1
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Lago S, Nadai M, Ruggiero E, Tassinari M, Marušič M, Tosoni B, Frasson I, Cernilogar FM, Pirota V, Doria F, Plavec J, Schotta G, Richter SN. The MDM2 inducible promoter folds into four-tetrad antiparallel G-quadruplexes targetable to fight malignant liposarcoma. Nucleic Acids Res 2021; 49:847-863. [PMID: 33410915 PMCID: PMC7826256 DOI: 10.1093/nar/gkaa1273] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Well-differentiated liposarcoma (WDLPS) is a malignant neoplasia hard to diagnose and treat. Its main molecular signature is amplification of the MDM2-containing genomic region. The MDM2 oncogene is the master regulator of p53: its overexpression enhances p53 degradation and inhibits apoptosis, leading to the tumoral phenotype. Here, we show that the MDM2 inducible promoter G-rich region folds into stable G-quadruplexes both in vitro and in vivo and it is specifically recognized by cellular helicases. Cell treatment with G-quadruplex-ligands reduces MDM2 expression and p53 degradation, thus stimulating cancer cell cycle arrest and apoptosis. Structural characterization of the MDM2 G-quadruplex revealed an extraordinarily stable, unique four-tetrad antiparallel dynamic conformation, amenable to selective targeting. These data indicate the feasibility of an out-of-the-box G-quadruplex-targeting approach to defeat WDLPS and all tumours where restoration of wild-type p53 is sought. They also point to G-quadruplex-dependent genomic instability as possible cause of MDM2 expansion and WDLPS tumorigenesis.
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Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Emanuela Ruggiero
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Martina Tassinari
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Maja Marušič
- Slovenian NMR center, National Institute of Chemistry, Hajdrihova, 19, Ljubljana SI-1000, Slovenia
| | - Beatrice Tosoni
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Germany
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, V. le Taramelli 10, 27100, Pavia, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, V. le Taramelli 10, 27100, Pavia, Italy
| | - Janez Plavec
- Slovenian NMR center, National Institute of Chemistry, Hajdrihova, 19, Ljubljana SI-1000, Slovenia
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Germany
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
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2
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Chebly A, Peloponese JM, Ségal-Bendirdjian E, Merlio JP, Tomb R, Chevret E. hMZF-2, the Elusive Transcription Factor. Front Genet 2021; 11:581115. [PMID: 33424921 PMCID: PMC7793725 DOI: 10.3389/fgene.2020.581115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/20/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Alain Chebly
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, Bordeaux, France.,Medical Genetics Unit (UGM), Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Jean-Marie Peloponese
- University of Montpellier, CNRS IRIM-UMR 9004, Research Institute in Infectiology of Montpellier, Montpellier, France
| | - Evelyne Ségal-Bendirdjian
- Université de Paris, INSERM UMR-S 1124, Team: Cellular Homeostasis, Cancer and Therapies, INSERM US36/CNRS UMS 2009, BioMedTech Facilities, Paris, France
| | - Jean-Philippe Merlio
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, Bordeaux, France.,Bordeaux University Hospital Center, Tumor Bank and Tumor Biology Laboratory, Pessac, France
| | - Roland Tomb
- Medical Genetics Unit (UGM), Faculty of Medicine, Saint Joseph University, Beirut, Lebanon.,Department of Dermatology, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Edith Chevret
- Bordeaux University, INSERM U1053 Bordeaux Research in Translational Oncology (BaRITOn), Cutaneous Lymphoma Oncogenesis Team, Bordeaux, France
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3
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Brix DM, Bundgaard Clemmensen KK, Kallunki T. Zinc Finger Transcription Factor MZF1-A Specific Regulator of Cancer Invasion. Cells 2020; 9:cells9010223. [PMID: 31963147 PMCID: PMC7016646 DOI: 10.3390/cells9010223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 12/11/2022] Open
Abstract
Over 90% of cancer deaths are due to cancer cells metastasizing into other organs. Invasion is a prerequisite for metastasis formation. Thus, inhibition of invasion can be an efficient way to prevent disease progression in these patients. This could be achieved by targeting the molecules regulating invasion. One of these is an oncogenic transcription factor, Myeloid Zinc Finger 1 (MZF1). Dysregulated transcription factors represent a unique, increasing group of drug targets that are responsible for aberrant gene expression in cancer and are important nodes driving cancer malignancy. Recent studies report of a central involvement of MZF1 in the invasion and metastasis of various solid cancers. In this review, we summarize the research on MZF1 in cancer including its function and role in lysosome-mediated invasion and in the expression of genes involved in epithelial to mesenchymal transition. We also discuss possible means to target it on the basis of the current knowledge of its function in cancer.
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Affiliation(s)
- Ditte Marie Brix
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (D.M.B.); (K.K.B.C.)
- Danish Medicines Council, Dampfærgevej 27-29, 2100 Copenhagen, Denmark
| | - Knut Kristoffer Bundgaard Clemmensen
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (D.M.B.); (K.K.B.C.)
| | - Tuula Kallunki
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (D.M.B.); (K.K.B.C.)
- Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence: ; Tel.: +45-35-25-7746
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4
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Zhang S, Shi W, Ramsay ES, Bliskovsky V, Eiden AM, Connors D, Steinsaltz M, DuBois W, Mock BA. The transcription factor MZF1 differentially regulates murine Mtor promoter variants linked to tumor susceptibility. J Biol Chem 2019; 294:16756-16764. [PMID: 31548308 DOI: 10.1074/jbc.ra119.009779] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/18/2019] [Indexed: 01/15/2023] Open
Abstract
Mechanistic target of rapamycin (MTOR) is a highly conserved serine/threonine kinase that critically regulates cell growth, proliferation, differentiation, and survival. Previously, we have implicated Mtor as a plasmacytoma-resistance locus, Pctr2, in mice. Here, we report that administration of the tumor-inducing agent pristane decreases Mtor gene expression to a greater extent in mesenteric lymph nodes of BALB/cAnPt mice than of DBA/2N mice. We identified six allelic variants in the Mtor promoter region in BALB/cAnPt and DBA/2N mice. To determine the effects of these variants on Mtor transcription, we constructed a series of luciferase reporters containing these promoter variants and transfected them into mouse plasmacytoma cells. We could attribute the differences in Mtor promoter activity between the two mouse strains to a C → T change at the -6 position relative to the transcriptional start site Tssr 40273; a T at this position in the BALB promoter creates a consensus binding site for the transcription factor MZF1 (myeloid zinc finger 1). Results from electrophoretic mobility shift assays and DNA pulldown assays with ChIP-PCR confirmed that MZF1 binds to the cis-element TGGGGA located in the -6/-1 Mtor promoter region. Of note, MZF1 significantly and differentially down-regulated Mtor promoter activity, with MZF1 overexpression reducing Mtor expression more strongly in BALB mice than in DBA mice. Moreover, MZF1 overexpression reduced Mtor expression in both fibroblasts and mouse plasmacytoma cells, and Mzf1 knockdown increased Mtor expression in BALB3T3 and NIH3T3 fibroblast cells. Our results provide evidence that MZF1 down-regulates Mtor expression in pristane-induced plasmacytomas in mice.
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Affiliation(s)
- Shuling Zhang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Wei Shi
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Edward S Ramsay
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Valery Bliskovsky
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Adrian Max Eiden
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel Connors
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Matthew Steinsaltz
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Wendy DuBois
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
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5
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Lee CJ, Hsu LS, Yue CH, Lin H, Chiu YW, Lin YY, Huang CY, Hung MC, Liu JY. MZF-1/Elk-1 interaction domain as therapeutic target for protein kinase Cα-based triple-negative breast cancer cells. Oncotarget 2018; 7:59845-59859. [PMID: 27542222 PMCID: PMC5312353 DOI: 10.18632/oncotarget.11337] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/06/2016] [Indexed: 12/31/2022] Open
Abstract
Recent reports demonstrate that the expression of protein kinase C alpha (PKCα) in triple-negative breast cancer (TNBC) correlates with decreased survival outcomes. However, off-target effects of targeting PKCα and limited understanding of the signaling mechanisms upstream of PKCα have hampered previous efforts to manipulate this ubiquitous gene. This study shows that the expression of both myeloid zinc finger 1 (MZF-1) and Ets-like protein-1 (Elk-1) correlates with PKCα expression in TNBC. We found that the acidic domain of MZF-1 and the heparin-binding domain of Elk-1 facilitate the heterodimeric interaction between the two genes before the complex formation binds to the PKCα promoter. Blocking the formation of the heterodimer by transfection of MZF-160-72 or Elk-1145-157 peptide fragments at the MZF-1 / Elk-1 interface decreases DNA-binding activity of the MZF-1 / Elk-1 complex at the PKCα promoter. Subsequently, PKCα expression, migration, tumorigenicity, and the epithelial-mesenchymal transition potential of TNBC cells decrease. These subsequent effects are reversed by transfection with full-length PKCα, confirming that the MZF-1/Elk-1 heterodimer is a mediator of PKCα in TNBC cells. These data suggest that the next therapeutic strategy in treating PKCα-related cancer will be developed from blocking MZF-1/Elk-1 interaction through their binding domain.
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Affiliation(s)
- Chia-Jen Lee
- Center for Molecular Medicine, China Medical University Hospital, Taichung 40402, Taiwan
| | - Li-Sung Hsu
- Institute of Biochemistry, Microbiology and Immunology, Medical College, Chung-Shan Medical University, Taichung 40201, Taiwan.,Clinical Laboratory, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
| | - Chia-Herng Yue
- Department of Surgery, Tungs' Taichung Metro Harbor Hospital, Taichung 435, Taiwan.,Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan
| | - Ho Lin
- Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan
| | - Yung-Wei Chiu
- Emergency Department and Center of Hyperbaric Oxygen Therapy, Tungs' Taichung Metro Harbor Hospital, Taichung 435, Taiwan
| | - Yu-Yu Lin
- Graduate Institute of Cancer Biology, China Medical University, Taichung 40402, Taiwan
| | - Chih-Yang Huang
- Graduate Institute of Chinese Medical Science, School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan.,Graduate Institute of Basic Medical Science, China Medical University, Taichung 40402, Taiwan.,Department of Health and Nutrition Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Mien-Chie Hung
- Center for Molecular Medicine, China Medical University Hospital, Taichung 40402, Taiwan.,Graduate Institute of Cancer Biology, China Medical University, Taichung 40402, Taiwan.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jer-Yuh Liu
- Center for Molecular Medicine, China Medical University Hospital, Taichung 40402, Taiwan.,Graduate Institute of Cancer Biology, China Medical University, Taichung 40402, Taiwan
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6
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miRNA-337-3p inhibits gastric cancer progression through repressing myeloid zinc finger 1-facilitated expression of matrix metalloproteinase 14. Oncotarget 2018; 7:40314-40328. [PMID: 27259238 PMCID: PMC5130010 DOI: 10.18632/oncotarget.9739] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/13/2016] [Indexed: 11/25/2022] Open
Abstract
Matrix metalloproteinase 14 (MMP-14), a membrane-anchored MMP that promotes the tumorigenesis and aggressiveness, is highly expressed in gastric cancer. However, the transcriptional regulators of MMP-14 expression in gastric cancer still remain largely unknown. In this study, through mining computational algorithm programs and chromatin immunoprecipitation datasets, we identified adjacent binding sites of myeloid zinc finger 1 (MZF1) and miRNA-337-3p (miR-337-3p) within the MMP-14 promoter. We demonstrated that MZF1 directly bound to the MMP-14 promoter to facilitate its nascent transcription and expression in gastric cancer cell lines. In contrast, endogenous miR-337-3p suppressed the MMP-14 expression through recognizing its binding site within MMP-14 promoter. Mechanistically, miR-337-3p repressed the binding of MZF1 to MMP-14 promoter via recruiting Argonaute 2 and inducing repressive chromatin remodeling. Gain- and loss-of-function studies demonstrated that miR-337-3p suppressed the growth, invasion, metastasis, and angiogenesis of gastric cancer cells in vitro and in vivo through repressing MZF1-facilitated MMP-14 expression. In clinical specimens and cell lines of gastric cancer, MZF1 was highly expressed and positively correlated with MMP-14 expression. Meanwhile, miR-337-3p was under-expressed and inversely correlated with MMP-14 levels. miR-337-3p was an independent prognostic factor for favorable outcome of gastric cancer, and patients with high MZF1 or MMP-14 expression had lower survival probability. Taken together, these data indicate that miR-337-3p directly binds to the MMP-14 promoter to repress MZF1-facilitatd MMP-14 expression, thus suppressing the progression of gastric cancer.
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7
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Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel) 2017; 8:genes8080192. [PMID: 28763006 PMCID: PMC5575656 DOI: 10.3390/genes8080192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
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8
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McKay GJ, Kavanagh DH, Crean JK, Maxwell AP. Bioinformatic Evaluation of Transcriptional Regulation of WNT Pathway Genes with reference to Diabetic Nephropathy. J Diabetes Res 2016; 2016:7684038. [PMID: 26697505 PMCID: PMC4677197 DOI: 10.1155/2016/7684038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 05/18/2015] [Accepted: 05/24/2015] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE WNT/β-catenin pathway members have been implicated in interstitial fibrosis and glomerular sclerosis disease processes characteristic of diabetic nephropathy (DN), processes partly controlled by transcription factors (TFs) that bind to gene promoter regions attenuating regulation. We sought to identify predicted cis-acting transcription factor binding sites (TFBSs) overrepresented within WNT pathway members. METHODS We assessed 62 TFBS motif frequencies from the JASPAR databases in 65 WNT pathway genes. P values were estimated on the hypergeometric distribution for each TF. Gene expression profiles of enriched motifs were examined in DN-related datasets to assess clinical significance. RESULTS Transcription factor AP-2 alpha (TFAP2A), myeloid zinc finger 1 (MZF1), and specificity protein 1 (SP1) were significantly enriched within WNT pathway genes (P values < 6.83 × 10(-29), 1.34 × 10(-11), and 3.01 × 10(-6), resp.). MZF1 expression was significantly increased in DN in a whole kidney dataset (fold change = 1.16; 16% increase; P = 0.03). TFAP2A expression was decreased in an independent dataset (fold change = -1.02; P = 0.03). No differential expression of SP1 was detected. CONCLUSIONS Three TFBS profiles are significantly enriched within WNT pathway genes highlighting the potential of in silico analyses for identification of pathway regulators. Modification of TF binding may possibly limit DN progression, offering potential therapeutic benefit.
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Affiliation(s)
- Gareth J. McKay
- Centre for Public Health, Queen's University Belfast, Belfast BT12 6BA, UK
- *Gareth J. McKay:
| | - David H. Kavanagh
- Centre for Public Health, Queen's University Belfast, Belfast BT12 6BA, UK
| | - John K. Crean
- Conway Institute, University College Dublin, Dublin 4, Ireland
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9
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CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells. Sci Rep 2015; 5:16791. [PMID: 26582124 PMCID: PMC4652170 DOI: 10.1038/srep16791] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/14/2015] [Indexed: 12/24/2022] Open
Abstract
In embryonic stem (ES) cells, developmental regulators have a characteristic bivalent chromatin signature marked by simultaneous presence of both activation (H3K4me3) and repression (H3K27me3) signals and are thought to be in a 'poised' state for subsequent activation or silencing during differentiation. We collected eleven pairs (H3K4me3 and H3K27me3) of ChIP sequencing datasets in human ES cells and eight pairs in murine ES cells, and predicted high-confidence (HC) bivalent promoters. Over 85% of H3K27me3 marked promoters were bivalent in human and mouse ES cells. We found that (i) HC bivalent promoters were enriched for developmental factors and were highly likely to be differentially expressed upon transcription factor perturbation; (ii) murine HC bivalent promoters were occupied by both polycomb repressive component classes (PRC1 and PRC2) and grouped into four distinct clusters with different biological functions; (iii) HC bivalent and active promoters were CpG rich while H3K27me3-only promoters lacked CpG islands. Binding enrichment of distinct sets of regulators distinguished bivalent from active promoters. Moreover, a 'TCCCC' sequence motif was specifically enriched in bivalent promoters. Finally, this analysis will serve as a resource for future studies to further understand transcriptional regulation during embryonic development.
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10
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Weber CE, Kothari AN, Wai PY, Li NY, Driver J, Zapf MAC, Franzen CA, Gupta GN, Osipo C, Zlobin A, Syn WK, Zhang J, Kuo PC, Mi Z. Osteopontin mediates an MZF1-TGF-β1-dependent transformation of mesenchymal stem cells into cancer-associated fibroblasts in breast cancer. Oncogene 2014; 34:4821-33. [PMID: 25531323 PMCID: PMC4476970 DOI: 10.1038/onc.2014.410] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 10/20/2014] [Accepted: 11/08/2014] [Indexed: 12/18/2022]
Abstract
Interactions between tumor cells and cancer-associated fibroblasts (CAFs) in the tumor microenvironment (TMEN) significantly influence cancer growth and metastasis. Transforming growth factor-β (TGF-β) is known to be a critical mediator of the CAF phenotype, and osteopontin (OPN) expression in tumors is associated with more aggressive phenotypes and poor patient outcomes. The potential link between these two pathways has not been previously addressed. Utilizing in vitro studies using human mesenchymal stem cells (MSCs) and MDA-MB231 (OPN+) and MCF7 (OPN−) human breast cancer cell lines, we demonstrate that OPN induces integrin-dependent MSC expression of TGF-β1 to mediate adoption of the CAF phenotype. This OPN-TGF-β1 pathway requires the transcription factor, myeloid zinc finger 1 (MZF1). In vivo studies with xenotransplant models in NOD-scid mice showed that OPN expression increases cancer growth and metastasis by mediating MSC-to-CAF transformation in a process that is MZF1- and TGF-β1-dependent. We conclude that tumor-derived OPN engenders MSC-to-CAF transformation in the microenvironment to promote tumor growth and metastasis via the OPN-MZF1-TGF-β1 pathway.
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Affiliation(s)
- C E Weber
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - A N Kothari
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - P Y Wai
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - N Y Li
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - J Driver
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - M A C Zapf
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - C A Franzen
- The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA.,Department of Urology, Loyola University Medical Center, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - G N Gupta
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA.,Department of Urology, Loyola University Medical Center, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - C Osipo
- The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - A Zlobin
- The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - W K Syn
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,Liver Unit, Barts Health NHS Trust, London, UK.,Regeneration and Repair, The Institute of Hepatology, London, UK
| | - J Zhang
- The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - P C Kuo
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - Z Mi
- Department of Surgery, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, USA.,The Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
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11
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Doppler SA, Werner A, Barz M, Lahm H, Deutsch MA, Dreßen M, Schiemann M, Voss B, Gregoire S, Kuppusamy R, Wu SM, Lange R, Krane M. Myeloid zinc finger 1 (Mzf1) differentially modulates murine cardiogenesis by interacting with an Nkx2.5 cardiac enhancer. PLoS One 2014; 9:e113775. [PMID: 25436607 PMCID: PMC4249966 DOI: 10.1371/journal.pone.0113775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/28/2014] [Indexed: 02/07/2023] Open
Abstract
Vertebrate heart development is strictly regulated by temporal and spatial expression of growth and transcription factors (TFs). We analyzed nine TFs, selected by in silico analysis of an Nkx2.5 enhancer, for their ability to transactivate the respective enhancer element that drives, specifically, expression of genes in cardiac progenitor cells (CPCs). Mzf1 showed significant activity in reporter assays and bound directly to the Nkx2.5 cardiac enhancer (Nkx2.5 CE) during murine ES cell differentiation. While Mzf1 is established as a hematopoietic TF, its ability to regulate cardiogenesis is completely unknown. Mzf1 expression was significantly enriched in CPCs from in vitro differentiated ES cells and in mouse embryonic hearts. To examine the effect of Mzf1 overexpression on CPC formation, we generated a double transgenic, inducible, tetOMzf1-Nkx2.5 CE eGFP ES line. During in vitro differentiation an early and continuous Mzf1 overexpression inhibited CPC formation and cardiac gene expression. A late Mzf1 overexpression, coincident with a second physiological peak of Mzf1 expression, resulted in enhanced cardiogenesis. These findings implicate a novel, temporal-specific role of Mzf1 in embryonic heart development. Thereby we add another piece of puzzle in understanding the complex mechanisms of vertebrate cardiac development and progenitor cell differentiation. Consequently, this knowledge will be of critical importance to guide efficient cardiac regenerative strategies and to gain further insights into the molecular basis of congenital heart malformations.
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Affiliation(s)
- Stefanie A. Doppler
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
- * E-mail:
| | - Astrid Werner
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
| | - Melanie Barz
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
| | - Harald Lahm
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
| | - Marcus-André Deutsch
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
| | - Martina Dreßen
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
- Clinical Cooperation Groups “Antigen-specific Immunotherapy” and “Immune-Monitoring”, Helmholtz Center Munich (Neuherberg), TUM, Munich, Germany
| | - Bernhard Voss
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
| | - Serge Gregoire
- Cardiovascular Research Center, Division of Cardiology, Harvard Medical School, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Rajarajan Kuppusamy
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sean M. Wu
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rüdiger Lange
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
- DZHK (German Center for Cardiovascular Research) – partner site Munich Heart Alliance, Munich, Germany
| | - Markus Krane
- Department of Experimental Surgery, Department of Cardiovascular Surgery, Deutsches Herzzentrum München, Technische Universität München (TUM), Munich, Germany
- DZHK (German Center for Cardiovascular Research) – partner site Munich Heart Alliance, Munich, Germany
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12
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Wright PW, Huehn A, Cichocki F, Li H, Sharma N, Dang H, Lenvik TR, Woll P, Kaufman D, Miller JS, Anderson SK. Identification of a KIR antisense lncRNA expressed by progenitor cells. Genes Immun 2013; 14:427-33. [PMID: 23863987 PMCID: PMC3808466 DOI: 10.1038/gene.2013.36] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 01/16/2023]
Abstract
Human NK cells express cell surface class I MHC receptors (killer cell immunoglobulin-like receptor, KIR) in a probabilistic manner. Previous studies have shown that a distal promoter acts in conjunction with a proximal bidirectional promoter to control the selective activation of KIR genes. We report here the presence of an intron 2 promoter in several KIR genes that produce a spliced antisense transcript. This long noncoding RNA (lncRNA) transcript contains antisense sequence complementary to KIR-coding exons 1 and 2 as well as the proximal promoter region of the KIR genes. The antisense promoter contains myeloid zinc finger 1 (MZF-1)-binding sites, a transcription factor found in hematopoietic progenitors and myeloid precursors. The KIR antisense lncRNA was detected only in progenitor cells or pluripotent cell lines, suggesting a function that is specific for stem cells. Overexpression of MZF-1 in developing NK cells led to decreased KIR expression, consistent with a role for the KIR antisense lncRNA in silencing KIR gene expression early in development.
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Affiliation(s)
- Paul W. Wright
- Lab of Experimental Immunology, SAIC-Frederick Inc., Frederick National Lab, Frederick, MD
| | - Andrew Huehn
- Cancer and Inflammation Program, CCR, National Cancer Institute, Frederick, MD
| | - Frank Cichocki
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN
| | - Hongchuan Li
- Lab of Experimental Immunology, SAIC-Frederick Inc., Frederick National Lab, Frederick, MD
| | - Neeraj Sharma
- Cancer and Inflammation Program, CCR, National Cancer Institute, Frederick, MD
| | - Hong Dang
- Cancer and Inflammation Program, CCR, National Cancer Institute, Frederick, MD
| | - Todd R. Lenvik
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN
| | - Petter Woll
- Stem Cell Institute, University of Minnesota, Minneapolis, MN
| | - Dan Kaufman
- Stem Cell Institute, University of Minnesota, Minneapolis, MN
| | - Jeffrey S. Miller
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN
| | - Stephen K. Anderson
- Lab of Experimental Immunology, SAIC-Frederick Inc., Frederick National Lab, Frederick, MD
- Cancer and Inflammation Program, CCR, National Cancer Institute, Frederick, MD
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13
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p55PIK transcriptionally activated by MZF1 promotes colorectal cancer cell proliferation. BIOMED RESEARCH INTERNATIONAL 2012; 2013:868131. [PMID: 23509792 PMCID: PMC3591147 DOI: 10.1155/2013/868131] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/31/2012] [Indexed: 01/23/2023]
Abstract
p55PIK, regulatory subunit of class IA phosphatidylinositol 3-kinase (PI3K), plays a crucial role in cell cycle progression by interaction with tumor repressor retinoblastoma (Rb) protein. A recent study showed that Rb protein can localize to the mitochondria in proliferative cells. Aberrant p55PIK expression may contribute to mitochondrial dysfunction in cancer progression. To reveal the mechanisms of p55PIK transcriptional regulation, the p55PIK promoter characteristics were analyzed. The data show that myeloid zinc finger 1, MZF1, is necessary for p55PIK gene transcription activation. ChIP (Chromatin immuno-precipitation) assay shows that MZF1 binds to the cis-element "TGGGGA" in p55PIK promoter. In MZF1 overexpressed cells, the promoter activity, expression of p55PIK, and cell proliferation rate were observed to be significantly enhanced. Whereas in MZF1-silenced cells, the promoter activity and expression of p55PIK and cell proliferation level was statistically decreased. In CRC tissues, MZF1 and p55PIK mRNA expression were increased (P = 0.046, P = 0.047, resp.). A strong positive correlation (Rs = 0.94) between MZF1 and p55PIK mRNA expression was observed. Taken together, we concluded that p55PIK is transcriptionally activated by MZF1, resulting in increased proliferation of colorectal cancer cells.
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14
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Sa-Nguanraksa D, O-Charoenrat P. The role of vascular endothelial growth factor a polymorphisms in breast cancer. Int J Mol Sci 2012. [PMID: 23203097 PMCID: PMC3509613 DOI: 10.3390/ijms131114845] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Breast cancer is the most common cancer in females and the leading cause of cancer death in women worldwide. Angiogenesis, the formation of new blood vessels, plays an important role in the development and progression of breast cancer. Vascular endothelial growth factor A (VEGFA), the key modulator of angiogenesis, is highly expressed in cancer tissue and correlates with its more aggressive features. Polymorphisms of VEGFA alter the levels of expression and subsequently influence the susceptibility and aggressiveness of breast cancer. Assessment of VEGFA polymorphisms may be used for the identification of patients suitable for anti-VEGFA therapy.
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Affiliation(s)
- Doonyapat Sa-Nguanraksa
- Division of Head-Neck and Breast Surgery, Department of Surgery, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
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15
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Li R, Ackerman WE, Summerfield TL, Yu L, Gulati P, Zhang J, Huang K, Romero R, Kniss DA. Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: translational systems approach to modeling human parturition. PLoS One 2011; 6:e20560. [PMID: 21655103 PMCID: PMC3107214 DOI: 10.1371/journal.pone.0020560] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/05/2011] [Indexed: 11/18/2022] Open
Abstract
A majority of the studies examining the molecular regulation of human labor have been conducted using single gene approaches. While the technology to produce multi-dimensional datasets is readily available, the means for facile analysis of such data are limited. The objective of this study was to develop a systems approach to infer regulatory mechanisms governing global gene expression in cytokine-challenged cells in vitro, and to apply these methods to predict gene regulatory networks (GRNs) in intrauterine tissues during term parturition. To this end, microarray analysis was applied to human amnion mesenchymal cells (AMCs) stimulated with interleukin-1β, and differentially expressed transcripts were subjected to hierarchical clustering, temporal expression profiling, and motif enrichment analysis, from which a GRN was constructed. These methods were then applied to fetal membrane specimens collected in the absence or presence of spontaneous term labor. Analysis of cytokine-responsive genes in AMCs revealed a sterile immune response signature, with promoters enriched in response elements for several inflammation-associated transcription factors. In comparison to the fetal membrane dataset, there were 34 genes commonly upregulated, many of which were part of an acute inflammation gene expression signature. Binding motifs for nuclear factor-κB were prominent in the gene interaction and regulatory networks for both datasets; however, we found little evidence to support the utilization of pathogen-associated molecular pattern (PAMP) signaling. The tissue specimens were also enriched for transcripts governed by hypoxia-inducible factor. The approach presented here provides an uncomplicated means to infer global relationships among gene clusters involved in cellular responses to labor-associated signals.
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Affiliation(s)
- Ruth Li
- Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research,
Department of Obstetrics and Gynecology, The Ohio State University, Columbus,
Ohio, United States of America
| | - William E. Ackerman
- Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research,
Department of Obstetrics and Gynecology, The Ohio State University, Columbus,
Ohio, United States of America
| | - Taryn L. Summerfield
- Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research,
Department of Obstetrics and Gynecology, The Ohio State University, Columbus,
Ohio, United States of America
| | - Lianbo Yu
- Center for Biostatistics, The Ohio State University, Columbus, Ohio,
United States of America
| | - Parul Gulati
- Center for Biostatistics, The Ohio State University, Columbus, Ohio,
United States of America
| | - Jie Zhang
- Department of Biomedical Informatics, The Ohio State University,
Columbus, Ohio, United States of America
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University,
Columbus, Ohio, United States of America
| | - Roberto Romero
- Perinatology Research Branch, Intramural Division, Eunice Kennedy Shriver
National Institute of Child Health and Human Development, National Institutes of
Health, Department of Health and Human Services, Bethesda, Maryland, United
States of America
- Hutzel Women's Hospital, Detroit, Michigan, United States of
America
| | - Douglas A. Kniss
- Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research,
Department of Obstetrics and Gynecology, The Ohio State University, Columbus,
Ohio, United States of America
- Department of Biomedical Engineering, The Ohio State University,
Columbus, Ohio, United States of America
- * E-mail:
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16
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Jiang W, Sequeira JM, Nakayama Y, Lai SC, Quadros EV. Characterization of the promoter region of TCblR/CD320 gene, the receptor for cellular uptake of transcobalamin-bound cobalamin. Gene 2010; 466:49-55. [PMID: 20627121 DOI: 10.1016/j.gene.2010.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 06/22/2010] [Accepted: 07/07/2010] [Indexed: 11/15/2022]
Abstract
Cellular uptake of cobalamin (Cbl) is mediated by the transcobalamin receptor (TCblR) that binds and internalizes transcobalamin (TC) saturated with Cbl. These receptors are expressed in actively proliferating cells and are down-regulated in quiescent cells. The 5' region of TCblR gene was analyzed for promoter activity to determine transcriptional regulation of TCblR expression. The region -668 to -455 appears to regulate TCblR expression. We have identified transcription factors MZF-1 (myeloid zinc finger 1)/RREB-1 (Ras-responsive element binding protein 1), C/EBP (CCAAT/enhancer binding protein)/HNF-3beta (hepatocyte nuclear factor 3) and AP-1(activator protein 1) as proteins likely to be involved in this regulation with the former region primarily involved in up regulation and the latter two regions involved in suppression of TCblR expression. These transcription factors are involved in cell proliferation and differentiation. Thus the cell cycle associated expression of TCblR appears to be tightly regulated in synchrony with the proliferative phase of the cell cycle.
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Affiliation(s)
- Wenxia Jiang
- School of Graduate Studies, SUNY-Downstate Medical Center, Brooklyn, NY 11203, USA
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17
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What is the role of alternate splicing in antigen presentation by major histocompatibility complex class I molecules? Immunol Res 2010; 46:32-44. [PMID: 19830395 DOI: 10.1007/s12026-009-8123-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The expression of major histocompatibility complex (MHC) class I molecules on the cell surface is critical for recognition by cytotoxic T lymphocytes (CTL). This recognition event leads to destruction of cells displaying MHC class I-viral peptide complexes or cells displaying MHC class I-mutant peptide complexes. Before they can be transported to the cell surface, MHC class I molecules must associate with their peptide ligand in the endoplasmic reticulum (ER) of the cell. Within the ER, numerous proteins assist in the appropriate assembly and folding of MHC class I molecules. These include the heterodimeric transporter associated with antigen processing (TAP1 and TAP2), the heterodimeric chaperone-oxidoreductase complex of tapasin and ERp57 and the general ER chaperones calreticulin and calnexin. Each of these accessory proteins has a well-defined role in antigen presentation by MHC class I molecules. However, alternate splice forms of MHC class I heavy chains, TAP and tapasin, have been reported suggesting additional complexity to the picture of antigen presentation. Here, we review the importance of these different accessory proteins and the progress in our understanding of alternate splicing in antigen presentation.
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18
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Kothinti RK, Blodgett AB, Petering DH, Tabatabai NM. Cadmium down-regulation of kidney Sp1 binding to mouse SGLT1 and SGLT2 gene promoters: possible reaction of cadmium with the zinc finger domain of Sp1. Toxicol Appl Pharmacol 2010; 244:254-62. [PMID: 20060848 DOI: 10.1016/j.taap.2009.12.038] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 12/19/2009] [Accepted: 12/21/2009] [Indexed: 02/04/2023]
Abstract
Cadmium (Cd) exposure causes glucosuria (glucose in the urine). Previously, it was shown that Cd exposure of primary cultures of mouse kidney cells (PMKC) decreased mRNA levels of the glucose transporters, SGLT1 and SGLT2 and that Sp1 from Cd-exposed cells displayed reduced binding to the GC boxes of the mouse SGLT1 promoter in vitro. Here, we identified a GC box upstream of mouse SGLT2 gene. ChIP assays on PMKC revealed that exposure to 5 microM Cd abolished Sp1 binding to SGLT1 GC box while it decreased Sp1 binding to SGLT2 GC sequence by 30% in vivo. The in vitro DNA binding assay, EMSA, demonstrated that binding of Sp1 from Cd (7.5 microM)-treated PMKC to the SGLT2 GC probe was 86% lower than in untreated cells. Sp1 is a zinc finger protein. Compared to PMKC exposed to 5 microM Cd alone, inclusion of 5 microM Zn restored SGLT1 and 2 mRNA levels by 15% and 30%, respectively. Cd (10 microM) decreased the binding of recombinant Sp1 (rhSp1) to SGLT1 and SGLT2 GC probes to 12% and 8% of untreated controls. Cd exerted no effect on GC-bound rhSp1. Co-treatment with Cd and Zn showed that added Zn significantly restored rhSp1 binding to the SGLT1 and SGLT2. Addition of Zn post Cd treatment was not stimulatory. We conclude that Cd can replace Zn in Sp1 DNA binding domain to reduce its binding to GC sites in mouse SGLT1 and SGLT2 promoters.
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Affiliation(s)
- Rajendra K Kothinti
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
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19
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Pikkarainen S, Kennedy RA, Marshall AK, Tham EL, Lay K, Kriz TA, Handa BS, Clerk A, Sugden PH. Regulation of expression of the rat orthologue of mouse double minute 2 (MDM2) by H(2)O(2)-induced oxidative stress in neonatal rat cardiac myocytes. J Biol Chem 2009; 284:27195-210. [PMID: 19638633 DOI: 10.1074/jbc.m109.037887] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mdm2 ubiquitin ligase is an important regulator of p53 abundance and p53-dependent apoptosis. Mdm2 expression is frequently regulated by a p53 Mdm2 autoregulatory loop whereby p53 stimulates Mdm2 expression and hence its own degradation. Although extensively studied in cell lines, relatively little is known about Mdm2 expression in heart where oxidative stress (exacerbated during ischemia-reperfusion) is an important pro-apoptotic stimulus. We demonstrate that Mdm2 transcript and protein expression are induced by oxidative stress (0.2 mm H(2)O(2)) in neonatal rat cardiac myocytes. In other cells, constitutive Mdm2 expression is regulated by the P1 promoter (5' to exon 1), with inducible expression regulated by the P2 promoter (in intron 1). In myocytes, H(2)O(2) increased Mdm2 expression from the P2 promoter, which contains two p53-response elements (REs), one AP-1 RE, and two Ets REs. H(2)O(2) did not detectably increase expression of p53 mRNA or protein but did increase expression of several AP-1 transcription factors. H(2)O(2) increased binding of AP-1 proteins (c-Jun, JunB, JunD, c-Fos, FosB, and Fra-1) to an Mdm2 AP-1 oligodeoxynucleotide probe, and chromatin immunoprecipitation assays showed it increased binding of c-Jun or JunB to the P2 AP-1 RE. Finally, antisense oligonucleotide-mediated reduction of H(2)O(2)-induced Mdm2 expression increased caspase 3 activation. Thus, increased Mdm2 expression is associated with transactivation at the P2 AP-1 RE (rather than the p53 or Ets REs), and Mdm2 induction potentially represents a cardioprotective response to oxidative stress.
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Affiliation(s)
- Sampsa Pikkarainen
- National Heart and Lung Institute Division, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
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20
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Saksena S, Dwivedi A, Singla A, Gill RK, Tyagi S, Borthakur A, Alrefai WA, Ramaswamy K, Dudeja PK. Characterization of the 5'-flanking region and regulation of expression of human anion exchanger SLC26A6. J Cell Biochem 2009; 105:454-66. [PMID: 18655181 DOI: 10.1002/jcb.21842] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
SLC26A6 (putative anion transporter 1, PAT1) has been shown to play an important role in mediating the luminal Cl(-)/OH(-)(HCO(3)(-)) exchange process in the intestine. Very little is known about the molecular mechanisms involved in the transcriptional regulation of intestinal SLC26A6 gene expression in the intestine. Current studies were, therefore, designed to clone and characterize the 5'-regulatory region of the human SLC26A6 gene and determine the mechanisms involved in its regulation. A 1,120 bp (p-964/+156) SLC26A6 promoter fragment cloned upstream to the luciferase reporter gene in pGL2-basic exhibited high promoter activity when transfected in Caco2 cells. Progressive deletions of the 5'-flanking region demonstrated that -214/-44 region of the promoter harbors cis-acting elements important for maximal SLC26A6 promoter activity. Since, diarrhea associated with inflammatory bowel diseases is attributed to increased secretion of pro-inflammatory cytokines, we examined the effects of IFNgamma (30 ng/ml, 24 h) on SLC26A6 function, expression and promoter activity. IFNgamma decreased both SLC26A6 mRNA and function and repressed SLC26A6 promoter activity. Deletion analysis indicated that IFNgamma response element is located between -414/-214 region and sequence analysis of this region revealed the presence of potential Interferon Stimulated Responsive Element (ISRE), a binding site (-318/-300 bp) for interferon regulatory factor-1 transcription factor (IRF-1). Mutations in the potential ISRE site abrogated the inhibitory effects of IFNgamma. These studies provided novel evidence for the involvement of IRF-1 in the regulation of SLC26A6 gene expression by IFNgamma in the human intestine.
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Affiliation(s)
- Seema Saksena
- Department of Medicine, University of Illinois at Chicago, Jesse Brown VA Medical Center, Chicago, Illinois 60612, USA.
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21
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Guo X, Silva JC. Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva. BMC Genomics 2008; 9:582. [PMID: 19055776 PMCID: PMC2612703 DOI: 10.1186/1471-2164-9-582] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 12/03/2008] [Indexed: 01/24/2023] Open
Abstract
Background Parasites in the genus Theileria cause lymphoproliferative diseases in cattle, resulting in enormous socio-economic losses. The availability of the genome sequences and annotation for T. parva and T. annulata has facilitated the study of parasite biology and their relationship with host cell transformation and tropism. However, the mechanism of transcriptional regulation in this genus, which may be key to understanding fundamental aspects of its parasitology, remains poorly understood. In this study, we analyze the evolution of non-coding sequences in the Theileria genome and identify conserved sequence elements that may be involved in gene regulation of these parasitic species. Results Intergenic regions and introns in Theileria are short, and their length distributions are considerably right-skewed. Intergenic regions flanked by genes in 5'-5' orientation tend to be longer and slightly more AT-rich than those flanked by two stop codons; intergenic regions flanked by genes in 3'-5' orientation have intermediate values of length and AT composition. Intron position is negatively correlated with intron length, and positively correlated with GC content. Using stringent criteria, we identified a set of high-quality orthologous non-coding sequences between T. parva and T. annulata, and determined the distribution of selective constraints across regions, which are shown to be higher close to translation start sites. A positive correlation between constraint and length in both intergenic regions and introns suggests a tight control over length expansion of non-coding regions. Genome-wide searches for functional elements revealed several conserved motifs in intergenic regions of Theileria genomes. Two such motifs are preferentially located within the first 60 base pairs upstream of transcription start sites in T. parva, are preferentially associated with specific protein functional categories, and have significant similarity to know regulatory motifs in other species. These results suggest that these two motifs are likely to represent transcription factor binding sites in Theileria. Conclusion Theileria genomes are highly compact, with selection seemingly favoring short introns and intergenic regions. Three over-represented sequence motifs were independently identified in intergenic regions of both Theileria species, and the evidence suggests that at least two of them play a role in transcriptional control in T. parva. These are prime candidates for experimental validation of transcription factor binding sites in this single-celled eukaryotic parasite. Sequences similar to two of these Theileria motifs are conserved in Plasmodium hinting at the possibility of common regulatory machinery across the phylum Apicomplexa.
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Affiliation(s)
- Xiang Guo
- The Institute for Genomic Research/J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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22
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McAlister VJ, Owens RA. Preferential integration of adeno-associated virus type 2 into a polypyrimidine/polypurine-rich region within AAVS1. J Virol 2007; 81:9718-26. [PMID: 17626070 PMCID: PMC2045435 DOI: 10.1128/jvi.00746-07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated virus type 2 (AAV2) preferentially integrates its genome into the AAVS1 locus on human chromosome 19. Preferential integration requires the AAV2 Rep68 or Rep78 protein (Rep68/78), a Rep68/78 binding site (RBS), and a nicking site within AAVS1 and may also require an RBS within the virus genome. To obtain further information that might help to elucidate the mechanism and preferred substrate configurations of preferential integration, we amplified junctions between AAV2 DNA and AAVS1 from AAV2-infected HeLaJW cells and cells with defective Artemis or xeroderma pigmentosum group A genes. We sequenced 61 distinct junctions. The integration junction sequences show the three classical types of nonhomologous-end-joining joints: microhomology at junctions (57%), insertion of sequences that are not normally contiguous with either the AAV2 or the AAVS1 sequences at the junction (31%), and direct joining (11%). These junctions were spread over 750 bases and were all downstream of the Rep68/78 nicking site within AAVS1. Two-thirds of the junctions map to 350 bases of AAVS1 that are rich in polypyrimidine tracts on the nicked strand. The majority of AAV2 breakpoints were within the inverted terminal repeat (ITR) sequences, which contain RBSs. We never detected a complete ITR at a junction. Residual ITRs at junctions never contained more than one RBS, suggesting that the hairpin form, rather than the linear ITR, is the more frequent integration substrate. Our data are consistent with a model in which a cellular protein other than Artemis cleaves AAV2 hairpins to produce free ends for integration.
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MESH Headings
- Binding Sites/physiology
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 19/metabolism
- Chromosomes, Human, Pair 19/virology
- DNA Breaks, Single-Stranded
- DNA-Binding Proteins/metabolism
- Dependovirus/genetics
- Dependovirus/metabolism
- Endonucleases
- Genome, Viral/physiology
- HeLa Cells
- Humans
- Models, Biological
- Nuclear Proteins/deficiency
- Nuclear Proteins/metabolism
- Quantitative Trait Loci/genetics
- Sequence Analysis, DNA
- Sequence Homology
- Terminal Repeat Sequences/physiology
- Viral Proteins/metabolism
- Virus Integration/physiology
- Xeroderma Pigmentosum Group A Protein/genetics
- Xeroderma Pigmentosum Group A Protein/metabolism
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Affiliation(s)
- Victor J McAlister
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health/DHHS, 8 Center Drive MSC 0840, Bethesda, MD 20892-0840, USA
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23
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Takahashi K, Matsumoto C, Ra C. FHL3 negatively regulates human high-affinity IgE receptor beta-chain gene expression by acting as a transcriptional co-repressor of MZF-1. Biochem J 2005; 386:191-200. [PMID: 15453830 PMCID: PMC1134781 DOI: 10.1042/bj20040775] [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] [Indexed: 11/17/2022]
Abstract
The high-affinity IgE receptor FcepsilonRI plays a key role in triggering allergic reactions. We recently reported that human FcepsilonRI beta-chain gene expression was down-regulated by a transcription factor, MZF-1, through an element in the fourth intron. In the present study, we found that this transcriptional repression by MZF-1 required FHL3 (four and a half LIM domain protein 3) as a cofactor. Yeast two-hybrid and immunoprecipitation assays demonstrated that FHL3 bound MZF-1 in vitro and in vivo. Overexpression of FHL3 in KU812 cells suppressed the beta-chain promoter activity through the element in the fourth intron in an MZF-1-dependent manner. Furthermore, results from pull-down assays and gel-filtration chromatography employing nuclear extracts indicated that MZF-1 and FHL3 formed a complex of high molecular mass with some additional proteins in the nucleus. Granulocyte-macrophage colony-stimulating factor, which was reported to decrease FcepsilonRI expression, induced the accumulation of FHL3 in the nucleus, in accordance with the repressive role of FHL3 in beta-chain gene expression.
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MESH Headings
- Cell Line, Tumor
- Cell Nucleus/chemistry
- Chromatography, Gel
- DNA, Complementary/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Down-Regulation/drug effects
- Down-Regulation/physiology
- Genes, Reporter
- Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology
- Humans
- Interleukin-3/pharmacology
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/physiology
- Introns/genetics
- Kruppel-Like Transcription Factors
- LIM Domain Proteins
- Leukemia, Basophilic, Acute/pathology
- Molecular Sequence Data
- Multigene Family
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Interaction Mapping
- Protein Structure, Tertiary
- Protein Transport
- Receptors, IgE/biosynthesis
- Receptors, IgE/genetics
- Recombinant Fusion Proteins/physiology
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Saccharomyces cerevisiae/metabolism
- Transcription Factors/genetics
- Transcription Factors/physiology
- Transcription, Genetic/drug effects
- Transcription, Genetic/physiology
- Transformation, Genetic
- Two-Hybrid System Techniques
- Zinc Fingers/genetics
- Zinc Fingers/physiology
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Affiliation(s)
- Kyoko Takahashi
- *Department of Molecular Cell Immunology and Allergology, Advanced Medical Research Center, Nihon University Graduate School of Medical Sciences, 30-1 Oyaguchi, Kami-machi, Itabashi-ku, Toyko 173-8610, Japan
| | - Chiyuki Matsumoto
- *Department of Molecular Cell Immunology and Allergology, Advanced Medical Research Center, Nihon University Graduate School of Medical Sciences, 30-1 Oyaguchi, Kami-machi, Itabashi-ku, Toyko 173-8610, Japan
- †Department of Dermatology, Surugadai Nihon University Hospital, 1-8-13 Kandasurugadai, Chiyoda-ku, Tokyo 101-8309, Japan
| | - Chisei Ra
- *Department of Molecular Cell Immunology and Allergology, Advanced Medical Research Center, Nihon University Graduate School of Medical Sciences, 30-1 Oyaguchi, Kami-machi, Itabashi-ku, Toyko 173-8610, Japan
- To whom correspondence should be addressed (email )
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24
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Follows GA, Tagoh H, Richards SJ, Melnik S, Dickinson H, de Wynter E, Lefevre P, Morgan GJ, Bonifer C. c-FMS chromatin structure and expression in normal and leukaemic myelopoiesis. Oncogene 2005; 24:3643-51. [PMID: 15806141 DOI: 10.1038/sj.onc.1208655] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The macrophage colony-stimulating factor receptor is encoded by the c-FMS gene, and it has been suggested that altered regulation of c-FMS expression may contribute to leukaemic transformation. c-FMS is expressed in pluripotent haemopoietic precursor cells and is subsequently upregulated during monocytic differentiation, but downregulated during granulopoiesis. We have examined transcription factor occupancy and aspects of chromatin structure of the critical c-FMS regulatory element located within the second intron (FIRE - fms intonic regulatory element) during normal and leukaemic myelopoiesis. Granulocytic differentiation from normal and leukaemic precursors is accompanied by loss of transcription factors at FIRE and downregulated c-FMS expression. The presence of AML1-ETO in leukaemic cells does not prevent this disassembly. In nonleukaemic cells, granulocytic differentiation is accompanied by reversal to a chromatin fine structure characteristic of c-FMS-nonexpressing cells. In addition, we show that low-level expression of the gene in leukaemic blast cells and granulocytes does not associate with increased CpG methylation across the c-FMS locus.
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25
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Follows GA, Tagoh H, Lefevre P, Morgan GJ, Bonifer C. Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci. Nucleic Acids Res 2004; 31:5805-16. [PMID: 14530429 PMCID: PMC219482 DOI: 10.1093/nar/gkg804] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The c-FMS gene encodes the macrophage colony-stimulating factor receptor (M-CSFR or CSF1-R), which is a tyrosine kinase growth factor receptor essential for macrophage development. We have previously characterized the chromatin features of the mouse gene; however, very little is known about chromatin structure and function of the human c-FMS locus. Here we present a side-by-side comparison of the chromatin structure, histone modification, transcription factor occupancy and cofactor recruitment of the human and the mouse c-FMS loci. We show that, similar to the mouse gene, the human c-FMS gene possesses a promoter and an intronic enhancer element (c-fms intronic regulatory element or FIRE). Both elements are evolutionarily conserved and specifically active in macrophages. However, we demonstrate by in vivo footprinting that both murine and human c-FMS cis-regulatory elements are recognised by an overlapping, but non-identical, set of transcription factors. Despite these differences, chromatin immunoprecipitation experiments show highly similar patterns of histone H3 modification and a similar distribution of chromatin modifying and remodelling activities at individual cis-regulatory elements and across the c-FMS locus. Our experiments support the hypothesis that the same regulatory principles operate at both genes via conserved cores of transcription factor binding sites.
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Affiliation(s)
- George A Follows
- Molecular Medicine Unit, University of Leeds, St James's University Hospital, Leeds LS9 7TF, UK
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26
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Shen CH, Steiner LA. Genome structure and thymic expression of an endogenous retrovirus in zebrafish. J Virol 2004; 78:899-911. [PMID: 14694121 PMCID: PMC368747 DOI: 10.1128/jvi.78.2.899-911.2004] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2003] [Accepted: 10/03/2003] [Indexed: 11/20/2022] Open
Abstract
In a search for previously unknown genes that are required for lymphocyte development in zebrafish, a retroviral sequence was identified in a subtracted thymus cDNA library and in genomic DNA libraries. The provirus is 11.2 kb and contains intact open reading frames for the gag, pol, and env genes, as well as nearly identical flanking long terminal repeat sequences. As determined by in situ hybridization, the thymus appears to be a major tissue for retroviral expression in both larval and adult fish. Several viral transcripts were found by Northern blotting in the adult thymus. The provirus was found at the same genomic locus in sperm from four fish, suggesting that it is an endogenous retrovirus. Phylogenetic analysis indicates that it is closest to, yet distinct from, the cluster of murine leukemia virus-related retroviruses, suggesting that this virus represents a new group of retroviruses.
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Affiliation(s)
- Ching-Hung Shen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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27
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Follows GA, Tagoh H, Lefevre P, Hodge D, Morgan GJ, Bonifer C. Epigenetic consequences of AML1-ETO action at the human c-FMS locus. EMBO J 2003; 22:2798-809. [PMID: 12773394 PMCID: PMC156747 DOI: 10.1093/emboj/cdg250] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Revised: 03/25/2003] [Accepted: 03/26/2003] [Indexed: 11/14/2022] Open
Abstract
Although many leukaemia-associated nuclear oncogenes are well characterized, little is known about the molecular details of how they alter gene expression. Here we examined transcription factor complexes and chromatin structure of the human c-FMS gene in normal and leukaemic cells. We demonstrate by in vivo footprinting and chromatin immunoprecipitation assays that this gene is bound by the transcription factor AML1 (RUNX1). In t(8;21) leukaemic cells expressing the aberrant fusion protein AML1-ETO, we demonstrate that this protein is part of a transcription factor complex binding to extended sequences of the c-FMS intronic regulatory region rather than the promoter. The AML1-ETO complex does not disrupt binding of other transcription factors, indicating that c-FMS is not irreversibly epigenetically silenced. However, AML1-ETO binding correlates with changes in the histone modification pattern and increased association of histone deacetylases. Our experiments provide for the first time a direct insight into the chromatin structure of an AML1-ETO-bound target gene.
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MESH Headings
- Acute Disease
- Base Sequence
- Binding Sites/genetics
- Cell Line
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 8/genetics
- Core Binding Factor Alpha 2 Subunit
- Gene Expression
- Gene Silencing
- Genes, fms
- HL-60 Cells
- HeLa Cells
- Histone Deacetylase 1
- Histone Deacetylases/metabolism
- Histones/chemistry
- Histones/metabolism
- Humans
- Introns
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Molecular Sequence Data
- Oncogene Proteins, Fusion/genetics
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- RUNX1 Translocation Partner 1 Protein
- Transcription Factors/genetics
- Translocation, Genetic
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Affiliation(s)
- George A Follows
- Molecular Medicine Unit, University of Leeds, St James's University Hospital, Leeds LS9 7TF, UK
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28
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Zelko IN, Folz RJ. Myeloid zinc finger (MZF)-like, Kruppel-like and Ets families of transcription factors determine the cell-specific expression of mouse extracellular superoxide dismutase. Biochem J 2003; 369:375-86. [PMID: 12374566 PMCID: PMC1223085 DOI: 10.1042/bj20021431] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2002] [Revised: 10/08/2002] [Accepted: 10/10/2002] [Indexed: 12/13/2022]
Abstract
Extracellular superoxide dismutase (EC-SOD or SOD3) is an important protective enzyme against the toxicity of superoxide radicals that are produced under both physiological and pathophysiological conditions. We have isolated and characterized over 11 kb of the mouse EC-SOD gene and its 5'- and 3'-flanking regions. The gene consists of two exons, with the entire coding region located within exon 2. In order to study the mechanism of cell-specific gene regulation for mouse EC-SOD, we characterized 2500 bp of its 5'-flanking region using cultured cells derived from mouse lung fibroblasts (MLg), kidney medulla (mIMCD3) and hepatocytes (Hepa 1-6). Real-time PCR showed that basal expression of EC-SOD was considerably higher in MLg cells compared with the other cell types. Reporter-gene assays revealed that the proximal promoter region was sufficient to support this high expression in MLg cells. Although no obvious TATA box was identified, our results show that a highly purine-rich region from -208 to +104 contains active binding sites for both the Kruppel-like and Ets families of transcription factors. Using electrophoretic mobility shift, DNase footprinting and reporter gene assays, we identified myeloid zinc finger 1 and gut-enriched Kruppel-like-factor-like nuclear transcription factors as repressors of EC-SOD expression, whereas nuclear transcription factors from the Ets family, such as Elf-1 and GA-binding protein alpha and beta, were potent activators of EC-SOD transcription. We propose a model that highlights competition between Ets activators and Kruppel-like repressors within the proximal promoter region that determines the level of EC-SOD expression in a particular cell type.
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Affiliation(s)
- Igor N Zelko
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, NC 27710, U.S.A
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29
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Higaki Y, Schullery D, Kawata Y, Shnyreva M, Abrass C, Bomsztyk K. Synergistic activation of the rat laminin gamma1 chain promoter by the gut-enriched Kruppel-like factor (GKLF/KLF4) and Sp1. Nucleic Acids Res 2002; 30:2270-9. [PMID: 12034813 PMCID: PMC117209 DOI: 10.1093/nar/30.11.2270] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Laminin is a multifunctional heterotrimeric protein present in extracellular matrix where it regulates processes that compose tissue architecture including cell differentiation. Laminin gamma1 is the most widely expressed laminin chain and its absence causes early lethality in mouse embryos. Laminin gamma1 chain gene (LAMC1) promoter contains several GC/GT-rich motifs including the bcn-1 element. Using the bcn-1 element as a bait in the yeast one-hybrid screen, we cloned the gut-enriched Kruppel-like factor (GKLF or KLF4) from a rat mesangial cell library. We show that GKLF binds bcn-1, but this binding is not required for the GKLF-mediated activation of the LAMC1 promoter. The activity of GKLF is dependent on a synergism with another Kruppel-like factor, Sp1. The LAMC1 promoter appears to have multiple GKLF- and Sp1-responsive elements which may account for the synergistic activation. We provide evidence that the synergistic action of GKLF and Sp1 is dependent on the promoter context and the integrity of GKLF activation and DNA-binding domain. GKLF is thought to participate in the switch from cell proliferation to differentiation. Thus, the Sp1-GKLF synergistic activation of the LAMC1 promoter may be one of the avenues for expression of laminin gamma1 chain when laminin is needed to regulate cell differentiation.
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Affiliation(s)
- Yuji Higaki
- Department of Medicine, Box 356521, University of Washington, Seattle, WA 98195, USA
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30
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Abstract
Granulocytes and monocytes develop from a common myeloid progenitor. Early granulopoiesis requires the C/EBPalpha, PU.1, RAR, CBF, and c-Myb transcription factors, and terminal neutrophil differentiation is dependent upon C/EBPepsilon, PU.1, Sp1, CDP, and HoxA10. Monopoiesis can be induced by Maf-B, c-Jun, or Egr-1 and is dependent upon PU.1, Sp1, and ICSBP. Signals eminating from cytokine receptors modulate factor activities but do not determine cell fates. Orchestration of the myeloid developmental program is achieved via cooperative gene regulation, via synergistic and inhibitory protein-protein interactions, via promoter auto-regulation and cross-regulation, via regulation of factor levels, and via induction of cell cycle arrest: For example, c-Myb and C/EBPalpha cooperate to activate the mim-1 and NE promoters, PU.1, C/EBPalpha, and CBF, regulate the NE, MPO, and M-CSF Receptor genes. PU.1:GATA-1 interaction and C/EBP suppression of FOG transcription inhibits erythroid and megakaryocyte gene expression. c-Jun:PU.1, ICSBP:PU.1, and perhaps Maf:Jun complexes induce monocytic genes. PU.1 and C/EBPalpha activate their own promoters, C/EBPalpha rapidly induces PU.1 and C/EBPepsilon RNA expression, and RARalpha activates the C/EBPepsilon promoter. Higher levels of PU.1 are required for monopoiesis than for B-lymphopoiesis, and higher C/EBP levels may favor granulopoiesis over monopoiesis. CBF and c-Myb stimulate proliferation whereas C/EBPalpha induces a G1/S arrest; cell cycle arrest is required for terminal myelopoiesis, perhaps due to expression of p53 or hypo-phosphorylated Rb.
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Affiliation(s)
- Alan D Friedman
- Division of Pediatric Oncology, Johns Hopkins University, Baltimore, Maryland, MD 21231, USA.
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31
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Kitagawa H, Taoka M, Tone Y, Sugahara K. Human glycosaminoglycan glucuronyltransferase I gene and a related processed pseudogene: genomic structure, chromosomal mapping and characterization. Biochem J 2001; 358:539-46. [PMID: 11535117 PMCID: PMC1222090 DOI: 10.1042/0264-6021:3580539] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Here we describe the characterization of the human glycosaminoglycan glucuronyltransferase I gene (GlcAT-I) and a related pseudogene. The GlcAT-I gene was localized to human chromosome 11q12-q13 by in situ hybridization of metaphase chromosomes. GlcAT-I spanned 7 kb of human genomic DNA and was divided into five exons. Northern blot analysis showed that GlcAT-I exhibited ubiquitous but markedly different expressions in the human tissues examined. The GlcAT-I promoter was approx. 3-fold more active in a melanoma cell line than in a hepatoma cell line, providing evidence for the differential regulation of the gene's expression. Stepwise 5' deletions of the promoter identified a strong enhancer element between -303 and -153 bp that included binding motifs for Ets, CREB (cAMP-response-element-binding protein) and STAT (signal transducers and activators of transcription). Screening of a human genomic library identified one additional distinct genomic clone containing an approx. 1.4 kb sequence region that shared an overall 95.3% nucleotide identity with exons 1-5 of GlcAT-I. However, a lack of intron sequences, as well as the presence of several nucleotide mutations, insertions and deletions that disrupted the potential GlcAT-I reading frame, suggested that the clone contained a processed pseudogene. The pseudogene was localized to chromosome 3. The human genome therefore contains two related GlcAT-I genes that are located on separate chromosomes.
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Affiliation(s)
- H Kitagawa
- Department of Biochemistry, Kobe Pharmaceutical University, Higashinada-ku, Kobe 658-8558, Japan.
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32
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Gaboli M, Kotsi PA, Gurrieri C, Cattoretti G, Ronchetti S, Cordon-Cardo C, Broxmeyer HE, Hromas R, Pandolfi PP. Mzf1 controls cell proliferation and tumorigenesis. Genes Dev 2001; 15:1625-30. [PMID: 11445537 PMCID: PMC312729 DOI: 10.1101/gad.902301] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
MZF1 is a transcription factor belonging to the Krüppel family of zinc finger proteins, expressed in totipotent hemopoietic cells as well as in myeloid progenitors. Here we have inactivated Mzfi1 by gene targeting. Mzf1(-/-) mice develop lethal neoplasias characterized by the infiltration and complete disruption of the liver architecture by a monomorphic population of cells of myeloid origin reminiscent of human chloromas. Mzf1 inactivation results in a striking increase of the autonomous cell proliferation and of the ability of Mzf1(-/-) hemopoietic progenitors to sustain long-term hemopoiesis. These findings demonstrate that Mzf1 can act as a tumor/growth suppressor in the hemopoietic compartment.
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Affiliation(s)
- M Gaboli
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, Sloan-Kettering Division, Graduate School of Medical Sciences, Cornell University, New York, New York 10021, USA
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33
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Affiliation(s)
- T Collins
- Department of Pathology, Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
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34
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Ponomarenko JV, Orlova GV, Ponomarenko MP, Lavryushev SV, Frolov AS, Zybova SV, Kolchanov NA. SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucleic Acids Res 2000; 28:205-8. [PMID: 10592226 PMCID: PMC102392 DOI: 10.1093/nar/28.1.205] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/1999] [Revised: 09/10/1999] [Accepted: 09/30/1999] [Indexed: 11/13/2022] Open
Abstract
SELEX_DB is a novel curated database on selected randomized DNA/RNA sequences designed for accumulation of experimental data on functional site sequences obtained by using SELEX and SELEX-like technologies from the pools of random sequences. This database also contains the programs for DNA/RNA functional site recognition within arbitrary nucleotide sequences. The first release of SELEX_DB has been installed under SRS and is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
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Affiliation(s)
- J V Ponomarenko
- Laboratory of Theoretical Genetics, Institute of Cytology, 10 Lavrentyev Avenue, Novosibirsk 630090, Russia.
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35
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Gobin SJP, Keijsers V, van Zutphen M, van den Elsen PJ. The Role of Enhancer A in the Locus-Specific Transactivation of Classical and Nonclassical HLA Class I Genes by Nuclear Factor κB. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.161.5.2276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
HLA class I expression is tightly controlled at the transcriptional level by several conserved regulatory elements in the proximal promoter region. In this study, the two putative κB motifs of enhancer A (κB1 and κB2) of the classical and nonclassical HLA class I genes were investigated for their binding properties of transcription factors and tested for their contribution to the NF-κB-induced route of transactivation. It was shown that NF-κB-induced transactivation through enhancer A is most important for the HLA-A locus, which contains two NF-κB binding sites. Although the enhancer A of HLA-B contains only one NF-κB binding site (κB1), there was still a moderate transactivation by NF-κB. Since HLA-F, which also possesses one NF-κB binding site but lacks protein binding to its κB2 site, was not transactivated by NF-κB, the NF-κB-mediated transactivation through the κB1 motif in HLA-B is most probably facilitated by binding of the transcription factor Sp1 to the upstream κB2 site. Thus, transcriptional regulation of HLA class I genes by NF-κB is restricted to the HLA-A and HLA-B loci.
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Affiliation(s)
- Sam J. P. Gobin
- Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Vivian Keijsers
- Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Marlijn van Zutphen
- Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter J. van den Elsen
- Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands
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36
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Yao YL, Dupont BR, Ghosh S, Fang Y, Leach RJ, Seto E. Cloning, chromosomal localization and promoter analysis of the human transcription factor YY1. Nucleic Acids Res 1998; 26:3776-83. [PMID: 9685495 PMCID: PMC147783 DOI: 10.1093/nar/26.16.3776] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Yin Yang 1 (YY1) is a protein that activates and represses transcription of a large number of cellular and viral genes. In addition, studies suggest that YY1 may play an important role in development and differentiation. Here, we report the isolation and analysis of a YY1 genomic clone from a lambda human liver library. Fluorescence in situ hybridization with the YY1 clone has localized the YY1 gene to chromosome 14 band q32. A major YY1 gene transcription initiation site has been mapped to 478 bp upstream of the ATG translation start site. The proximal promoter contains multiple Sp1 transcription factor binding sites but lacks a consensus TATA or CCAAT box. Transient transfections and detailed deletion analyses localized the promoter to no more than 277 bp upstream from the major transcription start site. Finally, we have found that overexpression of the adenovirus E1A protein represses expression of a reporter gene directed by the YY1 promoter.
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Affiliation(s)
- Y L Yao
- H. Lee Moffitt Cancer Center and Research Institute, Department of Microbiology and Immunology, College of Medicine, University of South Florida, 12902 Magnolia Drive, Tampa, FL 33612, USA
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37
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Murai K, Murakami H, Nagata S. Myeloid-specific transcriptional activation by murine myeloid zinc-finger protein 2. Proc Natl Acad Sci U S A 1998; 95:3461-6. [PMID: 9520388 PMCID: PMC19858 DOI: 10.1073/pnas.95.7.3461] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Myeloid zinc finger protein 2 (MZF-2) is a zinc-finger transcription factor that is expressed in myeloid cells, particularly in the cells committed to the neutrophilic lineage. Here we examine the ability of murine MZF-2 (mMZF-2) to activate transcription. The mMZF-2 protein binds to a DNA element (MZF-binding site) through its zinc-finger domain. When the intact mMZF-2 was cotransfected with a reporter gene, it did not activate transcription. However, N-terminal deletion mutants greatly enhanced transcription specifically in myeloid cells. Furthermore, in an in vivo competition assay, the middle region of MZF-2 inhibited the mMZF-2-mediated transcription activation. These results suggest that mMZF-2 is a transcriptional factor that can specifically work in myeloid cells and can be divided into at least three functional domains. The N-terminal domain inhibits transactivation by masking the effect of the activation domain. The middle region recruits a coactivator, which is responsible for myeloid-specific transcriptional activation. The C-terminal zinc-finger domain functions as a DNA-binding domain.
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Affiliation(s)
- K Murai
- Osaka Bioscience Institute, 6-2-4 Furuedai, Suita, Osaka 565, Japan
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38
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Shields JM, Yang VW. Identification of the DNA sequence that interacts with the gut-enriched Krüppel-like factor. Nucleic Acids Res 1998; 26:796-802. [PMID: 9443972 PMCID: PMC147321 DOI: 10.1093/nar/26.3.796] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gut-enriched Krüppel-like factor (GKLF) is a recently identified eukaryotic transcription factor that contains three C2H2zinc fingers. The amino acid sequence of the zinc finger portion of GKLF is closely related to several Krüppel proteins, including the lung Krüppel-like factor (LKLF), the erythroid Krüppel-like factor (EKLF) and the basic transcription element binding protein 2 (BTEB2). The DNA sequence to which GKLF binds has not been definitively established. In the present study we determined the DNA binding sequence of GKLF using highly purified recombinant GKLF in a target detection assay of an oligonucleotide library consisting of random sequences. Upon repeated rounds of selection and subsequent characterization of the selected sequences by base-specific mutagenesis a DNA with the sequence 5'-G/AG/AGGC/TGC/T-3' was found to contain the minimal essential binding site for GKLF. This sequence is present in the promoters of two previously characterized genes: the CACCC element of the beta-globin gene, which interacts with EKLF, and the basic transcription element (BTE) of the CYP1A1 gene, which interacts with Sp1 and several Sp1-like transcription factors. Moreover, the selected GKLF binding sequence was capable of mediating transactivation of a linked reporter gene by GKLF in co-transfection experiments. Our results establish GKLF as a sequence-specific transcription factor likely involved in regulation of expression of endogenous genes.
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Affiliation(s)
- J M Shields
- Department of Medicine and Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Shields JM, Christy RJ, Yang VW. Identification and characterization of a gene encoding a gut-enriched Krüppel-like factor expressed during growth arrest. J Biol Chem 1996; 271:20009-17. [PMID: 8702718 PMCID: PMC2330254 DOI: 10.1074/jbc.271.33.20009] [Citation(s) in RCA: 529] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A cDNA clone, named gut-enriched Krüppel-like factor (GKLF), was isolated from an NIH 3T3 library using a probe encoding the zinc finger region of the immediate-early transcription factor zif/268. The deduced GKLF amino acid sequence contains three tandem zinc fingers that are related to members of the Krüppel family of transcription factors. By indirect immunofluorescence, GKLF is localized to the cell nucleus. In cultured fibroblasts, GKLF mRNA is found in high levels in growth-arrested cells and is nearly undetectable in cells that are in the exponential phase of proliferation. The growth-arresting nature of GKLF is demonstrated by an inhibition of DNA synthesis in cells transfected with a GKLF-expressing plasmid construct. In the mouse, GKLF mRNA is present in select tissues and is most abundant in the colon, followed by the testis, lung, and small intestine. In situ hybridization experiments indicate that GKLF mRNA is enriched in epithelial cells located in the middle to upper crypt region of the colonic mucosa. Taken together, these results suggest that GKLF is potentially a negative regulator of cell growth in tissues such as the gut mucosa, where cell proliferation is intimately coupled to growth arrest and differentiation.
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Affiliation(s)
- Janiel M. Shields
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Robert J. Christy
- Center for Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center, San Antonio, Texas 78250
| | - Vincent W. Yang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
- ** To whom correspondence should be addressed: Dept. of Medicine, Ross 918, The Johns Hopkins University School of Medicine, 720 Rutland Ave., Baltimore, MD 21205. Tel.: 410-955-9691; Fax: 410-955-9677; E-mail:
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Filippova GN, Fagerlie S, Klenova EM, Myers C, Dehner Y, Goodwin G, Neiman PE, Collins SJ, Lobanenkov VV. An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol 1996; 16:2802-13. [PMID: 8649389 PMCID: PMC231272 DOI: 10.1128/mcb.16.6.2802] [Citation(s) in RCA: 426] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have isolated and analyzed human CTCF cDNA clones and show here that the ubiquitously expressed 11-zinc-finger factor CTCF is an exceptionally highly conserved protein displaying 93% identity between avian and human amino acid sequences. It binds specifically to regulatory sequences in the promoter-proximal regions of chicken, mouse, and human c-myc oncogenes. CTCF contains two transcription repressor domains transferable to a heterologous DNA binding domain. One CTCF binding site, conserved in mouse and human c-myc genes, is found immediately downstream of the major P2 promoter at a sequence which maps precisely within the region of RNA polymerase II pausing and release. Gel shift assays of nuclear extracts from mouse and human cells show that CTCF is the predominant factor binding to this sequence. Mutational analysis of the P2-proximal CTCF binding site and transient-cotransfection experiments demonstrate that CTCF is a transcriptional repressor of the human c-myc gene. Although there is 100% sequence identity in the DNA binding domains of the avian and human CTCF proteins, the regulatory sequences recognized by CTCF in chicken and human c-myc promoters are clearly diverged. Mutating the contact nucleotides confirms that CTCF binding to the human c-myc P2 promoter requires a number of unique contact DNA bases that are absent in the chicken c-myc CTCF binding site. Moreover, proteolytic-protection assays indicate that several more CTCF Zn fingers are involved in contacting the human CTCF binding site than the chicken site. Gel shift assays utilizing successively deleted Zn finger domains indicate that CTCF Zn fingers 2 to 7 are involved in binding to the chicken c-myc promoter, while fingers 3 to 11 mediate CTCF binding to the human promoter. This flexibility in Zn finger usage reveals CTCF to be a unique "multivalent" transcriptional factor and provides the first feasible explanation of how certain homologous genes (i.e., c-myc) of different vertebrate species are regulated by the same factor and maintain similar expression patterns despite significant promoter sequence divergence.
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Affiliation(s)
- G N Filippova
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA
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Perrotti D, Melotti P, Skorski T, Casella I, Peschle C, Calabretta B. Overexpression of the zinc finger protein MZF1 inhibits hematopoietic development from embryonic stem cells: correlation with negative regulation of CD34 and c-myb promoter activity. Mol Cell Biol 1995; 15:6075-87. [PMID: 7565760 PMCID: PMC230859 DOI: 10.1128/mcb.15.11.6075] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Zinc finger genes encode proteins that act as transcription factors. The myeloid zinc finger 1 (MZF1) gene encodes a zinc finger protein with two DNA-binding domains that recognize two distinct consensus sequences, is preferentially expressed in hematopoietic cells, and may be involved in the transcriptional regulation of hematopoiesis-specific genes. Reverse transcription-PCR analysis of human peripheral blood CD34+ cells cultured under lineage-restricted conditions demonstrated MZF1 expression during both myeloid and erythroid differentiation. Sequence analysis of the 5'-flanking region of the CD34 and c-myb genes, which are a marker of and a transcriptional factor required for hematopoietic proliferation and differentiation, respectively, revealed closely spaced MZF1 consensus binding sites found by electrophoretic mobility shift assays to interact with recombinant MZF1 protein. Transient or constitutive MZF1 expression in different cell types resulted in specific inhibition of chloramphenicol acetyltransferase activity driven by the CD34 or c-myb 5'-flanking region. To determine whether transcriptional modulation by MZF1 activity plays a role in hematopoietic differentiation, constructs containing the MZF1 cDNA under the control of different promoters were transfected into murine embryonic stem cells which, under defined in vitro culture conditions, generate colonies of multiple hematopoietic lineages. Constitutive MZF1 expression interfered with the ability of embryonic stem cells to undergo hematopoietic commitment and erythromyeloid colony formation and prevented the induced expression of CD34 and c-myb mRNAs during differentiation of these cells. These data indicate that MZF1 plays a critical role in hematopoiesis by modulating the expression of genes involved in this process.
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Affiliation(s)
- D Perrotti
- Department of Microbiology and Immunology, Jefferson Cancer Institute, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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