ESCs that are deficient for multiple H1 variants, we demonstrate the role of H1 in chromocenter clustering and transcriptional repression of major satellites. Thus, these results connect this important repressive mark with the well understood ESC epigenome and identify novel functions of H1 in mammalian genome organization.
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Affiliation(s)
- Kaixiang Cao
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nathalie Lailler
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yunzhe Zhang
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Ashwath Kumar
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Karan Uppal
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Zheng Liu
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Eva K. Lee
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Hongwei Wu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Magdalena Medrzycki
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chenyi Pan
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Po-Yi Ho
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Guy P. Cooper
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Xiao Dong
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Eric E. Bouhassira
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yuhong Fan
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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11
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Josse T, Mokrani-Benhelli H, Benferhat R, Shestakova E, Mansuroglu Z, Kakanakou H, Billecocq A, Bouloy M, Bonnefoy E. Association of the interferon-β gene with pericentromeric heterochromatin is dynamically regulated during virus infection through a YY1-dependent mechanism. Nucleic Acids Res 2012; 40:4396-411. [PMID: 22287632 PMCID: PMC3378888 DOI: 10.1093/nar/gks050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Nuclear architecture as well as gene nuclear positioning can modulate gene expression. In this work, we have analyzed the nuclear position of the interferon-β (IFN-β) locus, responsible for the establishment of the innate antiviral response, with respect to pericentromeric heterochromatin (PCH) in correlation with virus-induced IFN-β gene expression. Experiments were carried out in two different cell types either non-infected (NI) or during the time course of three different viral infections. In NI cells, we showed a monoallelic IFN-β promoter association with PCH that strongly decreased after viral infection. Dissociation of the IFN-β locus away from these repressive regions preceded strong promoter transcriptional activation and was reversible within 12 h after infection. No dissociation was observed after infection with a virus that abnormally maintained the IFN-β gene in a repressed state. Dissociation induced after virus infection specifically targeted the IFN-β locus without affecting the general structure and nuclear distribution of PCH clusters. Using cell lines stably transfected with wild-type or mutated IFN-β promoters, we identified the proximal region of the IFN-β promoter containing YY1 DNA-binding sites as the region regulating IFN-β promoter association with PCH before as well as during virus infection.
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Affiliation(s)
- T Josse
- Régulation de la Transcription et Maladies Génétiques, CNRS FRE3235, Université Paris Descartes, 45 rue des Saints Pères, 75270, Paris cedex 06, France
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12
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Kelly BL, Singh G, Aiyar A. Molecular and cellular characterization of an AT-hook protein from Leishmania. PLoS One 2011; 6:e21412. [PMID: 21731738 PMCID: PMC3121789 DOI: 10.1371/journal.pone.0021412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 05/27/2011] [Indexed: 11/26/2022] Open
Abstract
AT-rich DNA, and the proteins that bind it (AT-hook proteins), modulate chromosome structure and function in most eukaryotes. Unlike other trypanosomatids, the genome of Leishmania species is unusually GC-rich, and the regulation of Leishmania chromosome structure, replication, partitioning is not fully understood. Because AT-hook proteins modulate these functions in other eukaryotes, we examined whether AT-hook proteins are encoded in the Leishmania genome, to test their potential functions. Several Leishmania ORFs predicted to be AT-hook proteins were identified using in silico approaches based on sequences shared between eukaryotic AT-hook proteins. We have used biochemical, molecular and cellular techniques to characterize the L. amazonensis ortholog of the L. major protein LmjF06.0720, a potential AT-hook protein that is highly conserved in Leishmania species. Using a novel fusion between the AT-hook domain encoded by LmjF06.0720 and a herpesviral protein, we have demonstrated that LmjF06.0720 functions as an AT-hook protein in mammalian cells. Further, as observed for mammalian and viral AT-hook proteins, the AT-hook domains of LmjF06.0720 bind specific regions of condensed mammalian metaphase chromosomes, and support the licensed replication of DNA in mammalian cells. LmjF06.0720 is nuclear in Leishmania, and this localization is disrupted upon exposure to drugs that displace AT-hook proteins from AT-rich DNA. Coincidentally, these drugs dramatically alter the cellular physiology of Leishmania promastigotes. Finally, we have devised a novel peptido-mimetic agent derived from the sequence of LmjF06.0720 that blocks the proliferation of Leishmania promastigotes, and lowers amastigote parasitic burden in infected macrophages. Our results indicate that AT-hook proteins are critical for the normal biology of Leishmania. In addition, we have described a simple technique to examine the function of Leishmania chromatin-binding proteins in a eukaryotic context amenable to studying chromosome structure and function. Lastly, we demonstrate the therapeutic potential of compounds directed against AT-hook proteins in Leishmania.
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Affiliation(s)
- Ben L. Kelly
- Department of Microbiology, Immunology and Parasitology, Lousiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Gyanendra Singh
- Stanley S. Scott Cancer Center, Lousiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Ashok Aiyar
- Department of Microbiology, Immunology and Parasitology, Lousiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
- Stanley S. Scott Cancer Center, Lousiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
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Eilebrecht S, Brysbaert G, Wegert T, Urlaub H, Benecke BJ, Benecke A. 7SK small nuclear RNA directly affects HMGA1 function in transcription regulation. Nucleic Acids Res 2010; 39:2057-72. [PMID: 21087998 PMCID: PMC3064786 DOI: 10.1093/nar/gkq1153] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Non-coding (nc) RNAs are increasingly recognized to play important regulatory roles in eukaryotic gene expression. The highly abundant and essential 7SK ncRNA has been shown to negatively regulate RNA Polymerase II transcription by inactivating the positive transcription elongation factor b (P-TEFb) in cellular and Tat-dependent HIV transcription. Here, we identify a more general, P-TEFb-independent role of 7SK RNA in directly affecting the function of the architectural transcription factor and chromatin regulator HMGA1. An important regulatory role of 7SK RNA in HMGA1-dependent cell differentiation and proliferation regulation is uncovered with the identification of over 1500 7SK-responsive HMGA1 target genes. Elevated HMGA1 expression is observed in nearly every type of cancer making the use of a 7SK substructure in the inhibition of HMGA1 activity, as pioneered here, potentially useful in therapy. The 7SK-HMGA1 interaction not only adds an essential facet to the comprehension of transcriptional plasticity at the coupling of initiation and elongation, but also might provide a molecular link between HIV reprogramming of cellular gene expression-associated oncogenesis.
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Affiliation(s)
- Sebastian Eilebrecht
- Institut des Hautes Études Scientifiques & Centre National de la Recherche Scientifique USR3078, 35 route de Chartres, 91440 Bures sur Yvette, France
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14
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Identification of target genes for wild type and truncated HMGA2 in mesenchymal stem-like cells. BMC Cancer 2010; 10:329. [PMID: 20576167 PMCID: PMC2912264 DOI: 10.1186/1471-2407-10-329] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 06/25/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The HMGA2 gene, coding for an architectural transcription factor involved in mesenchymal embryogenesis, is frequently deranged by translocation and/or amplification in mesenchymal tumours, generally leading to over-expression of shortened transcripts and a truncated protein. METHODS To identify pathways that are affected by sarcoma-associated variants of HMGA2, we have over-expressed wild type and truncated HMGA2 protein in an immortalized mesenchymal stem-like cell (MSC) line, and investigated the localisation of these proteins and their effects on differentiation and gene expression patterns. RESULTS Over-expression of both transgenes blocked adipogenic differentiation of these cells, and microarray analysis revealed clear changes in gene expression patterns, more pronounced for the truncated protein. Most of the genes that showed altered expression in the HMGA2-overexpressing cells fell into the group of NF-kappaB-target genes, suggesting a central role for HMGA2 in this pathway. Of particular interest was the pronounced up-regulation of SSX1, already implicated in mesenchymal oncogenesis and stem cell functions, only in cells expressing the truncated protein. Furthermore, over-expression of both HMGA2 forms was associated with a strong repression of the epithelial marker CD24, consistent with the reported low level of CD24 in cancer stem cells. CONCLUSIONS We conclude that the c-terminal part of HMGA2 has important functions at least in mesenchymal cells, and the changes in gene expression resulting from overexpressing a protein lacking this domain may add to the malignant potential of sarcomas.
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Manabe T, Katayama T, Tohyama M. HMGA1a recognition candidate DNA sequences in humans. PLoS One 2009; 4:e8004. [PMID: 19956671 PMCID: PMC2777381 DOI: 10.1371/journal.pone.0008004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 10/30/2009] [Indexed: 12/17/2022] Open
Abstract
High mobility group protein A1a (HMGA1a) acts as an architectural transcription factor and influences a diverse array of normal biological processes. It binds AT-rich sequences, and previous reports have demonstrated HMGA1a binding to the authentic promoters of various genes. However, the precise sequences that HMGA1a binds to remain to be clarified. Therefore, in this study, we searched for the sequences with the highest affinity for human HMGA1a using an existing SELEX method, and then compared the identified sequences with known human promoter sequences. Based on our results, we propose the sequences “-(G/A)-G-(A/T)-(A/T)-A-T-T-T-” as HMGA1a-binding candidate sequences. Furthermore, these candidate sequences bound native human HMGA1a from SK-N-SH cells. When candidate sequences were analyzed by performing FASTAs against all known human promoter sequences, 500–900 sequences were hit by each one. Some of the extracted genes have already been proven or suggested as HMGA1a-binding promoters. The candidate sequences presented here represent important information for research into the various roles of HMGA1a, including cell differentiation, death, growth, proliferation, and the pathogenesis of cancer.
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Affiliation(s)
- Takayuki Manabe
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.
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16
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Characterization of a novel isoform of murine interferon regulatory factor 3. Biochem Biophys Res Commun 2008; 377:384-388. [DOI: 10.1016/j.bbrc.2008.09.147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 09/29/2008] [Indexed: 11/21/2022]
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17
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Mokrani H, Sharaf el Dein O, Mansuroglu Z, Bonnefoy E. Binding of YY1 to the proximal region of the murine beta interferon promoter is essential to allow CBP recruitment and K8H4/K14H3 acetylation on the promoter region after virus infection. Mol Cell Biol 2006; 26:8551-61. [PMID: 16954376 PMCID: PMC1636788 DOI: 10.1128/mcb.00420-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Virus-induced activation of the beta interferon (IFN-beta) gene requires orderly recruitment of chromatin-remodeling complexes and time-regulated acetylation of histone residues K8H4 and K14H3 on the promoter region. We have previously shown that transcription factor Yin Yang 1 (YY1) binds the murine IFN-beta promoter at two sites (-122 and -90) regulating promoter transcriptional capacity with a dual activator/repressor role. In this work we demonstrate that both YY1 -122 and -90 sites are required for CBP recruitment and K8H4/K14H3 acetylation to take place on the IFN-beta promoter region after virus infection. A single point mutation introduced at either one of these two sites inhibiting YY1 binding completely disrupted CBP recruitment and K8H4/K14H3 acetylation independently of HMGI or IRF3 binding to the promoter. We have previously demonstrated that YY1 represses the transcriptional capacity of the IFN-beta promoter through its -90 site via histone deacetylation. Here we demonstrate that, in vivo, the binding of YY1 to the -90 site is constant all through virus infection whereas the binding of YY1 to the -122 site is activated after infection. We discuss here the capacity of YY1 to either repress (through histone deacetylase recruitment) or activate (through CBP recruitment) IFN-beta gene expression according to the occupancy of either only its -90 site or both its -122 and -90 sites.
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Affiliation(s)
- Houda Mokrani
- Régulation de la Transcription et Maladies Génétiques, CNRS UPR2228, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris cedex 06, France
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18
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Klar M, Bode J. Enhanceosome formation over the beta interferon promoter underlies a remote-control mechanism mediated by YY1 and YY2. Mol Cell Biol 2005; 25:10159-70. [PMID: 16260628 PMCID: PMC1280260 DOI: 10.1128/mcb.25.22.10159-10170.2005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The expression of beta interferon genes from humans and mice is under the immediate control of a virus-responsive element (VRE) that terminates 110 bp upstream from the transcriptional start site. Whereas a wealth of information is available for the enhanceosome that is formed on the VRE upon the signals generated by viral infection, early observations indicating the existence of other far-upstream control elements have so far remained without a molecular fundament. Guided by a computational analysis of DNA structures, we could locate three as-yet-unknown transcription factor-binding regions at -0.5, -2, and -3 kb. Our present study delineates the interplay of factors YY1 and YY2 as it occurs at the sites at -3 kb and -2 kb (otherwise called HS1 and HS2), consistent with the idea that the novel factor YY2 antagonizes the negative actions exerted by YY1. Differences between the human and murine control regions will be described.
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Affiliation(s)
- Martin Klar
- German Research Center for Biotechnology (GBF), RDIF/Epigenetic Regulation, Mascheroder Weg 1, 38124 Braunschweig, Germany
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19
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Santoro R, De Lucia F. Many players, one goal: how chromatin states are inherited during cell division. Biochem Cell Biol 2005; 83:332-43. [PMID: 15959559 DOI: 10.1139/o05-021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Replication of genomic material is a process that requires not only high fidelity in the duplication of DNA sequences but also inheritance of the chromatin states. In the last few years enormous effort has been put into elucidating the mechanisms involved in the correct propagation of chromatin states. From all these studies it emerges that an epigenetic network is at the base of this process. A coordinated interplay between histone modifications and histone variants, DNA methylation, RNA components, ATP-dependent chromatin remodeling, and histone-specific assembly factors regulates establishment of the replication timing program, initiation of replication, and propagation of chromatin domains. The aim of this review is to examine, in light of recent findings, how so many players can be coordinated with each other to achieve the same goal, a correct inheritance of the chromatin state.
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Affiliation(s)
- Raffaella Santoro
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany.
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20
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Rouleux-Bonnin F, Bigot S, Bigot Y. Structural and transcriptional features of Bombus terrestris satellite DNA and their potential involvement in the differentiation process. Genome 2005; 47:877-88. [PMID: 15499402 DOI: 10.1139/g04-053] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A unique satellite DNA family was characterized in the genome of the bumble bee, Bombus terrestris. Sequence analysis revealed that it contains two wide palindromes of about 160 and 190 bp, respectively, that span 75% of the repeated unit. One feature of this satellite DNA is that it accounts for different amounts of genomic DNA in males and females. The DNA curvature and bendability were determined by migration on PAGE and by computer analysis. It has been correlated with the presence of dA/dT stretches repeated in phase with the helix turn and with the presence of the deformable dinucleotide CA-TG embedded in some of these A-T-rich regions. Transcription of the satellite DNA was also analyzed by Northern blot hybridization and RT-PCR. Multimeric transcripts spanning several satellite DNA units were found in RNA samples from males, workers, and queens. These transcripts resulted from a specific transcription occurring on one DNA strand in the embryos or on both DNA strands in imagoes. The involvement of DNA curvature in the organization of the satellite DNA and the function of the satellite transcripts is discussed.
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Affiliation(s)
- Florence Rouleux-Bonnin
- Laboratoire d'Etude des Parasites Génétiques (LEPG), UFR des Sciences et Techniques, Université François Rabelais, Parc Grandmont, 37200 Tours, France.
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21
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Flickinger RA. Transcriptional frequency and cell determination. J Theor Biol 2005; 232:151-6. [PMID: 15530486 DOI: 10.1016/j.jtbi.2004.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Revised: 05/17/2004] [Accepted: 05/19/2004] [Indexed: 01/19/2023]
Abstract
The relative base composition of DNA regulatory sequences of certain genes of undetermined multipotent progenitor cells may account for the frequency of transcription of these genes in cell determination. The sequences of these regulatory regions of cell determination genes that are more AT-rich would create the potential for transcription at a higher frequency due to their lower melting temperature, as well as propensity to bend. An increase of one or more of the high mobility group (HMG) chromatin proteins would preferentially bind the more AT-rich regulatory sequences, thereby increasing the rate of transcription. The amount of unphosphorylated H1 histone reacting with these same regulatory sites may decrease transcription frequency. The level of cell growth, i.e. total protein synthesis of a cell, is correlated positively with the synthesis of HMG proteins. H1 histone synthesis is linked to DNA replication. Unbalanced growth would alter the amounts of HMG proteins and H1 histone, thus changing transcriptional frequency. The greater the enrichment of AT sequences in the regulatory regions of the cell determination genes, the greater may be the extent of evolutionary conservation. Higher frequency of transcription of the cell determination genes with the more AT-rich regulatory sequences could account for the earlier expression of the more conserved cell determination genes during embryonic development. Preferential binding of H1 histone to the more AT-rich regulatory sequences would subsequently restrict their transcription before that of less conserved cell determination genes.
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Affiliation(s)
- R A Flickinger
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA.
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22
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Mesplède T, Navarro S, Génin P, Morin P, Island ML, Bonnefoy E, Civas A. Positive and negative control of virus-induced interferon-A gene expression. Autoimmunity 2004; 36:447-55. [PMID: 14984021 DOI: 10.1080/08916930310001602119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Transcriptional regulation is a consequence of the combination of both activation and repression for establishing specific patterns of eukaryotic gene expression. The regulation of the expression of type I interferon (IFN-A and -B) multigene family is controlled primarily at the transcriptional level and has been widely studied as a model to understand the mechanisms of stable repression, transient expression and postinduction repression of genes. The positive and negative regulatory elements required for this on/off switch have been defined within a complex 5' upstream region of their transcription start site. The differential expression pattern of IFN-A genes is thought to involve both substitutions in the virus responsive element (VRE-A) and presence or absence of the distal negative regulatory element (DNRE) which is delimited upstream of the VRE-A. The interferon regulatory factors (IRF)-3 and -7 binding to the VRE-A and interacting as homodimers or heterodimers participate in the virus-induced transcriptional activation of IFN-A family. This data and the presence of homeodomain protein pituitary homeobox 1 (Pitx1) binding to the distal DNRE, negatively regulating the IRF-3 and IRF-7 activities and interacting physically with IRF-3 and IRF-7 contribute to our understanding of the complex differential transcriptional activation and repression of the IFN-A genes.
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Affiliation(s)
- Thibault Mesplède
- UPR 2228-CNRS, Laboratoire de Régulation Transcriptionnelle et Maladies Génétiques, UFR Biomédicale des Saints-Peres, Université Paris V, 45, rue des Saints-Pères, 75270 Paris Cedex 06, France
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23
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Sumer H, Saffery R, Wong N, Craig JM, Choo KHA. Effects of Scaffold/Matrix Alteration on Centromeric Function and Gene Expression. J Biol Chem 2004; 279:37631-9. [PMID: 15220334 DOI: 10.1074/jbc.m401051200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have previously described a 3.5-Mb domain of enhance scaffold/matrix attachment region (S/MAR) at a human neocentromere, and normal expression of underlying genes within this region. We also reported that partial inhibition of histone deacetylation using 33 nmtrichostatin A (TSA) resulted in a shift in the position of the CENP-A-binding domain within the neocentromere, with no noticeable effects on mitotic segregation function. In this study, 33 nM TSA caused a reduction in the size of the enhanced S/MAR domain of one-half to 1.7 Mb. Treatment with a DNA-intercalating drug distamycin A (DST) at 75 microg/ml resulted in a size reduction of the enhanced S/MAR domain at the neocentromere of two-thirds to 1.2 Mb, and that of the CENP-A-binding domain of 40%, from 330 to 196 kb, with no significant shift in the position of the latter domain. Other DST effects include mitotic chromosomal missegregation, reduction in the levels of Topo IIalpha, CENP-A, CENP-C, and HP1alpha, and an increase in mitotic checkpoint protein BubR1. TSA or DST treatment similarly resulted in a significant reduction, by approximately 20 and 50%, respectively, in the size of the enhanced S/MAR domain at the alpha-satellite DNA of a native chromosome 10 centromere. Transcriptional competence within the neocentromere is overall not noticeably altered by either TSA or DST treatment, as is evident from the absence of any significant increase or decrease in the expression levels of 47 underlying genes tested. These results suggest that a substantial contraction of the S/MAR domain may not be deleterious to centromere function, that disruption of the S/MAR domain directly affects the binding properties of a host of scaffold/matrix and centromeric/pericentric proteins, and that the overall competence and regulation of transcription at the neocentromeric chromatin is similar to those found at the corresponding normal genomic sites.
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Affiliation(s)
- Huseyin Sumer
- Murdoch Childrens Research Institute, Department of Pediatrics, Royal Children's Hospital, Flemington Road, Melbourne 3052, Australia
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24
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Shestakova EA, Mansuroglu Z, Mokrani H, Ghinea N, Bonnefoy E. Transcription factor YY1 associates with pericentromeric gamma-satellite DNA in cycling but not in quiescent (G0) cells. Nucleic Acids Res 2004; 32:4390-9. [PMID: 15316102 PMCID: PMC514366 DOI: 10.1093/nar/gkh737] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pericentromeric gamma-satellite DNA is organized in constitutive heterochromatin structures. It comprises a 234 bp sequence repeated several thousands times surrounding the centromeric sequence of all murine chromosomes. Potential binding sites for transcription factor Yin Yang 1 (YY1), a repressor or activator of several cellular and viral genes, are present in pericentromeric gamma-satellite DNA. Using gel retardation and chromatin immunoprecipitation, we demonstrate in this work that YY1 specifically interacts in vitro and in vivo with gamma-satellite DNA. Using immunoFISH and confocal microscopy we show that YY1 specifically co-localizes with pericentromeric gamma-satellite DNA clusters organized in constitutive heterochromatin in murine L929 and 3T3 fibroblasts cell lines. Immunoelectron microscopy experiments further confirmed YY1 localization in heterochromatic areas. Overall, our results demonstrate for the first time that a fraction of YY1 is directly associated with constitutive heterochromatin structures. This association appears physiologically relevant since the association of YY1 with pericentromeric gamma-satellite DNA observed in cycling 3T3 fibroblasts strongly diminished in quiescent (G0) 3T3 fibroblasts. We discuss the implications of these results in the context of heterochromatin formation as well as with regard to the YY1-induced repression of euchromatic genes.
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Affiliation(s)
- Elena A Shestakova
- Régulation de la Transcription et Maladies Génétiques, CNRS UPR2228, IFR-95, Université René Descartes, 45 rue des Saints-Pères, 75270 Paris cedex 06, France
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25
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Massaad-Massade L, Tacine R, Dulauroy S, Reeves R, Barouki R. The functional interaction between HMGA1 and the estrogen receptor requires either the N- or the C-terminal domain of the receptor. FEBS Lett 2004; 559:89-95. [PMID: 14960313 DOI: 10.1016/s0014-5793(04)00032-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Revised: 01/09/2004] [Accepted: 01/09/2004] [Indexed: 11/21/2022]
Abstract
We have previously shown that HMGA1 enhances the transcriptional activity of promoters containing the estrogen response element (ERE) and increases binding of the estrogen receptor (ER) to ERE. Herein, we have assessed the transcriptional activity and ERE-binding ability of deleted ER fragments in absence or in presence of HMGA1. The HMGA1 protein stimulated binding and transcriptional activity by a factor of about 2-fold compared to the wild-type ER and both the N- and C-terminal ER deleted domains, but had no effect when both domains were deleted. These data show that HMGA1 cooperates with either the N- or the C-terminal transcriptional activation domain of the ER.
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Affiliation(s)
- Liliane Massaad-Massade
- Université René Descartes, Laboratoire de Toxicologie Moléculaire, U-490 INSERM, 45 rue des Saints-Pères, 75270 Paris Cedex, France.
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26
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The linker histones. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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27
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Iovanna JL. Expression of the stress-associated protein p8 is a requisite for tumor development. INTERNATIONAL JOURNAL OF GASTROINTESTINAL CANCER 2003; 31:89-98. [PMID: 12622419 DOI: 10.1385/ijgc:31:1-3:89] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We identified a new gene, called p8, because its expression was strongly induced during the acute phase of pancreatitis. Further experiments have shown that p8 mRNA is activated in response to several stresses and that its activation is not restricted to pancreatic cells. p8 is a nuclear protein and biochemical and biophysical studies have shown that p8 was very similar in many structural aspects to the HMG proteins, although sharing only low amino acid sequence homology. Also, p8 was found overexpressed in many human cancers. Therefore, we wondered whether the p8-mediated response to cellular stress was necessary for tumor establishment. Subcutaneous or intraperitoneal injections of transformed p8-expressing fibroblasts led to tumor formation in nude mice, but no tumor was observed with transformed p8-deficient cells. Restoring p8 expression in transformed p8-deficient fibroblasts led to tumor formation, demonstrating that p8 expression is crucial for tumor development and suggesting that the stress-response mechanisms governed by p8 are required for tumor establishment.
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Affiliation(s)
- Juan L Iovanna
- Centre de Recherche INSERM, EMI0116, 163 avenue de Luminy, Parc Scientifique et Technologique de Luminy, BP 172, 13009 Marseille, France.
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28
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Beitzel B, Bushman F. Construction and analysis of cells lacking the HMGA gene family. Nucleic Acids Res 2003; 31:5025-32. [PMID: 12930952 PMCID: PMC212792 DOI: 10.1093/nar/gkg684] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The high mobility group A (HMGA) family of non-histone chromosomal proteins is encoded by two related genes, HMGA1 and HMGA2. HMGA proteins are architectural transcription factors that have been found to regulate the transcription of a large number of genes. They are also some of the most commonly dysregulated genes in human neoplasias, highlighting a role in growth control. HMGA1 and HMGA2 have also been found to stimulate retroviral integration in vitro. In this study, we have cloned chicken HMGA1, and used the chicken DT40 B-cell lymphoma line to generate cells lacking HMGA1, HMGA2 and both in combination. We tested these lines for effects on cellular growth, gene control and retroviral integration. Surprisingly, we found that the HMGA gene family is dispensable for growth in DT40 cells, and that there is no apparent defect in retroviral integration in the absence of HMGA1 or HMGA2. We also analyzed the activity of approximately 4000 chicken genes, but found no significant changes. We conclude that HMGA proteins are not strictly required for growth control or retroviral integration in DT40 cells and may well be redundant with other factors.
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Affiliation(s)
- Brett Beitzel
- Infectious Disease Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
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29
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Weill L, Shestakova E, Bonnefoy E. Transcription factor YY1 binds to the murine beta interferon promoter and regulates its transcriptional capacity with a dual activator/repressor role. J Virol 2003; 77:2903-14. [PMID: 12584314 PMCID: PMC149748 DOI: 10.1128/jvi.77.5.2903-2914.2003] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2002] [Accepted: 11/20/2002] [Indexed: 12/31/2022] Open
Abstract
The induction of the beta interferon (IFN-beta) gene constitutes one of the first responses of the cell to virus infection. Its regulation is achieved through an intricate combination of virus-induced binding of transcription factors and local chromatin remodeling. In this work, we demonstrate that transcription factor YY1, known to interact with histone deacetylases (HDAC) and histone acetyltransferases, has a dual activator/repressor role during the regulation of the IFN-beta promoter activity. We show that YY1 specifically binds in vitro and in vivo to the murine IFN-beta promoter at positions -90 and -122. Overexpression of YY1 strongly repressed the transcriptional capacity of a stably integrated IFN-beta promoter fused to a chloramphenicol acetyltransferase reporter gene as well as the endogenous IFN activity of murine L929 cells via an HDAC activity. Stably integrated IFN-beta promoters mutated at the -90 site were no longer repressed by YY1, could no longer be activated by trichostatin A, displayed a retarded postinduction turn off, and a reduced virus-induced activity. Introduction of a mutation at the -122 site did not affect YY1-induced repression, but promoters with this mutation displayed a reduced virus-induced activity. Stably integrated full-length promoters (from position -330 to +20) mutated at both YY1-binding sites displayed extremely reduced promoter activities. We conclude that YY1 has a dual activator/repressor role on IFN-beta promoter activity depending on its binding site and time after infection.
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Affiliation(s)
- Laure Weill
- Régulation de la Transcription et Maladies Génétiques, CNRS UPR2228, UFR Biomédicale, 75270 Paris cedex 06, France
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30
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López-Rubio JJ, Elías-Arnanz M, Padmanabhan S, Murillo FJ. A repressor-antirepressor pair links two loci controlling light-induced carotenogenesis in Myxococcus xanthus. J Biol Chem 2002; 277:7262-70. [PMID: 11748235 DOI: 10.1074/jbc.m110351200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The light-inducible carB operon encodes all but one of the structural genes for carotenogenesis in Myxococcus xanthus. It is transcriptionally controlled by two proteins expressed from two unlinked genetic loci: CarS from the light-inducible carQRS operon, and CarA from the light-independent carA operon. CarA represses transcription from the carB promoter (P(B)) in the dark, and CarS counteracts this on illumination. The CarA sequence revealed a helix-turn-helix DNA-binding motif of the type found in bacterial MerR transcriptional factors, whereas CarS contains no known DNA-binding motif. Here, we examine the molecular interplay between CarA and CarS. We demonstrate the following. (i) Whereas CarS exhibits no DNA binding in vitro, CarA binds specifically to a region encompassing P(B) to form at least two distinct complexes. (ii) A palindrome located between positions -46 and -63 relative to the transcription start point is essential but not sufficient for the formation of the two CarA-DNA complexes observed. (iii) CarS abrogates the specific DNA binding of CarA. CarA is therefore a repressor and CarS an antirepressor. (iv) CarS physically interacts with CarA; thus, the functional interaction between them is mediated by protein-protein interactions.
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Affiliation(s)
- José Juan López-Rubio
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia 30071, Spain
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31
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Liu F, Chau KY, Arlotta P, Ono SJ. The HMG I proteins: dynamic roles in gene activation, development, and tumorigenesis. Immunol Res 2002; 24:13-29. [PMID: 11485207 DOI: 10.1385/ir:24:1:13] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The high mobility group I, Y, and I-C proteins are low-molecular-weight, nonhistone chromosomal proteins that play a general role modulating gene expression during development and the immune response. Consistent with their role in early development, all three proteins are expressed at high levels during embryogenesis, and their expression is markedly diminished in differentiated cells. Exceptions to the general repression of these genes in adult tissues involve (1) A burst of synthesis of the HMG I protein during the immune response (during lymphocyte activation and preceding cytokine/adhesion molecule gene expression), (2) A constitutive expression of the HMG I and Y proteins in photoreceptor cells, and (3) Derepression of HMG I, Y, and often I-C expression in neoplastic cells. Work from several laboratories has now uncovered how these proteins participate in gene activation: (1) By altering the chromatin structure around an inducible gene-and thus influencing accessibility of the locus to regulatory proteins-(2) By facilitating the loading of transcription factors onto the promoters, and (3) By bridging adjacent transcription factors on a promoter via protein/protein interactions. Despite the similar structures and biochemical properties of the three proteins, the work has also provided clues to a division of labor between these proteins. HMG I and Y have demonstrable roles in enhanceosome formation, whereas HMG I-C has a specific role in adipogenesis. C-terminal truncations of HMG I-C and wild-type HMG Y appear to function in a manner analogous to oncogenes, as assessed by cellular transforation assays and transgenic mice. Future work should clearly define the similarities and differences in the biological roles of the three proteins, and should evolve to include attempts at pharmaceutical intervention in disease, based upon structural information concerning HMG I interactions with DNA and with regulatory proteins.
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Affiliation(s)
- F Liu
- University College London, Institute of Ophthalmology, UK
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32
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Preferential damage to defined regions of genomic DNA by AT-specific anticancer drugs. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1067-568x(02)80003-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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33
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Abstract
Cell differentiation may depend in part upon a type of unbalanced growth in which several cell cycles occur with a reduced level of total protein synthesis. During this period the synthesis of the chromatin protein HMG-I/Y is reduced since its synthesis is correlated with that of total protein. The synthesis of histone H1 shows less reduction since its synthesis is entrained with that of DNA. This greater reduction of HMG-I/Y than of histone H1 is thought to delay or prevent replicon initiations within AT-enriched isochores. This shifts their time of replication from early to late S phase. This may restrict certain pathways of cell differentiation in multipotent progenitor cells and allow one particular type of differentiation.
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Affiliation(s)
- R Flickinger
- Department of Biological Sciences, State University of New York at Buffalo, 14260, USA
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35
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Bhattacharjee RN, Banks GC, Trotter KW, Lee HL, Archer TK. Histone H1 phosphorylation by Cdk2 selectively modulates mouse mammary tumor virus transcription through chromatin remodeling. Mol Cell Biol 2001; 21:5417-25. [PMID: 11463824 PMCID: PMC87264 DOI: 10.1128/mcb.21.16.5417-5425.2001] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional activation of the mouse mammary tumor virus (MMTV) promoter by ligand-bound glucocorticoid receptor (GR) is transient. Previously, we demonstrated that prolonged hormone exposure results in displacement of the transcription factor nuclear factor 1 (NF1) and the basal transcription complex from the promoter, the dephosphorylation of histone H1, and the establishment of a repressive chromatin structure. We have explored the mechanistic link between histone H1 dephosphorylation and silencing of the MMTV promoter by describing the putative kinase responsible for H1 phosphorylation. Both in vitro kinase assays and in vivo protein expression studies suggest that in hormone-treated cells the ability of cdk2 to phosphorylate histone H1 is decreased and the cdk2 inhibitory p21 protein level is increased. To address the role of cdk2 and histone H1 dephosphorylation in the silencing of the MMTV promoter, we used potent cdk2 inhibitors, Roscovitine and CVT-313, to generate an MMTV promoter which is associated predominantly with the dephosphorylated form of histone H1. Both Roscovitine and CVT-313 block phosphorylation of histone H1 and, under these conditions, the GR is unable to remodel chromatin, recruit transcription factors to the promoter, or stimulate MMTV mRNA accumulation. These results suggest a model where cdk2-directed histone H1 phosphorylation is a necessary condition to permit GR-mediated chromatin remodeling and activation of the MMTV promoter in vivo.
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Affiliation(s)
- R N Bhattacharjee
- Department of Obstetrics and Gynaecology, The University of Western Ontario, London, Ontario N6A 4L6, Canada
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36
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García-Montero AC, Vasseur S, Giono LE, Canepa E, Moreno S, Dagorn JC, Iovanna JL. Transforming growth factor beta-1 enhances Smad transcriptional activity through activation of p8 gene expression. Biochem J 2001; 357:249-53. [PMID: 11415456 PMCID: PMC1221948 DOI: 10.1042/0264-6021:3570249] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We report that exposure of mouse embryonic fibroblasts to transforming growth factor beta-1 (TGFbeta-1) (5 ng/ml) results in a strong activation of p8 mRNA expression that precedes the induction of cell growth. Involvement of the p8 promoter in the regulation was demonstrated by using a p8-chloramphenicol acetyltransferase construct. We therefore speculated that p8 might be a mediator of TGFbeta-1 in these cells. The incorporation of [(3)H]thymidine on treatment with TGFbeta-1 was indeed significantly higher in p8(+/+) fibroblasts than in p8(-/-) fibroblasts. Smad transcriptional activity was used as marker of the TGFbeta-1 signalling pathway, to probe the lower p8(-/-) response to TGFbeta-1. Two Smad-binding elements (SBEs)-luciferase constructs were transfected into p8(-/-) and p8(+/+) embryonic fibroblasts before treatment with TGFbeta-1. A lower level of Smad transactivation was observed in p8(-/-) embryonic fibroblasts, under basal conditions and after stimulation with TGFbeta-1. To test whether Smad underexpression in p8(-/-) cells was actually due to p8 depletion, p8(-/-) embryonic fibroblasts were transfected with a human p8 expression plasmid together with an SBE-luciferase construct. The expression of p8 restored Smad transactivation in unstimulated and TGFbeta-1-treated cells to the level found in p8(+/+) cells. We concluded that TGFbeta-1 activates p8 expression, which in turn enhances the Smad-transactivating function responsible for TGFbeta-1 activity.
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Reeves R, Beckerbauer L. HMGI/Y proteins: flexible regulators of transcription and chromatin structure. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1519:13-29. [PMID: 11406267 DOI: 10.1016/s0167-4781(01)00215-9] [Citation(s) in RCA: 285] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The mammalian HMGI/Y (HMGA) non-histone proteins participate in a wide variety of cellular processes including regulation of inducible gene transcription, integration of retroviruses into chromosomes and the induction of neoplastic transformation and promotion of metastatic progression of cancer cells. Recent advances have contributed greatly to our understanding of how the HMGI/Y proteins participate in the molecular mechanisms underlying these biological events. All members of the HMGI/Y family of 'high mobility group' proteins are characterized by the presence of multiple copies of a conserved DNA-binding peptide motif called the 'AT hook' that preferentially binds to the narrow minor groove of stretches of AT-rich sequence. The mammalian HMGI/Y proteins have little, if any, secondary structure in solution but assume distinct conformations when bound to substrates such as DNA or other proteins. Their intrinsic flexibility allows the HMGI/Y proteins to participate in specific protein-DNA and protein-protein interactions that induce both structural changes in chromatin substrates and the formation of stereospecific complexes called 'enhanceosomes' on the promoter/enhancer regions of genes whose transcription they regulate. The formation of such regulatory complexes is characterized by reciprocal inductions of conformational changes in both the HMGI/Y proteins themselves and in their interacting substrates. It may well be that the inherent flexibility of the HMGI/Y proteins, combined with their ability to undergo reversible disordered-to-ordered structural transitions, has been a significant factor in the evolutionary selection of these proteins for their functional role(s) in cells.
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Affiliation(s)
- R Reeves
- Department of Biochemistry/Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA.
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38
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Shestakova E, Bandu MT, Doly J, Bonnefoy E. Inhibition of histone deacetylation induces constitutive derepression of the beta interferon promoter and confers antiviral activity. J Virol 2001; 75:3444-52. [PMID: 11238870 PMCID: PMC114137 DOI: 10.1128/jvi.75.7.3444-3452.2001] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2000] [Accepted: 01/03/2001] [Indexed: 11/20/2022] Open
Abstract
The induction of alpha/beta interferon (IFN-alpha/beta) genes constitutes one of the first responses of the cell to virus infection. The IFN-beta gene is constitutively repressed in uninfected cells and is transiently activated after virus infection. In this work we demonstrate that histone deacetylation regulates the silent state of the murine IFN-beta gene. Using chromatin immunoprecipitation (ChIP) assays, we show a direct in vivo correlation between the transcriptionally silent state and a state of hypoacetylation of histone H4 on the IFN-beta promoter region. Trichostatin A (TSA), a specific inhibitor of histone deacetylases, induced strong, constitutive derepression of the murine IFN-beta promoter stably integrated into a chromatin context, as well as the hyperacetylation of histone H4, without requiring de novo protein synthesis. We also show in this work that TSA treatment strongly enhances the endogenous IFN level and confers an antiviral state to murine fibroblastic L929 cells. Inhibition of histone deacetylation with TSA protected the cells against the lost of viability induced by vesicular stomatitis virus (VSV) and inhibited VSV multiplication. Using antibodies neutralizing IFN-alpha/beta, we show that the antiviral state induced by TSA is due to TSA-induced IFN production. The demonstration of the predominant role of histone deacetylation during the regulation of the constitutive repressed state of the IFN-beta promoter constitutes an interesting advance on the understanding of the negative regulation of this gene and opens up the possibility of new therapeutic perspectives.
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Affiliation(s)
- E Shestakova
- Laboratoire de Régulation de la Transcription et Maladies Génétiques, CNRS, UPR2228, UFR Biomédicale, Université René Descartes, 75270 Paris Cedex 06, France
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39
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Pałyga J, Górnicka-Michalska E, Kowalski A, Ksiazkiewicz J. Natural allelic variation of duck erythrocyte histone H1b. Int J Biochem Cell Biol 2000; 32:665-75. [PMID: 10785363 DOI: 10.1016/s1357-2725(99)00153-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In our previous work (J. Palyga, Genetic polymorphisms of histone H1. b in duck erythrocytes. Hereditas 114, 85-89, 1991) we reported a genetic polymorphism of duck erythrocyte histone H1.b. Here, we screened H1 preparations in a two-dimensional polyacrylamide gel to refine the distribution of allelic forms of H1.b in fifteen duck populations. We have revealed that the frequency of H1.b allelic variants was significantly different among many conservative and breeding duck groups. While b(1) and b(3) were common in all populations screened, the allele b(2), with a slightly lower apparent molecular weight, was confined mainly to brown-feathered ducks (Khaki Campbell and Orpington) and descendent lines. The C- and N-terminal peptides released upon cleavage with N-bromosuccinimide and Staphylococcus aureus protease V8 from duck allelic histones H1. b2 and H1.b3, respectively, migrated differently in the gel, probably as a result of potential amino acid variation in a C-terminal domain.
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Affiliation(s)
- J Pałyga
- Department of Genetics, Wyzsza Szkola Pedagogiczna, ul. Konopnickiej 15, 25-406, Kielce, Poland.
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40
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Slama-Schwok A, Zakrzewska K, Léger G, Leroux Y, Takahashi M, Käs E, Debey P. Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence. Biophys J 2000; 78:2543-59. [PMID: 10777751 PMCID: PMC1300844 DOI: 10.1016/s0006-3495(00)76799-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Using spectroscopic methods, we have studied the structural changes induced in both protein and DNA upon binding of the High-Mobility Group I (HMG-I) protein to a 21-bp sequence derived from mouse satellite DNA. We show that these structural changes depend on the stoichiometry of the protein/DNA complexes formed, as determined by Job plots derived from experiments using pyrene-labeled duplexes. Circular dichroism and melting temperature experiments extended in the far ultraviolet range show that while native HMG-I is mainly random coiled in solution, it adopts a beta-turn conformation upon forming a 1:1 complex in which the protein first binds to one of two dA.dT stretches present in the duplex. HMG-I structure in the 1:1 complex is dependent on the sequence of its DNA target. A 3:1 HMG-I/DNA complex can also form and is characterized by a small increase in the DNA natural bend and/or compaction coupled to a change in the protein conformation, as determined from fluorescence resonance energy transfer (FRET) experiments. In addition, a peptide corresponding to an extended DNA-binding domain of HMG-I induces an ordered condensation of DNA duplexes. Based on the constraints derived from pyrene excimer measurements, we present a model of these nucleated structures. Our results illustrate an extreme case of protein structure induced by DNA conformation that may bear on the evolutionary conservation of the DNA-binding motifs of HMG-I. We discuss the functional relevance of the structural flexibility of HMG-I associated with the nature of its DNA targets and the implications of the binding stoichiometry for several aspects of chromatin structure and gene regulation.
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Affiliation(s)
- A Slama-Schwok
- INRA 806/EA2703 Muséum National d'Histoire Naturelle, Institut de Biologie Physico-Chimique, Paris, France.
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Vyas DR, McCarthy JJ, Tsika RW. Nuclear protein binding at the beta-myosin heavy chain A/T-rich element is enriched following increased skeletal muscle activity. J Biol Chem 1999; 274:30832-42. [PMID: 10521475 DOI: 10.1074/jbc.274.43.30832] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In adult mouse skeletal muscle, beta-myosin heavy chain (betaMyHC) gene expression is primarily restricted to slow-type I fibers but can be induced in fast-type II fibers by mechanical overload (MOV). Our previous transgenic analyses have delimited an 89-base pair (bp) MOV-responsive region (-293 to -205), and shown that mutation of the MCAT and C-rich elements within this region did not abolish betaMyHC transgene induction by MOV. In this study we describe an A/T-rich element (betaA/T-rich; -269 5'-GGAGATATTTTT-3' -258) located within this 89-bp region that, only under MOV conditions, revealed enriched binding as characterized by electrophoretic mobility shift assays and dimethyl sulfate and diethyl pyrocarbonate interference footprinting. Direct, competition, and supershift electrophoretic mobility shift assays revealed highly enriched specific binding activity at the betaA/T-rich element that was antigenically distinct from GATA-4, MEF2A-D, SRF, and Oct-1, nuclear proteins that were previously shown to bind A/T-rich elements. In vitro translated GATA-4, MEF2C, SRF, and Oct-1 bound to consensus GATA, MEF2, SRE, and Oct-1 elements, respectively, but not to the betaA/T-rich element. Two-dimensional UV cross-linking of the bromodeoxyuridine-substituted betaA/T-rich element with mechanically overloaded plantaris (MOV-P) nuclear extract detected two proteins (44 and 48 kDa). Our results indicate that the betaA/T-rich element may function in vivo as a betaMyHC MOV-inducible element during hypertrophy of adult skeletal muscle by binding two distinct proteins identified only in MOV-P nuclear extract.
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Affiliation(s)
- D R Vyas
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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