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Abstract
Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here, we identify 6703 and 1536 protein–protein interactions for 109 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis identifies more high-confidence interactions, highlighting the transient and dynamic nature of many of the TF interactions. By performing clustering and correlation analyses, we identify subgroups of TFs associated with specific biological functions, such as RNA splicing or chromatin remodeling. We also observe 202 TF-TF interactions, of which 118 are interactions with nuclear factor 1 (NFI) family members, indicating uncharacterized cross-talk between NFI signaling and other TF signaling pathways. Moreover, TF interactions with basal transcription machinery are mainly observed through TFIID and SAGA complexes. This study provides a rich resource of human TF interactions and also act as a starting point for future studies aimed at understanding TF-mediated transcription. Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here the authors identify 6703 and 1536 protein–protein interactions for 109 different human TFs through BioID and AP-MS analyses, respectively.
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Chen T, Wang X, Li C, Zhang H, Liu Y, Han D, Li Y, Li Z, Luo D, Zhang N, Zheng M, Chen B, Wang L, Zhao W, Yang Q. CircHIF1A regulated by FUS accelerates triple-negative breast cancer progression by modulating NFIB expression and translocation. Oncogene 2021; 40:2756-2771. [PMID: 33714984 DOI: 10.1038/s41388-021-01739-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 01/31/2023]
Abstract
Emerging evidence has demonstrated that circular RNAs (circRNAs) play critical roles in the development and progression of human cancer. However, the biological functions and underlying mechanisms of circRNAs in triple-negative breast cancer (TNBC) remain to be investigated. In our present study, we found that the novel circRNA circHIF1A was significantly overexpressed in breast cancer tissues and that it was associated with metastasis, poor prognosis, and the TNBC subtype. Gain- and loss-of-function experiments were conducted to investigate the biological roles of circHIF1A in TNBC. Overexpression of circHIF1A significantly promoted TNBC growth and metastasis in vitro and in vivo, while knockdown of circHIF1A exerted the opposite effects. Mechanistically, circHIF1A modulated the expression and translocation of NFIB through posttranscriptional and posttranslational modifications, resulting in the activation of the AKT/STAT3 signaling pathway and inhibition of P21. The RNA binding protein FUS could regulate the biogenesis of circHIF1A by interacting with the flanking intron, and FUS was transcriptionally regulated by NFIB, thus forming the circHIF1A/NFIB/FUS positive feedback loop. Moreover, circHIF1A could be packaged into exosomes and was upregulated in the plasma of breast cancer patients. Our findings indicated that circHIF1A played a critical role in the growth and metastasis of TNBC via a positive feedback loop and that circHIF1A could be a promising biomarker for breast cancer diagnosis and a potential therapeutic target for TNBC treatment.
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Affiliation(s)
- Tong Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xiaolong Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Chen Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Hanwen Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Ying Liu
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Dianwen Han
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yaming Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Zheng Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Dan Luo
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Ning Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Meizhu Zheng
- Department of Breast Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Bing Chen
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Lijuan Wang
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Wenjing Zhao
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China. .,Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, China. .,Research Institute of Breast Cancer, Shandong University, Jinan, Shandong, China.
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Vo TM, Burchett R, Brun M, Monckton EA, Poon HY, Godbout R. Effects of nuclear factor I phosphorylation on calpastatin ( CAST) gene variant expression and subcellular distribution in malignant glioma cells. J Biol Chem 2019; 294:1173-1188. [PMID: 30504225 DOI: 10.1074/jbc.ra118.004787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 11/29/2018] [Indexed: 12/20/2022] Open
Abstract
Malignant glioma (MG) is the most lethal primary brain tumor. In addition to having inherent resistance to radiation treatment and chemotherapy, MG cells are highly infiltrative, rendering focal therapies ineffective. Genes involved in MG cell migration and glial cell differentiation are up-regulated by hypophosphorylated nuclear factor I (NFI), which is dephosphorylated by the phosphatase calcineurin in MG cells. Calcineurin is cleaved and thereby activated by calpain proteases, which are, in turn, inhibited by calpastatin (CAST). Here, we show that the CAST gene is a target of NFI and has NFI-binding sites in its intron 3 region. We also found that NFI-mediated regulation of CAST depends on NFI's phosphorylation state. We noted that occupation of CAST intron 3 by hypophosphorylated NFI results in increased activation of an alternative promoter. This activation resulted in higher levels of CAST transcript variants, leading to increased levels of CAST protein that lacks the N-terminal XL domain. CAST was primarily present in the cytoplasm of NFI-hypophosphorylated MG cells, with a predominantly perinuclear immunostaining pattern. NFI knockdown in NFI-hypophosphorylated MG cells increased CAST levels at the plasma membrane. These results suggest that NFI plays an integral role in the regulation of CAST variants and CAST subcellular distribution. Along with the previous findings indicating that NFI activity is regulated by calcineurin, these results provide a foundation for further investigations into the possibility of regulatory cross-talk between NFI and the CAST/calpain/calcineurin signaling pathway in MG cells.
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Affiliation(s)
- The Minh Vo
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Rebecca Burchett
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Miranda Brun
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Elizabeth A Monckton
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Ho-Yin Poon
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada.
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Piper M, Gronostajski R, Messina G. Nuclear Factor One X in Development and Disease. Trends Cell Biol 2018; 29:20-30. [PMID: 30287093 DOI: 10.1016/j.tcb.2018.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023]
Abstract
The past decade has seen incredible advances in the field of stem cell biology that have greatly improved our understanding of development and provided important insights into pathological processes. Transcription factors (TFs) play a central role in mediating stem cell proliferation, quiescence, and differentiation. One TF that contributes to these processes is Nuclear Factor One X (NFIX). Recently, NFIX activity has been shown to be essential in multiple organ systems and to have important translational impacts for human health. Here, we describe recent studies showing the contribution of NFIX to muscle development and muscular dystrophies, hematopoiesis, cancer, and neural stem cell biology, highlighting the importance of this knowledge in the development of therapeutic targets.
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Affiliation(s)
- Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Richard Gronostajski
- Department of Biochemistry, Genetics, Genomics & Bioinformatics Graduate Program, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Graziella Messina
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy.
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Brun M, Jain S, Monckton EA, Godbout R. Nuclear Factor I Represses the Notch Effector HEY1 in Glioblastoma. Neoplasia 2018; 20:1023-1037. [PMID: 30195713 PMCID: PMC6138789 DOI: 10.1016/j.neo.2018.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/17/2018] [Accepted: 08/20/2018] [Indexed: 01/16/2023] Open
Abstract
Glioblastomas (GBMs) are highly aggressive brain tumors with a dismal prognosis. Nuclear factor I (NFI) is a family of transcription factors that controls glial cell differentiation in the developing central nervous system. NFIs have previously been shown to regulate the expression of astrocyte markers such as glial fibrillary acidic protein (GFAP) in both normal brain and GBM cells. We used chromatin immunoprecipitation (ChIP)–on-chip to identify additional NFI targets in GBM cells. Analysis of our ChIP data revealed ~400 putative NFI target genes including an effector of the Notch signaling pathway, HEY1, implicated in the maintenance of neural stem cells. All four NFIs (NFIA, NFIB, NFIC, and NFIX) bind to NFI recognition sites located within 1 kb upstream of the HEY1 transcription site. We further showed that NFI negatively regulates HEY1 expression, with knockdown of all four NFIs in GBM cells resulting in increased HEY1 RNA levels. HEY1 knockdown in GBM cells decreased cell proliferation, increased cell migration, and decreased neurosphere formation. Finally, we found a general correlation between elevated levels of HEY1 and expression of the brain neural stem/progenitor cell marker B-FABP in GBM cell lines. Knockdown of HEY1 resulted in an increase in the RNA levels of the GFAP astrocyte differentiation marker. Overall, our data indicate that HEY1 is negatively regulated by NFI family members and is associated with increased proliferation, decreased migration, and increased stem cell properties in GBM cells.
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Affiliation(s)
- Miranda Brun
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada, T6G 1Z2
| | - Saket Jain
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada, T6G 1Z2
| | - Elizabeth A Monckton
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada, T6G 1Z2
| | - Roseline Godbout
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada, T6G 1Z2.
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Abstract
Long noncoding RNAs (lncRNAs) are an important group of pervasive noncoding RNAs (>200nt) proposed to be crucial regulators of numerous physiological and pathological processes. Through interactions with RNA, chromatin, and protein, lncRNAs modulate mRNA stability, chromatin structure, and the function of proteins (including transcription factors). In addition, to their well-known roles in the modulation of cell growth, apoptosis, neurological disease progression and cancer metastasis, these large molecules have also been identified as likely mediators of lipid metabolism. In particular, lncRNAs orchestrate adipogenesis; fatty acid, cholesterol, and phospholipid metabolism and transport; and the formation of high-density and low-density lipoproteins (HDLs and LDLs). LncRNAs also appear to target several transcription factors that play essential roles in the regulation of lipid metabolism, such as liver X receptors (LXRs), sterol regulatory element binding proteins (SREBPs), and peroxisome proliferator-activated receptor γ (PPARγ). Better understanding the regulatory roles of lncRNAs in dyslipidemia, atherosclerosis, and adipogenesis will reveal appropriate strategies to treat these diseases. In this review, we review recent progress in lncRNA-mediated regulation of lipid metabolism, as well as its role in the regulation of adipogenesis.
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Relationship between long noncoding RNAs and physiological risk factors of cardiovascular disease. J Clin Lipidol 2017; 11:617-623. [DOI: 10.1016/j.jacl.2017.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 03/16/2017] [Accepted: 03/19/2017] [Indexed: 01/09/2023]
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Archer K, Broskova Z, Bayoumi AS, Teoh JP, Davila A, Tang Y, Su H, Kim IM. Long Non-Coding RNAs as Master Regulators in Cardiovascular Diseases. Int J Mol Sci 2015; 16:23651-67. [PMID: 26445043 PMCID: PMC4632719 DOI: 10.3390/ijms161023651] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/21/2015] [Accepted: 09/28/2015] [Indexed: 12/21/2022] Open
Abstract
Cardiovascular disease is the leading cause of death in the United States, accounting for nearly one in every seven deaths. Over the last decade, various targeted therapeutics have been introduced, but there has been no corresponding improvement in patient survival. Since the mortality rate of cardiovascular disease has not been significantly decreased, efforts have been made to understand the link between heart disease and novel therapeutic targets such as non-coding RNAs. Among multiple non-coding RNAs, long non-coding RNA (lncRNA) has emerged as a novel therapeutic in cardiovascular medicine. LncRNAs are endogenous RNAs that contain over 200 nucleotides and regulate gene expression. Recent studies suggest critical roles of lncRNAs in modulating the initiation and progression of cardiovascular diseases. For example, aberrant lncRNA expression has been associated with the pathogenesis of ischemic heart failure. In this article, we present a synopsis of recent discoveries that link the roles and molecular interactions of lncRNAs to cardiovascular diseases. Moreover, we describe the prevalence of circulating lncRNAs and assess their potential utilities as biomarkers for diagnosis and prognosis of heart disease.
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Affiliation(s)
- Krystal Archer
- Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
| | - Zuzana Broskova
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
| | - Ahmed S Bayoumi
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
| | - Jian-peng Teoh
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
| | - Alec Davila
- Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
| | - Yaoliang Tang
- Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
| | - Il-man Kim
- Vascular Biology Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
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Wang Y, Huang C, Chintagari NR, Xi D, Weng T, Liu L. miR-124 regulates fetal pulmonary epithelial cell maturation. Am J Physiol Lung Cell Mol Physiol 2015; 309:L400-13. [PMID: 26071557 DOI: 10.1152/ajplung.00356.2014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 06/08/2015] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs are a family of small noncoding RNAs that regulate the expression of their target proteins at the posttranscriptional level. Their functions cover almost every aspect of cell physiology. However, the roles of microRNAs in fetal lung development are not completely understood. The objective of this study is to investigate the regulation and molecular mechanisms of alveolar epithelial cell maturation during fetal lung development by miR-124. We discovered that miR-124 was downregulated during rat fetal lung development and predominantly expressed in the epithelial cells at late stage of the lung development. Overexpression of miR-124 with an adenovirus vector led to the inhibition of epithelial maturation in rat fetal lung organ cultures and fetal alveolar epithelial type II cells, as demonstrated by a decrease in the type II cell marker expression and an increase in glycogen content. We further demonstrated by luciferase reporter assays that miR-124 inhibited the NF-κB, cAMP/PKA, and MAPK/ERK pathways. In addition, nuclear factor I/B (NFIB), a critical protein in fetal lung maturation, was validated as a direct target of miR-124. Furthermore, miR-124 expression was induced by the Wnt/β-catenin signaling pathway through a direct interaction of LEF1 and the miR-124 promoter region. We concluded that miR-124 downregulation is critical to fetal lung epithelial maturation and miR-124 inhibits this maturation process at least partially through the inhibition of NFIB.
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Affiliation(s)
- Yang Wang
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Chaoqun Huang
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma
| | - Narendranath Reddy Chintagari
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Dong Xi
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Tingting Weng
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and
| | - Lin Liu
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma; and Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma
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Duval C, Zaniolo K, Leclerc S, Salesse C, Guérin SL. Characterization of the human α9 integrin subunit gene: Promoter analysis and transcriptional regulation in ocular cells. Exp Eye Res 2015; 135:146-63. [PMID: 25746835 DOI: 10.1016/j.exer.2015.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/26/2015] [Accepted: 03/02/2015] [Indexed: 11/29/2022]
Abstract
α9β1 is the most recent addition to the integrin family of membrane receptors and consequently remains the one that is the least characterized. To better understand how transcription of the human gene encoding the α9 subunit is regulated, we cloned the α9 promoter and characterized the regulatory elements that are required to ensure its transcription. Transfection of α9 promoter/CAT plasmids in primary cultured human corneal epithelial cells (HCECs) and uveal melanoma cell lines demonstrated the presence of both negative and positive regulatory elements along the α9 promoter and positioned the basal α9 promoter to within 118 bp from the α9 mRNA start site. In vitro DNaseI footprinting and in vivo ChIP analyses demonstrated the binding of the transcription factors Sp1, c-Myb and NFI to the most upstream α9 negative regulatory element. The transcription factors Sp1 and NFI were found to bind the basal α9 promoter individually but Sp1 binding clearly predominates when both transcription factors are present in the same extract. Suppression of Sp1 expression through RNAi also caused a dramatic reduction in the expression of the α9 gene. Most of all, addition of tenascin-C (TNC), the ligand of α9β1, to the tissue culture plates prior to seeding HCECs increased α9 transcription whereas it simultaneously decreased expression of the α5 integrin subunit gene. This dual regulatory action of TNC on the transcription of the α9 and α5 genes suggests that both these integrins must work together to appropriately regulate cell adhesion, migration and differentiation that are hallmarks of tissue wound healing.
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Affiliation(s)
- Céline Duval
- Centre Universitaire d'Ophtalmologie-Recherche, Axe Médecine Régénératrice, Hôpital du Saint-Sacrement, Centre de Recherche FRQS du CHU de Québec, Québec, Canada
| | - Karine Zaniolo
- Centre Universitaire d'Ophtalmologie-Recherche, Axe Médecine Régénératrice, Hôpital du Saint-Sacrement, Centre de Recherche FRQS du CHU de Québec, Québec, Canada
| | - Steeve Leclerc
- Centre Universitaire d'Ophtalmologie-Recherche, Axe Médecine Régénératrice, Hôpital du Saint-Sacrement, Centre de Recherche FRQS du CHU de Québec, Québec, Canada
| | - Christian Salesse
- Centre Universitaire d'Ophtalmologie-Recherche, Axe Médecine Régénératrice, Hôpital du Saint-Sacrement, Centre de Recherche FRQS du CHU de Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Sylvain L Guérin
- Centre Universitaire d'Ophtalmologie-Recherche, Axe Médecine Régénératrice, Hôpital du Saint-Sacrement, Centre de Recherche FRQS du CHU de Québec, Québec, Canada; Département d'Ophtalmologie, Faculté de Médecine, Université Laval, Québec, QC, Canada.
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11
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Mellas RE, Kim H, Osinski J, Sadibasic S, Gronostajski RM, Cho M, Baker OJ. NFIB regulates embryonic development of submandibular glands. J Dent Res 2014; 94:312-9. [PMID: 25403566 DOI: 10.1177/0022034514559129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
NFIB (nuclear factor I B) is a NFI transcription factor family member, which is essential for the development of a variety of organ systems. Salivary gland development occurs through several stages, including prebud, bud, pseudoglandular, canalicular, and terminal. Although many studies have been done to understand mouse submandibular gland (SMG) branching morphogenesis, little is known about SMG cell differentiation during the terminal stages. The goal of this study was to determine the role of NFIB during SMG development. We analyzed SMGs from wild-type and Nfib-deficient mice (Nfib (-/-)). At embryonic (E) day 18.5, SMGs from wild-type mice showed duct branching morphogenesis and differentiation of tubule ductal cells into tubule secretory cells. In contrast, SMGs from Nfib (-/-) mice at E18.5 failed to differentiate into tubule secretory cells while branching morphogenesis was unaffected. SMGs from wild-type mice at E16.5 displayed well-organized cuboidal inner terminal tubule cells. However, SMGs from Nfib (-/-) at E16.5 displayed disorganized inner terminal tubule cells. SMGs from wild-type mice at E18.5 became fully differentiated, as indicated by a high degree of apicobasal polarization (i.e., presence of apical ZO-1 and basolateral E-cadherin) and columnar shape. Furthermore, SMGs from wild-type mice at E18.5 expressed the protein SMGC, a marker for tubule secretory cells. However, SMGs from Nfib (-/-) mice at E18.5 showed apicobasal polarity, but they were disorganized and lost the ability to secrete SMGC. These findings indicate that the transcription factor NFIB is not required for branching morphogenesis but plays a key role in tubule cell differentiation during mouse SMG development.
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Affiliation(s)
- R E Mellas
- School of Dentistry University of Utah, Salt Lake City, UT, USA
| | - H Kim
- Department of Restorative Dentistry, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - J Osinski
- Department of Biochemistry, Developmental Genomics Group, Center of Excellence in Bioinformatics and Life Science, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - S Sadibasic
- Department of Restorative Dentistry, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - R M Gronostajski
- Department of Biochemistry, Developmental Genomics Group, Center of Excellence in Bioinformatics and Life Science, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - M Cho
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - O J Baker
- School of Dentistry University of Utah, Salt Lake City, UT, USA
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12
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Hu YW, Zhao JY, Li SF, Huang JL, Qiu YR, Ma X, Wu SG, Chen ZP, Hu YR, Yang JY, Wang YC, Gao JJ, Sha YH, Zheng L, Wang Q. RP5-833A20.1/miR-382-5p/NFIA-dependent signal transduction pathway contributes to the regulation of cholesterol homeostasis and inflammatory reaction. Arterioscler Thromb Vasc Biol 2014; 35:87-101. [PMID: 25265644 DOI: 10.1161/atvbaha.114.304296] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Cardiovascular disease caused by atherosclerosis is the number one cause of death in Western countries and threatens to become the major cause of morbidity and mortality worldwide. Long noncoding RNAs are emerging as new players in gene regulation, but how long noncoding RNAs operate in the development of atherosclerosis remains unclear. APPROACH AND RESULTS Using microarray analysis, we found that long noncoding RNA RP5-833A20.1 expression was upregulated, whereas nuclear factor IA (NFIA) expression was downregulated in human acute monocytic leukemia macrophage-derived foam cells. Moreover, we showed that long noncoding RNA RP5-833A20.1 may decreases NFIA expression by inducing hsa-miR-382-5p expression in vitro. We found that the RP5-833A20.1/hsa-miR-382-5p/NFIA pathway is essential to the regulation of cholesterol homeostasis and inflammatory responses in human acute monocytic leukemia macrophages. Lentivirus-mediated NFIA overexpression increased high-density lipoprotein cholesterol circulation, reduced low-density lipoprotein cholesterol, and very-low-density lipoprotein cholesterol circulation, decreased circulation of inflammatory cytokines, including interleukin-1β, interleukin-6, tumor necrosis factor-α, and C-reactive protein, enhanced reverse cholesterol transport, and promoted regression of atherosclerosis in apolipoprotein E-deficient mice. CONCLUSIONS Our findings indicated that the RP5-833A20.1/miR-382-5p/NFIA pathway was essential to the regulation of cholesterol homeostasis and inflammatory reactions and suggested that NFIA may represent a therapeutic target to ameliorate cardiovascular disease.
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Affiliation(s)
- Yan-Wei Hu
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Yi Zhao
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shu-Fen Li
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jin-Lan Huang
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu-Rong Qiu
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xin Ma
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shao-Guo Wu
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Ping Chen
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ya-Rong Hu
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jun-Yao Yang
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan-Chao Wang
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ji-Juan Gao
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan-Hua Sha
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lei Zheng
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Qian Wang
- From the Laboratory Medicine Center (Y.-W.H., J.-Y.Z., S.-F.L., J.-L.H., Y.-R.Q., S.-G.W., Z.-P.C., Y.-R.H., J.-Y.Y., Y.-C.W., J.-J.G., Y.-H.S., L.Z., Q.W.) and Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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Duval C, Gaudreault M, Vigneault F, Touzel-Deschênes L, Rochette PJ, Masson-Gadais B, Germain L, Guérin SL. Rescue of the transcription factors Sp1 and NFI in human skin keratinocytes through a feeder-layer-dependent suppression of the proteasome activity. J Mol Biol 2012; 418:281-99. [PMID: 22420942 DOI: 10.1016/j.jmb.2012.01.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/17/2012] [Accepted: 01/19/2012] [Indexed: 12/01/2022]
Abstract
Co-culturing human skin keratinocytes along with a feeder layer has proven to considerably improve their proliferative properties by delaying massive induction of terminal differentiation. Through a yet unclear mechanism, we recently reported that irradiated 3T3 (i3T3) fibroblasts used as a feeder layer increase the nuclear content of Sp1, a positive transcription factor (TF) that plays a critical role in many cellular functions including cell proliferation, into both adult skin keratinocytes and newborn skin keratinocytes. In this study, we examined the influence of i3T3 on the expression and DNA binding of NFI, another TF important for cell proliferation and cell cycle progression, and attempted to decipher the mechanism by which the feeder layer contributes at maintaining higher levels of these TFs in skin keratinocytes. Our results indicate that co-culturing both adult skin keratinocytes and newborn skin keratinocytes along with a feeder layer dramatically increases glycosylation of NFI and may prevent it from being degraded by the proteasome.
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Affiliation(s)
- Céline Duval
- LOEX/CUO-Recherche, Hôpital du Saint-Sacrement, Centre de Recherche du CHA, Québec, QC, Canada G1S4L8
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14
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Hsu YC, Osinski J, Campbell CE, Litwack ED, Wang D, Liu S, Bachurski CJ, Gronostajski RM. Mesenchymal nuclear factor I B regulates cell proliferation and epithelial differentiation during lung maturation. Dev Biol 2011; 354:242-52. [PMID: 21513708 DOI: 10.1016/j.ydbio.2011.04.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/04/2011] [Accepted: 04/06/2011] [Indexed: 01/01/2023]
Abstract
The Nuclear factor I (NFI) transcription factor family consists of four genes (Nfia, Nfib, Nfic and Nfix) that regulate the development of multiple organ systems in mice and humans. Nfib is expressed in both lung mesenchyme and epithelium and mice lacking Nfib have severe lung maturation defects and die at birth. Here we continue our analysis of the phenotype of Nfib⁻/⁻ lungs and show that Nfib specifically in lung mesenchyme controls late epithelial and mesenchymal cell proliferation and differentiation. There are more PCNA, BrdU, PHH3 and Ki67 positive cells in Nfib⁻/⁻ lungs than in wild type lungs at E18.5 and this increase in proliferation marker expression is seen in both epithelial and mesenchymal cells. The loss of Nfib in all lung cells decreases the expression of markers for alveolar epithelial cells (Aqp5 and Sftpc), Clara cells (Scgb1a1) and ciliated cells (Foxj1) in E18.5 lungs. To test for a specific role of Nfib in lung mesenchyme we generated and analyzed Nfib(flox/flox), Dermo1-Cre mice. Loss of Nfib only in mesenchyme results in decreased Aqp5, Sftpc and Foxj1 expression, increased cell proliferation, and a defect in sacculation similar to that seen in Nfib⁻/⁻ mice. In contrast, mesenchyme specific loss of Nfib had no effect on the expression of Scgb1a1 in the airway. Microarray and QPCR analyses indicate that the loss of Nfib in lung mesenchyme affects the expression of genes associated with extracellular matrix, cell adhesion and FGF signaling which could affect distal lung maturation. Our data indicate that mesenchymal Nfib regulates both mesenchymal and epithelial cell proliferation through multiple pathways and that mesenchymal NFI-B-mediated signals are essential for the maturation of distal lung epithelium.
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Affiliation(s)
- Yu-Chih Hsu
- Department of Biochemistry, Developmental Genomics Group, Center of Excellence in Bioinformatics and Life Science, State University of New York at Buffalo, 701 Ellicott St. Buffalo, NY 14203, USA
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15
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DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I. Proc Natl Acad Sci U S A 2009; 106:12049-54. [PMID: 19584245 DOI: 10.1073/pnas.0812894106] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The conserved nuclear factor I (NFI) family of transcription factors is unique to animals and essential for mammalian development. The Caenorhabditis elegans genome encodes a single NFI family member, whereas vertebrate genomes encode 4 distinct NFI protein subtypes (A, B, C, and X). NFI-1-deficient worms exhibit abnormalities, including reduced lifespan, defects in movement and pharyngeal pumping, and delayed egg-laying. To explore the functional basis of these phenotypes, we sought to comprehensively identify NFI-1-bound loci in C. elegans. We first established NFI-1 DNA-binding specificity using an in vitro DNA-selection strategy. Analysis yielded a consensus motif of TTGGCA(N)(3)TGCCAA, which occurs 586 times in the genome, a 100-fold higher frequency than expected. We next asked which sites were occupied by NFI-1 in vivo by performing chromatin immunoprecipitation of NFI-1 followed by microarray hybridization. Only 55 genomic locations were identified, an unexpectedly small target set. In vivo NFI-1 binding sites tend to be upstream of genes involved in core cellular processes, such as chromatin remodeling, mRNA splicing, and translation. Remarkably, 59 out of 70 (84%) of the C. briggsae orthologs of the identified targets contain conserved NFI binding sites in their promoters. These experiments provide a foundation for understanding how NFI-1 is recruited to unexpectedly few in vivo sites to perform its developmental functions, despite a vast over-representation of its binding motif.
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16
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Nuclear factor one transcription factors in CNS development. Mol Neurobiol 2009; 39:10-23. [PMID: 19058033 DOI: 10.1007/s12035-008-8048-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 11/12/2008] [Indexed: 01/22/2023]
Abstract
Transcription factors are key regulators of central nervous system (CNS) development and brain function. Research in this area has now uncovered a new key player-the nuclear factor one (NFI) gene family. It has been almost a decade since the phenotype of the null mouse mutant for the nuclear factor one A transcription factor was reported. Nfia null mice display a striking brain phenotype including agenesis of the corpus callosum and malformation of midline glial populations needed to guide axons of the corpus callosum across the midline of the developing brain. Besides NFIA, there are three other NFI family members in vertebrates: NFIB, NFIC, and NFIX. Since generation of the Nfia knockout (KO) mice, KO mice for all other family members have been generated, and defects in one or more organ systems have been identified for all four NFI family members (collectively referred to as NFI here). Like the Nfia KO mice, the Nfib and Nfix KO mice also display a brain phenotype, with the Nfib KO forebrain phenotype being remarkably similar to that of Nfia. Over the past few years, studies have highlighted NFI as a key payer in a variety of CNS processes including axonal outgrowth and guidance and glial and neuronal cell differentiation. Here, we discuss the importance and role of NFI in these processes in the context of several CNS systems including the neocortex, hippocampus, cerebellum, and spinal cord at both cellular and molecular levels.
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17
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Ho PS. Thermogenomics: thermodynamic-based approaches to genomic analyses of DNA structure. Methods 2008; 47:159-67. [PMID: 18848994 DOI: 10.1016/j.ymeth.2008.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 09/12/2008] [Indexed: 10/21/2022] Open
Abstract
The postgenomic era is all about learning about function by comparing genomic sequences within and between organisms. This review describes an approach that applies detailed thermodynamic information, as opposed to sequence motif searches, to analyze genomes (thermogenomics) for the occurrence of sequences with the potential to form left-handed Z-DNA and those that bind the eukaryotic nuclear factor I (NFI) transcriptional regulators. Such thermogenomic strategies allow us to address the questions of whether Z-DNA forming sequences can potentially function in regulating transcription of eukaryotic genes and how such function may emerge relative to other GC-rich elements, such as NFI recognition sites, to become a transcriptional coactivator.
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Affiliation(s)
- P Shing Ho
- Department of Biochemistry and Molecular Biology, 1870 Campus Delivery, 316 MRB Building, Colorado State University, Fort Collins, CO 80523-1870, USA.
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Campbell CE, Piper M, Plachez C, Yeh YT, Baizer JS, Osinski JM, Litwack ED, Richards LJ, Gronostajski RM. The transcription factor Nfix is essential for normal brain development. BMC DEVELOPMENTAL BIOLOGY 2008; 8:52. [PMID: 18477394 PMCID: PMC2414869 DOI: 10.1186/1471-213x-8-52] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 05/13/2008] [Indexed: 11/15/2022]
Abstract
Background The Nuclear Factor I (NFI) multi-gene family encodes site-specific transcription factors essential for the development of a number of organ systems. We showed previously that Nfia-deficient mice exhibit agenesis of the corpus callosum and other forebrain defects; Nfib-deficient mice have defects in lung maturation and show callosal agenesis and forebrain defects resembling those seen in Nfia-deficient animals, while Nfic-deficient mice have defects in tooth root formation. Recently the Nfix gene has been disrupted and these studies indicated that there were largely uncharacterized defects in brain and skeletal development in Nfix-deficient mice. Results Here we show that disruption of Nfix by Cre-recombinase mediated excision of the 2nd exon results in defects in brain development that differ from those seen in Nfia and Nfib KO mice. In particular, complete callosal agenesis is not seen in Nfix-/- mice but rather there appears to be an overabundance of aberrant Pax6- and doublecortin-positive cells in the lateral ventricles of Nfix-/- mice, increased brain weight, expansion of the cingulate cortex and entire brain along the dorsal ventral axis, and aberrant formation of the hippocampus. On standard lab chow Nfix-/- animals show a decreased growth rate from ~P8 to P14, lose weight from ~P14 to P22 and die at ~P22. If their food is supplemented with a soft dough chow from P10, Nfix-/- animals show a lag in weight gain from P8 to P20 but then increase their growth rate. A fraction of the animals survive to adulthood and are fertile. The weight loss correlates with delayed eye and ear canal opening and suggests a delay in the development of several epithelial structures in Nfix-/- animals. Conclusion These data show that Nfix is essential for normal brain development and may be required for neural stem cell homeostasis. The delays seen in eye and ear opening and the brain morphology defects appear independent of the nutritional deprivation, as rescue of perinatal lethality with soft dough does not eliminate these defects.
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Affiliation(s)
- Christine E Campbell
- Dept. of Biochemistry and New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 3435 Main St,, Buffalo, NY 14214, USA.
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Lin YL, Wang YH, Lee HJ. Transcriptional regulation of the human TR2 orphan receptor gene by nuclear factor 1-A. Biochem Biophys Res Commun 2006; 350:430-6. [PMID: 17010934 DOI: 10.1016/j.bbrc.2006.09.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 09/14/2006] [Indexed: 11/15/2022]
Abstract
The human testicular receptor 2 (TR2), a member of the nuclear hormone receptor superfamily, has no identified ligand yet. Previous evidence demonstrated that a 63bp DNA fragment, named the promoter activating cis-element (PACE), has been identified as a positive regulatory region in the 5' promoter region of the human TR2 gene. In the present report, the human nuclear factor 1-A (NF1-A) was identified as a transcriptional activator to recognize the center of the PACE, called the PACE-C. NF1-A could bind to the 18bp PACE-C region, and enhance about 13- to 17-fold of the luciferase reporter gene activity via the PACE-C in dose-dependent and orientation-independent manners. This transcriptional activation was further confirmed by real-time RT-PCR assay. In conclusion, our results indicated that NF1-A transcription factor plays an important role in the transcriptional activation of the TR2 gene expression via the PACE-C in the minimal promoter region.
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Affiliation(s)
- Yun-Lu Lin
- Department of Life Science, National Dong Hwa University, Hualien 97401, Taiwan
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Lazakovitch E, Kalb JM, Matsumoto R, Hirono K, Kohara Y, Gronostajski RM. nfi-I affects behavior and life-span in C. elegans but is not essential for DNA replication or survival. BMC DEVELOPMENTAL BIOLOGY 2005; 5:24. [PMID: 16242019 PMCID: PMC1277823 DOI: 10.1186/1471-213x-5-24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 10/20/2005] [Indexed: 11/10/2022]
Abstract
BACKGROUND The Nuclear Factor I (one) (NFI) family of transcription/replication factors plays essential roles in mammalian gene expression and development and in adenovirus DNA replication. Because of its role in viral DNA replication NFI has long been suspected to function in host DNA synthesis. Determining the requirement for NFI proteins in mammalian DNA replication is complicated by the presence of 4 NFI genes in mice and humans. Loss of individual NFI genes in mice cause defects in brain, lung and tooth development, but the presence of 4 homologous NFI genes raises the issue of redundant roles for NFI genes in DNA replication. No NFI genes are present in bacteria, fungi or plants. However single NFI genes are present in several simple animals including Drosophila and C. elegans, making it possible to test for a requirement for NFI in multicellular eukaryotic DNA replication and development. Here we assess the functions of the single nfi-1 gene in C. elegans. RESULTS C. elegans NFI protein (CeNFI) binds specifically to the same NFI-binding site recognized by vertebrate NFIs. nfi-1 encodes alternatively-spliced, maternally-inherited transcripts that are expressed at the single cell stage, during embryogenesis, and in adult muscles, neurons and gut cells. Worms lacking nfi-1 survive but have defects in movement, pharyngeal pumping and egg-laying and have a reduced life-span. Expression of the muscle gene Ce titin is decreased in nfi-1 mutant worms. CONCLUSION NFI gene function is not needed for survival in C. elegans and thus NFI is likely not essential for DNA replication in multi-cellular eukaryotes. The multiple defects in motility, egg-laying, pharyngeal pumping, and reduced lifespan indicate that NFI is important for these processes. Reduction in Ce titin expression could affect muscle function in multiple tissues. The phenotype of nfi-1 null worms indicates that NFI functions in multiple developmental and behavioral systems in C. elegans, likely regulating genes that function in motility, egg-laying, pharyngeal pumping and lifespan maintenance.
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Affiliation(s)
- Elena Lazakovitch
- Dept. of Biochemistry, SUNY at Buffalo, 140 Farber Hall, 3435 Main St., Buffalo, NY, 14214, USA
| | - John M Kalb
- Dept. of Biology, Canisius College, Buffalo, NY, USA
| | - Reiko Matsumoto
- Dept. of Biochemistry, SUNY at Buffalo, 140 Farber Hall, 3435 Main St., Buffalo, NY, 14214, USA
| | - Keiko Hirono
- CREST and Gene Network Lab, National Institute of Genetics, Mishima, Japan
| | - Yuji Kohara
- CREST and Gene Network Lab, National Institute of Genetics, Mishima, Japan
| | - Richard M Gronostajski
- Dept. of Biochemistry, SUNY at Buffalo, 140 Farber Hall, 3435 Main St., Buffalo, NY, 14214, USA
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Steele-Perkins G, Plachez C, Butz KG, Yang G, Bachurski CJ, Kinsman SL, Litwack ED, Richards LJ, Gronostajski RM. The transcription factor gene Nfib is essential for both lung maturation and brain development. Mol Cell Biol 2005; 25:685-98. [PMID: 15632069 PMCID: PMC543431 DOI: 10.1128/mcb.25.2.685-698.2005] [Citation(s) in RCA: 228] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phylogenetically conserved nuclear factor I (NFI) gene family encodes site-specific transcription factors essential for the development of a number of organ systems. We showed previously that Nfia-deficient mice exhibit agenesis of the corpus callosum and other forebrain defects, whereas Nfic-deficient mice have agenesis of molar tooth roots and severe incisor defects. Here we show that Nfib-deficient mice possess unique defects in lung maturation and exhibit callosal agenesis and forebrain defects that are similar to, but more severe than, those seen in Nfia-deficient animals. In addition, loss of Nfib results in defects in basilar pons formation and hippocampus development that are not seen in Nfia-deficient mice. Heterozygous Nfib-deficient animals also exhibit callosal agenesis and delayed lung maturation, indicating haploinsufficiency at the Nfib locus. The similarity in brain defects in Nfia- and Nfib-deficient animals suggests that these two genes may cooperate in late fetal forebrain development, while Nfib is essential for late fetal lung maturation and development of the pons.
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Affiliation(s)
- George Steele-Perkins
- State University of New York at Buffalo, Dept. of Biochemistry, 140 Farber Hall, 3435 Main St., Buffalo, NY 14214-3000, USA
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Elemento O, Tavazoie S. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol 2005; 6:R18. [PMID: 15693947 PMCID: PMC551538 DOI: 10.1186/gb-2005-6-2-r18] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Revised: 10/29/2004] [Accepted: 12/03/2004] [Indexed: 11/10/2022] Open
Abstract
We describe a powerful new approach for discovering globally conserved regulatory elements between two genomes. The method is fast, simple and comprehensive, without requiring alignments. Its application to pairs of yeasts, worms, flies and mammals yields a large number of known and novel putative regulatory elements. Many of these are validated by independent biological observations, have spatial and/or orientation biases, are co-conserved with other elements and show surprising conservation across large phylogenetic distances.
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Affiliation(s)
- Olivier Elemento
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Saeed Tavazoie
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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Stefancsik R, Sarkar S. Relationship between the DNA binding domains of SMAD and NFI/CTF transcription factors defines a new superfamily of genes. ACTA ACUST UNITED AC 2004; 14:233-9. [PMID: 14631647 DOI: 10.1080/1085566031000141126] [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: 10/27/2022]
Abstract
Transcription factors of the SMAD family relay signals from cell surface receptors to the nucleus in response to TGF-beta related soluble factors. Members of the nuclear factor I/CAAT box binding family (NFI/CTF) have been implicated as regulators of diverse biological processes such as adenovirus replication and transcription of TGF-responsive genes. There are highly conserved DNA binding domains in SMAD and NFI/CTF transcription factors that allow sequence specific DNA binding for members of each family. However, no homology relationship has been established for the DNA binding domains present in these families. For a better understanding of the structure and evolution of SMAD genes, we carried out a sensitive PSI-BLAST database search. This revealed significant similarities between the DNA binding domains of SMADs and NFI/CTF transcription factors. Enhanced graphic matrix analysis and multiple sequence alignment of the amino acid sequences of the SMAD and NFI/CTF DNA binding domains also show that these two classes of domains share considerable structural similarity. These results strongly suggest that these two classes of factors share a homologous DNA binding domain presumably resulting from a common ancestry. In contrast, the C-terminal transcription modulation domains of both SMAD and NFI/CTF families do not show any sequence similarity. Based on the structural relationship of their DNA binding domains, we propose that the SMAD and NFI/CTF transcription factors belong to new superfamily of genes.
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Affiliation(s)
- Raymund Stefancsik
- Department of Anatomy and Cellular Biology, Graduate Program in Cell, Molecular and Developmental Biology, Sackler School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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Yeung LHY, Read JT, Sorenson P, Nelson CC, Jia W, Rennie PS. Identification and characterization of a prostate-specific androgen-independent protein-binding site in the probasin promoter. Biochem J 2003; 371:843-55. [PMID: 12540291 PMCID: PMC1223328 DOI: 10.1042/bj20021816] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2002] [Revised: 01/22/2003] [Accepted: 01/23/2003] [Indexed: 01/03/2023]
Abstract
In this study we investigated the combination of transcription factors and proteins binding to the proximal part of the prostate-specific probasin (PB) promoter. Using DNaseI in vitro footprinting, several protected regions were identified on the proximal PB promoter (nucleotides -286 to +28 relative to the transcription start site) when nuclear extracts from LNCaP, a human prostate cancer cell line, were used. Four of the protected areas were observed only when LNCaP nuclear extracts treated with synthetic androgen (10 nM R1881) were used. Two other regions, referred to as FPI and FPII, showed protection regardless of the presence or absence of androgen. When DNaseI footprinting was done using other prostate and non-prostate nuclear extracts, protection of the FPII region was only seen in prostate cell lines. These androgen-independent regions were further tested for tissue and binding specificity using the electrophoretic mobility-shift assay. Eight complexes formed with the FPI probe while four complexes were observed with the FPII probe on incubation with the tested nuclear extracts. Methylation protection assays reveal that prostate cancer cell lines yield slightly different protection patterns for some of the protein complexes formed with non-prostate-derived cell lines, suggesting the presence of prostate-enriched or -exclusive proteins. Site-directed mutagenesis of the protected nucleotides within FPII resulted in a significant reduction in expression from the PB promoter. Identification of proteins binding to the FPII region revealed the participation of nuclear factor I (NF-I) or a closely related protein, although other unknown proteins are also involved. Defining the DNA and protein components that dictate prostate-specific expression of the PB promoter in an androgen-independent manner would provide a strong basis for the design and development of a gene therapy for systemic treatment of androgen-independent prostate cancer.
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Affiliation(s)
- Lillian H Y Yeung
- Department of Pathology and Laboratory Medicine, University of British Columbia, and The Prostate Centre, Vancouver General Hospital, Canada.
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Kido K, Bannert H, Gronostajski RM, Flügel RM. Bel1-mediated transactivation of the spumaretroviral internal promoter is repressed by nuclear factor I. J Biol Chem 2003; 278:11836-42. [PMID: 12446690 DOI: 10.1074/jbc.m208963200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gene expression of the internal and long terminal repeat promoters of the spuma retrovirus is specifically activated by the transactivator Bel1, the key regulator of viral gene expression. Bel1 directly binds to and activates DNA target sites of viral promoters and those of distinct cellular genes. To determine the contribution of cellular transcription factors to viral transactivation, the viral internal promoter (IP) was analyzed by transient expression, electrophoretic mobility shift assays), and supershifts. Here we report that Bel1-mediated transactivation of the full-length and shortened versions of the Bel1 response element (BRE) were repressed by nuclear factor I (NFI). Electrophoretic mobility shift assays using nuclear extracts from transfected 293T cells revealed that different DNA-protein complexes consisting of DNA target sites of NFI and Bel1 proteins were formed. The specificity of the repressor and transactivator DNA binding was shown by NFI- and Bel1-specific antibodies that led to supershifts of the different nuclear protein-oligodeoxynucleotide complexes. The specificity of the complexes was confirmed by using unlabeled, shortened, and mutated IP.BRE oligodeoxynucleotides in competition experiments with the authentic IP.BRE. Cotransfection of the infectious spumavirus DNA genome with a human NFI-X1 expression plasmid into cell cultures greatly reduced the expression of viral structural and Bel1 proteins. These data demonstrate the relevance of NFI-mediated repression of Bel1-driven transactivation in vivo.
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Affiliation(s)
- Kenji Kido
- Division of Retroviral Gene Expression, Research Program Applied Tumor Virology German Cancer Research Center, Im Neuenheimer Feld 242, 69009 Heidelberg, Germany
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Sheeter D, Du P, Rought S, Richman D, Corbeil J. Surface CD4 expression modulated by a cellular factor induced by HIV type 1 infection. AIDS Res Hum Retroviruses 2003; 19:117-23. [PMID: 12639247 DOI: 10.1089/088922203762688621] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) alters gene expression in infected cells, leading to cellular dysfunction. We uncovered a number of host cell genes that are modulated in both CD4(+) T cell lines and primary CD4(+) T lymphocytes infected with HIV-1, using high-density oligonucleotide probe microarray technology. We focused on one gene in particular, nuclear factor I-B2 (NFI-B2), because of its high level of expression. NFI-B2 is a member of the nuclear factor I family of nuclear proteins, which are known to be involved in viral and cellular transcription. To better understand the role of NFI-B2 during HIV-1 infection, we generated a Jurkat T cell line that constitutively expressed NFI-B2. After infection with HIV-1, these cells produced fewer viruses because of a downregulation of surface CD4 expression. The surface expression of the coreceptor, CXCR4, remained unchanged. Furthermore, levels of CD4 mRNA were reduced in NFI-B2-producing cells, suggesting that expression of NFI-B2 impairs CD4 transcription. Modulation of NFI-B2 by HIV-1 may represent yet another mechanism by which HIV infection reduces cell surface expression of CD4.
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Affiliation(s)
- Dennis Sheeter
- Department of Medicine, University of California San Diego, La Jolla, California 92093-0679, USA
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27
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Zambotti A, Makhluf H, Shen J, Ducy P. Characterization of an osteoblast-specific enhancer element in the CBFA1 gene. J Biol Chem 2002; 277:41497-506. [PMID: 12186862 DOI: 10.1074/jbc.m204271200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cbfa1 is a critical regulator of cell differentiation expressed only in the osteochondrogenic lineage. To define the molecular basis of this cell-specific expression we analyzed the murine Cbfa1 promoter. Here we show that the first 976 bp of this promoter are specifically active in osteoblastic cells. Within this region DNase I footprinting delineated a 40-bp area (CE1) protected differently by nuclear extracts from osteoblastic cells and from non-osteoblastic cells. When multimerized, CE1 conferred an osteoblast-specific activity to a heterologous promoter in DNA transfection experiments; this enhancing ability was conserved between mouse, rat, and human CE1 present in the respective Cbfa1 promoters. CE1 site-specific mutagenesis determined that it binds NF1- and AP1-like activities. Further analyses revealed that the NF1 site acts as a repressor in non-osteoblastic cells due to the binding of NF1-A, a NF1 isoform not expressed in osteoblastic cells. In contrast, the AP1 site mediates an osteoblast-specific activation caused by the preferential binding of FosB to CE1 in osteoblastic cells. In summary, this study identified an osteoblast-specific enhancer in the Cbfa1 promoter whose activity is achieved by the combination of an inhibitory and an activatory mechanism.
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Affiliation(s)
- Adriana Zambotti
- Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, Texas 77030, USA
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28
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Kane R, Murtagh J, Finlay D, Marti A, Jaggi R, Blatchford D, Wilde C, Martin F. Transcription factor NFIC undergoes N-glycosylation during early mammary gland involution. J Biol Chem 2002; 277:25893-903. [PMID: 11991954 DOI: 10.1074/jbc.m202469200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of a 74-kDa nuclear factor I (NFI) protein is triggered in early involution in the mouse mammary gland, and its expression correlates with enhanced occupation of a twin (NFI) binding element in the clusterin promoter, a gene whose transcription is induced at this time (Furlong, E. E., Keon, N. K., Thornton, F. D., Rein, T., and Martin, F. (1996) J. Biol. Chem. 271, 29688-29697). We now identify this 74-kDa NFI as an NFIC isoform based on its interaction in Western analysis with two NFIC-specific antibodies. A transition from the expression of a 49-kDa NFIC in lactation to the expression of the 74-kDa NFIC in early involution is demonstrated. We show that the 74-kDa NFIC binds specifically to concanavalin A (ConA) and that this binding can be reversed by the specific ConA ligands, methyl alpha-D-mannopyranoside and methyl alpha-D-glucopyranoside. In addition, its apparent molecular size was reduced to approximately 63 kDa by treatment with the peptide N-glycosidase. The 49-kDa lactation-associated NFIC did not bind ConA nor was it affected by peptide N-glycosidase. Tunicamycin, a specific inhibitor of N-glycosylation, blocked formation of the 74-kDa NFI in involuting mouse mammary gland in vivo when delivered from implanted Elvax depot pellets. Finally, the production of the ConA binding activity could be reiterated in "mammospheres" formed from primary mouse mammary epithelial cells associated with a laminin-rich extracellular matrix. Synthesis of the 74-kDa NFIC was also inhibited in this setting by tunicamycin. Thus, involution triggers the production of an NFIC isoform that is post-translationally modified by N-glycosylation. We further show, by using quantitative competitive reverse transcriptase-PCR, that there is increased expression of the major mouse mammary NFIC mRNA transcript, mNFIC2, in early involution, suggesting that the involution-associated change in NFIC expression also has a transcriptional contribution.
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Affiliation(s)
- Rosemary Kane
- Conway Institute of Biomolecular and Biomedical Research and Department of Pharmacology, University College Dublin, Belfield, Dublin 4, Ireland
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29
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Monaco MC, Sabath BF, Durham LC, Major EO. JC virus multiplication in human hematopoietic progenitor cells requires the NF-1 class D transcription factor. J Virol 2001; 75:9687-95. [PMID: 11559801 PMCID: PMC114540 DOI: 10.1128/jvi.75.20.9687-9695.2001] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
JCV, a small DNA virus of the polyomavirus family, has been shown to infect glial cells of the central nervous system, hematopoietic progenitor cells, and immune system lymphocytes. A family of DNA binding proteins called nuclear factor-1 (NF-1) has been linked with site-coding specific transcription of cellular and viral genes and replication of some viruses, including JC virus (JCV). It is unclear which NF-1 gene product must be expressed by cells to promote JCV multiplication. Previously, it was shown that elevated levels of NF-1 class D mRNA were expressed by human brain cells that are highly susceptible to JCV infection but not by JCV nonpermissive HeLa cells. Recently, we reported that CD34(+) precursor cells of the KG-1 line, when treated with the phorbol ester phorbol 12-myristate 13-acetate (PMA), differentiated to cells with macrophage-like characteristics and lost susceptibility to JCV infection. These studies have now been extended by asking whether loss of JCV susceptibility by PMA-treated KG-1 cells is linked with alterations in levels of NF-1 class D expression. Using reverse transcription-PCR, we have found that PMA-treated KG-1 cells express mRNA that codes for all four classes of NF-1 proteins, although different levels of RNA expression were observed in the hematopoietic cells differentiated into macrophages. Northern hybridization confirms that the expression of NF-1 class D gene is lower in JCV nonpermissive PMA-treated KG-1 cells compared with non-PMA-treated cells. Further, using gel mobility shift assays, we were able to show the induction of specific NF-1-DNA complexes in KG-1 cells undergoing PMA treatment. The binding increases in direct relation to the duration of PMA treatment. These results suggest that the binding pattern of NF-1 class members may change in hematopoietic precursor cells, such as KG-1, as they undergo differentiation to macrophage-like cells. Transfection of PMA-treated KG-1 cells with an NF-1 class D expression vector restored the susceptibility of these cells to JCV infection, while the transfection of PMA-treated KG-1 cells with NF-1 class A, B, and C vectors was not able to restore JCV susceptibility. These data collectively suggest that selective expression of NF-1 class D has a regulatory role in JCV multiplication.
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Affiliation(s)
- M C Monaco
- Laboratory of Molecular Medicine and Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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30
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Norquay LD, Jin Y, Surabhi RM, Gietz RD, Tanese N, Cattini PA. A member of the nuclear factor-1 family is involved in the pituitary repression of the human placental growth hormone genes. Biochem J 2001; 354:387-95. [PMID: 11171118 PMCID: PMC1221667 DOI: 10.1042/0264-6021:3540387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The human growth hormone (GH) gene family consists of five tandemly arranged and highly related genes, including the chorionic somatomammotropins (CSs), at a single locus on chromosome 17. Despite striking homologies in promoter and flanking DNA sequences, the genes within this locus have different tissue-specific patterns of expression: GH-N is expressed almost exclusively in the somatotrophs of the anterior pituitary; the remaining genes, including CS-A, are expressed in placental syncytiotrophoblast. Previously we proposed that active repression of the placental gene promoters in pituitary GC cells is mediated by upstream 'P' sequences and, specifically, a 263 bp region containing two 'P' sequence elements (PSE-A and PSE-B) and corresponding factors (PSF-A and PSF-B). We have now examined the possibility that PSF-A and PSF-B are members of the nuclear factor (NF)-1 family. Transcripts of NF-1A, NF-1C and NF-1X, but not of NF-1B, were readily detected in GC cells. High-affinity binding of NF-1 to PSE-B, but not to PSE-A, was confirmed by competition of DNA-protein interactions by using NF-1 DNA elements and antibodies. Functionally, a NF-1 element was able to substitute for PSE-B as a promoter-specific repressor in GC cells after gene transfer. However, there was a difference in the magnitude of repression exerted by the NF-1 and PSF-B elements on the CS-A promoter and, with the use of mutations, this difference was shown to be consistent with variations in NF-1-binding sequences. These results indicate that PSF-B, but not PSF-A, is a member of the NF-1 family, which participates in the PSF complex and in the repression of the CS-A promoter in pituitary GC cells.
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Affiliation(s)
- L D Norquay
- Gene Technology Group and Department of Physiology, University of Manitoba, 730 William Avenue, Winnipeg, Manitoba, Canada R3E 3J7
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31
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Nakazato M, Chung HK, Ulianich L, Grassadonia A, Suzuki K, Kohn LD. Thyroglobulin repression of thyroid transcription factor 1 (TTF-1) gene expression is mediated by decreased DNA binding of nuclear factor I proteins which control constitutive TTF-1 expression. Mol Cell Biol 2000; 20:8499-512. [PMID: 11046146 PMCID: PMC102156 DOI: 10.1128/mcb.20.22.8499-8512.2000] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Follicular thyroglobulin (TG) selectively suppresses the expression of thyroid-restricted transcription factors, thereby altering the expression of thyroid-specific proteins. In this study, we investigated the molecular mechanism by which TG suppresses the prototypic thyroid-restricted transcription factor, thyroid transcription factor 1 (TTF-1), in rat FRTL-5 thyrocytes. We show that the region between bp -264 and -153 on the TTF-1 promoter contains two nuclear factor I (NFI) elements whose function is involved in TG-mediated suppression. Thus, NFI binding to these elements is critical for constitutive expression of TTF-1; TG decreases NFI binding to the NFI elements in association with TG repression. NFI is a family of transcription factors that is ubiquitously expressed and contributes to constitutive and cell-specific gene expression. In contrast to the contribution of NFI proteins to constitutive gene expression in other systems, we demonstrate that follicular TG transcriptionally represses all NFI RNAs (NFI-A, -B, -C, and -X) in association with decreased NFI binding and that the RNA levels decrease as early as 4 h after TG treatment. Although TG treatment for 48 h results in a decrease in NFI protein-DNA complexes measured in DNA mobility shift assays, NFI proteins are still detectable by Western analysis. We show, however, that the binding of all NFI proteins is redox regulated. Thus, diamide treatment of nuclear extracts strongly reduces the binding of NFI proteins, and the addition of higher concentrations of dithiothreitol to nuclear extracts from TG-treated cells restores NFI-DNA binding to levels in extracts from untreated cells. We conclude that NFI binding to two NFI elements, at bp -264 to -153, positively regulates TTF-1 expression and controls constitutive TTF-1 levels. TG mediates the repression of TTF-1 gene expression by decreasing NFI RNA and protein levels, as well as by altering the binding activity of NFI, which is redox controlled.
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Affiliation(s)
- M Nakazato
- Cell Regulation Section, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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32
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Abstract
The Nuclear Factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression. The classes of genes whose expression is modulated by NFI include those that are ubiquitously expressed, as well as those that are hormonally, nutritionally, and developmentally regulated. The NFI family is composed of four members in vertebrates (NFI-A, NFI-B, NFI-C and NFI-X), and the four NFI genes are expressed in unique, but overlapping, patterns during mouse embryogenesis and in the adult. Transcripts of each NFI gene are differentially spliced, yielding as many as nine distinct proteins from a single gene. Products of the four NFI genes differ in their abilities to either activate or repress transcription, likely through fundamentally different mechanisms. Here, we will review the properties of the NFI genes and proteins and their known functions in gene expression and development.
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Affiliation(s)
- R M Gronostajski
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Case Western Reserve University, OH 44195, USA.
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33
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Roulet E, Bucher P, Schneider R, Wingender E, Dusserre Y, Werner T, Mermod N. Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J Mol Biol 2000; 297:833-48. [PMID: 10736221 DOI: 10.1006/jmbi.2000.3614] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Accurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction tools, we have begun a systematic study of the sequence-specific DNA-binding of a transcription factor belonging to the CTF/NFI family. Using a systematic collection of rationally designed oligonucleotides combined with an in vitro DNA binding assay, we found that the sequence specificity of this protein cannot be represented by a simple consensus sequence or weight matrix. For instance, CTF/NFI uses a flexible DNA binding mode that allows for variations of the binding site length. From the experimental data, we derived a novel prediction method using a generalised profile as a binding site predictor. Experimental evaluation of the generalised profile indicated that it accurately predicts the binding affinity of the transcription factor to natural or synthetic DNA sequences. Furthermore, the in vitro measured binding affinities of a subset of oligonucleotides were found to correlate with their transcriptional activities in transfected cells. The combined computational-experimental approach exemplified in this work thus resulted in an accurate prediction method for CTF/NFI binding sites potentially functioning as regulatory regions in vivo.
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Affiliation(s)
- E Roulet
- Laboratory of Molecular Biotechnology, Centre for Biotechnology UNIL-EPFL and Institute of Animal Biology University of Lausanne, Lausanne, CH-1015, Switzerland
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34
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Edenberg HJ. Regulation of the mammalian alcohol dehydrogenase genes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2000; 64:295-341. [PMID: 10697413 DOI: 10.1016/s0079-6603(00)64008-4] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This review focuses on the regulation of the mammalian medium-chain alcohol dehydrogenase (ADH) genes. This family of genes encodes enzymes involved in the reversible oxidation of alcohols to aldehydes. Interest in these enzymes is increased because of their role in the metabolism of beverage alcohol as well as retinol, and their influence on the risk for alcoholism. There are six known classes ADH genes that evolved from a common ancestor. ADH genes differ in their patterns of expression: most are expressed in overlapping tissue-specific patterns, but class III ADH genes are expressed ubiquitously. All have proximal promoters with multiple cis-acting elements. These elements, and the transcription factors that can interact with them, are being defined. Subtle differences in sequence can affect affinity for these factors, and thereby influence the expression of the genes. This provides an interesting system in which to examine the evolution of tissue specificity. Among transcription factors that are important in multiple members of this gene family are the C/EBPs, Sp1,USF, and AP1, HNF-1, CTF/NF-1, glucocorticoid, and retinoic acid receptors, and several as-yet unidentified negative elements, are important in at least one of the genes. There is evidence that cis-acting elements located far from the proximal promoter are necessary for proper expression. Three of the genes have upstream AUGs in the 5' nontranslated regions of their mRNA, unusual for mammalian genes. The upstream AUGs have been shown to significantly affect expression of the human ADH5 gene.
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Affiliation(s)
- H J Edenberg
- Department of Biochemistry, Indiana University School of Medicine, Indianapolis 46202, USA
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35
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Bandyopadhyay SK, de La Motte CA, Williams BR. Induction of E-selectin expression by double-stranded RNA and TNF-alpha is attenuated in murine aortic endothelial cells derived from double-stranded RNA-activated kinase (PKR)-null mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 164:2077-83. [PMID: 10657661 DOI: 10.4049/jimmunol.164.4.2077] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The adherence of leukocytes on the endothelium is mediated in part by the transient expression of the E-selectin adhesion molecule. Because we have previously shown that the dsRNA-activated kinase PKR mediates dsRNA induction of NF-kappaB, we used murine aortic endothelial (MuAE) cells isolated from wild-type and PKR-null mice to investigate the role of PKR in the induction of E-selectin expression by dsRNA (pIC) and TNF-alpha. E-selectin mRNA and protein expression was inducible by both pIC and TNF-alpha in wild-type MuAE cells, whereas induction of E-selectin expression by these agents was defective in PKR-null MuAE cells. Induction of E-selectin promoter activity and NF-kappaB DNA binding activity were substantially reduced in pIC- or TNF-alpha-treated PKR-null cells, indicating a role for PKR in both pIC and TNF-alpha induction of E-selectin via an NF-kappaB-dependent pathway. In PKR-null cells, pIC-mediated degradation of IkappaBbeta is deficient. Activation of this pathway requires the PKR-dependent degradation of the IkappaBbeta protein. Moreover, both phosphorylated and unphosphorylated activating transcription factor 2 DNA-binding activities were reduced in PKR-null aortic endothelial cells. These results indicate that the PKR is required for full activation of E-selectin expression by pIC and TNF-alpha in primary mouse aortic endothelial cells identifying activating transcription factor 2 as a new target for PKR-dependent regulation and suggest a role for PKR in leukocyte adhesion.
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MESH Headings
- Animals
- Aorta
- Cells, Cultured
- Cyclic AMP Response Element-Binding Protein/antagonists & inhibitors
- Cyclic AMP Response Element-Binding Protein/genetics
- Cyclic AMP Response Element-Binding Protein/metabolism
- E-Selectin/biosynthesis
- E-Selectin/genetics
- E-Selectin/metabolism
- Endothelium, Vascular/cytology
- Endothelium, Vascular/enzymology
- Endothelium, Vascular/metabolism
- Enzyme Activation/immunology
- Enzyme Induction/drug effects
- Enzyme Induction/genetics
- Enzyme Induction/immunology
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/immunology
- Luciferases/biosynthesis
- Luciferases/genetics
- Macromolecular Substances
- Mice
- Mice, Knockout
- Promoter Regions, Genetic/drug effects
- Promoter Regions, Genetic/immunology
- Protein Binding/drug effects
- Protein Binding/immunology
- RNA, Double-Stranded/pharmacology
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/biosynthesis
- Tumor Necrosis Factor-alpha/pharmacology
- eIF-2 Kinase/deficiency
- eIF-2 Kinase/genetics
- eIF-2 Kinase/physiology
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Affiliation(s)
- S K Bandyopadhyay
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA.
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36
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das Neves L, Duchala CS, Tolentino-Silva F, Haxhiu MA, Colmenares C, Macklin WB, Campbell CE, Butz KG, Gronostajski RM, Godinho F. Disruption of the murine nuclear factor I-A gene (Nfia) results in perinatal lethality, hydrocephalus, and agenesis of the corpus callosum. Proc Natl Acad Sci U S A 1999; 96:11946-51. [PMID: 10518556 PMCID: PMC18392 DOI: 10.1073/pnas.96.21.11946] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phylogenetically conserved nuclear factor I (NFI) family of transcription/replication proteins is essential both for adenoviral DNA replication and for the transcription of many cellular genes. We showed previously that the four murine NFI genes (Nfia, Nfib, Nfic, and Nfix) are expressed in unique but overlapping patterns during mouse development and in adult tissues. Here we show that disruption of the Nfia gene causes perinatal lethality, with >95% of homozygous Nfia(-/-) animals dying within 2 weeks after birth. Newborn Nfia(-/-) animals lack a corpus callosum and show ventricular dilation indicating early hydrocephalus. Rare surviving homozygous Nfia(-/-) mice lack a corpus callosum, show severe communicating hydrocephalus, a full-axial tremor indicative of neurological defects, male-sterility, low female fertility, but near normal life spans. These findings indicate that while the Nfia gene appears nonessential for cell viability and DNA replication in embryonic stem cells and fibroblasts, loss of Nfia function causes severe developmental defects. This finding of an NFI gene required for a developmental process suggests that the four NFI genes may have distinct roles in vertebrate development.
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Affiliation(s)
- L das Neves
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland OH 44195, USA
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37
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Park GT, Morasso MI. Regulation of the Dlx3 homeobox gene upon differentiation of mouse keratinocytes. J Biol Chem 1999; 274:26599-608. [PMID: 10473625 PMCID: PMC1317293 DOI: 10.1074/jbc.274.37.26599] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Distal-less Dlx3 homeodomain gene is expressed in terminally differentiated murine epidermal cells, and there is evidence to support an essential role as a transcriptional regulator of the terminal differentiation process in these cells. In an attempt to determine the factors that induce Dlx3 gene expression, we have cloned the 1.2-kilobase pair proximal region of murine gene and analyzed its cis-regulatory elements and potential trans-acting factors. The proximal region of the Dlx3 gene has a canonical TATA box and CCAAT box, and the transcription start site was located 205 base pairs upstream from the initiation of translation site. Serial deletion analysis showed that the region between -84 and -34 confers the maximal promoter activity both in undifferentiated and differentiated primary mouse keratinocytes. Gel retardation assays and mutational analysis demonstrated that the transcriptional regulator NF-Y (also referred to as CBF) binds to a CCAAT box motif within this region and is responsible for the majority of the Dlx3 promoter activity. In addition, an Sp1-binding site was located immediately upstream of transcription start site that acts as a positive regulatory element of the Dlx3 promoter, independent of the CCAAT box motif. Importantly, elements residing between +30 to +60 of the Dlx3 gene are responsible for the Ca(2+)-dependent induction of Dlx3 during keratinocyte differentiation.
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Affiliation(s)
- Geon Tae Park
- From the Laboratory of Skin Biology, NIAMS, National Institutes of Health, Bethesda, Maryland 20892
| | - Maria I. Morasso
- From the Laboratory of Skin Biology, NIAMS, National Institutes of Health, Bethesda, Maryland 20892
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38
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de Jong RN, van der Vliet PC. Mechanism of DNA replication in eukaryotic cells: cellular host factors stimulating adenovirus DNA replication. Gene 1999; 236:1-12. [PMID: 10433960 DOI: 10.1016/s0378-1119(99)00249-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Replication of adenovirus (Ad) DNA depends on interactions between three viral and three cellular proteins. Human transcription factors NFI and Oct-1 recruit the Ad DNA polymerase to the origin of DNA replication as a complex with the Ad protein primer pTP. High affinity and specificity DNA binding to recognition sites in this origin by the transcription factors stimulate and stabilize pre-initiation complex formation to compensate for the low binding specificity of the pTP/pol complex. In this review, we discuss the properties of NFI and Oct-1 and the mechanism by which they enhance initiation of DNA replication. We propose a model that describes the dynamics of initiation and elongation as well as the assembly and disassembly of the pre-initiation complex.
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Affiliation(s)
- R N de Jong
- Laboratory for Physiological Chemistry and Centre for Biomedical Genetics, Utrecht University, Utrecht, The Netherlands
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39
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de Parseval A, Elder JH. Demonstration that orf2 encodes the feline immunodeficiency virus transactivating (Tat) protein and characterization of a unique gene product with partial rev activity. J Virol 1999; 73:608-17. [PMID: 9847366 PMCID: PMC103867 DOI: 10.1128/jvi.73.1.608-617.1999] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The long PCR technique was used to amplify the three size classes of viral mRNAs produced in cells infected by feline immunodeficiency virus (FIV). We identified in the env region a new splice acceptor site that generated two transcripts, each coding for an 11-kDa protein, p11(rev), whose function is unknown. The small-size class of mRNAs included two bicistronic orf2/rev mRNAs and two rev-like mRNAs, consisting only of the second exon of rev and coding for a 15-kDa protein, p15(rev). p15(rev) contained the minimal effector domain of Rev and was sufficient to mediate partial Rev activity. The bicistronic mRNAs encoded two distinct proteins, one of 23 kDa corresponding to Rev and a 9-kDa protein encoded by the orf2 gene. The orf2 gene product is a protein of 79 amino acids with characteristics similar to those of the Tat (transactivator) proteins of the ungulate lentiviruses. Transient expression assays, using the FIV long terminal repeat (LTR) to drive transcription of the bacterial gene for chloramphenicol acetyltransferase demonstrated that the orf2 gene transactivates gene expression an average of 14- to 20-fold above the basal level. Deletion mutants of the FIV LTR were generated to locate sequences responsive to transactivation mediated by the orf2 gene. A 5' deletion mutant that removed the AP1 site resulted in residual low-level transactivation by orf2. Further experiments using LTR mutants with internal deletions identified three regions located between positions -126 and -47 relative to the cap site that were important for orf2-directed transactivation. These regions include the AP1 site, a C/EBP tandem repeat, and an ATF site.
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Affiliation(s)
- A de Parseval
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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40
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Jump DB, Badin MV, Thelen A. The CCAAT box binding factor, NF-Y, is required for thyroid hormone regulation of rat liver S14 gene transcription. J Biol Chem 1997; 272:27778-86. [PMID: 9346922 DOI: 10.1074/jbc.272.44.27778] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Triiodothyronine (T3) activates rat liver S14 gene transcription through T3 receptors (TRbeta) binding distal thyroid hormone response elements located between -2.8 and -2.5 kilobase pairs upstream from the transcription start site. Previous studies suggested that proximal promoter elements located between -220 to -80 base pairs upstream from the 5' end of the S14 gene were involved in hormone activation of the S14 gene. This report identifies an inverted CCAAT box (or Y box) at -104ATTGG-100 as a core cis-regulatory element. Gel shift studies using rat liver nuclear proteins show that at least three CCAAT-binding factors interact with this region as follows: NF-Y and c/EBP-related proteins formed major complexes, whereas NF-1/CTF forms a minor complex in gel shift assay. Mutation of the Y box indicated that loss of NF-Y binding, but not c/EBP or NF-1, correlated closely with a decline in basal activity and a loss of T3-mediated transactivation. Substitution of the S14 Y box in reporter genes with elements binding only NF-Y elevated basal activity and T3-mediated transactivation, whereas substitution with elements binding c/EBP-related proteins or SP1 displayed low basal activity and T3-mediated transactivation. These studies indicate that NF-Y and TRbeta functionally interact to confer T3 control to the S14 gene.
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Affiliation(s)
- D B Jump
- Department of Physiology, Michigan State University, East Lansing, Michigan 48824, USA.
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41
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Tarapore P, Richmond C, Zheng G, Cohen SB, Kelder B, Kopchick J, Kruse U, Sippel AE, Colmenares C, Stavnezer E. DNA binding and transcriptional activation by the Ski oncoprotein mediated by interaction with NFI. Nucleic Acids Res 1997; 25:3895-903. [PMID: 9380514 PMCID: PMC146989 DOI: 10.1093/nar/25.19.3895] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Ski oncoprotein has been found to bind non-specifically to DNA in association with unindentified nuclear factors. In addition, Ski has been shown to activate transcription of muscle-specific and viral promoters/enhancers. The present study was undertaken to identify Ski's DNA binding and transcriptional activation partners by identifying specific DNA binding sites. We used nuclear extracts from a v-Ski-transduced mouse L-cell line and selected Ski-bound sequences from a pool of degenerate oligonucleotides with anti-Ski monoclonal antibodies. Two sequences were identified by this technique. The first (TGGC/ANNNNNT/GCCAA) is the previously identified binding site of the nuclear factor I (NFI) family of transcription factors. The second (TCCCNNGGGA) is the binding site of Olf-1/EBF. By electophoretic mobility shift assays we find that Ski is a component of one or more NFI complexes but we fail to detect Ski in Olf-1/EBF complexes. We show that Ski binds NFI proteins and activates transcription of NFI reporters, but only in the presence of NFI. We also find that homodimerization of Ski is essential for co-activation with NFI. However, the C-terminal dimerization domain of c-Ski, which is missing in v-Ski, can be substituted by the leucine zipper domain of GCN4.
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Affiliation(s)
- P Tarapore
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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42
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Osada S, Daimon S, Nishihara T, Imagawa M. Identification of DNA binding-site preferences for nuclear factor I-A. FEBS Lett 1996; 390:44-6. [PMID: 8706826 DOI: 10.1016/0014-5793(96)00622-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nuclear factor I (NFI) proteins constitute a large family of DNA binding proteins. These proteins promote the initiation of adenovirus replication and regulate the transcription of viral and cellular genes. The binding sites for NFI have been reported in a wide variety of promoters, and they exhibit flexibility in their sequences. To clarify the DNA binding site of NFI-A, one of the NFI proteins, we performed a polymerase chain reaction-mediated random site selection, and determined the optimal sequence as 5'-TTGGCANNNN(G/T)CCA(G/A)-3'.
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Affiliation(s)
- S Osada
- Department of Environmental Biochemistry, Faculty of Pharmaceutical Sciences, Osaka University, Japan
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43
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Puzianowska-Kuznicka M, Shi YB. Nuclear factor I as a potential regulator during postembryonic organ development. J Biol Chem 1996; 271:6273-82. [PMID: 8626421 DOI: 10.1074/jbc.271.11.6273] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Nuclear factor I (NFI) family members are transcription factors that are believed to also participate in DNA replication. We have cloned two Xenopus laevis NFIs that are up-regulated by thyroid hormone. They are 84-95% identical to their counterparts in birds and mammals. In contrast, the two Xenopus NFIs are much less homologous to each other, sharing only 58% homology, which largely resides in the DNA binding domain at the amino terminus. However, both NFIs can bind to a consensus NFI binding site and activate the transcription of a promoter bearing the site. Northern blot reveals that both NFI genes are regulated in tissue- and developmental stage-dependent manners. They are first activated, independently of thyroid hormone, to low levels at stages 23/24, around the onset of larval organogenesis. After stage 54, their mRNA levels are dramatically upregulated by endogenous thyroid hormone, and high levels of their expression correlate with organ-specific metamorphosis. Furthermore, gel mobility shift assay indicates that the NFI proteins are present in different organs and that their levels are regulated similarly to the mRNA levels. These results strongly suggest that NFIs play important roles during postembryonic organ development, in contrast to the general belief that NFIs are ubiquitous factors.
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Affiliation(s)
- M Puzianowska-Kuznicka
- Laboratory of Molecular Embryology, NICHD, National Institutes of Health, Bethesda, Maryland 20892-5430, USA
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44
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Rein T, Förster R, Krause A, Winnacker EL, Zorbas H. Organization of the alpha-globin promoter and possible role of nuclear factor I in an alpha-globin-inducible and a noninducible cell line. J Biol Chem 1995; 270:19643-50. [PMID: 7642653 DOI: 10.1074/jbc.270.33.19643] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nuclear factor I (NFI) was suggested to be involved in the expression of the human alpha-globin gene. Two established cell lines, which express alpha-globin differentially, were therefore compared for differences in binding of NFI at the alpha-globin promoter in vivo. HeLa cells, in which alpha-globin is repressed, show a high density promoter occupation with several proteins associated with structurally distorted DNA. Cell line K562, which is inducible for alpha-globin, surprisingly was found to be heterogeneous consisting mainly of cells (approximately 95%) unable to express alpha-globin. However, the promoter of the nonexpressing K562 cells was clearly different from that of HeLa cells, being occupied only at basal transcriptional elements. Therefore, the alpha-globin gene in these K562 cells may not be truly repressed, but in an intermediate state between repression and active transcription. The NFI site of the alpha-globin promoter appeared occupied in HeLa but free of proteins in K562 cells. All cells of both cell lines produce NFI, but the composition and DNA binding affinity of NFI species differ significantly between the two cell lines. Therefore, distinct forms of NFI may repress alpha-globin transcription in HeLa cells. However, NFI is apparently not involved in establishing the latent transcriptional state of the majority of K562 cells.
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Affiliation(s)
- T Rein
- Institut für Biochemie, Ludwig-Maximilans-Universität München, Germany
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45
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Li S, Rosen JM. Nuclear factor I and mammary gland factor (STAT5) play a critical role in regulating rat whey acidic protein gene expression in transgenic mice. Mol Cell Biol 1995; 15:2063-70. [PMID: 7891701 PMCID: PMC230433 DOI: 10.1128/mcb.15.4.2063] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The rat whey acidic protein (WAP) gene contains a mammary gland-specific and hormonally regulated DNase I-hypersensitive site 830 to 720 bp 5' to the site of transcription initiation. We have reported previously that nuclear factor I (NFI) binding at a palindromic site and binding at a half-site are the major DNA-protein interactions detected within this tissue-specific nuclease-hypersensitive region. We now show that point mutations introduced into these NFI-binding sites dramatically affect WAP gene expression in transgenic mice. Transgene expression was totally abrogated when the palindromic NFI site or both binding sites were mutated, suggesting that NFI is a key regulator of WAP gene expression. In addition, a recognition site for mammary gland factor (STAT5), which mediates prolactin induction of milk protein gene expression, was also identified immediately proximal to the NFI-binding sites. Mutation of this site reduced transgene expression by approximately 90% per gene copy, but did not alter tissue specificity. These results suggest that regulation of WAP gene expression is determined by the cooperative interactions among several enhancers that constitute a composite response element.
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Affiliation(s)
- S Li
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030
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46
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Identification of a conserved oxidation-sensitive cysteine residue in the NFI family of DNA-binding proteins. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43973-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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47
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Bois-Joyeux B, Danan JL. Members of the CAAT/enhancer-binding protein, hepatocyte nuclear factor-1 and nuclear factor-1 families can differentially modulate the activities of the rat alpha-fetoprotein promoter and enhancer. Biochem J 1994; 301 ( Pt 1):49-55. [PMID: 7518671 PMCID: PMC1137141 DOI: 10.1042/bj3010049] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The promoter of the rat alpha-fetoprotein (AFP) gene, which makes the expression of the developmentally regulated AFP gene specific to the liver, is a putative target for transcription factors of the CAAT/enhancer-binding protein (C/EBP), hepatocyte nuclear factor-1 (HNF-1) and nuclear factor-1 (NF-1) families. We have evaluated the influence of these factors on the activity of the AFP promoter by transfection of HepG2 hepatoma cells with the appropriate expression vector plus a CAT plasmid under the control of the AFP promoter. A similar plasmid bearing the rat albumin promoter was used as a control. C/EBP alpha, C/EBP beta and D-binding protein (DBP) acted as trans-activators on the AFP promoter, whereas liver inhibitory protein (LIP), a truncated form of C/EBP beta, was a potent negative regulator of the promoter. C/EBP alpha also bound to and stimulated the activity of the AFP enhancer at -2.5 kb. Interestingly, HNF-1 beta was found to be more potent than HNF-1 alpha in activating the AFP promoter. This effect was specific, as it did not occur with the rat albumin promoter. HNF-1 beta, which is produced earlier than HNF-1 alpha during liver development, would thus have the greater influence on the AFP promoter in early development. Both HNF-1s allowed expression of the AFP promoter in cells of nonhepatic origin. Overexpression of NF-1 induced a specific decrease in the activity of the AFP promoter. This strongly suggests that competition between NF-1 and HNF-1 for binding to their overlapping binding sites on the AFP promoter is critical for modulating its activity. Thus changing combinations of these trans-acting factors may tightly modulate the AFP promoter activity in the course of liver development and carcinogenesis.
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Affiliation(s)
- B Bois-Joyeux
- Centre de Recherche sur l'Endocrinologie Moléculaire et le Développement, CNRS UPR 1511, Meudon, France
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Le HB, Vaisanen PA, Johnson JL, Raney AK, McLachlan A. Regulation of transcription from the human muscle phosphofructokinase P2 promoter by the Sp1 transcription factor. DNA Cell Biol 1994; 13:473-85. [PMID: 8024691 DOI: 10.1089/dna.1994.13.473] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The human muscle phosphofructokinase (HPFKM) p2 promoter contains sequence elements that are similar to the Sp1 transcription factor binding site consensus sequence. DNase I footprinting identified four regions of the HPFKM p2 promoter that bound purified Sp1. Gel retardation analysis using HeLa S3 nuclear extracts and purified Sp1 protein demonstrated that each of the four recognition elements bound the Sp1 transcription factor. The function of the HPFKM p2 promoter elements was examined in transient transfection assays using these binding sites cloned into a minimal promoter element. In Drosophila Schneider line-2 cells, each of these regulatory regions trans-activated transcription from a minimal promoter element in response to exogenously expressed Sp1. In addition, transcription from the HPFKM p2 promoter was shown to be trans-activated by exogenously expressed Sp1 in Drosophila Schneider line-2 cells. Deletion analysis of the HPFKM p2 promoter demonstrated that the promoter region between -66 and +16 was sufficient to confer sp1 responsiveness. This promoter region includes one of the regulatory elements footprinted by the purified Sp1 transcription factor and mediates the majority of the transcriptional activity from the HPFKM p2 promoter in the human cervical carcinoma cell line HeLa S3. This demonstrates that the HPFKM p2 promoter contains four functional Sp1 binding sites that may contribute to the level of transcription from this promoter in a variety of cell types.
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Affiliation(s)
- H B Le
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037
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49
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Li S, Rosen J. Distal regulatory elements required for rat whey acidic protein gene expression in transgenic mice. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)36779-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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50
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Transcription of the histone H5 gene is regulated by three differentiation-specific enhancers. Mol Cell Biol 1993. [PMID: 8336726 DOI: 10.1128/mcb.13.8.4904] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Histone H5, an early marker of the avian erythroid lineage, is expressed at low levels in early erythroid precursors and at higher levels in more mature cells. We show that the increase in H5 expression is due to transcriptional activation of the H5 gene following differentiation of precursor CFU(E). We have found and characterized two upstream enhancers, E1 (between -2233 and -1878 from the site of transcription initiation, +1) and E3 (between -1321 and -1163), and confirmed the presence of a downstream enhancer (C. D. Trainor, S. J. Stamler, and J. D. Engel, Nature [London] 328:827-830, 1987) E7 (between +846 and +1181) which are responsible for the increase in H5 gene transcription. The enhancers had a weak effect in nondifferentiated CFU(E) but a strong effect when the cells were induced to differentiate. Cooperation among the three enhancers, however, was not required for H5 gene activity in the differentiated cells. The enhancers contain binding sites for several ubiquitous and erythroid cell-specific nuclear proteins, including GATA-1, as demonstrated with GATA-1-specific antibodies. Although the GATA sites were required for enhancer function, the concentration of GATA-1, GATA-2, and GATA-3 decreased during cell differentiation, and overexpression of these factors had little effect on H5 transcription. Hence, the differentiation-specific effect of the enhancers is not mediated by changes in relative levels of the GATA factors. Functional analysis of the H5 promoter indicated that the requirement of several elements, including a GC box necessary for transcription enhancement, did not change during the early stages of CFU(E) differentiation. However, the UPE, a positive element in proliferating CFU(E) recognized by the transcription factor H4TF2, was dispensable in the differentiated cells. These results suggest that as the cells enter the final stages of differentiation, there is a reprogramming of the regulatory factors that control H5 transcription and that the enhancers rescue and increase the activity of the promoter.
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