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Dinh NTM, Nguyen TM, Park MK, Lee CH. Y-Box Binding Protein 1: Unraveling the Multifaceted Role in Cancer Development and Therapeutic Potential. Int J Mol Sci 2024; 25:717. [PMID: 38255791 PMCID: PMC10815159 DOI: 10.3390/ijms25020717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Y-box binding protein 1 (YBX1), a member of the Cold Shock Domain protein family, is overexpressed in various human cancers and is recognized as an oncogenic gene associated with poor prognosis. YBX1's functional diversity arises from its capacity to interact with a broad range of DNA and RNA molecules, implicating its involvement in diverse cellular processes. Independent investigations have unveiled specific facets of YBX1's contribution to cancer development. This comprehensive review elucidates YBX1's multifaceted role in cancer across cancer hallmarks, both in cancer cell itself and the tumor microenvironment. Based on this, we proposed YBX1 as a potential target for cancer treatment. Notably, ongoing clinical trials addressing YBX1 as a target in breast cancer and lung cancer have showcased its promise for cancer therapy. The ramp up in in vitro research on targeting YBX1 compounds also underscores its growing appeal. Moreover, the emerging role of YBX1 as a neural input is also proposed where the high level of YBX1 was strongly associated with nerve cancer and neurodegenerative diseases. This review also summarized the up-to-date advanced research on the involvement of YBX1 in pancreatic cancer.
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Affiliation(s)
- Ngoc Thi Minh Dinh
- College of Pharmacy, Dongguk University, Goyang 10326, Republic of Korea; (N.T.M.D.); (T.M.N.)
| | - Tuan Minh Nguyen
- College of Pharmacy, Dongguk University, Goyang 10326, Republic of Korea; (N.T.M.D.); (T.M.N.)
| | - Mi Kyung Park
- Department of BioHealthcare, Hwasung Medi-Science University, Hwaseong-si 18274, Republic of Korea
| | - Chang Hoon Lee
- College of Pharmacy, Dongguk University, Goyang 10326, Republic of Korea; (N.T.M.D.); (T.M.N.)
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2
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YB-1 as an Oncoprotein: Functions, Regulation, Post-Translational Modifications, and Targeted Therapy. Cells 2022; 11:cells11071217. [PMID: 35406781 PMCID: PMC8997642 DOI: 10.3390/cells11071217] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/26/2022] [Accepted: 04/02/2022] [Indexed: 02/04/2023] Open
Abstract
Y box binding protein 1 (YB-1) is a protein with a highly conserved cold shock domain (CSD) that also belongs to the family of DNA- and RNA-binding proteins. YB-1 is present in both the nucleus and cytoplasm and plays versatile roles in gene transcription, RNA splicing, DNA damage repair, cell cycle progression, and immunity. Cumulative evidence suggests that YB-1 promotes the progression of multiple tumor types and serves as a potential tumor biomarker and therapeutic target. This review comprehensively summarizes the emerging functions, mechanisms, and regulation of YB-1 in cancers, and further discusses targeted strategies.
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3
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Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control. Biomolecules 2020; 10:biom10040591. [PMID: 32290447 PMCID: PMC7226217 DOI: 10.3390/biom10040591] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.
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4
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Liu TT, Arango-Argoty G, Li Z, Lin Y, Kim SW, Dueck A, Ozsolak F, Monaghan AP, Meister G, DeFranco DB, John B. Noncoding RNAs that associate with YB-1 alter proliferation in prostate cancer cells. RNA (NEW YORK, N.Y.) 2015; 21:1159-72. [PMID: 25904138 PMCID: PMC4436668 DOI: 10.1261/rna.045559.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
The highly conserved, multifunctional YB-1 is a powerful breast cancer prognostic indicator. We report on a pervasive role for YB-1 in which it associates with thousands of nonpolyadenylated short RNAs (shyRNAs) that are further processed into small RNAs (smyRNAs). Many of these RNAs have previously been identified as functional noncoding RNAs (http://www.johnlab.org/YB1). We identified a novel, abundant, 3'-modified short RNA antisense to Dicer1 (Shad1) that colocalizes with YB-1 to P-bodies and stress granules. The expression of Shad1 was shown to correlate with that of YB-1 and whose inhibition leads to an increase in cell proliferation. Additionally, Shad1 influences the expression of additional prognostic markers of cancer progression such as DLX2 and IGFBP2. We propose that the examination of these noncoding RNAs could lead to better understanding of prostate cancer progression.
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Affiliation(s)
- Teresa T Liu
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Gustavo Arango-Argoty
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Zhihua Li
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Yuefeng Lin
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Sang Woo Kim
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Anne Dueck
- University of Regensburg, Biochemistry I, 93053 Regensburg, Bavaria, Germany
| | - Fatih Ozsolak
- Helicos BioSciences Corporation, Cambridge, Massachusetts 02139, USA
| | - A Paula Monaghan
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Gunter Meister
- University of Regensburg, Biochemistry I, 93053 Regensburg, Bavaria, Germany
| | - Donald B DeFranco
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Bino John
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
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Leiprecht N, Notz E, Schuetz J, Haedicke J, Stubenrauch F, Iftner T. A novel recombinant papillomavirus genome enabling in vivo RNA interference reveals that YB-1, which interacts with the viral regulatory protein E2, is required for CRPV-induced tumor formation in vivo. Am J Cancer Res 2014; 4:222-33. [PMID: 24959377 PMCID: PMC4065403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/23/2014] [Indexed: 06/03/2023] Open
Abstract
YB-1 is considered a negative prognostic marker for different types of cancer. Increased YB-1 protein levels in tumor cells indicate a worse prognosis. In a preceding study comparing the transcripts of CRPV-induced benign papillomas to mRNA levels of malignant epithelial tumors, we identified YB-1 as a gene that is up-regulated in papillomavirus-associated carcinomas and which causes an invasive phenotype in CRPV-positive cells in vitro. Here we demonstrate that YB-1 is a previously unknown factor required for papillomavirus-induced tumor development in the rabbit animal model system. By infecting the animals with a novel recombinant shRNA-expressing CRPV genome, we show that knock-down of YB-1 dramatically reduces papillomavirus-dependent tumor formation in vivo. Consistent with previous reports showing a nuclear distribution of YB-1 proteins as a hallmark of malignancy, we demonstrate a predominantly nuclear localization of YB-1 in CRPV-immortalized cells. Furthermore we give evidence of YB-1 regulating the CRPV URR and thereby viral gene expression and we identified YB-1 as a novel interactor of the CRPV regulatory protein E2. Taken together we hypothesize that YB-1 is essential for papillomavirus-induced tumor formation probably by regulating viral gene expression including expression of the oncogenes E6 and E7.
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Affiliation(s)
- Natalie Leiprecht
- Medical Virology, Division of Experimental Virology, University Hospital Tübingen Germany
| | - Ekaterina Notz
- Medical Virology, Division of Experimental Virology, University Hospital Tübingen Germany
| | - Johanna Schuetz
- Medical Virology, Division of Experimental Virology, University Hospital Tübingen Germany
| | - Juliane Haedicke
- Medical Virology, Division of Experimental Virology, University Hospital Tübingen Germany
| | - Frank Stubenrauch
- Medical Virology, Division of Experimental Virology, University Hospital Tübingen Germany
| | - Thomas Iftner
- Medical Virology, Division of Experimental Virology, University Hospital Tübingen Germany
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6
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Y-box binding protein 1--a prognostic marker and target in tumour therapy. Eur J Cell Biol 2013; 93:61-70. [PMID: 24461929 DOI: 10.1016/j.ejcb.2013.11.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/22/2013] [Accepted: 11/28/2013] [Indexed: 01/11/2023] Open
Abstract
Y-box binding protein 1 (YB-1) is a multifunctional protein involved in various cellular processes including both transcriptional and translational regulation of target gene expression. Significantly increased YB-1 levels have been reported in a number of human malignancies and shown to be associated with poor prognosis and disease recurrence. Indeed, YB-1 can act as a versatile oncoprotein playing an important role in tumour cell proliferation and progression. Consequently, YB-1 not only proves to be a good prognostic tumour marker, but also may be a promising emerging molecular target for the development of new therapeutical strategies. In this review, we discuss both the role of YB-1 in cancer and specifically in malignant melanoma as well as possible translations into the clinics derived thereof.
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Wang XL, Zhang YX, Yang CG, Zhang B, Chen SL. Cloning, characterization and expression analysis of a cold shock domain family member YB-1 in turbot Scophthalmus maximus. FISH & SHELLFISH IMMUNOLOGY 2012; 33:1215-1221. [PMID: 22982328 DOI: 10.1016/j.fsi.2012.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 08/11/2012] [Accepted: 09/03/2012] [Indexed: 06/01/2023]
Abstract
The Y-box proteins are a family of highly conserved nucleic acid binding proteins. In this report we have identified a new member, YB-1 from turbot (Scophthalmus maximus) spleen cDNA library. The full-length cDNA sequence of turbot YB-1 was obtained and then the expression at transcriptional level was researched by qRT-PCR. In normal organs, the expression of YB-1 was higher in liver, brain, gill and heart, respectively. YB-1 had the highest expression level at gastrula stage during the early stages of embryo development. In the liver, kidney and spleen, the turbot YB-1 expression level was the highest at 72 h after challenge with lymphocystis disease virus (LCDV) and the highest at 12 h after challenge with Vibrio anguillarum (V. anguillarum). Furthermore, the expression of turbot YB-1 also distinctly increased in turbot kidney cells (TK) at 24 h after challenge with V. anguillarum and LCDV. These results indicated that the turbot YB-1 protein may play a significant role in the immune response of turbot.
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Affiliation(s)
- Xian-Li Wang
- Translational Center for Stem Cell Research, Tongji Hospital, Stem Cell Research Center, Tongji University School of Medicine, Shanghai 200065, China
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8
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Cellular localization of Y-box binding protein 1 in brain tissue of rats, macaques, and humans. BMC Neurosci 2009; 10:28. [PMID: 19323802 PMCID: PMC2666744 DOI: 10.1186/1471-2202-10-28] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 03/26/2009] [Indexed: 01/01/2023] Open
Abstract
Background The Y-box binding protein 1 (YB-1) is considered to be one of the key regulators of transcription and translation. However, so far only limited knowledge exists regarding its cellular distribution in the adult brain. Results Analysis of YB-1 immunolabelling as well as double-labelling with the neuronal marker NeuN in rat brain tissue revealed a predominant neuronal expression in the dentate gyrus, the cornu ammonis pyramidal cell layer, layer III of the piriform cortex as well as throughout all layers of the parahippocampal cortex. In the hilus of the hippocampus single neurons expressed YB-1. The neuronal expression pattern was comparable in the hippocampus and parahippocampal cortex of adult macaques and humans. Double-labelling of YB-1 with the endothelial cell marker Glut-1, the multidrug transporter P-glycoprotein, and the astrocytic marker GFAP did not indicate a co-localization. Following status epilepticus in rats, no induction of YB-1 occurred in brain capillary endothelial cells and neurons. Conclusion In conclusion, our study demonstrates that YB-1 is predominantly expressed in neurons in the adult brain of rats, macaques and humans. Lack of a co-localization with Glut-1 and P-glycoprotein argues against a direct role of YB-1 in the regulation of blood-brain barrier P-glycoprotein.
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Klenova E, Scott AC, Roberts J, Shamsuddin S, Lovejoy EA, Bergmann S, Bubb VJ, Royer HD, Quinn JP. YB-1 and CTCF differentially regulate the 5-HTT polymorphic intron 2 enhancer which predisposes to a variety of neurological disorders. J Neurosci 2004; 24:5966-73. [PMID: 15229244 PMCID: PMC6729234 DOI: 10.1523/jneurosci.1150-04.2004] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The serotonin transporter (5-HTT) gene contains a variable number tandem repeat (VNTR) domain within intron 2 that is often associated with a number of neurological conditions, including affective disorders. The implications of this polymorphism are not yet understood, however, we have previously demonstrated that the 5-HTT VNTR is a transcriptional regulatory domain, and the allelic variation supports differential reporter gene expression in vivo and in vitro. The aim of this study was to identify transcription factors responsible for the regulation of this VNTR. Using a yeast one-hybrid screen, we found the transcription factor Y box binding protein 1 (YB-1) interacts with the 5-HTT VNTR. Consistent with this, we demonstrate in a reporter gene assay that the polymorphic VNTR domains differentially respond to exogenous YB-1 and that YB-1 will bind to the VNTR in vitro in a sequence-specific manner. Interestingly, the transcription factor CCTC-binding factor (CTCF), previously shown to interact with YB-1, interferes with the ability of the VNTR to support YB-1-directed reporter gene expression. In addition, CTCF blocks the binding of YB-1 to its DNA recognition sequences in vitro, thus providing a possible mechanism of regulation of YB-1 activation of the VNTR by CTCF. Therefore, we have identified YB-1 and CTCF as transcription factors responsible, at least in part, for modulation of VNTR function as a transcriptional regulatory domain. Our data suggest a novel mechanism that explains, in part, the ability of the distinct VNTR copy numbers to support differential reporter gene expression based on YB-1 binding sites.
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Affiliation(s)
- Elena Klenova
- Department of Biological Sciences, University of Essex, Essex CO4 3SQ, United Kingdom.
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10
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Ohba H, Chiyoda T, Endo E, Yano M, Hayakawa Y, Sakaguchi M, Darnell RB, Okano HJ, Okano H. Sox21 is a repressor of neuronal differentiation and is antagonized by YB-1. Neurosci Lett 2004; 358:157-60. [PMID: 15039105 DOI: 10.1016/j.neulet.2004.01.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 01/08/2004] [Accepted: 01/09/2004] [Indexed: 10/26/2022]
Abstract
Sox21, a high-mobility group box transcription factor, is expressed throughout the immature neural stem/progenitor population in ventricular zone but not in the cortical plate in embryonic mouse brain and its expression is restricted to the subventricular zone in the adult brain. In undifferentiated PC12 cells, endogenous Sox21 expression is detected but its expression ceases during the nerve growth factor (NGF)-induced neuronal differentiation. Overexpression of Sox21 results in a substantial repression of NGF-induced neurite outgrowth in PC12 cells. Further, we biochemically identified a Sox21-associating protein, Y-box binding protein 1 which not only binds to Sox21 but also partially restores NGF-induced neurite outgrowth of PC12 cells inhibited by Sox21. These results suggest that Sox21 is a repressor of neuronal differentiation in the developing nervous system.
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Affiliation(s)
- Hiroyuki Ohba
- CREST-JST and Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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11
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Holm PS, Lage H, Bergmann S, Jürchott K, Glockzin G, Bernshausen A, Mantwill K, Ladhoff A, Wichert A, Mymryk JS, Ritter T, Dietel M, Gänsbacher B, Royer HD. Multidrug-resistant cancer cells facilitate E1-independent adenoviral replication: impact for cancer gene therapy. Cancer Res 2004; 64:322-8. [PMID: 14729641 DOI: 10.1158/0008-5472.can-0482-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Resistance to chemotherapy is responsible for a failure of current treatment regimens in cancer patients. We have reported previously that the Y-box protein YB-1 regulates expression of the P-glycoprotein gene mdr1, which plays a major role in the development of a multidrug resistant-tumor phenotype. YB-1 predicts drug resistance and patient outcome in breast cancer. Thus, YB-1 is a promising target for new therapeutic approaches to defeat multidrug resistance. In drug-resistant cancer cells and in adenovirus-infected cells YB-1 is found in the nucleus. Nuclear accumulation of YB-1 in adenovirus-infected cells is a function of the E1 region, and we have shown that YB-1 facilitates adenovirus replication. Here we report that E1A-deleted or mutant adenovirus vectors, such as Ad312 and Ad520, replicate efficiently in multidrug-resistant (MDR) cancer cells and induce an adenovirus cytopathic effect resulting in host cell lysis. Thus, replication-defective adenoviruses are a previously unrecognized vector system for a selective elimination of MDR cancer cells. Our work forms the basis for the development of novel oncolytic adenovirus vectors for the treatment of MDR malignant diseases in the clinical setting.
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Affiliation(s)
- Per S Holm
- Institut für Experimentelle Onkologie und Therapieforschung, Technische Universität München, Klinikum Rechts der Isar, München, Germany.
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Funakoshi T, Kobayashi S, Ohashi S, Sato TA, Anzai K. Isolation and characterization of brain Y-box protein: developmentally regulated expression, polyribosomal association and dendritic localization. ACTA ACUST UNITED AC 2003; 118:1-9. [PMID: 14559349 DOI: 10.1016/s0169-328x(03)00328-0] [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] [Indexed: 10/27/2022]
Abstract
Y-box proteins are DNA- and RNA-binding proteins and control specific gene expression at both transcriptional and translational levels. Particularly in germ cells, it has been reported that Y-box proteins bind to paternal or maternal mRNAs to form mRNPs, mask them from translation and control cell maturation. In this study, we cloned cDNA for a Y-box protein from rat brain. A deduced amino acid sequence of the protein was very similar to that of several other Y-box proteins, and we termed the protein rBYB1 (rat brain Y-box protein 1). rBYB1 was found to be considerably expressed in the cytoplasm of pre- and early postnatal brains, and then decreased to adult levels with brain development. Further, we found rBYB1 to be distributed in both polyribosomal and nonpolyribosomal (mRNP) fractions on a sucrose density gradient, and to be associated with polyribosomes via RNA in the higher-density fractions. Moreover, rBYB1 was localized in dendrites of the primary hippocampal neurons. We compared these sucrose gradient and intracellular rBYB1 localization results with those for fragile X mental retardation protein (FMRP), which is known to be an mRNA-binding and polyribosome-associating translational regulator distributed in neuronal dendrites. Our results suggest that in the brain of prenatal and newborn animals, rBYB1 may function in storage and/or translational regulation of mRNAs involved in the rapid progress of the postnatal brain, and in mature neurons, it may also participate in the control of protein synthesis in dendrites.
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Affiliation(s)
- Tomoko Funakoshi
- Department of Biochemistry, College of Pharmacy, Nihon University, Narashinodai, Funabashi, Chiba 274-8555, Japan
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13
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Jurchott K, Bergmann S, Stein U, Walther W, Janz M, Manni I, Piaggio G, Fietze E, Dietel M, Royer HD. YB-1 as a cell cycle-regulated transcription factor facilitating cyclin A and cyclin B1 gene expression. J Biol Chem 2003; 278:27988-96. [PMID: 12695516 DOI: 10.1074/jbc.m212966200] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of the Y-box protein YB-1 is increased in proliferating normal and cancer cells, but its role in cell proliferation and cell cycle progression is unclear. We have identified a cell cycle-dependent relocalization of YB-1 from the cytoplasm to the nucleus at the G1/S phase transition and demonstrate that both the charged zipper and the cold shock domain are involved in regulating this process. Using cell lines that constitutively overexpress YB-1, we show that nuclear accumulation of YB-1 is associated with increased cyclin A and cyclin B1 mRNA and protein expression. We provide evidence that deregulated YB-1 expression is linked to adhesion-independent cell proliferation through the induction of cyclin A. Thus, we have identified YB-1 as a cell cycle stage-specific transcription factor important for cell proliferation.
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Affiliation(s)
- Karsten Jurchott
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13092 Berlin, Germany.
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14
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Firulli AB, Thattaliyath BD. Transcription factors in cardiogenesis: the combinations that unlock the mysteries of the heart. INTERNATIONAL REVIEW OF CYTOLOGY 2002; 214:1-62. [PMID: 11893163 DOI: 10.1016/s0074-7696(02)14002-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Heart formation is one of the first signs of organogenesis within the developing embryo and this process is conserved from flies to man. Completing the genetic roadmap of the molecular mechanisms that control the cell specification and differentiation of cells that form the developing heart has been an exciting and fast-moving area of research in the fields of molecular and developmental biology. At the core of these studies is an interest in the transcription factors that are responsible for initiation of a pluripotent cell to become programmed to the cardiac lineage and the subsequent transcription factors that implement the instructions set up by the cells commitment decision. To gain a better understanding of these pathways, cardiac-expressed transcription factors have been identified, cloned, overexpressed, and mutated to try to determine function. Although results vary depending on the gene in question, it is clear that there is a striking evolutionary conservation of the cardiogenic program among species. As we move up the evolutionary ladder toward man, we encounter cases of functional redundancy and combinatorial interactions that reflect the complex networks of gene expression that orchestrate heart development. This review focuses on what is known about the transcription factors implicated in heart formation and the role they play in this intricate genetic program.
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Affiliation(s)
- Anthony B Firulli
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio 78229, USA
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15
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Stein U, Jürchott K, Walther W, Bergmann S, Schlag PM, Royer HD. Hyperthermia-induced nuclear translocation of transcription factor YB-1 leads to enhanced expression of multidrug resistance-related ABC transporters. J Biol Chem 2001; 276:28562-9. [PMID: 11369762 DOI: 10.1074/jbc.m100311200] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genotoxic stress leads to nuclear translocation of the Y-box transcription factor YB-1 and enhanced expression of the multidrug resistance gene MDR1. Because hyperthermia is used for the treatment of colon cancer in combination with chemoradiotherapy, we investigated the influence of hyperthermia on YB-1 activity and the expression of multidrug resistance-related genes. Here we report that hyperthermia causes YB-1 translocation from the cytoplasm into the nucleus of human colon carcinoma cells HCT15 and HCT116. Nuclear translocation of YB-1 was associated with increased MDR1 and MRP1 gene activity, which is reflected in strong efflux pump activity. However, a combination of hyperthermia and drug treatment effectively reduced cell survival of the HCT15 and HCT116 cells. These results demonstrate that activation of MDR1 and MRP1 gene expression and increased efflux pump activity after hyperthermia were insufficient to cause an increase in drug resistance in colon cancer cell lines. The ability of hyperthermia to abrogate drug resistance in the presence of an increase in functional MDR proteins may provide an explanation for the efficacious results seen in the clinic in colon cancer patients treated with a combination of hyperthermia and chemotherapy.
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Affiliation(s)
- U Stein
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle Strasse 10, 13092 Berlin, Germany.
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16
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Diamond P, Shannon MF, Vadas MA, Coles LS. Cold shock domain factors activate the granulocyte-macrophage colony-stimulating factor promoter in stimulated Jurkat T cells. J Biol Chem 2001; 276:7943-51. [PMID: 11116154 DOI: 10.1074/jbc.m009836200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cold shock domain (CSD) family members have been shown to play roles in either transcriptional activation or repression of many genes in various cell types. We have previously shown that CSD proteins dbpAv and dbpB (also known as YB-1) act to repress granulocyte-macrophage colony-stimulating factor transcription in human embryonic lung (HEL) fibroblasts via binding to single-stranded DNA regions across the promoter. Here we show that the same CSD factors are involved in granulocyte-macrophage colony-stimulating factor transcriptional activation in Jurkat T cells. Unlike the mechanisms of CSD repression in HEL fibroblasts, CSD-mediated activation in Jurkat T cells is not mediated through DNA binding but presumably through protein-protein interactions via the C terminus of the CSD protein with transcription factors such as RelA/NF-kappaB p65. We demonstrate that Jurkat T cells lack truncated CSD factor subtypes present in HEL fibroblasts, which raises the possibility that the cellular content of CSD proteins may determine their final role as activators or repressors of transcription.
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Affiliation(s)
- P Diamond
- Division of Human Immunology, Hanson Centre for Cancer Research, Institute of Medical and Veterinary Science, Frome Road, Adelaide, South Australia, 5000, Australia.
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Coles LS, Diamond P, Occhiodoro F, Vadas MA, Shannon MF. An ordered array of cold shock domain repressor elements across tumor necrosis factor-responsive elements of the granulocyte-macrophage colony-stimulating factor promoter. J Biol Chem 2000; 275:14482-93. [PMID: 10799531 DOI: 10.1074/jbc.275.19.14482] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The tumor necrosis factor-alpha-responsive region of the human granulocyte-macrophage colony-stimulating factor (GM-CSF) promoter (-114 to -31) encompasses binding sites for NF-kappaB, CBF, AP-1, ETS, and NFAT families of transcription factors. We show both here and previously that mutation of any one of these binding sites greatly reduces tumor necrosis factor-alpha induction of the GM-CSF promoter. Interspersed between these elements are sequences that when mutated lead to an increase in GM-CSF promoter activity. We have previously shown that two of these repressor elements bind proteins known as cold shock domain (CSD) factors and that overexpression of CSD proteins leads to repression of GM-CSF promoter activity in fibroblasts. CSD proteins are single strand DNA- and RNA-binding proteins that contact 5'-CCTG-3' sequences in the GM-CSF repressor elements. We show here that two newly identified repressor sequences in the proximal promoter can also bind CSD proteins. We have characterized the CSD-containing protein complexes that bind to the GM-CSF promoter and identified a novel protein related to mitochondrial single strand binding protein that forms part of one of these complexes. The four CSD-binding sites on the promoter occur in pairs on opposite strands of the DNA and appear to form an ordered array of binding elements. A similar ordered array of CSD sites are present in the promoters of the granulocyte colony-stimulating factor and interleukin-3 genes, implying a common mechanism for negative regulation of these myeloid growth factors.
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Affiliation(s)
- L S Coles
- Division of Human Immunology, Hanson Centre for Cancer Research, Institute of Medical and Veterinary Science, Frome Road, Adelaide, South Australia, 5000, Australia.
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18
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Kaltreider RC, Pesce CA, Ihnat MA, Lariviere JP, Hamilton JW. Differential effects of arsenic(III) and chromium(VI) on nuclear transcription factor binding. Mol Carcinog 1999. [DOI: 10.1002/(sici)1098-2744(199907)25:3<219::aid-mc8>3.0.co;2-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Wada MR, Ohtani Y, Shibata Y, Tanaka KJ, Tanimoto N, Nishikata T. An alternatively spliced gene encoding a Y-box protein showing maternal expression and tissue-specific zygotic expression in the ascidian embryo. Dev Growth Differ 1998; 40:631-40. [PMID: 9865973 DOI: 10.1046/j.1440-169x.1998.t01-4-00007.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An ascidian Y-box protein gene was cloned, designated as CiYB, which consists of a highly conserved cold shock domain and an auxiliary tail domain with alternating modules of acidic and basic amino acids. CiYB is a single copy gene in the ascidian genome. During oogenesis and early development, CiYB produces three different transcripts (CiYB1, CiYB2 and CiYB3) by alternate splicing. CiYB1 and CiYB2 were expressed during oogenesis, suggesting that they are recruited into maternal ribonucleoprotein particles. According to gel mobility shift assay, the CiYB1 protein has the ability to bind RNA. The sequence preference of RNA binding is similar to that of the Xenopus Y-box protein (FRGY2), which is a major component of the maternal messenger ribonucleoprotein particles (mRNP) in the oocyte. These results suggest that the ascidian Y-box protein may have an important role for masking and translational regulation of maternal mRNA. Furthermore, CiYB1, CiYB2 and CiYB3 were expressed zygotically in a tissue restricted manner. CiYB1 was expressed specifically in muscle precursor blastomeres and tail muscle cells suggesting its important role in muscle differentiation.
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Affiliation(s)
- M R Wada
- Department of Biology, Faculty of Science, Konan University, Kobe, Japan.
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20
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Matsumoto K, Wolffe AP. Gene regulation by Y-box proteins: coupling control of transcription and translation. Trends Cell Biol 1998; 8:318-23. [PMID: 9704408 DOI: 10.1016/s0962-8924(98)01300-2] [Citation(s) in RCA: 244] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Y-box proteins are multifunctional regulators of gene expression. In somatic cells, they have the capacity to exert positive and negative effects on both transcription and translation. In Xenopus oocytes, they help to mask maternal mRNA and couple the transcription of mRNA in the nucleus to its translational fate in the cytoplasm. This review describes how the capacity of the Y-box proteins to destabilize both RNA and DNA duplexes, together with their distribution between nuclear and cytoplasmic compartments, might explain these multiple roles.
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Affiliation(s)
- K Matsumoto
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892-5431, USA
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21
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Franco GR, Garratt RC, Tanaka M, Simpson AJ, Pena SD. Characterization of a Schistosoma mansoni gene encoding a homologue of the Y-box binding protein. Gene 1997; 198:5-16. [PMID: 9370259 DOI: 10.1016/s0378-1119(97)00261-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have cloned and characterized a Schistosoma mansoni cDNA encoding a basic protein homologous to the human Y-box binding protein 1 (YB-1). The 1.3-kb S. mansoni YB-1 transcript, which was shown to be expressed in various stages of the parasite life cycle, codes for a protein of 217 amino acids containing, towards its N-terminus, a nucleic acid binding motif, known as the cold-shock domain (CSD). This domain is 64% identical to the cold-shock domain of other members of the Y-box binding protein family and 43% identical to the cold-shock protein CspA of Escherichia coli. In S. mansoni YB-1, the cold-shock domain possess some structural characteristics that permit dimer formation as occurs in the Bacillus subtilis cold-shock protein CspB. The C-terminal region of S. mansoni YB-1 differs from the other Y-box binding proteins because of the presence of tandem repeats of Arg and Gly, suggesting the formation of a fibroin-like beta-sandwich structure. This novel folding pattern for the C-terminus of S. mansoni YB-1 might suggest a distinct specific function for this protein in the parasite.
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Affiliation(s)
- G R Franco
- Departamento de Bioquímica e Immunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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22
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Sundseth R, MacDonald G, Ting J, King AC. DNA elements recognizing NF-Y and Sp1 regulate the human multidrug-resistance gene promoter. Mol Pharmacol 1997; 51:963-71. [PMID: 9187262 DOI: 10.1124/mol.51.6.963] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Regulation of the human multidrug resistance gene (hMDR1) was studied by mapping DNA elements in the proximal promoter necessary for efficient transcription. Transient transfection analysis in tumor cell lines (HCT116, HepG2, and Saos2) of promoter deletions identified several regulatory domains. These cell lines expressed hMDR1 mRNA. Removal of an element between +25 and +158 reduced promoter activity by 2-3-fold, whereas deletion of sequences from approximately -5000 to -138 base pairs gave a approximately 2-fold increase. The activity of the hMDR1 promoter (-137 to +25) was comparable in activity to the SV40 early promoter and enhancer combination. Deletion of the hMDR1 promoter between -86 and -44 reduced activity by 5-10-fold, identifying an important regulatory region. This minimal region (-88 to -37) activated transcription when inserted upstream of a synthetic promoter, suggesting that it acts independently of other regulatory sequences. Two DNA elements within 85 base pairs of the transcriptional start site were required to confer efficient gene expression. A double-point mutation in the Y box (inverted CCAAT box) between -70 and -80 reduced activity of the promoter by 5-10-fold, and a single-point mutation at -52 within a GC-rich element reduced activity by 3-fold. Thus, both the Y-box and GC elements must each remain intact for optimal promoter activity. DNA-binding analyses suggest that the transcription factor NF-Y, but not YB-1 or c/EBP, is most likely responsible for controlling the activity of the Y-box element in these tumor cell lines. DNA-binding analyses also suggest that Sp1, alone or in combination with other nuclear factors, likely controls the activity of the GC element.
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Affiliation(s)
- R Sundseth
- Division of Molecular Genetics and Microbiology, Wellcome Research Laboratories, Research Triangle Park, North Carolina 27709, USA
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23
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Bargou RC, Jürchott K, Wagener C, Bergmann S, Metzner S, Bommert K, Mapara MY, Winzer KJ, Dietel M, Dörken B, Royer HD. Nuclear localization and increased levels of transcription factor YB-1 in primary human breast cancers are associated with intrinsic MDR1 gene expression. Nat Med 1997; 3:447-50. [PMID: 9095180 DOI: 10.1038/nm0497-447] [Citation(s) in RCA: 330] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Breast cancers are either primarily resistant to chemotherapy (intrinsic resistance), or respond to chemotherapy but later recur with a multidrug-resistant phenotype because of overexpression of the multidrug transporter P-glycoprotein. The MDR1 gene encoding P-glycoprotein may be transcriptionally regulated by a Y-box transcription factor. We now report that, in multidrug-resistant MCF-7 breast cancer cells, nuclear localization of YB-1 is associated with MDR-1 gene expression. In drug-sensitive MCF-7 cells, however, YB-1 was localized to the cytoplasm. Regulated overexpression of YB-1 in drug-sensitive diploid breast epithelial cells induced MDR-1 gene expression and multidrug resistance. In 27 out of 27 untreated primary breast cancers, YB-1 protein was expressed in the cytoplasm although it was undetectable in normal breast tissue of these patients. In a subgroup of tumors (9/27), however, YB-1 was also localized to the nucleus and, in these cases, high levels of P-glycoprotein were present. These results show that in a subset of untreated primary breast cancers, nuclear localization of YB-1 protein is associated with intrinsic multidrug resistance. Our data show that YB-1 has an important role in controlling MDR1 gene transcription and this finding provides a basis for the analysis of molecular mechanisms responsible for intrinsic multidrug resistance in human breast cancer.
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Affiliation(s)
- R C Bargou
- Humboldt Universität zu Berlin, Universitätsklinikum Rudolf Virchow, Robert-Rössle Klinik, Germany
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24
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Coles LS, Diamond P, Occhiodoro F, Vadas MA, Shannon MF. Cold shock domain proteins repress transcription from the GM-CSF promoter. Nucleic Acids Res 1996; 24:2311-7. [PMID: 8710501 PMCID: PMC145951 DOI: 10.1093/nar/24.12.2311] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The human granulocyte-macrophage colony stimulating factor (GM-CSF) gene promoter binds a sequence-specific single-strand DNA binding protein termed NF-GMb. We previously demonstrated that the NF-GMb binding sites were required for repression of tumor necrosis factor-alpha (TNF-alpha) induction of the proximal GM-CSF promoter sequences in fibroblasts. We now describe the isolation of two different cDNA clones that encode cold shock domain (CSD) proteins with NF-GMb binding characteristics. One is identical to the previously reported CSD protein dbpB and the other is a previously unreported variant of the dbpA CSD factor. This is the first report of CSD factors binding to a cytokine gene. Nuclear NF-GMb and expressed CSD proteins have the same binding specificity for the GM-CSF promoter and other CSD binding sites. We present evidence that CSD factors are components of the nuclear NF-GMb complex. We also demonstrate that overexpression of the CSD proteins leads to complete repression of the proximal GM-CSF promoter containing the NF-GMb/CSD binding sites. Surprisingly, we show that CSD overexpression can also directly repress a region of the promoter which apparently lacks NF-GMb/CSD binding sites. NF-GMb/CSD factors may hence be acting by two different mechanisms. We discuss the potential importance of CSD factors in maintaining strict regulation of the GM-CSF gene.
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Affiliation(s)
- L S Coles
- Division of Human Immunology, Hanson Centre for Cancer Research, Institute of Medical and Veterinary Science, Adelaide, South Australia, Australia
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25
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Sapru MK, Gao JP, Walke W, Burmeister M, Goldman D. Cloning and characterization of a novel transcriptional repressor of the nicotinic acetylcholine receptor delta-subunit gene. J Biol Chem 1996; 271:7203-11. [PMID: 8636158 DOI: 10.1074/jbc.271.12.7203] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have identified a negative cis-acting regulatory element in the nicotinic acetylcholine receptor delta-subunit gene's promoter. This element resides within a previously identified 47-base pair activity-dependent enhancer. Proteins that bind this region of DNA were cloned from a lambdagt11 innervated muscle expression library. Two cDNAs (MY1 and MY1a) were isolated that encode members of the Y-box family of transcription factors. MY1/1a RNAs are expressed at relatively high levels in heart, skeletal muscle, testis, glia, and specific regions of the central nervous system. MY1/1a are nuclear proteins that bind specifically to the coding strand of the 47-base pair enhancer and suppress delta-promoter activity in a sequence-specific manner. These results suggest a novel mechanism of repression by MY1/1a, which may contribute to the low level expression of the delta-subunit gene in innervated muscle. Finally, the gene encoding MY1/1a, Yb2, maps to the mid-distal region of mouse chromosome 6.
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Affiliation(s)
- M K Sapru
- Mental Health Research Institute, University of Michigan, Ann Arbor, 48109, USA
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26
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Duh JL, Zhu H, Shertzer HG, Nebert DW, Puga A. The Y-box motif mediates redox-dependent transcriptional activation in mouse cells. J Biol Chem 1995; 270:30499-507. [PMID: 8530481 DOI: 10.1074/jbc.270.51.30499] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We show here that the OxyR response element (ORE) in the bacterial oxyR promoter can also function as a redox-dependent enhancer in mammalian cells. Fusion of ORE to an SV40 basal promoter driving chloramphenicol acetyltransferase (CAT) expression confers H2O2 inducibility to expression of the cat gene in mouse Hepa-1 hepatoma cells. Nuclear extracts from these cells contain DNA-binding proteins that specifically interact with ORE DNA, cannot be completed by cognate oligonucleotides to AP-1 or NF kappa B, and are constitutively expressed, since treatment with H2O2 causes no detectable changes in binding activity or DNA-protein interaction. Recombinant cDNA clones that express ORE-binding proteins were isolated from a mouse hepatoma expression library and found to be representatives of two different members of the murine Y-box family of transcription factors. Canonical Y-box and ORE oligonucleotides compete with each other for binding to Y-box proteins in gel shift assays and antibodies to FRGY2, a Xenopus Y-box protein, supershift both Y-box and ORE DNA-protein complexes. In addition, antisense oligonucleotides to mouse YB-1 mRNA abolish induction of ORE-mediated cat expression by H2O2, and luciferase reporter constructs containing ORE, or the Y-box from the human MHC class II HLA-DQ gene, exhibit identical dose-dependent H2O2 inducibilities, which can be abolished by addition of 2-mercaptoethanol to the culture medium. These results suggest that the Y-box proteins may be an integral component of a eukaryotic redox signaling pathway.
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Affiliation(s)
- J L Duh
- Department of Environmental Health, University of Cincinnati Medical Center, Ohio 45267-0056, USA
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27
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Giffin W, Haché RJ. Nuclear factor binding to a DNA sequence element that represses MMTV transcription induces a structural transition and leads to the contact of single-stranded binding proteins with DNA. DNA Cell Biol 1995; 14:1025-35. [PMID: 8534369 DOI: 10.1089/dna.1995.14.1025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
NRE1 is a DNA sequence element in the long terminal repeat of mouse mammary tumor virus through which viral transcription is repressed. In addition to double-stranded DNA binding, both upper- and lower-stranded NRE1 binding activities occur in nuclear extracts. All three binding activities appear to be important for transcriptional effects. We report that occupancy of NRE1 within linear double-stranded NRE1 induces a structural transition in upstream flanking DNA that is facilitated by Mg2+. This transition was reflected by the striking DNase I sensitivity of the DNA. As Mg2+ concentration was increased, discrete DNase I hypersensitivity on one face of the DNA progressed to complete degradation of template. On the DNA face opposite the DNase I hypersensitivity, Mg2+ promoted regularly spaced cleavage by the single-strand-specific cleavage agents KMnO4 and S1 nuclease. Induction of degradation by DNase I occurred independently of MMTV sequences flanking NRE1, because nuclear extract-dependent DNase I sensitivity was conferred to an unrelated DNA fragment by introduction of a 23-bp NRE1-containing oligonucleotide. UV protein-DNA cross-linking revealed that addition of Mg2+ to a double-stranded NRE1 DNA binding assay induced conversion from a double- to a single-stranded protein-DNA cross-linking pattern. Thus, nuclear factor binding to NRE1 induces changes in DNA topology that promote the direct contact of single-stranded NRE1 binding factors with DNA.
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Affiliation(s)
- W Giffin
- Department of Medicine, University of Ottawa, Loeb Institute for Medical Research, Ottawa Civic Hospital, Ontario, Canada
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28
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Kudo S, Mattei MG, Fukuda M. Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 231:72-82. [PMID: 7628487 DOI: 10.1111/j.1432-1033.1995.tb20672.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Human DNA-binding proteins, dbpA and dbpB (YB-1), are members of a protein family containing a cold-shock domain, and are regarded as transcriptional regulators. Here, we isolated genomic fragments of these genes and characterized their transcriptional regulation. Analysis of lambda phage genomic clones revealed that the dbpA gene consists of 10 exons spanning a 24-kb genomic region. The cold-shock domain, composed of about 70 amino acid residues, is encoded separately by exons 2-5. The exon 6, encoding 69 amino acid residues, was found to be an alternative exon. Northern-blot analysis showed that both genes were highly expressed in skeletal muscle and heart compared with in other tissues. The dbpA gene contains no typical TATA box or CAAT box at the immediate 5' region, but a sequence similar to an initiator consensus sequence was revealed at a major transcription-start site. A transient expression assay using the chloramphenicol acetyltransferase reporter gene revealed that the sequence located at positions -17 to +70 relative to the major transcription-start site was critical for promoter function. Within this region, the consensus sequence for serum-response element, CC(A/T)6GG, is present at positions -13 to -4 in addition to the initiator sequence. Immunofluorescence showed the cellular localization of dbpA to be both in the cytoplasm and nucleus, particularly at the perinuclear region. In situ hybridization demonstrated the localization of the dbpA gene on chromosome 12 band p13.1, whereas dbpB-(YB-1)-related genes were dispersed on many chromosomes with strongest hybridization signals on chromosome 1. All 16 dbpB (YB-1) clones, isolated from the same genomic library used for dbpA genomic cloning, were processed genes because of their intronless structures and multiple mutations. One of these processed genes possesses an open reading frame, which encodes most of the amino acid residues of dbpB (YB-1). These results indicate that dbpA and dbpB (YB-1) genes evolved in different fashions after deviation from a common ancestral gene.
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Affiliation(s)
- S Kudo
- La Jolla Cancer Research Foundation, CA 92037, USA
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29
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MacDonald GH, Itoh-Lindstrom Y, Ting JP. The transcriptional regulatory protein, YB-1, promotes single-stranded regions in the DRA promoter. J Biol Chem 1995; 270:3527-33. [PMID: 7876087 DOI: 10.1074/jbc.270.8.3527] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
YB-1 is a member of a newly defined family of DNA- and RNA-binding proteins, the Y box factors. These proteins have been shown to affect gene expression at both the transcriptional and translational levels. Recently, we showed that YB-1 represses interferon-gamma-induced transcription of class II human major histocompatibility (MHC) genes (1). Studies in this report characterize the DNA binding properties of purified, recombinant YB-1 on the MHC class II DRA promoter. The generation of YB-1-specific antibodies further permitted an analysis of the DNA binding properties of endogenous YB-1. YB-1 specifically binds single-stranded templates of the DRA promoter with greater affinity than double-stranded templates. The single-stranded DNA binding sites of YB-1 were mapped to the X box, whereas the double-stranded binding sites were mapped to the Y box of the DRA promoter, by methylation interference analysis. Most significantly, YB-1 can induce or stabilize single-stranded regions in the X and Y elements of the DRA promoter, as revealed by mung bean nuclease analysis. In concert with the findings that YB-1 represses DRA transcription, this study of YB-1 binding properties suggests a model of repression in which YB-1 binding results in single-stranded regions within the promoter, thus preventing loading and/or function of other DRA-specific transactivating factors.
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Affiliation(s)
- G H MacDonald
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill 27599-7295
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30
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Abstract
Members of the Y-box (YB) family of transcription factors are expressed in a wide range of cell types and are implicated in the regulation of a rapidly increasing number of genes. Although the biological activities of YB proteins appear to be varied, distinct patterns, relating to the timing of their expression and the identity of their target genes, are beginning to emerge. A recent report by Ito et al. focusses attention on cell proliferation and adds support to earlier suggestions that a primary function of YB proteins is to help activate growth-associated genes.
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Affiliation(s)
- M Ladomery
- School of Biological and Medical Sciences, University of St Andrews, Fife, Scotland
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31
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Ladomery M, Sommerville J. Binding of Y-box proteins to RNA: involvement of different protein domains. Nucleic Acids Res 1994; 22:5582-9. [PMID: 7530842 PMCID: PMC310120 DOI: 10.1093/nar/22.25.5582] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Eukaryotic Y-box proteins are reported to interact with a wide variety of nucleic acid structures to act as transcription factors and mRNA masking proteins. The modular structure of Y-box proteins includes a highly conserved N-terminal cold-shock domain (CSD, equivalent to the bacterial cold-shock proteins) plus four basic C-terminal domains containing arginine clusters and aromatic residues. In addition, the basic domains are separated by acidic regions which contain several potential sites for serine/threonine phosphorylation. The interaction of Y-box proteins, isolated from Xenopus oocytes (FRGY2 type), with RNA molecules has been studied by UV crosslinking and protein fragmentation. We have identified two distinct binding activities. The CSD interacts preferentially with the polypurines poly(A,G) and poly(G) but not poly(A), this activity being sensitive to 5 mM MgCl2 but not to 5 mM spermidine. In the presence of 1 mM MgCl2 or 1 mM spermidine, the basic domains interact preferentially with poly(C,U), this activity being sensitive to 0.5 M NaCl. Binding of the basic domains is also sensitive to low concentrations of heparin. The basic domains can be crosslinked individually to labelled RNA. These results are discussed with reference to the various specificities noted in the binding of Y-box proteins to RNA and DNA.
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Affiliation(s)
- M Ladomery
- School of Biological and Medical Sciences, University of St Andrews, Fife, UK
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32
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Ito K, Tsutsumi K, Kuzumaki T, Gomez PF, Otsu K, Ishikawa K. A novel growth-inducible gene that encodes a protein with a conserved cold-shock domain. Nucleic Acids Res 1994; 22:2036-41. [PMID: 8029009 PMCID: PMC308118 DOI: 10.1093/nar/22.11.2036] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We have isolated a cDNA that encodes a novel member of the Y-box binding protein family, termed as RYB-a (Rat Y-box Binding protein-a). RYB-a is a 31 kDa protein that contains a conserved cold-shock domain and an amino acid alignment similar to those of charge zipper proteins. Expression of RYB-a mRNA was highly abundant in the skeletal muscle, spleen, and fetal liver. The expression is very low in new-born and adult livers, suggesting its expression is under developmental regulation. In addition, the expression of RYB-a mRNA was induced in the liver during regeneration and by stimulation of quiescent fibroblast cells with serum. Induction in the fibroblasts was inhibited by treating the cell with a specific tyrosine kinase inhibitor, genistein or by detachment of cell-adhesion. Since both treatments are known to inhibit G1 cells to enter S phase, RYB-a gene is thought to be a member of growth-inducible genes.
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Affiliation(s)
- K Ito
- Department of Biochemistry, Yamagata University School of Medicine, Japan
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33
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A human protein containing a “cold shock” domain binds specifically to H-DNA upstream from the human gamma-globin genes. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)36764-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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34
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Familari M, Almouzni G, Wolffe AP. Isolation of a potentially functional Y-box protein (MSY-1) processed pseudogene from mouse: evolutionary relationships within the EF1A/dbpB/YB-1 gene family. Gene 1994; 141:255-9. [PMID: 8163198 DOI: 10.1016/0378-1119(94)90581-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A processed pseudogene from Mus musculus, designated psi MSY-2, was obtained with a MSY-1 cDNA (encoding mouse Y-box factor 1) probe. Mouse psi MSY-2 is intronless and has an ORF with an in-frame translational stop. The pseudogene has repeat sequences at the 5' and 3' boundaries, suggestive of an origin as a retroposon, and exhibits mutagenesis of CpG residues at a frequency at least tenfold higher than predicted from random mutagenesis. This indicates that 'repeat-induced point mutagenesis' or ripping has occurred. We find that the mouse genome contains many DNA sequences with homology to a cDNA encoding the DNA-binding domain of the Y-box proteins. We estimate that there are at least 15 copies per haploid genome.
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Affiliation(s)
- M Familari
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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35
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Wolffe AP. Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins. Bioessays 1994; 16:245-51. [PMID: 8031301 DOI: 10.1002/bies.950160407] [Citation(s) in RCA: 286] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Y-box proteins are the most evolutionarily conserved nucleic acid binding proteins yet defined in bacteria, plants and animals. The central nucleic acid binding domain of the vertebrate proteins is 43% identical to a 70-amino-acid-long protein (CS7.4) from E. coli. The structure of this domain consists of an antiparallel five-stranded beta-barrel that recognizes both DNA and RNA. The diverse biological roles of these Y-box proteins range from the control of the E. coli cold-shock stress response to the translational masking of messenger RNA in vertebrate gametes. This review discusses the organization of the prokaryotic and eukaryotic Y-box proteins, how they interact with nucleic acids, and their biological roles, both proven and potential.
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Affiliation(s)
- A P Wolffe
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892
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Giffin W, Torrance H, Saffran H, MacLeod H, Haché R. Repression of mouse mammary tumor virus transcription by a transcription factor complex. Binding of individual components to separated DNA strands. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42278-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Kashanchi F, Duvall JF, Dittmer J, Mireskandari A, Reid RL, Gitlin SD, Brady JN. Involvement of transcription factor YB-1 in human T-cell lymphotropic virus type I basal gene expression. J Virol 1994; 68:561-5. [PMID: 8254772 PMCID: PMC236322 DOI: 10.1128/jvi.68.1.561-565.1994] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sequences which control basal human T-cell lymphotropic virus type I (HTLV-I) transcription likely play an important role in initiation and maintenance of virus replication. We previously identified and analyzed a 45-nucleotide sequence (downstream regulatory element 1 [DRE 1]), +195 to +240, at the boundary of the R/U5 region of the long terminal repeat which is required for HTLV-I basal transcription. We identified a protein, p37, which specifically bound to DRE 1. An affinity column fraction, containing p37, stimulated HTLV-I transcription approximately 12-fold in vitro. We now report the identification of a cDNA clone (15B-7), from a Jurkat expression library, that binds specifically to the DRE 1 regulatory sequence. Binding of the cDNA fusion protein, similarly to the results obtained with purified Jurkat protein, was decreased by introduction of site-specific mutations in the DRE 1 regulatory sequence. In vitro transcription and translation of 15B-7 cDNA produced a fusion protein which bound specifically to the HTLV-I +195 to +240 oligonucleotide. The partial cDNA encodes a protein which is homologous to the C-terminal 196 amino acids of the 36-kDa transcription factor, YB-1. Cotransfection of a YB-1 expression plasmid increases HTLV-I basal transcription approximately 14-fold in Jurkat T lymphocytes. On the basis of the molecular weight, DNA-binding characteristics, and in vivo transactivation activity, we suggest that the previously identified DRE 1-binding protein, p37, is YB-1.
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Affiliation(s)
- F Kashanchi
- Laboratory of Molecular Virology, National Institutes of Health, Bethesda, Maryland 20892
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Ozer J, Chalkley R, Sealy L. Characterization of rat pseudogenes for enhancer factor I subunit A: ripping provides clues to the evolution of the EFIA/dbpB/YB-1 multigene family. Gene 1993; 133:187-95. [PMID: 8224907 DOI: 10.1016/0378-1119(93)90637-i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Genomic Southern blot analysis of rat EFIA (gene encoding enhancer factor I subunit A) reveals a complex band pattern when cDNA subfragment probes are used. Screening a rat genomic library with a rat EFIA cDNA probe yields two different processed EFIA pseudogenes, designated rat psi EFIA#(2/3) and #(4/7), in addition to two other different, but less extensively characterized clones. psi EFIA#(4/7) has no open reading frame (ORF) sequences. psi EFIA#(2/3) contains two ORFs (83 and 178 codons), the products of which (if expressed) might be negative-acting EFIA transcription factors. Located nearly 0.6 kb upstream from psi EFIA#(2/3) is a perfect 69-bp dinucleotide (CT) tandem repeat, a sequence element associated with other isolated pseudogenes. Additionally, the 3' end of this processed gene is interrupted by an unusual retroposon, an inverted dimeric B1-like short interspersed repetitive element (SINE). The isolation of several independent clones of the same EFIA processed pseudogenes indicates that they comprise a significant component of the rat EFIA copy multiplicity. The phenomenon of repeat induced point mutagenesis (ripping) at rat EFIA pseudogene CpG doublets occurs at a frequency at least 6.5 times higher than predicted from random mutagenesis. This is consonant with the proposal that ripping may be the mechanism which inactivates the ectopic recombination potential of the rat EFIA pseudogenes.
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Affiliation(s)
- J Ozer
- Department of Cell Biology, Vanderbilt University School of Medicine, Nashville 37232
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Abstract
A cDNA expression library constructed from day 9 embryonic liver was screened with a previously identified protein binding site in the flanking region of the liver-specific, estrogen-dependent avian apoVLDLII gene. Two of the clones isolated were shown to encode the chicken homolog of the Y-box binding protein, YB-1 (dbpb), which we have designated chkYB-1. This protein was originally identified in avian extracts by virtue of its ability to bind to two reverse CCAAT motifs in the Rous sarcoma virus enhancer. Since its identification, additional nucleic acid binding properties have been ascribed to its homologs, or closely related proteins, in other species. We have determined the sequence of chkYB-1, investigated its ability to bind to sites known to be involved in tissue-specific expression in the liver, and examined factors influencing its hepatic expression. These studies have demonstrated that the level of chkYB-1 mRNA in the liver decreases steadily throughout embryogenesis and for several weeks posthatching until adult levels are attained. We present several lines of evidence that YB-1 expression in the liver is positively associated with DNA synthesis or cell proliferation. Its binding characteristics indicate that the protein can interact specifically with a number of binding sites for liver-enriched or specific factors. In addition, although it is not particularly asymmetric in terms of base composition, we find a marked preference in binding to the pyrimidine-rich strand of these sites regardless of the presence or polarity of an intact CCAAT box. The increased levels of expression of YB-1 during proliferation combined with its binding characteristics suggest that it may be involved in the reduced expression of liver-specific genes observed at early stages of development or during liver regeneration.
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Grant CE, Deeley RG. Cloning and characterization of chicken YB-1: regulation of expression in the liver. Mol Cell Biol 1993; 13:4186-96. [PMID: 8321222 PMCID: PMC359968 DOI: 10.1128/mcb.13.7.4186-4196.1993] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A cDNA expression library constructed from day 9 embryonic liver was screened with a previously identified protein binding site in the flanking region of the liver-specific, estrogen-dependent avian apoVLDLII gene. Two of the clones isolated were shown to encode the chicken homolog of the Y-box binding protein, YB-1 (dbpb), which we have designated chkYB-1. This protein was originally identified in avian extracts by virtue of its ability to bind to two reverse CCAAT motifs in the Rous sarcoma virus enhancer. Since its identification, additional nucleic acid binding properties have been ascribed to its homologs, or closely related proteins, in other species. We have determined the sequence of chkYB-1, investigated its ability to bind to sites known to be involved in tissue-specific expression in the liver, and examined factors influencing its hepatic expression. These studies have demonstrated that the level of chkYB-1 mRNA in the liver decreases steadily throughout embryogenesis and for several weeks posthatching until adult levels are attained. We present several lines of evidence that YB-1 expression in the liver is positively associated with DNA synthesis or cell proliferation. Its binding characteristics indicate that the protein can interact specifically with a number of binding sites for liver-enriched or specific factors. In addition, although it is not particularly asymmetric in terms of base composition, we find a marked preference in binding to the pyrimidine-rich strand of these sites regardless of the presence or polarity of an intact CCAAT box. The increased levels of expression of YB-1 during proliferation combined with its binding characteristics suggest that it may be involved in the reduced expression of liver-specific genes observed at early stages of development or during liver regeneration.
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Affiliation(s)
- C E Grant
- Cancer Research Laboratories, Queen's University, Kingston, Ontario, Canada
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Ozer J, Chalkley R, Sealy L. Isolation of the CCAAT transcription factor subunit EFIA cDNA and a potentially functional EFIA processed pseudogene from Bos taurus: insights into the evolution of the EFIA/dbpB/YB-1 gene family. Gene 1993; 124:223-30. [PMID: 8444345 DOI: 10.1016/0378-1119(93)90397-l] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The genomic copy multiplicity of the CCAAT transcription complex component enhancer factor I subunit A (EFIA) has been examined. When a mammalian genomic Southern blot was hybridized to a rat EFIA cDNA, a complex pattern consisting of numerous related sequences was found in all the species examined, with Bos taurus being the least complex. An EFIA#1 cDNA from Bos taurus was isolated from a primary lung endothelial cell cDNA library by screening with the 1489-bp rat EFIA cDNA. The deduced bovine EFIA#1 amino acid (aa) sequence is 98% identical to rat EFIA and 100% identical to human EFIA/DbpB/YB-1 family member DNA-binding protein B (DbpB). In addition, a processed EFIA pseudogene from Bos taurus, designated bovine psi EFIA#1, was obtained from a genomic library by screening with a rat EFIA cDNA probe. The bovine psi EFIA#1 gene has an ORF which, if expressed, would encode a 140-aa sequence, with aa 31-140 having 84% identity to bovine EFIA#1. The genomic cloning data indicate that processed pseudogenes are partially responsible for the complexity of the EFIA genomic Southern blots. The phenomenon of 'repeat induced point mutation' (ripping) at bovine psi EFIA#1 gene CpG dinucleotides occurs at a 6.5-fold higher frequency than expected from random mutagenesis. Therefore, ripping is likely to be the mechanism by which the bovine EFIA#1 pseudogene's ectopic recombination potential was inactivated.
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Affiliation(s)
- J Ozer
- Department of Cell Biology, Vanderbilt University Medical Center, Nashville, TN 37232
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Affiliation(s)
- D M Kingsley
- Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, California 94305-5427
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