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Nourisa J, Passemiers A, Shakeri F, Omidi M, Helmholz H, Raimondi D, Moreau Y, Tomforde S, Schlüter H, Luthringer-Feyerabend B, Cyron CJ, Aydin RC, Willumeit-Römer R, Zeller-Plumhoff B. Gene regulatory network analysis identifies MYL1, MDH2, GLS, and TRIM28 as the principal proteins in the response of mesenchymal stem cells to Mg 2+ ions. Comput Struct Biotechnol J 2024; 23:1773-1785. [PMID: 38689715 PMCID: PMC11058716 DOI: 10.1016/j.csbj.2024.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
Magnesium (Mg)-based implants have emerged as a promising alternative for orthopedic applications, owing to their bioactive properties and biodegradability. As the implants degrade, Mg2+ ions are released, influencing all surrounding cell types, especially mesenchymal stem cells (MSCs). MSCs are vital for bone tissue regeneration, therefore, it is essential to understand their molecular response to Mg2+ ions in order to maximize the potential of Mg-based biomaterials. In this study, we conducted a gene regulatory network (GRN) analysis to examine the molecular responses of MSCs to Mg2+ ions. We used time-series proteomics data collected at 11 time points across a 21-day period for the GRN construction. We studied the impact of Mg2+ ions on the resulting networks and identified the key proteins and protein interactions affected by the application of Mg2+ ions. Our analysis highlights MYL1, MDH2, GLS, and TRIM28 as the primary targets of Mg2+ ions in the response of MSCs during 1-21 days phase. Our results also identify MDH2-MYL1, MDH2-RPS26, TRIM28-AK1, TRIM28-SOD2, and GLS-AK1 as the critical protein relationships affected by Mg2+ ions. By offering a comprehensive understanding of the regulatory role of Mg2+ ions on MSCs, our study contributes valuable insights into the molecular response of MSCs to Mg-based materials, thereby facilitating the development of innovative therapeutic strategies for orthopedic applications.
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Affiliation(s)
- Jalil Nourisa
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
| | | | - Farhad Shakeri
- Institute of Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Maryam Omidi
- Institute of Clinical Chemistry/Central Laboratories, University Medical Center Hamburg, Hamburg, Germany
| | - Heike Helmholz
- Institute of Metallic Biomaterials, Helmholtz Zentrum Hereon, Geesthacht, Germany
| | | | | | - Sven Tomforde
- Department of Computer Science, Intelligent Systems, University of Kiel, Kiel, Germany
| | - Hartmuth Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, University of Hamburg, Hamburg, Germany
| | | | - Christian J. Cyron
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
- Institute for Continuum and Material Mechanics, Hamburg University of Technology, Hamburg, Germany
| | - Roland C. Aydin
- Institute of Material Systems Modeling, Helmholtz Zentrum Hereon, Geesthacht, Germany
- Institute for Continuum and Material Mechanics, Hamburg University of Technology, Hamburg, Germany
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Park HH, Kim HR, Park SY, Hwang SM, Hong SM, Park S, Kang HC, Morgan MJ, Cha JH, Lee D, Roe JS, Kim YS. RIPK3 activation induces TRIM28 derepression in cancer cells and enhances the anti-tumor microenvironment. Mol Cancer 2021; 20:107. [PMID: 34419074 PMCID: PMC8379748 DOI: 10.1186/s12943-021-01399-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022] Open
Abstract
Background Necroptosis is emerging as a new target for cancer immunotherapy as it is now recognized as a form of cell death that increases tumor immunogenicity, which would be especially helpful in treating immune-desert tumors. De novo synthesis of inflammatory proteins during necroptosis appears especially important in facilitating increased anti-tumor immune responses. While late-stage transcription mediated by NF-κB during cell death is believed to play a role in this process, it is otherwise unclear what cell signaling events initiate this transactivation of inflammatory genes. Methods We employed tandem-affinity purification linked to mass spectrometry (TAP-MS), in combination with the analysis of RNA-sequencing (RNA-Seq) datasets to identify the Tripartite Motif Protein 28 (TRIM28) as a candidate co-repressor. Comprehensive biochemical and molecular biology techniques were used to characterize the role of TRIM28 in RIPK3 activation-induced transcriptional and immunomodulatory events. The cell composition estimation module was used to evaluate the correlation between RIPK3/TRIM28 levels and CD8+ T cells or dendritic cells (DC) in all TCGA tumors. Results We identified TRIM28 as a co-repressor that regulates transcriptional activity during necroptosis. Activated RIPK3 phosphorylates TRIM28 on serine 473, inhibiting its chromatin binding activity, thereby contributing to the transactivation of NF-κB and other transcription factors, such as SOX9. This leads to elevated cytokine expression, which then potentiates immunoregulatory processes, such as DC maturation. The expression of RIPK3 has a significant positive association with the tumor-infiltrating immune cells populations in various tumor type, thereby activating anti-cancer responses. Conclusion Our data suggest that RIPK3 activation-dependent derepression of TRIM28 in cancer cells leads to increased immunostimulatory cytokine production in the tumor microenvironment, which then contributes to robust cytotoxic anti-tumor immunity. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01399-3.
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Affiliation(s)
- Han-Hee Park
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, South Korea.,Department of Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea
| | - Hwa-Ryeon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Sang-Yeong Park
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, South Korea.,Department of Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea
| | - Sung-Min Hwang
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Sun Mi Hong
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Sangwook Park
- Department of Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Ho Chul Kang
- Department of Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Michael J Morgan
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK, 74464, USA
| | - Jong-Ho Cha
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, 22212, South Korea.,Department of Biomedical Science and Engineering, Graduate School, Inha University, Incheon, 22212, South Korea
| | - Dakeun Lee
- Department of Pathology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Jae-Seok Roe
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea.
| | - You-Sun Kim
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, South Korea. .,Department of Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea.
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Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia. Genes (Basel) 2019; 10:genes10090716. [PMID: 31527520 PMCID: PMC6771147 DOI: 10.3390/genes10090716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/17/2019] [Accepted: 09/10/2019] [Indexed: 11/17/2022] Open
Abstract
B-cell acute lymphoblastic leukemia is the most commonly diagnosed childhood malignancy worldwide; more than 50% of these cases are diagnosed in Mexico. Although the five-year survival rate is >80%, 30% of patients experience relapse with poor prognosis. Cancer-associated gene expression profiles have been identified in several malignancies, and some transcripts have been used to predict disease prognosis. The human transcriptome is incompletely elucidated; moreover, more than 80% of transcripts can be processed via alternative splicing (AS), which increases transcript and protein diversity. The human transcriptome is divided; coding RNA accounts for 2%, and the remaining 98% is noncoding RNA. Noncoding RNA can undergo AS, promoting the diversity of noncoding transcripts. We designed specific primers to amplify previously reported alternative transcript variants of ZNF695 and showed that six ZNF695 transcript variants are co-expressed in cancer cell lines. The amplicons were sequenced and identified. Additionally, we analyzed the expression of these six transcript variants in bone marrow from B-cell acute lymphoblastic leukemia patients and observed that ZNF695 transcript variants one and three were the predominant variants expressed in leukemia. Moreover, our results showed the co-expression of coding and long noncoding RNA. Finally, we observed that long noncoding RNA ZNF695 expression predicted survival rates.
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Stelloo S, Nevedomskaya E, Kim Y, Hoekman L, Bleijerveld OB, Mirza T, Wessels LFA, van Weerden WM, Altelaar AFM, Bergman AM, Zwart W. Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis. Oncogene 2017; 37:313-322. [PMID: 28925401 DOI: 10.1038/onc.2017.330] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/10/2017] [Accepted: 08/06/2017] [Indexed: 12/13/2022]
Abstract
Androgen receptor (AR) is a key player in prostate cancer development and progression. Here we applied immunoprecipitation mass spectrometry of endogenous AR in LNCaP cells to identify components of the AR transcriptional complex. In total, 66 known and novel AR interactors were identified in the presence of synthetic androgen, most of which were critical for AR-driven prostate cancer cell proliferation. A subset of AR interactors required for LNCaP proliferation were profiled using chromatin immunoprecipitation assays followed by sequencing, identifying distinct genomic subcomplexes of AR interaction partners. Interestingly, three major subgroups of genomic subcomplexes were identified, where selective gain of function for AR genomic action in tumorigenesis was found, dictated by FOXA1 and HOXB13. In summary, by combining proteomic and genomic approaches we reveal subclasses of AR transcriptional complexes, differentiating normal AR behavior from the oncogenic state. In this process, the expression of AR interactors has key roles by reprogramming the AR cistrome and interactome in a genomic location-specific manner.
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Affiliation(s)
- S Stelloo
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E Nevedomskaya
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Y Kim
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L Hoekman
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - O B Bleijerveld
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - T Mirza
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - W M van Weerden
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A F M Altelaar
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, The Netherlands Proteomics Centre, Utrecht University, Utrecht, The Netherlands
| | - A M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - W Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Fadda A, Syed N, Mackeh R, Papadopoulou A, Suzuki S, Jithesh PV, Kino T. Genome-wide Regulatory Roles of the C2H2-type Zinc Finger Protein ZNF764 on the Glucocorticoid Receptor. Sci Rep 2017; 7:41598. [PMID: 28139699 PMCID: PMC5282477 DOI: 10.1038/srep41598] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/23/2016] [Indexed: 01/13/2023] Open
Abstract
The C2H2-type zinc finger protein ZNF764 acts as an enhancer for several steroid hormone receptors, and haploinsufficiency of this gene may be responsible for tissue resistance to multiple steroid hormones including glucocorticoids observed in a patient with 16p11.2 microdeletion. We examined genome-wide regulatory actions of ZNF764 on the glucocorticoid receptor (GR) in HeLa cells as a model system. ZNF764- and GR-binding sites demonstrated similar distribution in various genomic features. They positioned predominantly around 50-500 kbs from the transcription start sites of their nearby genes, and were closely localized with each other, overlapping in ~37% of them. ZNF764 demonstrated differential on/off effects on GR-binding and subsequent mRNA expression: some genes were highly dependent on the presence/absence of ZNF764, but others were not. Pathway analysis revealed that these 3 gene groups were involved in distinct cellular activities. ZNF764 physically interacted with GR at ligand-binding domain through its KRAB domain, and both its physical interaction to GR and zinc finger domain appear to be required for ZNF764 to regulate GR transcriptional activity. Thus, ZNF764 is a cofactor directing GR transcriptional activity toward specific biologic pathways by changing GR binding and transcriptional activity on the glucocorticoid-responsive genes.
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Affiliation(s)
- Abeer Fadda
- Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Najeeb Syed
- Division of Biomedical Informatics, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Rafah Mackeh
- Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Anna Papadopoulou
- Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shigeru Suzuki
- Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Pediatrics, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Puthen V. Jithesh
- Division of Biomedical Informatics, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Tomoshige Kino
- Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
- Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Agustín-Pavón C, Mielcarek M, Garriga-Canut M, Isalan M. Deimmunization for gene therapy: host matching of synthetic zinc finger constructs enables long-term mutant Huntingtin repression in mice. Mol Neurodegener 2016; 11:64. [PMID: 27600816 PMCID: PMC5013590 DOI: 10.1186/s13024-016-0128-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 08/27/2016] [Indexed: 12/29/2022] Open
Abstract
Background Synthetic zinc finger (ZF) proteins can be targeted to desired DNA sequences and are useful tools for gene therapy. We recently developed a ZF transcription repressor (ZF-KOX1) able to bind to expanded DNA CAG-repeats in the huntingtin (HTT) gene, which are found in Huntington’s disease (HD). This ZF acutely repressed mutant HTT expression in a mouse model of HD and delayed neurological symptoms (clasping) for up to 3 weeks. In the present work, we sought to develop a long-term single-injection gene therapy approach in the brain. Method Since non-self proteins can elicit immune and inflammatory responses, we designed a host-matched analogue of ZF-KOX1 (called mZF-KRAB), to treat mice more safely in combination with rAAV vector delivery. We also tested a neuron-specific enolase promoter (pNSE), which has been reported as enabling long-term transgene expression, to see whether HTT repression could be observed for up to 6 months after AAV injection in the brain. Results After rAAV vector delivery, we found that non-self proteins induce significant inflammatory responses in the brain, in agreement with previous studies. Specifically, microglial cells were activated at 4 and 6 weeks after treatment with non-host-matched ZF-KOX1 or GFP, respectively, and this was accompanied by a moderate neuronal loss. In contrast, the host-matched mZF-KRAB did not provoke these effects. Nonetheless, we found that using a pCAG promoter (CMV early enhancer element and the chicken β-actin promoter) led to a strong reduction in ZF expression by 6 weeks after injection. We therefore tested a new non-viral promoter to see whether the host-adapted ZF expression could be sustained for a longer time. Vectorising mZF-KRAB with a promoter-enhancer from neuron-specific enolase (Eno2, rat) resulted in up to 77 % repression of mutant HTT in whole brain, 3 weeks after bilateral intraventricular injection of 1010 virions. Importantly, repressions of 48 % and 23 % were still detected after 12 and 24 weeks, respectively, indicating that longer term effects are possible. Conclusion Host-adapted ZF-AAV constructs displayed a reduced toxicity and a non-viral pNSE promoter improved long-term ZF protein expression and target gene repression. The optimized constructs presented here have potential for treating HD. Electronic supplementary material The online version of this article (doi:10.1186/s13024-016-0128-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carmen Agustín-Pavón
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.,Current address: Predepartmental Unit of Medicine, Faculty of Health Sciences, University Jaume I, Av. de Vicent Sos Baynat, s/n 12071, Castelló de la Plana, Spain
| | - Michal Mielcarek
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Mireia Garriga-Canut
- Cell and Developmental Biology Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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Anifandis G, Messini CI, Dafopoulos K, Messinis IE. Genes and Conditions Controlling Mammalian Pre- and Post-implantation Embryo Development. Curr Genomics 2015; 16:32-46. [PMID: 25937812 PMCID: PMC4412963 DOI: 10.2174/1389202916666141224205025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/20/2014] [Accepted: 12/23/2014] [Indexed: 01/06/2023] Open
Abstract
Embryo quality during the in vitro developmental period is of great clinical importance. Experimental genetic studies during this period have demonstrated the association between specific gene expression profiles and the production of healthy blastocysts. Although the quality of the oocyte may play a major role in embryo development, it has been well established that the post - fertilization period also has an important and crucial role in the determination of blastocyst quality. A variety of genes (such as OCT, SOX2, NANOG) and their related signaling pathways as well as transcription molecules (such as TGF-β, BMP) have been implicated in the pre- and post-implantation period. Furthermore, DNA methylation has been lately characterized as an epigenetic mark since it is one of the most important processes involved in the maintenance of genome stability. Physiological embryo development appears to depend upon the correct DNA methylation pattern. Due to the fact that soon after fertilization the zygote undergoes several morphogenetic and developmental events including activation of embryonic genome through the transition of the maternal genome, a diverse gene expression pattern may lead to clinically important conditions, such as apoptosis or the production of a chromosomically abnormal embryo. The present review focused on genes and their role during pre-implantation embryo development, giving emphasis on the various parameters that may alter gene expression or DNA methylation patterns. The pre-implantation embryos derived from in vitro culture systems (in vitro fertilization) and the possible effects on gene expression after the prolonged culture conditions are also discussed.
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Affiliation(s)
- G Anifandis
- Department of Obstetrics and Gynaecology ; Embryology Lab, University of Thessalia, School of Health Sciences, Faculty of Medicine, Larisa, Greece
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The B-subdomain of the Xenopus laevis XFIN KRAB-AB domain is responsible for its weaker transcriptional repressor activity compared to human ZNF10/Kox1. PLoS One 2014; 9:e87609. [PMID: 24498343 PMCID: PMC3912051 DOI: 10.1371/journal.pone.0087609] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 12/23/2013] [Indexed: 12/12/2022] Open
Abstract
The Krüppel-associated box (KRAB) domain interacts with the nuclear hub protein TRIM28 to initiate or mediate chromatin-dependent processes like transcriptional repression, imprinting or suppression of endogenous retroviruses. The prototype KRAB domain initially identified in ZNF10/KOX1 encompasses two subdomains A and B that are found in hundreds of zinc finger transcription factors studied in human and murine genomes. Here we demonstrate for the first time transcriptional repressor activity of an amphibian KRAB domain. After sequence correction, the updated KRAB-AB domain of zinc finger protein XFIN from the frog Xenopus laevis was found to confer transcriptional repression in reporter assays in Xenopus laevis A6 kidney cells as well as in human HeLa, but not in the minnow Pimephales promelas fish cell line EPC. Binding of the XFIN KRAB-AB domain to human TRIM28 was demonstrated in a classical co-immunoprecipitation approach and visualized in a single-cell compartmentalization assay. XFIN-AB displayed reduced potency in repression as well as lower strength of interaction with TRIM28 compared to ZNF10 KRAB-AB. KRAB-B subdomain swapping between the two KRAB domains indicated that it was mainly the KRAB-B subdomain of XFIN that was responsible for its lower capacity in repression and binding to human TRIM28. In EPC fish cells, ZNF10 and XFIN KRAB repressor activity could be partially restored to low levels by adding exogenous human TRIM28. In contrast to XFIN, we did not find any transcriptional repression activity for the KRAB-like domain of human PRDM9 in HeLa cells. PRDM9 is thought to harbor an evolutionary older domain related to KRAB whose homologs even occur in invertebrates. Our results support the notion that functional bona fide KRAB domains which confer transcriptional repression and interact with TRIM28 most likely co-evolved together with TRIM28 at the beginning of tetrapode evolution.
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Weaver JR, Bartolomei MS. Chromatin regulators of genomic imprinting. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1839:169-77. [PMID: 24345612 DOI: 10.1016/j.bbagrm.2013.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 12/05/2013] [Accepted: 12/10/2013] [Indexed: 02/04/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon in which genes are expressed monoallelically in a parent-of-origin-specific manner. Each chromosome is imprinted with its parental identity. Here we will discuss the nature of this imprinting mark. DNA methylation has a well-established central role in imprinting, and the details of DNA methylation dynamics and the mechanisms that target it to imprinted loci are areas of active investigation. However, there is increasing evidence that DNA methylation is not solely responsible for imprinted expression. At the same time, there is growing appreciation for the contributions of post-translational histone modifications to the regulation of imprinting. The integration of our understanding of these two mechanisms is an important goal for the future of the imprinting field. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Jamie R Weaver
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, 9-123 Smilow Center for Translational Research, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, 9-123 Smilow Center for Translational Research, Philadelphia, PA 19104, USA.
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Santoni de Sio FR, Barde I, Offner S, Kapopoulou A, Corsinotti A, Bojkowska K, Genolet R, Thomas JH, Luescher IF, Pinschewer D, Harris N, Trono D. KAP1 regulates gene networks controlling T-cell development and responsiveness. FASEB J 2012; 26:4561-75. [PMID: 22872677 DOI: 10.1096/fj.12-206177] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chromatin remodeling at specific genomic loci controls lymphoid differentiation. Here, we investigated the role played in this process by Kruppel-associated box (KRAB)-associated protein 1 (KAP1), the universal cofactor of KRAB-zinc finger proteins (ZFPs), a tetrapod-restricted family of transcriptional repressors. T-cell-specific Kap1-deleted mice displayed a significant expansion of immature thymocytes, imbalances in CD4(+)/CD8(+) cell ratios, and altered responses to TCR and TGFβ stimulation when compared to littermate KAP1 control mice. Transcriptome and chromatin studies revealed that KAP1 binds T-cell-specific cis-acting regulatory elements marked by the H3K9me3 repressive mark and enriched in Ikaros/NuRD complexes. Also, KAP1 directly controls the expression of several genes involved in TCR and cytokine signaling. Among these, regulation of FoxO1 seems to play a major role in this system. Likely responsible for tethering KAP1 to at least part of its genomic targets, a small number of KRAB-ZFPs are selectively expressed in T-lymphoid cells. These results reveal the so far unsuspected yet important role of KAP1-mediated epigenetic regulation in T-lymphocyte differentiation and activation.
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Kino T, Pavlatou MG, Moraitis AG, Nemery RL, Raygada M, Stratakis CA. ZNF764 haploinsufficiency may explain partial glucocorticoid, androgen, and thyroid hormone resistance associated with 16p11.2 microdeletion. J Clin Endocrinol Metab 2012; 97:E1557-66. [PMID: 22577170 PMCID: PMC3410270 DOI: 10.1210/jc.2011-3493] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Nuclear hormone receptors exert their transcriptional effects through shared cofactor molecules; thus, defects in such intermediate proteins may be associated with multiple hormone resistance. Microdeletion of small chromosomal segments results in hereditary or sporadic diseases by affecting expression of residing genes. OBJECTIVES We describe a 7-yr-old boy with partial resistance to glucocorticoids, thyroid hormones, and possibly androgens. He was diagnosed as being in the autism spectrum disorder and had developmental delay and several facial morphological manifestations. We explored genes responsible for multiple hormone resistance of this case. RESULTS We found in this patient an approximately 1.1-Mb heterozygous 16p11.2 microdeletion, which included an approximately 500-kb unique deletion along with the common, previously reported approximately 600-kb 16p11.2 microdeletion. The small interfering RNA-based screening revealed that knockdown of ZNF764, which is located in the deleted segment unique to our case, significantly reduced glucocorticoid-, androgen-, and thyroid hormone-induced transcriptional activity of their responsive genes in HeLa cells, whereas its overexpression enhanced their transcriptional activity. The activities of the estrogen and progesterone receptors, cAMP response element-binding protein, and p53 were not affected in these cells. ZNF764 (zinc finger protein 764) expression was reduced in the patient's peripheral blood mononuclear cells, whereas exogenously supplemented ZNF764 recovered responsiveness to glucocorticoids in the patient's Epstein-Barr virus-transformed lymphocytes. The effect of ZNF764 on the glucocorticoid receptor transcriptional activity was mediated through cooperation with a general nuclear hormone receptor coactivator, transcriptional intermediary factor 1. CONCLUSIONS ZNF764 haploinsufficiency caused by microdeletion may be responsible for the partial multiple hormone resistance observed in our patient. ZNF764 appears to be involved in glucocorticoid, androgen, and thyroid hormone action.
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Affiliation(s)
- Tomoshige Kino
- Unit on Molecular Hormone Actio, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-1109, USA.
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12
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Wu J, Cui N, Wang R, Li J, Wong J. A role for CARM1-mediated histone H3 arginine methylation in protecting histone acetylation by releasing corepressors from chromatin. PLoS One 2012; 7:e34692. [PMID: 22723830 PMCID: PMC3377634 DOI: 10.1371/journal.pone.0034692] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 03/05/2012] [Indexed: 12/21/2022] Open
Abstract
Arginine methylation broadly occurs in histones and has been linked to transcriptional regulation, cell cycle regulation and DNA repair. While numerous proteins (histone code effectors) that specifically recognize or read the methylated lysine residues in core histones have been identified, little is known for effectors specific for methylated arginines in histones. In this study, we attempted to identify effector(s) recognizing asymmetrically methylated R17 and R26 in H3, which are catalyzed by CARM1/PRMT4, through an unbiased biochemical approach. Although we have yet to identify such effector using this approach, we find that these modifications function cooperatively with histone acetylation to inhibit the binding of the nucleosome remodeling and deacetylase complex (NuRD) and TIF1 family corepressors to H3 tail in vitro. In support of this finding, we show that overexpression of CARM1 in 293 T cells leads to reduced association of NuRD with chromatin, whereas knockdown of CARM1 in HeLa cells leads to increased association of NuRD with chromatin and decreased level of histone acetylation. Furthermore, in the Carm1−/− MEF cells there is an increased association of NuRD and TIF1β with chromatin and a global decrease in histone acetylation. By chromatin immunoprecipitation assay, we show that overexpression of CARM1 results in reduced association of NuRD complex and TIF1β with an episomal reporter and that CARM1 is required in MEF cells for LPS-induced dissociation of NuRD from a NF-κb target gene. Taking together, our study provides evidence for a role of CARM1-mediated arginine methylation in regulation of histone acetylation and transcription: facilitating transcription by discharging corepressors from chromatin.
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Affiliation(s)
- Jing Wu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Nan Cui
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Rui Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- * E-mail:
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13
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Shibata M, Blauvelt KE, Liem KF, García-García MJ. TRIM28 is required by the mouse KRAB domain protein ZFP568 to control convergent extension and morphogenesis of extra-embryonic tissues. Development 2012; 138:5333-43. [PMID: 22110054 DOI: 10.1242/dev.072546] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
TRIM28 is a transcriptional regulator that is essential for embryonic development and is implicated in a variety of human diseases. The roles of TRIM28 in distinct biological processes are thought to depend on its interaction with factors that determine its DNA target specificity. However, functional evidence linking TRIM28 to specific co-factors is scarce. chatwo, a hypomorphic allele of Trim28, causes embryonic lethality and defects in convergent extension and morphogenesis of extra-embryonic tissues. These phenotypes are remarkably similar to those of mutants in the Krüppel-associated box (KRAB) zinc finger protein ZFP568, providing strong genetic evidence that ZFP568 and TRIM28 control morphogenesis through a common molecular mechanism. We determined that chatwo mutations decrease TRIM28 protein stability and repressive activity, disrupting both ZFP568-dependent and ZFP568-independent roles of TRIM28. These results, together with the analysis of embryos bearing a conditional inactivation of Trim28 in embryonic-derived tissues, revealed that TRIM28 is differentially required by ZFP568 and other factors during the early stages of mouse embryogenesis. In addition to uncovering novel roles of TRIM28 in convergent extension and morphogenesis of extra-embryonic tissues, our characterization of chatwo mutants demonstrates that KRAB domain proteins are essential to determine some of the biological functions of TRIM28.
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Affiliation(s)
- Maho Shibata
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853, USA
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14
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Bartolomei MS, Ferguson-Smith AC. Mammalian genomic imprinting. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a002592. [PMID: 21576252 DOI: 10.1101/cshperspect.a002592] [Citation(s) in RCA: 365] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Normal mammalian development requires a maternal and paternal contribution, which is attributed to imprinted genes, or genes that are expressed from a single parental allele. Approximately 100 imprinted genes have been reported in mammals thus far. Imprinted genes are controlled by cis-acting regulatory elements, termed imprinting control regions (ICRs), which have parental-specific epigenetic modifications, including DNA methylation. ICRs are methylated by de novo DNA methyltransferases during germline development; these parental-specific modifications must be maintained following fertilization when the genome is extensively reprogrammed. Many imprinted genes reside in ∼1-megabase clusters, with two major mechanisms of imprinting regulation currently recognized, CTCF-dependent insulators and long noncoding RNAs. Unclustered imprinted genes are generally regulated by germline-derived differential promoter methylation. Here, we describe the identification and functions of imprinted genes, cis-acting control sequences, trans-acting factors, and imprinting mechanisms in clusters. Finally, we define questions that require more extensive research.
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Affiliation(s)
- Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19063, USA.
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15
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Aucagne R, Droin N, Paggetti J, Lagrange B, Largeot A, Hammann A, Bataille A, Martin L, Yan KP, Fenaux P, Losson R, Solary E, Bastie JN, Delva L. Transcription intermediary factor 1γ is a tumor suppressor in mouse and human chronic myelomonocytic leukemia. J Clin Invest 2011; 121:2361-70. [PMID: 21537084 PMCID: PMC3104753 DOI: 10.1172/jci45213] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 03/08/2011] [Indexed: 12/27/2022] Open
Abstract
Transcription intermediary factor 1γ (TIF1γ) was suggested to play a role in erythropoiesis. However, how TIF1γ regulates the development of different blood cell lineages and whether TIF1γ is involved in human hematological malignancies remain to be determined. Here we have shown that TIF1γ was a tumor suppressor in mouse and human chronic myelomonocytic leukemia (CMML). Loss of Tif1g in mouse HSCs favored the expansion of the granulo-monocytic progenitor compartment. Furthermore, Tif1g deletion induced the age-dependent appearance of a cell-autonomous myeloproliferative disorder in mice that recapitulated essential characteristics of human CMML. TIF1γ was almost undetectable in leukemic cells of 35% of CMML patients. This downregulation was related to the hypermethylation of CpG sequences and specific histone modifications in the gene promoter. A demethylating agent restored the normal epigenetic status of the TIF1G promoter in human cells, which correlated with a reestablishment of TIF1γ expression. Together, these results demonstrate that TIF1G is an epigenetically regulated tumor suppressor gene in hematopoietic cells and suggest that changes in TIF1γ expression may be a biomarker of response to demethylating agents in CMML.
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MESH Headings
- Aged
- Aged, 80 and over
- Aging/genetics
- Animals
- Antimetabolites, Antineoplastic/pharmacology
- Antimetabolites, Antineoplastic/therapeutic use
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Azacitidine/therapeutic use
- Base Sequence
- Cell Differentiation
- DNA Methylation
- Decitabine
- Female
- Gene Expression Regulation, Leukemic
- Genes, Tumor Suppressor
- Hematopoiesis/genetics
- Hematopoiesis/physiology
- Hematopoietic Stem Cells/pathology
- Humans
- Leukemia, Myelomonocytic, Chronic/drug therapy
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/pathology
- Male
- Mice
- Mice, Knockout
- Middle Aged
- Molecular Sequence Data
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Promoter Regions, Genetic
- Receptor, Macrophage Colony-Stimulating Factor/biosynthesis
- Receptor, Macrophage Colony-Stimulating Factor/genetics
- Specific Pathogen-Free Organisms
- Transcription Factors/deficiency
- Transcription Factors/genetics
- Transcription Factors/physiology
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Affiliation(s)
- Romain Aucagne
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Nathalie Droin
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Jérôme Paggetti
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Brice Lagrange
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Anne Largeot
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Arlette Hammann
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Amandine Bataille
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Laurent Martin
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Kai-Ping Yan
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Pierre Fenaux
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Régine Losson
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Eric Solary
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Jean-Noël Bastie
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
| | - Laurent Delva
- Inserm UMR 866, University of Burgundy, Dijon, France.
IFR “Santé-STIC,” University of Burgundy, Dijon, France.
Inserm UMR 1009, Integrated Research Cancer Institute Villejuif (IRCIV), Institut Gustave Roussy, Villejuif, France.
Flow Cytometry Facility,
Cellular Imagery Facility, and
Department of Pathology, University Hospital, Dijon, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics, CNRS UMR 7104, Inserm U964, Louis Pasteur University, Collège de France, Illkirch, France.
University Hospital, Assistance Publique–Hôpitaux de Paris (AP-HP) and University of Paris 13, Bobigny, France.
University Hospital, Clinical Hematology Department, Dijon, France
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16
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Transcription cofactors TRIM24, TRIM28, and TRIM33 associate to form regulatory complexes that suppress murine hepatocellular carcinoma. Proc Natl Acad Sci U S A 2011; 108:8212-7. [PMID: 21531907 DOI: 10.1073/pnas.1101544108] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
TRIM24 (TIF1α), TRIM28 (TIF1β), and TRIM33 (TIF1γ) are three related cofactors belonging to the tripartite motif superfamily that interact with distinct transcription factors. TRIM24 interacts with the liganded retinoic acid (RA) receptor to repress its transcriptional activity. Germ line inactivation of TRIM24 in mice deregulates RA-signaling in hepatocytes leading to the development of hepatocellular carcinoma (HCC). Here we show that TRIM24 can be purified as at least two macromolecular complexes comprising either TRIM33 or TRIM33 and TRIM28. Somatic hepatocyte-specific inactivation of TRIM24, TRIM28, or TRIM33 all promote HCC in a cell-autonomous manner in mice. Moreover, HCC formation upon TRIM24 inactivation is strongly potentiated by further loss of TRIM33. These results demonstrate that the TIF1-related subfamily of TRIM proteins interact both physically and functionally to modulate HCC formation in mice.
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17
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Abstract
Krüppel-type or C2H2 zinc fingers represent a dominant DNA-binding motif in eukaryotic transcription factor (TF) proteins. In Krüppel-type (KZNF) TFs, KZNF motifs are arranged in arrays of three to as many as 40 tandem units, which cooperate to define the unique DNA recognition properties of the protein. Each finger contains four amino acids located at specific positions, which are brought into direct contact with adjacent nucleotides in the DNA sequence as the KZNF array winds around the major groove of the alpha helix. This arrangement creates an intimate and potentially predictable relationship between the amino acid sequence of KZNF arrays and the nucleotide sequence of target binding sites. The large number of possible combinations and arrangements of modular KZNF motifs, and the increasing lengths of KZNF arrays in vertebrate species, has created huge repertoires of functionally unique TF proteins. The properties of this versatile DNA-binding motif have been exploited independently many times over the course of evolution, through attachment to effector motifs that confer activating, repressing or other activities to the proteins. Once created, some of these novel inventions have expanded in specific evolutionary clades, creating large families of TFs that are lineage- or species-unique. This chapter reviews the properties and their remarkable evolutionary history of eukaryotic KZNF TF proteins, with special focus on large families that dominate the TF landscapes in different metazoan species.
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Affiliation(s)
- Lisa Stubbs
- Department of Cell and Developmental Biology, Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA,
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18
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19
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Groner AC, Meylan S, Ciuffi A, Zangger N, Ambrosini G, Dénervaud N, Bucher P, Trono D. KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet 2010; 6:e1000869. [PMID: 20221260 PMCID: PMC2832679 DOI: 10.1371/journal.pgen.1000869] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 02/02/2010] [Indexed: 01/05/2023] Open
Abstract
Krüppel-associated box domain-zinc finger proteins (KRAB–ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB–mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB–containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB–mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 β (HP1β) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1–dependent transcriptional repression at an endogenous KRAB–ZFP gene cluster, where KAP1 binds to the 3′ end of genes and mediates propagation of H3K9me3 and HP1β towards their 5′ end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB–ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB–ZFPs and KAP1. The regulation of gene activity by transcription factors is crucial to the function of all cells. Here, we studied the mechanisms of action of the largest family of gene regulators encoded by the human genome, the so-called KRAB–containing zinc finger proteins (KRAB–ZFPs), which in concert with their universal cofactor KAP1 act as transcriptional repressors. For this, we used two parallel approaches. First, by targeting an ectopic KRAB domain to hundreds of different genes, we found that KRAB/KAP1 can repress promoters located several tens of kilobases from the repressor DNA docking site. We further could show that KRAB induces such long-range effects by mediating the spread of repressive chromatin marks along the body of the gene, resulting in a block of transcriptional initiation at the promoter. In a second set of experiments, we analyzed an endogenous KRAB–ZFP gene cluster, where we could also document KAP1–dependent heterochromatin spreading and transcriptional repression. Together, these results support a model whereby KRAB–ZFPs and KAP1 can mediate long-range transcriptional repression through the spread of silencing chromatin marks. This study thus provides insight into KRAB/KAP1–induced gene regulation at KRAB–ZFP gene clusters, and will further help interpret genome-wide studies of KRAB–ZFPs and KAP1 DNA binding patterns.
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Affiliation(s)
- Anna C. Groner
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Frontiers-in-Genetics National Center of Competence in Research, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sylvain Meylan
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Frontiers-in-Genetics National Center of Competence in Research, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Nadine Zangger
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Frontiers-in-Genetics National Center of Competence in Research, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Giovanna Ambrosini
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Dénervaud
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Philipp Bucher
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Frontiers-in-Genetics National Center of Competence in Research, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- * E-mail:
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20
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Losson R, Nielsen AL. The NIZP1 KRAB and C2HR domains cross-talk for transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:463-8. [PMID: 20176155 DOI: 10.1016/j.bbagrm.2010.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 02/08/2010] [Accepted: 02/16/2010] [Indexed: 01/10/2023]
Abstract
The NSD1 histone methyltransferase is involved in the outgrowth disorders Sotos and Weaver syndromes and childhood acute myeloid leukemia. NSD1 is a bona fida transcriptional co-repressor for Nizp1 which is a protein including SCAN, KRAB, C2HR and zinc-finger domains. In this study the Nizp1 KRAB-domain was identified to possess an intrinsic transcriptional activation capacity suppressed in cis by the presence of the C2HR domain. Oppositely, the KRAB-domain supported C2HR domain mediated transcriptional repression. The presence of the KRAB-domain resulted in increased NSD1 co-repressor association with the C2HR domain. This study shows a new function of the KRAB-domain, C2HR-domain, and the associated factors to confer Nizp1 mediated transcriptional regulation.
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Affiliation(s)
- Regine Losson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics, Illkirch, France
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21
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Peng H, Ivanov AV, Oh HJ, Lau YFC, Rauscher FJ. Epigenetic gene silencing by the SRY protein is mediated by a KRAB-O protein that recruits the KAP1 co-repressor machinery. J Biol Chem 2010; 284:35670-80. [PMID: 19850934 DOI: 10.1074/jbc.m109.032086] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The sex determination transcription factor SRY is a cell fate-determining transcription factor that mediates testis differentiation during embryogenesis. It may function by repressing the ovarian determinant gene, RSPO1, action in the ovarian developmental pathway and activates genes, such as SOX9, important for testis differentiation at the onset of gonadogenesis. Further, altered expression of SRY and related SOX genes contribute to oncogenesis in many human cancers. Little is known of the mechanisms by which SRY regulates its target genes. Recently a KRAB domain protein (KRAB-O) that lacks a zinc finger motif has been demonstrated to interact with SRY and hypothesized to function as an adaptor molecule for SRY by tethering the KAP1-NuRD-SETDB1-HP1 silencing machinery to repress SRY targets. We have critically examined this hypothesis by reconstituting and characterizing SRY-KRAB-O-KAP1 interactions. These recombinant molecules can form a ternary complex by direct and high affinity interactions. The KRAB-O protein can simultaneously bind KAP1 and SRY in a noncompetitive but also noncooperative manner. An extensive mutagenesis analysis suggests that different surfaces on KRAB-O are utilized for these independent interactions. Transcriptional repression by SRY requires binding to KRAB-O, thus bridging to the KAP1 repression machinery. This repression machinery is recruited to SRY target promoters in chromatin templates via SRY. These results suggest that SRY has co-opted the KRAB-O protein to recruit the KAP1 repression machinery to sex determination target genes. Other KRAB domain proteins, which lack a zinc finger DNA-binding motif, may function in similar roles as adaptor proteins for epigenetic gene silencing.
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22
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Imprinting and epigenetic changes in the early embryo. Mamm Genome 2009; 20:532-43. [PMID: 19760320 DOI: 10.1007/s00335-009-9225-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 06/18/2009] [Indexed: 10/20/2022]
Abstract
Imprinted genes are epigenetically regulated so that only one allele is expressed in a parent-of-origin-dependent manner. Although they represent a small subset of the mammalian genome, imprinted genes are essential for normal development. The regulatory mechanisms underlying imprinting are complex and have been the subject of extensive investigation. DNA methylation is the best-established epigenetic mark that is critical for the allele-specific expression of imprinted genes. This mark must be correctly established in the germline, maintained throughout life, and erased and reestablished in the germline the next generation. These events coincide with the genome-wide epigenetic reprogramming that occurs during gametogenesis and early embryogenesis; therefore, the establishment and maintenance of DNA methylation must be tightly regulated. Studies on enzymes that participate in both de novo methylation and its maintenance (i.e., the DNMT family) have provided information on how methylation influences imprinting. However, many aspects of the regulation of DNA methylation are unknown, including how methylation complexes are targeted and the molecular mechanisms underlying DNA demethylation. In this review we focus on the epigenetic changes that occur in the germline and early embryo, with an emphasis on imprinting. We summarize recent findings on factors influencing DNA methylation establishment, maintenance, and erasure that have further elucidated the mechanisms of imprinting, while highlighting topics that require further investigation.
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Abstract
Genomic imprinting refers to an epigenetic mark that distinguishes parental alleles and results in a monoallelic, parental-specific expression pattern in mammals. Few phenomena in nature depend more on epigenetic mechanisms while at the same time evading them. The alleles of imprinted genes are marked epigenetically at discrete elements termed imprinting control regions (ICRs) with their parental origin in gametes through the use of DNA methylation, at the very least. Imprinted gene expression is subsequently maintained using noncoding RNAs, histone modifications, insulators, and higher-order chromatin structure. Avoidance is manifest when imprinted genes evade the genome-wide reprogramming that occurs after fertilization and remain marked with their parental origin. This review summarizes what is known about the establishment and maintenance of imprinting marks and discusses the mechanisms of imprinting in clusters. Additionally, the evolution of imprinted gene clusters is described. While considerable information regarding epigenetic control of imprinting has been obtained recently, much remains to be learned.
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Affiliation(s)
- Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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Yang Z, Wen HJ, Minhas V, Wood C. The zinc finger DNA-binding domain of K-RBP plays an important role in regulating Kaposi's sarcoma-associated herpesvirus RTA-mediated gene expression. Virology 2009; 391:221-31. [PMID: 19592062 DOI: 10.1016/j.virol.2009.06.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 04/24/2009] [Accepted: 06/09/2009] [Indexed: 01/10/2023]
Abstract
K-RBP is a KRAB-containing zinc finger protein with multiple zinc finger motifs and represses Kaposi's sarcoma-associated herpesvirus (KSHV) transactivator RTA-mediated transactivation of several viral lytic gene promoters, including the ORF57 promoter. Whether K-RBP binds DNA through its zinc fingers and the role of zinc finger domain in repressing gene expression are unclear. Here we report that K-RBP binds DNA through its zinc finger domain and the target DNA sequences contain high GC content. Furthermore, K-RBP binds to KSHV ORF57 promoter, which contains a GC-rich motif. K-RBP suppresses the basal ORF57 promoter activity as well as RTA-mediated activation. The zinc finger domain of K-RBP is sufficient for the suppression of ORF57 promoter activation mediated by the viral transactivator RTA. Finally, we show that K-RBP inhibits RTA binding to ORF57 promoter. These findings suggest that the DNA-binding activity of K-RBP plays an important role in repressing viral promoter activity.
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Affiliation(s)
- Zhilong Yang
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln NE 68583, USA
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25
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Rambaud J, Desroches J, Balsalobre A, Drouin J. TIF1beta/KAP-1 is a coactivator of the orphan nuclear receptor NGFI-B/Nur77. J Biol Chem 2009; 284:14147-56. [PMID: 19321449 PMCID: PMC2682863 DOI: 10.1074/jbc.m809023200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 03/25/2009] [Indexed: 01/02/2023] Open
Abstract
In efforts to define mechanisms of transcriptional activation by the orphan nuclear receptor NGFI-B (Nur77), we identified TIF1beta by mass spectrometry within a nuclear protein complex containing NGFI-B. TIF1beta, also known as KAP-1 (KRAB domain-associated protein) or KRIP-1, acts as a transcriptional corepressor for many transcription factors, in particular for the Krüppel-associated box domain-containing zinc finger transcription factors. TIF1beta is also an intrinsic component of two chromatin remodeling and histone deacetylase complexes, the N-CoR1 and nucleosome remodeling and deacetylation complexes. In contrast to these activities, we report that TIF1beta is a coactivator of NGFI-B and that it is as potent as the SRC coactivators in this context. Using pull-down assays and immunoprecipitation, we showed that TIF1beta interacts directly with NGFI-B and with other Nur family members. NGFI-B is an important mediator of hypothalamic corticotropin-releasing hormone (CRH) activation of proopiomelanocortin (POMC) transcription, and TIF1beta enhances transcription mediated through the NGFI-B target, the Nur response element (NurRE). The NurRE binds Nur factor dimers and is responsive to signaling pathways. In keeping with the role of NGFI-B as mediator of CRH signaling, we found that TIF1beta is recruited to the POMC promoter following CRH stimulation and that TIF1beta potentiates CRH and protein kinase A signaling through the NurRE; it acts synergistically with the SRC2 coactivator. However, the actions of TIF1beta and SRC2 were mapped to different NGFI-B AF-1 subdomains. Taken together, these results indicate that TIF1beta is an important coactivator of NGFI-B-dependent transcription.
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Affiliation(s)
- Juliette Rambaud
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, Montréal, Quebec H2W 1R7, Canada
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26
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Li X, Ito M, Zhou F, Youngson N, Zuo X, Leder P, Ferguson-Smith AC. A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev Cell 2008; 15:547-57. [PMID: 18854139 DOI: 10.1016/j.devcel.2008.08.014] [Citation(s) in RCA: 448] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 06/20/2008] [Accepted: 08/25/2008] [Indexed: 10/21/2022]
Abstract
The mechanisms responsible for maintaining genomic methylation imprints in mouse embryos are not understood. We generated a knockout mouse in the Zfp57 locus encoding a KRAB zinc finger protein. Loss of just the zygotic function of Zfp57 causes partial neonatal lethality, whereas eliminating both the maternal and zygotic functions of Zfp57 results in a highly penetrant embryonic lethality. In oocytes, absence of Zfp57 results in failure to establish maternal methylation imprints at the Snrpn imprinted region. Intriguingly, methylation imprints are reacquired specifically at the maternally derived Snrpn imprinted region when the zygotic Zfp57 is present in embryos. This suggests that there may be DNA methylation-independent memory for genomic imprints. Zfp57 is also required for the postfertilization maintenance of maternal and paternal methylation imprints at multiple imprinted domains. The effects on genomic imprinting are consistent with the maternal-zygotic lethality of Zfp57 mutants.
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Affiliation(s)
- Xiajun Li
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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27
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Riclet R, Chendeb M, Vonesch JL, Koczan D, Thiesen HJ, Losson R, Cammas F. Disruption of the interaction between transcriptional intermediary factor 1{beta} and heterochromatin protein 1 leads to a switch from DNA hyper- to hypomethylation and H3K9 to H3K27 trimethylation on the MEST promoter correlating with gene reactivation. Mol Biol Cell 2008; 20:296-305. [PMID: 18923144 DOI: 10.1091/mbc.e08-05-0510] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Here, we identified the imprinted mesoderm-specific transcript (MEST) gene as an endogenous TIF1beta primary target gene and demonstrated that transcriptional intermediary factor (TIF) 1beta, through its interaction with heterochromatin protein (HP) 1, is essential in establishing and maintaining a local heterochromatin-like structure on MEST promoter region characterized by H3K9 trimethylation and hypoacetylation, H4K20 trimethylation, DNA hypermethylation, and enrichment in HP1 that correlates with preferential association to foci of pericentromeric heterochromatin and transcriptional repression. On disruption of the interaction between TIF1beta and HP1, TIF1beta is released from the promoter region, and there is a switch from DNA hypermethylation and histone H3K9 trimethylation to DNA hypomethylation and histone H3K27 trimethylation correlating with rapid reactivation of MEST expression. Interestingly, we provide evidence that the imprinted MEST allele DNA methylation is insensitive to TIF1beta loss of function, whereas the nonimprinted allele is regulated through a distinct TIF1beta-DNA methylation mechanism.
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Affiliation(s)
- Raphaël Riclet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université Louis Pasteur/Collège de France, Illkirch-Cedex, France
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28
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Zeng L, Yap KL, Ivanov AV, Wang X, Mujtaba S, Plotnikova O, Rauscher FJ, Zhou MM. Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. Nat Struct Mol Biol 2008; 15:626-33. [PMID: 18488044 DOI: 10.1038/nsmb.1416] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Accepted: 03/14/2008] [Indexed: 12/30/2022]
Abstract
The tandem PHD finger-bromodomain, found in many chromatin-associated proteins, has an important role in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). Here we report the three-dimensional solution structure of the tandem PHD finger-bromodomain of KAP1. The structure reveals a distinct scaffold unifying the two protein modules, in which the first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other. A comprehensive mutation-based structure-function analysis correlating transcriptional repression, ubiquitin-conjugating enzyme 9 (UBC9) binding and SUMOylation shows that the PHD finger and the bromodomain of KAP1 cooperate as one functional unit to facilitate lysine SUMOylation, which is required for KAP1 co-repressor activity in gene silencing. These results demonstrate a previously unknown unified function for the tandem PHD finger-bromodomain as an intramolecular small ubiquitin-like modifier (SUMO) E3 ligase for transcriptional silencing.
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Affiliation(s)
- Lei Zeng
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, 1425 Madison Avenue, New York, New York 10029, USA
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29
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Mysliwiec MR, Kim TG, Lee Y. Characterization of zinc finger protein 496 that interacts with Jumonji/Jarid2. FEBS Lett 2007; 581:2633-40. [PMID: 17521633 PMCID: PMC2002548 DOI: 10.1016/j.febslet.2007.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 04/23/2007] [Accepted: 05/03/2007] [Indexed: 10/23/2022]
Abstract
Jumonij (JMJ)/Jarid2 plays important roles in embryonic development and functions as a transcriptional repressor. Using yeast two-hybrid screening, we have identified a cofactor of JMJ, the zinc finger protein 496 (Zfp496) that contains a SCAN, KRAB and zinc finger domain. Our molecular analyses indicate that Zfp496 functions as a transcriptional activator. Further, Zfp496 inhibits the transcriptional repression of JMJ and JMJ represses the transcriptional activation of Zfp496. This study demonstrates that JMJ physically and functionally interacts with Zfp496, which will provide important insights into endogenous target gene regulation by both factors.
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30
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O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet 2007; 3:e89. [PMID: 17542650 PMCID: PMC1885280 DOI: 10.1371/journal.pgen.0030089] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 04/19/2007] [Indexed: 12/13/2022] Open
Abstract
We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts. We found that in each of the cell types the two modifications were differentially enriched at the promoters of the two largest classes of transcription factors. Specifically, zinc finger (ZNF) genes were bound by H3me3K9 and homeobox genes were bound by H3me3K27. We have previously shown that the Polycomb repressive complex 2 is responsible for mediating trimethylation of lysine 27 of histone H3 in human cancer cells. In contrast, there is little overlap between H3me3K9 targets and components of the Polycomb repressive complex 2, suggesting that a different histone methyltransferase is responsible for the H3me3K9 modification. Previous studies have shown that SETDB1 can trimethylate H3 on lysine 9, using in vitro or artificial tethering assays. SETDB1 is thought to be recruited to chromatin by complexes containing the KAP1 corepressor. To determine if a KAP1-containing complex mediates trimethylation of the identified H3me3K9 targets, we performed ChIP-chip assays and identified KAP1 target genes using human 5-kb promoter arrays. We found that a large number of genes of ZNF transcription factors were bound by both KAP1 and H3me3K9 in normal and cancer cells. To expand our studies of KAP1, we next performed a complete genomic analysis of KAP1 binding using a 38-array tiling set, identifying ~7,000 KAP1 binding sites. The identified KAP1 targets were highly enriched for C2H2 ZNFs, especially those containing Krüppel-associated box (KRAB) domains. Interestingly, although most KAP1 binding sites were within core promoter regions, the binding sites near ZNF genes were greatly enriched within transcribed regions of the target genes. Because KAP1 is recruited to the DNA via interaction with KRAB-ZNF proteins, we suggest that expression of KRAB-ZNF genes may be controlled via an auto-regulatory mechanism involving KAP1. Methylation of lysines 9 or 27 of histone H3 (H3me3K9 or H3me3K27, respectively) has been associated with silenced chromatin. However, a comprehensive comparison of the regions of the genome bound by these two types of modified histone H3 has not been performed. Therefore, we compared the binding patterns of H3me3K9 and H3me3K27 at ~26,000 human promoters in four different cell populations. Our studies indicated that the two marks segregate differentially with the two most common types of transcriptional regulators; H3me3K27 is highly enriched at homeobox genes and H3me3K9 is highly enriched at zinc-finger genes (ZNFs). We showed that many of the promoters bound by H3me3K9 are also bound by the corepressor KAP1. A genome-wide screen for KAP1 target genes revealed a difference in the location of KAP1 binding sites in the ZNF genes versus other targets. In general, KAP1 binding sites were localized to core promoter regions. However, KAP1 binding sites associated with ZNF genes are near the 3′ end of the coding region. Our results suggest that the KRAB-ZNF family members participate in an autoregulatory loop involving binding of the KAP1 protein to the 3′ end of the ZNF target genes, resulting in trimethylation of H3K9 and transcriptional repression.
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Affiliation(s)
- Henriette O'Geen
- Department of Pharmacology, University of California Davis, Davis, California, United States of America
- The Genome Center, University of California Davis, Davis, California, United States of America
| | - Sharon L Squazzo
- Department of Pharmacology, University of California Davis, Davis, California, United States of America
- The Genome Center, University of California Davis, Davis, California, United States of America
| | - Sushma Iyengar
- Department of Pharmacology, University of California Davis, Davis, California, United States of America
- The Genome Center, University of California Davis, Davis, California, United States of America
| | - Kim Blahnik
- Department of Pharmacology, University of California Davis, Davis, California, United States of America
- The Genome Center, University of California Davis, Davis, California, United States of America
| | - John L Rinn
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Roland Green
- NimbleGen Systems, Madison, Wisconsin, United States of America
| | - Peggy J Farnham
- Department of Pharmacology, University of California Davis, Davis, California, United States of America
- The Genome Center, University of California Davis, Davis, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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31
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Yang Z, Wood C. The transcriptional repressor K-RBP modulates RTA-mediated transactivation and lytic replication of Kaposi's sarcoma-associated herpesvirus. J Virol 2007; 81:6294-306. [PMID: 17409159 PMCID: PMC1900108 DOI: 10.1128/jvi.02648-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The replication and transcription activator (RTA) protein of Kaposi's sarcoma (KS)-associated herpesvirus (KSHV)/human herpesvirus 8 functions as the key regulator to induce KSHV lytic replication from latency through activation of the lytic cascade of KSHV. Elucidation of the host factors involved in RTA-mediated transcriptional activation is pivotal for understanding the transition between viral latency and lytic replication. KSHV-RTA binding protein (K-RBP) was previously isolated as a cellular RTA binding protein of unknown function. Sequence analysis showed that K-RBP contains a Kruppel-associated box (KRAB) at the N terminus and 12 adjacent zinc finger motifs. In similarity to other KRAB-containing zinc finger proteins, K-RBP is a transcriptional repressor. Mutational analysis revealed that the KRAB domain is responsible for the transcriptional suppression activity of this protein and that the repression is histone deacetylase independent. K-RBP was found to repress RTA-mediated transactivation and interact with TIF1beta (transcription intermediary factor 1beta), a common corepressor of KRAB-containing protein, to synergize with K-RBP in repression. Overexpression and knockdown experiment results suggest that K-RBP is a suppressor of RTA-mediated KSHV reactivation. Our findings suggest that the KRAB-containing zinc finger protein K-RBP can suppress RTA-mediated transactivation and KSHV lytic replication and that KSHV utilizes this protein as a regulator to maintain a balance between latency and lytic replication.
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Affiliation(s)
- Zhilong Yang
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska, E249 Beadle Center, P.O. Box 880666, Lincoln, NE 68588-0666, USA
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32
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Peng H, Gibson LC, Capili AD, Borden KLB, Osborne MJ, Harper SL, Speicher DW, Zhao K, Marmorstein R, Rock TA, Rauscher FJ. The structurally disordered KRAB repression domain is incorporated into a protease resistant core upon binding to KAP-1-RBCC domain. J Mol Biol 2007; 370:269-89. [PMID: 17512541 DOI: 10.1016/j.jmb.2007.03.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 02/05/2007] [Accepted: 03/19/2007] [Indexed: 12/13/2022]
Abstract
The KRAB domain is a 75 amino acid transcriptional repression module that is encoded by more than 400 zinc finger protein genes, making it the most abundant repression domain in the human proteome. KRAB-mediated gene silencing requires a direct high affinity interaction with the RBCC domain of KAP-1 co-repressor. The structures of the free KRAB domain or the KRAB-RBCC complex are unknown. To address this, we have performed a systematic biophysical analysis of all KRAB isoforms using purified recombinant proteins. All KRAB domains are predominantly monomeric either alone or in a complex with KAP-1-RBCC protein, while a KRAB-SCAN isoform exists as a stable dimer. The KRAB:KAP-1-RBCC interaction requires only the A box in the context of the KRAB(Ab) or KRAB(AC) but both A and B boxes in the context of KRAB(AB). All isoforms bind the KAP-1-RBCC in a stable, zinc dependent fashion with a stoichiometry of KRAB1:3 RBCC with a zinc content of four atoms per RBCC monomer. Limited proteolysis, mass spectrometry and N-terminal sequence analyses suggest that a core complex comprises the entire RBCC domain of KAP-1 and the AB box of the KRAB domain rendering it resistant to proteolysis. NMR spectroscopy showed that unbound KRAB domain does not exist as a well-folded globular protein in solution but may fold into an ordered structure upon binding to the KAP-1-RBCC protein. This is the first example of a structurally disordered repressor domain that is the most widely conserved silencing domain in tetrapods.
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Affiliation(s)
- Hongzhuang Peng
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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33
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Sripathy SP, Stevens J, Schultz DC. The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression. Mol Cell Biol 2006; 26:8623-38. [PMID: 16954381 PMCID: PMC1636786 DOI: 10.1128/mcb.00487-06] [Citation(s) in RCA: 241] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
KAP1/TIF1beta is proposed to be a universal corepressor protein for the KRAB zinc finger protein (KRAB-zfp) superfamily of transcriptional repressors. To characterize the role of KAP1 and KAP1-interacting proteins in transcriptional repression, we investigated the regulation of stably integrated reporter transgenes by hormone-responsive KRAB and KAP1 repressor proteins. Here, we demonstrate that depletion of endogenous KAP1 levels by small interfering RNA (siRNA) significantly inhibited KRAB-mediated transcriptional repression of a chromatin template. Similarly, reduction in cellular levels of HP1alpha/beta/gamma and SETDB1 by siRNA attenuated KRAB-KAP1 repression. We also found that direct tethering of KAP1 to DNA was sufficient to repress transcription of an integrated transgene. This activity is absolutely dependent upon the interaction of KAP1 with HP1 and on an intact PHD finger and bromodomain of KAP1, suggesting that these domains function cooperatively in transcriptional corepression. The achievement of the repressed state by wild-type KAP1 involves decreased recruitment of RNA polymerase II, reduced levels of histone H3 K9 acetylation and H3K4 methylation, an increase in histone occupancy, enrichment of trimethyl histone H3K9, H3K36, and histone H4K20, and HP1 deposition at proximal regulatory sequences of the transgene. A KAP1 protein containing a mutation of the HP1 binding domain failed to induce any change in the histone modifications associated with DNA sequences of the transgene, implying that HP1-directed nuclear compartmentalization is required for transcriptional repression by the KRAB/KAP1 repression complex. The combination of these data suggests that KAP1 functions to coordinate activities that dynamically regulate changes in histone modifications and deposition of HP1 to establish a de novo microenvironment of heterochromatin, which is required for repression of gene transcription by KRAB-zfps.
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Affiliation(s)
- Smitha P Sripathy
- Case Western Reserve University, Department of Pharmacology and Case Comprehensive Cancer Center, Cleveland, Ohio 44106-4965, USA
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34
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Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res 2006; 16:669-77. [PMID: 16606702 PMCID: PMC1457042 DOI: 10.1101/gr.4842106] [Citation(s) in RCA: 241] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array of DNA-binding zinc-finger motifs, are specific to tetrapod vertebrates and represent the largest class of ZNF proteins in mammals. To define the full repertoire of human KRAB-ZNF proteins, we searched the genome sequence for key motifs and then constructed and manually curated gene models incorporating those sequences. The resulting gene catalog contains 423 KRAB-ZNF protein-coding loci, yielding alternative transcripts that altogether predict at least 742 structurally distinct proteins. Active rounds of segmental duplication, involving single genes or larger regions and including both tandem and distributed duplication events, have driven the expansion of this mammalian gene family. Comparisons between the human genes and ZNF loci mined from the draft mouse, dog, and chimpanzee genomes not only identified 103 KRAB-ZNF genes that are conserved in mammals but also highlighted a substantial level of lineage-specific change; at least 136 KRAB-ZNF coding genes are primate specific, including many recent duplicates. KRAB-ZNF genes are widely expressed and clustered genes are typically not coregulated, indicating that paralogs have evolved to fill roles in many different biological processes. To facilitate further study, we have developed a Web-based public resource with access to gene models, sequences, and other data, including visualization tools to provide genomic context and interaction with other public data sets.
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Affiliation(s)
| | | | | | | | | | | | | | - Elbert Branscomb
- Microbial Systems Divisions, Biosciences, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Lisa Stubbs
- Genome Biology
- Corresponding author.E-mail ; fax (925) 422-2099
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35
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Oh HJ, Lau YFC. KRAB: a partner for SRY action on chromatin. Mol Cell Endocrinol 2006; 247:47-52. [PMID: 16414182 DOI: 10.1016/j.mce.2005.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Revised: 12/01/2005] [Accepted: 12/02/2005] [Indexed: 01/10/2023]
Abstract
The sex determining region Y (SRY/Sry) gene is necessary and sufficient for testis determination and differentiation in mammals. SRY/Sry encodes a putative transcription factor with a high mobility group (HMG) DNA-binding domain. The spatiotemporal regulation of Sry expression suggests that a brief action of SRY in a limited number of progenitor cells (pre-Sertoli cells) before the onset of default ovarian differentiation is sufficient to switch on testicular differentiation. Recent identification and characterization of the Krüppel-associated box only (KRAB-O) protein as an SRY-interacting protein have provided experimental evidence supporting an interesting model for SRY function. In this model, SRY recruits the KRAB-KAP1 (KRAB-associating protein 1) complex as a chromatin modulator, which provides a molecular mechanism of SRY as a transcription factor. Moreover, the sufficiency of a brief action of SRY for testis differentiation can be partly explained by the heritability of KRAB-mediated chromatin remodeling. Although it is currently uncertain whether KRAB-O is the only KRAB protein with which SRY interacts, we hypothesize that KRAB-O or yet-to-be identified KRAB-containing proteins might play various roles in sex determination and gonadal differentiation.
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Affiliation(s)
- Hyun Ju Oh
- Department of Medicine, VA Medical Center, University of California at San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA
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36
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Cammas F, Herzog M, Lerouge T, Chambon P, Losson R. Association of the transcriptional corepressor TIF1beta with heterochromatin protein 1 (HP1): an essential role for progression through differentiation. Genes Dev 2004; 18:2147-60. [PMID: 15342492 PMCID: PMC515292 DOI: 10.1101/gad.302904] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The transcriptional intermediary factor 1beta (TIF1beta) is a corepressor for KRAB-domain-containing zinc finger proteins and is believed to play essential roles in cell physiology by regulating chromatin organization at specific loci through association with chromatin remodeling and histone-modifying activities and recruitment of heterochromatin protein 1 (HP1) proteins. In this study, we have engineered a modified embryonal carcinoma F9 cell line (TIF1beta(HP1box/-)) expressing a mutated TIF1beta protein (TIF1beta(HP1box)) unable to interact with HP1 proteins. Phenotypic analysis of TIF1beta(HP1box/-) and TIF1beta(+/-) cells shows that TIF1beta-HP1 interaction is not required for differentiation of F9 cells into primitive endoderm-like (PrE) cells on retinoic acid (RA) treatment but is essential for further differentiation into parietal endoderm-like (PE) cells on addition of cAMP and for differentiation into visceral endoderm-like cells on treatment of vesicles with RA. Complementation experiments reveal that TIF1beta-HP1 interaction is essential only during a short window of time within early differentiating PrE cells to establish a selective transmittable competence to terminally differentiate on further cAMP inducing signal. Moreover, the expression of three endoderm-specific genes, GATA6, HNF4, and Dab2, is down-regulated in TIF1beta(HP1box/-) cells compared with wild-type cells during PrE differentiation. Collectively, these data demonstrate that the interaction between TIF1beta and HP1 proteins is essential for progression through differentiation by regulating the expression of endoderm differentiation master players.
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Affiliation(s)
- Florence Cammas
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP/Collège de France, BP10142, 67404 Illkirch, France
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37
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Yan KP, Dollé P, Mark M, Lerouge T, Wendling O, Chambon P, Losson R. Molecular cloning, genomic structure, and expression analysis of the mouse transcriptional intermediary factor 1 gamma gene. Gene 2004; 334:3-13. [PMID: 15256250 DOI: 10.1016/j.gene.2004.02.056] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2003] [Revised: 02/19/2004] [Accepted: 02/27/2004] [Indexed: 12/31/2022]
Abstract
Human transcriptional intermediary factor 1 gamma (Tif1gamma), also known as Ret fused gene 7 (RFG7), is a member of a novel family of transcriptional coregulator-encoding genes which function in cell differentiation and development. Here, we report the structure and expression pattern of the mouse Tif1gamma gene. This gene comprises 20 coding exons spanning about 77 kb of genomic DNA on chromosome 3F2, and encodes a 1142-amino-acid protein with 96% identity to the human protein. The locations of exon/intron boundaries correlated well with those for the regions of conserved amino acid sequences (RBCC motif, PHD finger and bromodomain). In situ hybridization analysis of the TIF1gamma mRNA on sections from staged mouse embryos revealed a low level of ubiquitous expression at midgestation, and higher expression levels within the brain and spinal cord epithelium at later developmental stages. Prominent expression was also found in developing sensory epithelia (cochlea, retina, olfactory epithelium), and in several developing organs including the thymus, lung, stomach, intestine, liver, and kidney cortex. In the adult mouse, Tif1gamma mRNA was detected by Northern blot analysis in all tissues examined, with the highest expression level in testis. In situ hybridization and immunohistochemistry studies revealed that expression of the Tif1gamma mRNA and protein varied according to the stage of the seminiferous epithelium cycle. Taken together, these results indicate-and serve as a basis for investigating-a possible involvement of Tif1gamma in the control of embryonic development and spermatogenesis.
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Affiliation(s)
- Kai-Ping Yan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP/Collège de France, BP 10142, 67 404 Illkirch Cedex, France
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38
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Ransom DG, Bahary N, Niss K, Traver D, Burns C, Trede NS, Paffett-Lugassy N, Saganic WJ, Lim CA, Hersey C, Zhou Y, Barut BA, Lin S, Kingsley PD, Palis J, Orkin SH, Zon LI. The zebrafish moonshine gene encodes transcriptional intermediary factor 1gamma, an essential regulator of hematopoiesis. PLoS Biol 2004; 2:E237. [PMID: 15314655 PMCID: PMC509301 DOI: 10.1371/journal.pbio.0020237] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Accepted: 05/26/2004] [Indexed: 11/18/2022] Open
Abstract
Hematopoiesis is precisely orchestrated by lineage-specific DNA-binding proteins that regulate transcription in concert with coactivators and corepressors. Mutations in the zebrafish moonshine (mon) gene specifically disrupt both embryonic and adult hematopoiesis, resulting in severe red blood cell aplasia. We report that mon encodes the zebrafish ortholog of mammalian transcriptional intermediary factor 1gamma (TIF1gamma) (or TRIM33), a member of the TIF1 family of coactivators and corepressors. During development, hematopoietic progenitor cells in mon mutants fail to express normal levels of hematopoietic transcription factors, including gata1, and undergo apoptosis. Three different mon mutant alleles each encode premature stop codons, and enforced expression of wild-type tif1gamma mRNA rescues embryonic hematopoiesis in homozygous mon mutants. Surprisingly, a high level of zygotic tif1gamma mRNA expression delineates ventral mesoderm during hematopoietic stem cell and progenitor formation prior to gata1 expression. Transplantation studies reveal that tif1gamma functions in a cell-autonomous manner during the differentiation of erythroid precursors. Studies in murine erythroid cell lines demonstrate that Tif1gamma protein is localized within novel nuclear foci, and expression decreases during erythroid cell maturation. Our results establish a major role for this transcriptional intermediary factor in the differentiation of hematopoietic cells in vertebrates.
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Affiliation(s)
- David G Ransom
- Division of Hematology/Oncology, Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
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39
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Nielsen AL, Jørgensen P, Lerouge T, Cerviño M, Chambon P, Losson R. Nizp1, a novel multitype zinc finger protein that interacts with the NSD1 histone lysine methyltransferase through a unique C2HR motif. Mol Cell Biol 2004; 24:5184-96. [PMID: 15169884 PMCID: PMC419876 DOI: 10.1128/mcb.24.12.5184-5196.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Haploinsufficiency of the NSD1 gene is a hallmark of Sotos syndrome, and rearrangements of this gene by translocation can cause acute myeloid leukemia. The NSD1 gene product is a SET-domain histone lysine methyltransferase that has previously been shown to interact with nuclear receptors. We describe here a novel NSD1-interacting protein, Nizp1, that contains a SCAN box, a KRAB-A domain, and four consensus C2H2-type zinc fingers preceded by a unique finger derivative, referred to herein as the C2HR motif. The C2HR motif functions to mediate protein-protein interaction with the cysteine-rich (C5HCH) domain of NSD1 in a Zn(II)-dependent fashion, and when tethered to RNA polymerase II promoters, represses transcription in an NSD1-dependent manner. Mutations of the cysteine or histidine residues in the C2HR motif abolish the interaction of Nizp1 with NSD1 and compromise the ability of Nizp1 to repress transcription. Interestingly, converting the C2HR motif into a canonical C2H2 zinc finger has a similar effect. Thus, Nizp1 contains a novel type of zinc finger motif that functions as a docking site for NSD1 and is more than just a degenerate evolutionary remnant of a C2H2 motif.
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40
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Looman C, Hellman L, Abrink M. A novel Krüppel-Associated Box identified in a panel of mammalian zinc finger proteins. Mamm Genome 2004; 15:35-40. [PMID: 14727140 DOI: 10.1007/s00335-003-3022-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2003] [Accepted: 08/21/2003] [Indexed: 12/29/2022]
Abstract
Krüppel-related zinc finger proteins probably constitute the largest individual family of transcription factors in mammals. These proteins often carry a potent repressor domain called the Krüppel Associated Box (KRAB), which is known to effectively repress transcription through interaction with transcriptional intermediary factor 1beta (TIF1beta). Here we report the isolation and characterization of a novel human KRAB A zinc finger protein, HZF12. The gene encoding HZF12 is located on Chromosome (Chr) 19p13.11-p12, and a 4.4-kb transcript from this gene is expressed in a variety of adult and fetal tissues. Two additional, larger transcripts are expressed in testis only. Interestingly, the KRAB A domain of HZF12 is followed by a 21-amino acid domain, encoded by a separate exon. This domain, which we designate KRAB C, was also identified in more than 25 additional human, mouse, and rat KRAB zinc finger proteins. On the basis of results from a previous study, we conclude that this novel KRAB domain strengthens the interaction with TIF1beta, thereby improving the ability of these KRAB zinc finger proteins to recruit TIF1beta to specific sites.
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Affiliation(s)
- Camilla Looman
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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41
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Ayyanathan K, Lechner MS, Bell P, Maul GG, Schultz DC, Yamada Y, Tanaka K, Torigoe K, Rauscher FJ. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. Genes Dev 2003; 17:1855-69. [PMID: 12869583 PMCID: PMC196232 DOI: 10.1101/gad.1102803] [Citation(s) in RCA: 288] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Heterochromatin protein 1 (HP1) is a key component of constitutive heterochromatin in Drosophila and is required for stable epigenetic gene silencing classically observed as position effect variegation. Less is known of the family of mammalian HP1 proteins, which may be euchromatic, targeted to expressed loci by repressor-corepressor complexes, and retained there by Lys 9-methylated histone H3 (H3-MeK9). To characterize the physical properties of euchromatic loci bound by HP1, we developed a strategy for regulated recruitment of HP1 to an expressed transgene in mammalian cells by using a synthetic, hormone-regulated KRAB repression domain. We show that its obligate corepressor, KAP1, can coordinate all the machinery required for stable gene silencing. In the presence of hormone, the transgene is rapidly silenced, spatially recruited to HP1-rich nuclear regions, assumes a compact chromatin structure, and is physically associated with KAP1, HP1, and the H3 Lys 9-specific methyltransferase, SETDB1, over a highly localized region centered around the promoter. Remarkably, silencing established by a short pulse of hormone is stably maintained for >50 population doublings in the absence of hormone in clonal-cell populations, and the silent transgenes in these clones show promoter hypermethylation. Thus, like variegation in Drosophila, recruitment of mammalian HP1 to a euchromatic promoter can establish a silenced state that is epigenetically heritable.
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42
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Looman C, Abrink M, Mark C, Hellman L. KRAB zinc finger proteins: an analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution. Mol Biol Evol 2002; 19:2118-30. [PMID: 12446804 DOI: 10.1093/oxfordjournals.molbev.a004037] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Krüppel-related zinc finger proteins, with 564 members in the human genome, probably constitute the largest individual family of transcription factors in mammals. Approximately 30% of these proteins carry a potent repressor domain called the Krüppel associated box (KRAB). Depending on the structure of the KRAB domain, these proteins have been further divided into three subfamilies (A + B, A + b, and A only). In addition, some KRAB zinc finger proteins contain another conserved motif called SCAN. To study their molecular evolution, an extensive comparative analysis of a large panel of KRAB zinc finger genes was performed. The results show that both the KRAB A + b and the KRAB A subfamilies have their origin in a single member or a few closely related members of the KRAB A + B family. The KRAB A + B family is also the most prevalent among the KRAB zinc finger genes. Furthermore, we show that internal duplications of individual zinc finger motifs or blocks of several zinc finger motifs have occurred quite frequently within this gene family. However, zinc finger motifs are also frequently lost from the open reading frame, either by functional inactivation by point mutations or by the introduction of a stop codon. The introduction of a stop codon causes the exclusion of part of the zinc finger region from the coding region and the formation of graveyards of degenerate zinc finger motifs in the 3'-untranslated region of these genes. Earlier reports have shown that duplications of zinc finger genes commonly occur throughout evolution. We show that there is a relatively low degree of sequence conservation of the zinc finger motifs after these duplications. In many cases this may cause altered binding specificities of the transcription factors encoded by these genes. The repetitive nature of the zinc finger region and the structural flexibility within the zinc finger motif make these proteins highly adaptable. These factors may have been of major importance for their massive expansion in both number and complexity during metazoan evolution.
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Affiliation(s)
- Camilla Looman
- The Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden
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43
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Xu D, Ye D, Fisher M, Juliano RL. Selective inhibition of P-glycoprotein expression in multidrug-resistant tumor cells by a designed transcriptional regulator. J Pharmacol Exp Ther 2002; 302:963-71. [PMID: 12183653 DOI: 10.1124/jpet.102.033639] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Selective inhibition of the multidrug resistance 1 (MDR1) gene and its product, the P-glycoprotein, a membrane transporter responsible for multidrug resistance, could be an important approach for enhancing cancer therapeutics. An emerging strategy for selective gene regulation involves designed zinc finger proteins that can recognize specific sequences in the promoter regions of disease-related genes. Herein, we investigate the behavior of clones of multidrug-resistant NCI/ADR-RES breast carcinoma cells displaying ponasterone-inducible expression of a designed transcriptional repressor targeted to the MDR1 promoter. The controlled production of this novel repressor resulted in major reductions in P-glycoprotein levels in these otherwise highly drug-resistant tumor cells. The regulated reduction of MDR1 expression in NCI/ADR-RES cells was accompanied by a marked increase in the rate of uptake of the P-glycoprotein substrate rhodamine 123. In addition, the cytotoxicity profile of the antitumor drug doxorubicin was dramatically altered in the induced cells compared with controls. The expression levels of other genes were examined both by a DNA array analysis of approximately 2000 genes and by biochemical techniques. Although some changes were observed in mRNA levels of nontargeted genes, the most dramatic effect by far was on MDR1, indicating that the action of the designed transcriptional repressor was quite selective. This study suggests that designed transcriptional regulators can be used to strongly and selectively influence expression of cancer-related genes, even under circumstances of extensive amplification of the target gene.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B/antagonists & inhibitors
- ATP Binding Cassette Transporter, Subfamily B/biosynthesis
- Antibiotics, Antineoplastic/pharmacology
- Antineoplastic Agents/pharmacology
- Blotting, Northern
- Blotting, Western
- Doxorubicin/pharmacology
- Flow Cytometry
- Fluorescent Dyes
- Gene Expression Regulation, Neoplastic/genetics
- Genes, MDR/genetics
- Humans
- Oligonucleotide Array Sequence Analysis
- Plasmids/genetics
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Repressor Proteins/biosynthesis
- Repressor Proteins/genetics
- Rhodamine 123
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- Dong Xu
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 29799, USA
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44
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Tian Y, Breedveld GJ, Huang S, Oostra BA, Heutink P, Lo WHY. Characterization of ZNF333, a novel double KRAB domain containing zinc finger gene on human chromosome 19p13.1. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1577:121-5. [PMID: 12151103 DOI: 10.1016/s0167-4781(02)00397-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ZNF333 is a novel human KRAB-zinc finger protein gene on chromosome 19p13.1 encompassing 14 exons. ZNF333 is highly expressed in heart and encodes a 665 amino acid protein that contains a rare combination of double KRAB-domains, each consisting of a classical KRAB-A and a highly divergent KRAB-B box at the N-terminus. ZNF333 further contains 10 C2H2 zinc finger motifs at the C-terminus.
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Affiliation(s)
- Yong Tian
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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45
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Peng H, Feldman I, Rauscher FJ. Hetero-oligomerization among the TIF family of RBCC/TRIM domain-containing nuclear cofactors: a potential mechanism for regulating the switch between coactivation and corepression. J Mol Biol 2002; 320:629-44. [PMID: 12096914 DOI: 10.1016/s0022-2836(02)00477-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The RING-B box-coiled-coil (RBCC) motif (also re-named recently as the tripartite motif (TRIM)) is a widely distributed motif that is hypothesized to be a protein-protein interface. The RBCC/TRIM domain of the corepressor KAP-1 is both necessary and sufficient to interact directly with the transcription repressor KRAB domain. Each subdomain of the KAP-1-RBCC contributes directly to the oligomerization and/or ligand recognition. Little is known about the function or the natural binding ligands for the RBCC/TRIM domain of the other TIF family members. In order to investigate whether hetero-oligomerization might be a biological regulatory mechanism, we have evaluated the hetero-oligomerization potential of the TIF family members including KAP-1, TIF1alpha, TIF1gamma, and the RBCC/TRIM family members including PML1, and MID1. We have reconstituted and characterized the oligomerization for these proteins using baculovirus and mammalian expression systems by biochemical approaches. Our data indicate that the RBCC/TRIM domains of KAP-1, TIF1alpha and TIF1gamma exist in a homo-oligomeric state. However, there is little cross-talk between KAP-1 and other TIF family members, suggesting that a high degree of specificity for oligomerization interface and ligand recognition is intrinsically built into the RBCC/TRIM domain of KAP-1. Finally, we demonstrate that TIF1alpha interacts with TIF1gamma and the coiled-coil region of TIF1gamma is necessary for this interaction. The hetero-oligomerization between TIF1alpha and TIF1gamma implies a potential regulatory mechanism for transcriptional regulation.
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Affiliation(s)
- Hongzhuang Peng
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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46
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Tanaka K, Tsumaki N, Kozak CA, Matsumoto Y, Nakatani F, Iwamoto Y, Yamada Y. A Krüppel-associated box-zinc finger protein, NT2, represses cell-type-specific promoter activity of the alpha 2(XI) collagen gene. Mol Cell Biol 2002; 22:4256-67. [PMID: 12024037 PMCID: PMC133841 DOI: 10.1128/mcb.22.12.4256-4267.2002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Type XI collagen is composed of three chains, alpha 1(XI), alpha 2(XI), and alpha 3(XI), and plays a critical role in the formation of cartilage collagen fibrils and in skeletal morphogenesis. It was previously reported that the -530-bp promoter segment of the alpha 2(XI) collagen gene (Col11a2) was sufficient for cartilage-specific expression and that a 24-bp sequence from this segment was able to switch promoter activity from neural tissues to cartilage in transgenic mice when this sequence was placed in the heterologous neurofilament light gene (NFL) promoter. To identify a protein factor that bound to the 24-bp sequence of the Col11a2 promoter, we screened a mouse limb bud cDNA expression library in the yeast one-hybrid screening system and obtained the cDNA clone NT2. Sequence analysis revealed that NT2 is a zinc finger protein consisting of a Krüppel-associated box (KRAB) and is a homologue of human FPM315, which was previously isolated by random cloning and sequencing. The KRAB domain has been found in a number of zinc finger proteins and implicated as a transcriptional repression domain, although few target genes for KRAB-containing zinc finger proteins has been identified. Here, we demonstrate that NT2 functions as a negative regulator of Col11a2. In situ hybridization analysis of developing mouse cartilage showed that NT2 mRNA is highly expressed by hypertrophic chondrocytes but is minimally expressed by resting and proliferating chondrocytes, in an inverse correlation with the expression patterns of Col11a2. Gel shift assays showed that NT2 bound a specific sequence within the 24-bp site of the Col11a2 promoter. We found that Col11a2 promoter activity was inhibited by transfection of the NT2 expression vector in RSC cells, a chondrosarcoma cell line. The expression vector for mutant NT2 lacking the KRAB domain failed to inhibit Col11a2 promoter activity. These results demonstrate that KRAB-zinc finger protein NT2 inhibits transcription of its physiological target gene, suggesting a novel regulatory mechanism of cartilage-specific expression of Col11a2.
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Affiliation(s)
- Kazuhiro Tanaka
- Craniofacial Developmental Biology and Regeneration Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
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47
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Benzel I, Barde YA, Casademunt E. Strain-specific complementation between NRIF1 and NRIF2, two zinc finger proteins sharing structural and biochemical properties. Gene 2001; 281:19-30. [PMID: 11750124 DOI: 10.1016/s0378-1119(01)00730-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The zinc finger protein NRIF (neurotrophin receptor interacting factor) was originally identified by virtue of its interaction with the neurotrophin receptor p75NTR and its participation in embryonic apoptosis. Targeted deletion of the nrif gene in mice is embryonically lethal in the C57BL6 genetic background, where it blocks cell cycle progression, but not in the Sv129 strain. We have now identified a second, highly homologous nrif gene, designated nrif2, encoding a protein with similar structural and biochemical properties as well as subcellular distribution as NRIF1, and whose over-expression in transfected fibroblasts also correlates with impaired BrdU incorporation. Unexpectedly, the nrif2 transcript becomes significantly upregulated in nrif1-/- mice only in Sv129, the genetic background where the mutants are viable, suggesting that the functional complementation of the two nrif genes may be strain-specific.
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MESH Headings
- Amino Acid Sequence
- Animals
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Cycle
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA-Binding Proteins
- Gene Expression
- Genetic Complementation Test
- Intracellular Signaling Peptides and Proteins
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Inbred Strains
- Mice, Knockout
- Mice, Transgenic
- Molecular Sequence Data
- Mutation
- Protein Binding
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor, Nerve Growth Factor
- Receptors, Nerve Growth Factor/genetics
- Receptors, Nerve Growth Factor/metabolism
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- I Benzel
- Department of Neurobiochemistry, Max Planck Institute of Neurobiology, Am Klopferspitz 18a, 82152 Martinsried, Germany
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Wang S, Liu S, Wu MH, Geng Y, Wood C. Identification of a cellular protein that interacts and synergizes with the RTA (ORF50) protein of Kaposi's sarcoma-associated herpesvirus in transcriptional activation. J Virol 2001; 75:11961-73. [PMID: 11711586 PMCID: PMC116091 DOI: 10.1128/jvi.75.24.11961-11973.2001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lytic reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV), or human herpesvirus 8, from latency requires transcriptional transactivation by the viral protein RTA encoded by the ORF50 gene. Very little is known about how RTA functions and the cellular factors that may be involved in its transactivation function. Using the yeast two-hybrid system, we have identified a human cellular protein that can interact with KSHV RTA. The cellular protein, referred to as the human hypothetical protein MGC2663 by GenBank, is encoded by human chromosome 19. This protein is 554 amino acids (aa) in size and displays sequence similarity with members of the Krueppel-associated box-zinc finger proteins (KRAB-ZFPs). MGC2663 expression could be detected in all primate cell lines tested, and its expression level was neither stimulated nor inhibited by RTA. MGC2663 specifically synergizes with RTA to activate viral transcription, and overexpression of MGC2663 in the presence of RTA further enhances RTA transactivation of several viral promoters that were identified as targets for RTA. Coimmunoprecipitation and pull-down assays further demonstrated that MGC2663 interacts with RTA both in vivo and in vitro, and the N-terminal 273 aa of KSHV RTA and the potential zinc finger domain of MGC2663 are required for their interaction. Our results indicate that this novel human cellular protein, MGC2663, named K-RBP (KSHV RTA binding protein) due to its RTA binding feature, specifically interacts with the KSHV RTA protein and functions as a cellular RTA cofactor to activate viral gene expression. Though its normal cellular function needs to be further studied, K-RBP may play a significant role in mediating RTA transactivation in vivo.
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Affiliation(s)
- S Wang
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68588, USA
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Mark C, Looman C, Abrink M, Hellman L. Molecular cloning and preliminary functional analysis of two novel human KRAB zinc finger proteins, HKr18 and HKr19. DNA Cell Biol 2001; 20:275-86. [PMID: 11410164 DOI: 10.1089/104454901750232472] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
cDNA clones encoding two novel human KRAB zinc finger proteins, HKr18 and HKr19, were isolated from a human testis cDNA library. Their corresponding genes were later identified in sequences originating from chromosomes 19 and 7, respectively. On the basis of the collected information from gene and cDNA sequences, Hkr18 was found to be a protein of 94 kDa with 20 zinc finger motifs in its C terminus. The HKr19 is a smaller protein, with a molecular weight of 56 kDa containing 11 zinc finger motifs. Both HKr18 and HKr19 contained a KRAB A as well as a KRAB B domain in their N termini. Northern blot analysis showed expression of HKr18 in all human tissues tested, indicating a ubiquitous expression pattern. In contrast, HKr19 showed a more restricted tissue distribution, with detectable expression primarily in testis and fetal tissues. The HKr19 protein is a member of the large ZNF91 subfamily of KRAB zinc finger genes. A PCR-based analysis of the expression of HKr19 and other closely related genes showed that lymphoid, myeloid, and nonhematopoietic cells expressed different sets of these genes. This latter finding indicates that some members of the ZNF91 family may be involved in regulating lineage commitment during hematopoietic development. Transfection of various parts of HKr19 into human embryonic kidney cells (HEK 293 cells) showed that the entire protein and its zinc finger region were toxic to these cells when expressed at high levels. In contrast, the KRAB domain and the linker region seemed to be well tolerated.
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Affiliation(s)
- C Mark
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala, Sweden
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