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Nagda BM, Nguyen VM, White RT. promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting DNA Promoter Sequences. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:208-214. [PMID: 38051616 DOI: 10.1109/tcbb.2023.3339597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Accurate identification of DNA promoter sequences is of crucial importance in unraveling the underlying mechanisms that regulate gene transcription. Initiation of transcription is controlled through regulatory transcription factors binding to promoter core regions in the DNA sequence. Detection of promoter regions is necessary if we are to build genetic regulatory networks for biomedical and clinical applications, and for identification of rarely expressed genes. We propose a novel ensemble learning technique using deep recurrent neural networks with convolutional feature extraction and hard negative pattern mining to detect several types of promoter sequences, including promoter sequences with the TATA-box and without the TATA-box, within DNA sequences of four different species. Using extensive independent tests and previously published results, we demonstrate that our method sets a new state-of-the-art of over 98% Matthews correlation coefficient in all eight organism categories for recognizing the stretch of base pairs that code for the promoter region within DNA sequences.
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Contreras‐Marciales ADP, López‐Guzmán SF, Benítez‐Hess ML, Oviedo N, Hernández‐Sánchez J. Characterization of the promoter region of the murine Catsper2 gene. FEBS Open Bio 2022; 12:2236-2249. [PMID: 36345591 PMCID: PMC9714369 DOI: 10.1002/2211-5463.13518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
CATSPER2 (Cation channel sperm-associated protein 2) protein, which is part of the calcium CATSPER channel located in the membrane of the flagellar principal piece of the sperm cell, is only expressed in the testis during spermatogenesis. Deletions or mutations in the Catsper2 gene are associated with the deafness-infertility syndrome (DIS) and non-syndromic male infertility. However, the mechanisms by which Catsper2 is regulated are unknown. Here, we report the characterization of the promoter region of murine Catsper2 and the role of CTCF and CREMτ in its transcription. We report that the promoter region has transcriptional activity in both directions, as determined by observing luciferase activity in mouse Sertoli and GC-1 spg transfected cells. WGBS data analysis indicated that a CpG island identified in silico is non-methylated; Chromatin immunoprecipitation (ChIP)-seq data analysis revealed that histone marks H3K4me3 and H3K36me3 are present in the promoter and body of the Catsper2 gene respectively, indicating that Catsper2 is subject to epigenetic regulation. In addition, the murine Catsper2 core promoter was delimited to a region between -54/+189 relative to the transcription start site (TSS), where three CTCF and one CRE binding site were predicted. The functionality of these sites was determined by mutation of the CTCF sites and deletion of the CRE site. Finally, ChIP assays confirmed that CREMτ and CTCF bind to the Catsper2 minimal promoter region. This study represents the first functional analysis of the murine Catsper2 promoter region and the mechanisms that regulate its expression.
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Affiliation(s)
- Andrea del Pilar Contreras‐Marciales
- Departamento de Genética y Biología MolecularCentro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV)Ciudad de MéxicoMexico
| | - Sergio Federico López‐Guzmán
- Departamento de Genética y Biología MolecularCentro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV)Ciudad de MéxicoMexico
| | - María Luisa Benítez‐Hess
- Departamento de Genética y Biología MolecularCentro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV)Ciudad de MéxicoMexico
| | - Norma Oviedo
- Unidad de Investigación Médica en Inmunología e Infectología, Centro Médico Nacional, La RazaInstituto Mexicano del Seguro SocialCiudad de MéxicoMexico
| | - Javier Hernández‐Sánchez
- Departamento de Genética y Biología MolecularCentro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV)Ciudad de MéxicoMexico
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Xiong J, Liu L, Ma X, Li F, Tang C, Li Z, Lü B, Zhou T, Lian X, Chang Y, Tang M, Xie S, Lu X. Characterization of PtAOS1 Promoter and Three Novel Interacting Proteins Responding to Drought in Poncirus trifoliata. Int J Mol Sci 2020; 21:ijms21134705. [PMID: 32630273 PMCID: PMC7370134 DOI: 10.3390/ijms21134705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 11/16/2022] Open
Abstract
Jasmonic acid (JA) plays a crucial role in various biological processes including development, signal transduction and stress response. Allene oxide synthase (AOS) catalyzing (13S)-hydroperoxyoctadecatrienoic acid (13-HPOT) to an unstable allene oxide is involved in the first step of JA biosynthesis. Here, we isolated the PtAOS1 gene and its promoter from trifoliate orange (Poncirus trifoliata). PtAOS1 contains a putative chloroplast targeting sequence in N-terminal and shows relative to pistachio (Pistacia vera) AOS. A number of stress-, light- and hormone-related cis-elements were found in the PtAOS1 promoter which may be responsible for the up-regulation of PtAOS1 under drought and JA treatments. Transient expression in tobacco (Nicotiana benthamiana) demonstrated that the P-532 (-532 to +1) fragment conferring drive activity was a core region in the PtAOS1 promoter. Using yeast one-hybrid, three novel proteins, PtDUF886, PtDUF1685 and PtRAP2.4, binding to P-532 were identified. The dual luciferase assay in tobacco illustrated that all three transcription factors could enhance PtAOS1 promoter activity. Genes PtDUF1685 and PtRAP2.4 shared an expression pattern which was induced significantly by drought stress. These findings should be available evidence for trifoliate orange responding to drought through JA modulation.
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Affiliation(s)
- Jiang Xiong
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Lian Liu
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Xiaochuan Ma
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Feifei Li
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
- Institute of Horticulture, Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Chaolan Tang
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Zehang Li
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Biwen Lü
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Tie Zhou
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Xuefei Lian
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Yuanyuan Chang
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Mengjing Tang
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Shenxi Xie
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
| | - Xiaopeng Lu
- Department of Horticulture, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.X.); (L.L.); (X.M.); (F.L.); (C.T.); (Z.L.); (B.L.); (T.Z.); (X.L.); (Y.C.); (M.T.); (S.X.)
- National Centre for Citrus Improvement, Changsha 410128, China
- Correspondence: ; Tel./Fax: +86-0731-84618171
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Tello J, Torres-Pérez R, Flutre T, Grimplet J, Ibáñez J. VviUCC1 Nucleotide Diversity, Linkage Disequilibrium and Association with Rachis Architecture Traits in Grapevine. Genes (Basel) 2020; 11:E598. [PMID: 32485819 PMCID: PMC7348735 DOI: 10.3390/genes11060598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/25/2022] Open
Abstract
Cluster compactness is a trait with high agronomic relevance, affecting crop yield and grape composition. Rachis architecture is a major component of cluster compactness determinism, and is a target trait toward the breeding of grapevine varieties less susceptible to pests and diseases. Although its genetic basis is scarcely understood, a preliminary result indicated a possible involvement of the VviUCC1 gene. The aim of this study was to characterize the VviUCC1 gene in grapevine and to test the association between the natural variation observed for a series of rachis architecture traits and the polymorphisms detected in the VviUCC1 sequence. This gene encodes an uclacyanin plant-specific cell-wall protein involved in fiber formation and/or lignification processes. A high nucleotide diversity in the VviUCC1 gene promoter and coding regions was observed, but no critical effects were predicted in the protein domains, indicating a high level of conservation of its function in the cultivated grapevine. After correcting statistical models for genetic stratification and linkage disequilibrium effects, marker-trait association results revealed a series of single nucleotide polymorphisms (SNPs) significantly associated with cluster compactness and rachis traits variation. Two of them (Y-984 and K-88) affected two common cis-transcriptional regulatory elements, suggesting an effect on phenotype via gene expression regulation. This work reinforces the interest of further studies aiming to reveal the functional effect of the detected VviUCC1 variants on grapevine rachis architecture.
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Affiliation(s)
- Javier Tello
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain; (R.T.-P.); (J.G.); (J.I.)
| | - Rafael Torres-Pérez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain; (R.T.-P.); (J.G.); (J.I.)
- Servicio de Bioinformática para Genómica y Proteómica (BioinfoGP), Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Timothée Flutre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France;
| | - Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain; (R.T.-P.); (J.G.); (J.I.)
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain
| | - Javier Ibáñez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain; (R.T.-P.); (J.G.); (J.I.)
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Ali S, Kim WC. A Fruitful Decade Using Synthetic Promoters in the Improvement of Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1433. [PMID: 31737027 PMCID: PMC6838210 DOI: 10.3389/fpls.2019.01433] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/16/2019] [Indexed: 05/17/2023]
Abstract
Advances in plant biotechnology provide various means to improve crop productivity and greatly contributing to sustainable agriculture. A significant advance in plant biotechnology has been the availability of novel synthetic promoters for precise spatial and temporal control of transgene expression. In this article, we review the development of various synthetic promotors and the rise of their use over the last several decades for regulating the transcription of various transgenes. Similarly, we provided a brief description of the structure and scope of synthetic promoters and the engineering of their cis-regulatory elements for different targets. Moreover, the functional characteristics of different synthetic promoters, their modes of regulating the expression of candidate genes in response to different conditions, and the resulting plant trait improvements reported in the past decade are discussed.
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An Y, Wang YT, Ma YT, Wulasihan M, Huang Y, Adi D, Yang YN, Ma X, Li XM, Xie X, Huang D, Liu F, Chen BD. IL-10 genetic polymorphisms were associated with valvular calcification in Han, Uygur and Kazak populations in Xinjiang, China. PLoS One 2015; 10:e0128965. [PMID: 26039365 PMCID: PMC4454577 DOI: 10.1371/journal.pone.0128965] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/04/2015] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Valvular calcification occurs via ongoing endothelial injury associated with inflammation. IL-10 is an anti-inflammatory cytokine and 75% of the variation in IL-10 production is genetically determined. However, the relationship between genetic polymorphisms of IL-10 and valvular calcification has not been studied. The objective of this study was to investigate the association between valvular calcification and IL-10 genetic polymorphisms in the Han, Uygur and Kazak populations in China. PATIENTS AND METHODS All of the participants were selected from subjects participating in the Cardiovascular Risk Survey (CRS) study. The single nucleotide polymorphisms (SNPs) rs1800871 and rs1800872 of the IL-10 gene were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three independent case-control studies involving the Han population, the Uygur population and the Kazak population were used in the analysis. RESULTS For the Han and Kazak populations, rs1800871 was found to be associated with valvular calcification in the recessive model, and the difference remained statistically significant following multivariate adjustment (p<0.001, p=0.031, respectively). For the Han, Uygur and Kazak populations, rs1800872 was found to be associated with valvular calcification in the dominant model, and the difference remained statistically significant following multivariate adjustment (p<0.001, p=0.009, and p=0.023,respectively). CONCLUSION Both rs1800871 and rs1800872 of the IL-10 gene are associated with valvular calcification in the Han and Kazak populations in China. Rs1800872 is also associated with valvular calcification in the Uygur population.
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Affiliation(s)
- Yong An
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Yong-Tao Wang
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Yi-Tong Ma
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
- * E-mail: (YTM); (MW)
| | - Muhuyati Wulasihan
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- * E-mail: (YTM); (MW)
| | - Ying Huang
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Dilare Adi
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Yi-Ning Yang
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Xiang Ma
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Xiao-Mei Li
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Xiang Xie
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Ding Huang
- Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 P.R. China
| | - Fen Liu
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
| | - Bang-Dang Chen
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054 P.R. China
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Dutt M, Dhekney SA, Soriano L, Kandel R, Grosser JW. Temporal and spatial control of gene expression in horticultural crops. HORTICULTURE RESEARCH 2014; 1:14047. [PMID: 26504550 PMCID: PMC4596326 DOI: 10.1038/hortres.2014.47] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/19/2014] [Accepted: 08/06/2014] [Indexed: 05/05/2023]
Abstract
Biotechnology provides plant breeders an additional tool to improve various traits desired by growers and consumers of horticultural crops. It also provides genetic solutions to major problems affecting horticultural crops and can be a means for rapid improvement of a cultivar. With the availability of a number of horticultural genome sequences, it has become relatively easier to utilize these resources to identify DNA sequences for both basic and applied research. Promoters play a key role in plant gene expression and the regulation of gene expression. In recent years, rapid progress has been made on the isolation and evaluation of plant-derived promoters and their use in horticultural crops, as more and more species become amenable to genetic transformation. Our understanding of the tools and techniques of horticultural plant biotechnology has now evolved from a discovery phase to an implementation phase. The availability of a large number of promoters derived from horticultural plants opens up the field for utilization of native sequences and improving crops using precision breeding. In this review, we look at the temporal and spatial control of gene expression in horticultural crops and the usage of a variety of promoters either isolated from horticultural crops or used in horticultural crop improvement.
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Affiliation(s)
- Manjul Dutt
- Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
| | - Sadanand A Dhekney
- Department of Plant Sciences, Sheridan Research and Extension Center, University of Wyoming, Sheridan, WY 82801, USA
| | - Leonardo Soriano
- Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
- Universidade de Sao Paulo, Centro de Energia Nuclear na Agricultura, Piracicaba, Brazil
| | - Raju Kandel
- Department of Plant Sciences, Sheridan Research and Extension Center, University of Wyoming, Sheridan, WY 82801, USA
| | - Jude W Grosser
- Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
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Chai KH, McLoughlin DM, Chan TF, Chan HYE, Lau KF. Genomic organization and promoter cloning of the human X11α gene APBA1. DNA Cell Biol 2011; 31:651-9. [PMID: 22136355 DOI: 10.1089/dna.2011.1447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X11α is a brain specific multi-modular protein that interacts with the Alzheimer's disease amyloid precursor protein (APP). Aggregation of amyloid-β peptide (Aβ), an APP cleavage product, is believed to be central to the pathogenesis of Alzheimer's disease. Recently, overexpression of X11α has been shown to reduce Aβ generation and to ameliorate memory deficit in a transgenic mouse model of Alzheimer's disease. Therefore, manipulating the expression level of X11α may provide a novel route for the treatment of Alzheimer's disease. Human X11α is encoded by the gene APBA1. As evidence suggests that X11α expression can be regulated at transcription level, we have determined the gene structure and cloned the promoter of APBA1. APBA1 spans over 244 kb on chromosome 9 and is composed of 13 exons and has multiple transcription start sites. A putative APBA1 promoter has been identified upstream of exon 1 and functional analysis revealed that this is highly active in neurons. By deletion analysis, the minimal promoter was found to be located between -224 and +14, a GC-rich region that contains a functional Sp3 binding site. In neurons, overexpression of Sp3 stimulates the APBA1 promoter while an Sp3 inhibitor suppresses the promoter activity. Moreover, inhibition of Sp3 reduces endogenous X11α expression and promotes the generation of Aβ. Our findings reveal that Sp3 play an essential role in APBA1 transcription.
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Affiliation(s)
- Ka-Ho Chai
- Biochemistry Program, School Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong SAR
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Niewiadomska-Cimicka A, Schmidt M, Ożyhar A, Jones D, Jones G, Kochman M. Juvenile hormone binding protein core promoter is TATA-driven with a suppressory element. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:226-35. [DOI: 10.1016/j.bbagrm.2011.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 01/10/2011] [Accepted: 02/05/2011] [Indexed: 11/29/2022]
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10
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Yu HT, Chan WWL, Chai KH, Lee CWC, Chang RCC, Yu MS, McLoughlin DM, Miller CCJ, Lau KF. Transcriptional regulation of human FE65, a ligand of Alzheimer's disease amyloid precursor protein, by Sp1. J Cell Biochem 2010; 109:782-93. [PMID: 20091743 DOI: 10.1002/jcb.22457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
FE65 is a neuronal-enriched adaptor protein that binds to the Alzheimer's disease amyloid precursor protein (APP). FE65 forms a transcriptionally active complex with the APP intracellular domain (AICD). The precise gene targets for this complex are unclear but several Alzheimer's disease-linked genes have been proposed. Additionally, evidence suggests that FE65 influences APP metabolism. The mechanism by which FE65 expression is regulated is as yet unknown. To gain insight into the regulatory mechanism, we cloned a 1.6 kb fragment upstream of the human FE65 gene and found that it possesses particularly strong promoter activity in neurones. To delineate essential regions in the human FE65 promoter, a series of deletion mutants were generated. The minimal FE65 promoter was located between -100 and +5, which contains a functional Sp1 site. Overexpression of the transcription factor Sp1 potentiates the FE65 promoter activity. Conversely, suppression of the FE65 promoter was observed in cells either treated with an Sp1 inhibitor or in which Sp1 was knocked down. Furthermore, reduced levels of Sp1 resulted in downregulation of endogenous FE65 mRNA and protein. These findings reveal that Sp1 plays a crucial role in transcriptional control of the human FE65 gene.
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Affiliation(s)
- Hoi-Tin Yu
- Department of Biochemistry (Science), The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR
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Warnatz HJ, Querfurth R, Guerasimova A, Cheng X, Haas SA, Hufton AL, Manke T, Vanhecke D, Nietfeld W, Vingron M, Janitz M, Lehrach H, Yaspo ML. Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Res 2010; 38:6112-23. [PMID: 20494980 PMCID: PMC2952857 DOI: 10.1093/nar/gkq402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Given the inherent limitations of in silico studies relying solely on DNA sequence analysis, the functional characterization of mammalian promoters and associated cis-regulatory elements requires experimental support, which demands cloning and analysis of putative promoter regions. Focusing on human chromosome 21, we cloned 182 gene promoters of 2500 bp in length and conducted reporter gene assays on transfected-cell arrays. We found 56 promoters that were active in HEK293 cells, while another 49 promoters could be activated by treatment of cells with Trichostatin A or depletion of serum. We observed high correlations between promoter activities and endogenous transcript levels, RNA polymerase II occupancy, CpG islands and core promoter elements. Truncation of a subset of 62 promoters to ∼500 bp revealed that truncation rarely resulted in loss of activity, but rather in loss of responses to external stimuli, suggesting the presence of cis-regulatory response elements within distal promoter regions. In these regions, we found a strong enrichment of transcription factor binding sites that could potentially activate gene expression in the presence of stimuli. This study illustrates the modular functional architecture of chromosome 21 promoters and helps to reveal the complex mechanisms governing transcriptional regulation.
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Affiliation(s)
- Hans-Jörg Warnatz
- Department for Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
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12
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Sharma AK, Sharma MK. Plants as bioreactors: Recent developments and emerging opportunities. Biotechnol Adv 2009; 27:811-832. [PMID: 19576278 PMCID: PMC7125752 DOI: 10.1016/j.biotechadv.2009.06.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 06/15/2009] [Accepted: 06/16/2009] [Indexed: 12/18/2022]
Abstract
In recent years, the use of plants as bioreactors has emerged as an exciting area of research and significant advances have created new opportunities. The driving forces behind the rapid growth of plant bioreactors include low production cost, product safety and easy scale up. As the yield and concentration of a product is crucial for commercial viability, several strategies have been developed to boost up protein expression in transgenic plants. Augmenting tissue-specific transcription, elevating transcript stability, tissue-specific targeting, translation optimization and sub-cellular accumulation are some of the strategies employed. Various kinds of products that are currently being produced in plants include vaccine antigens, medical diagnostics proteins, industrial and pharmaceutical proteins, nutritional supplements like minerals, vitamins, carbohydrates and biopolymers. A large number of plant-derived recombinant proteins have reached advanced clinical trials. A few of these products have already been introduced in the market.
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Affiliation(s)
- Arun K Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Manoj K Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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13
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Hazelton S, Spurlock D, Bidwell C, Donkin S. Cloning the Genomic Sequence and Identification of Promoter Regions of Bovine Pyruvate Carboxylase. J Dairy Sci 2008; 91:91-9. [DOI: 10.3168/jds.2007-0542] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Mannini R, Rivieccio V, D'Auria S, Tanfani F, Ausili A, Facchiano A, Facchiano A, Pedone C, Grimaldi G. Structure/function of KRAB repression domains: Structural properties of KRAB modules inferred from hydrodynamic, circular dichroism, and FTIR spectroscopic analyses. Proteins 2005; 62:604-16. [PMID: 16385564 DOI: 10.1002/prot.20792] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The abundant zinc finger proteins (ZFPs) sharing the KRAB motif, a potent transcription repression domain, direct the assembly on templates of multiprotein repression complexes. A pivotal step in this pathway is the assembly of a KRAB domain-directed complex with a primary corepressor, KAP1/KRIP-1/TIF1beta. The structure/function dependence of KRAB/TIF1beta protein-protein interaction and properties of the complex, therefore, play pivotal roles in diverse cellular processes depending on KRAB-ZFPs regulation. KRAB domains are functionally bipartite. The 42 amino acid-long KRAB-A module, indeed, is necessary and sufficient for transcriptional repression and for the interaction with the tripartite RBCC region of TIF1beta, while the KRAB-B motif seems to potentiate the assembly of the complex. The structural properties of KRAB-A and KRAB-AB domains from the human ZNF2 protein have been investigated by characterizing highly purified lone (A) and composite (AB) modules. Hydrodynamic and spectroscopic features, investigated by means of gel filtration, circular dichroism, and infrared spectroscopy, provide evidence that both KRAB-A and KRAB-AB domains present low compactness, structural disorder, residual secondary structure content, flexibility, and tendency to molecular aggregation. Comparative analysis among KRAB-A and KRAB-AB modules suggests that the presence of the -B module may influence the properties of lone KRAB-A by affecting the structural flexibility and stability of the conformers. The combined experimental data and the intrinsic features of KRAB-A and KRAB-AB primary structures indicate a potential role of specific subregions within the modules in driving structural flexibility, which is proposed to be of importance for their function.
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Affiliation(s)
- Riccardo Mannini
- Istituto di Genetica e Biofisica Adriano Buzzati-Traverso, CNR, Italy
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15
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Oh JH, Yang JO, Hahn Y, Kim MR, Byun SS, Jeon YJ, Kim JM, Song KS, Noh SM, Kim S, Yoo HS, Kim YS, Kim NS. Transcriptome analysis of human gastric cancer. Mamm Genome 2005; 16:942-54. [PMID: 16341674 DOI: 10.1007/s00335-005-0075-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Accepted: 08/09/2005] [Indexed: 12/01/2022]
Abstract
To elucidate the genetic events associated with gastric cancer, 124,704 cDNA clones were collected from 37 human gastric cDNA libraries, including 20 full-length enriched cDNA libraries of gastric cancer cell lines and tissues from Korean patients. An analysis of the collected ESTs revealed that 97,930 high-quality ESTs coalesced into 13,001 clusters, of which 11,135 clusters (85.6%) were annotated to known ESTs. The analysis of the full-length cDNAs also revealed that 4862 clusters (51.7%) contained at least one putative full-length cDNA clone with an initiation codon, with the average length of the 5' UTR of 140 bp. A large number appear to have a diverse transcription start site (TSS). An examination of the TSS of some genes, such as TEGT and GAPD, using 5' RACE revealed that the predicted TSSs are actually found in human gastric cancer cells and that several TSSs differ depending on the specific gastric cell line. Furthermore, of the human gastric ESTs, 766 genes (9.5%) were present as putative alternatively spliced variants. Confirmation of the predicted spliced isoforms using RT-PCR showed that the predicted isoforms exist in gastric cancer cells and some isoforms coexist in gastric cell lines. These results provide potentially useful information for elucidating the molecular mechanisms associated with gastric oncogenesis.
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Affiliation(s)
- Jung-Hwa Oh
- Laboratory of Human Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon , 305-333, Korea
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16
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Zhou J, Fan C, Zhong Y, Liu Y, Liu M, Zhou A, Ren K, Zhang J. Genomic organization, promoter characterization and roles of Sp1 and AP-2 in the basal transcription of mousePDIP1gene. FEBS Lett 2005; 579:1715-22. [PMID: 15757666 DOI: 10.1016/j.febslet.2005.02.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 01/31/2005] [Accepted: 02/04/2005] [Indexed: 11/25/2022]
Abstract
The mouse polymerase delta-interacting protein 1 gene, PDIP1, is mapped to chromosome 7F3 region, spans approximately 16.7kb, and is organized into six exons. The transcription start site (TSS) was determined to be G, corresponding to position of 162-bp upstream of the translation start codon. The promoter region was found to lack TATA box or CCAAT box, instead, a CpG island was detected surrounding TSS. The region from -162 to +114 is required for basal transcriptional regulation of mouse PDIP1 gene, contains two AP-2 and two Sp1 binding sites. The Sp1 site upstream of TSS activates, while the other Sp1 site and two AP-2 sites suppress the transcription activity of mouse PDIP1 gene.
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Affiliation(s)
- Jianlin Zhou
- Department of Biochemistry and Molecular Biology, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, China
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17
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Luk JM, Tong MK, Mok BW, Tam PC, Yeung WSB, Lee KF. Sp1 site is crucial for the mouse claudin-19 gene expression in the kidney cells. FEBS Lett 2005; 578:251-6. [PMID: 15589828 DOI: 10.1016/j.febslet.2004.11.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Revised: 10/25/2004] [Accepted: 11/02/2004] [Indexed: 12/11/2022]
Abstract
Members of the claudin family play important roles in the formation of tight junctions in the kidneys, liver and intestine. Claudin-19 (Cldn19), a newly identified member of this family, is highly expressed in the kidney of the mouse. To have a better understanding on mouse claudin-19 gene expression, a 0.9-kb DNA fragment containing the 5'-flanking region of the Cldn19 gene was isolated. DNA sequence comparison between the mouse and human Cldn19 promoter regions exhibited little homology. One transcription initiation site was located at 104 nucleotides upstream of the start codon (ATG) of the Cldn19 gene. The mouse claudin-19 promoter lacked typical CAAT or GC-box. Deletion constructs of the 0.9-kb DNA fragment were generated and fused to a promoterless luciferase (Luc) reporter plasmid. Transfection studies using various kidney cell lines (MDCK, mIMCD3 and HEK293) revealed that the minimal promoter fragment resided in the -39 to -108 region, which contained a number of binding sites for transcription factors including Sp1. Site-directed mutagenesis using specific oligo probes confirmed that Sp1 was crucial for Cldn19 transactivation in the three cell lines studied. Electromobility shift assay confirmed that the nuclear extracts of these cells bound to the Sp1 oligo derived from Cldn19 promoter, but not to the mutated Sp1 oligo probe. Moreover, this DNA-protein complex would be recognized by Sp1 antibody, indicating specific Sp1 binding. Collectively, our data suggest that Sp1 binds to the claudin-19 promoter region and is responsible for its expression in the kidney cell lines in vitro.
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Affiliation(s)
- John M Luk
- Department of Surgery, Hong Kong Jockey Club Clinical Research Centre, Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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18
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McLeod A, Smart CD, Fry WE. Core promoter structure in the oomycete Phytophthora infestans. EUKARYOTIC CELL 2004; 3:91-9. [PMID: 14871940 PMCID: PMC329498 DOI: 10.1128/ec.3.1.91-99.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have investigated the core promoter structure of the oomycete Phytophthora infestans. The transcriptional start sites (TSS) of three previously characterized P. infestans genes, Piexo1, Piexo3, and Piendo1, were determined by primer extension analyses. The TSS regions were homologous to a previously identified 16-nucleotide (nt) core sequence that overlaps the TSS in most oomycete genes. The core promoter regions of Piexo1 and Piendo1 were investigated by using a transient protoplast expression assay and the reporter gene beta-glucuronidase. Mutational analyses of the promoters of Piexo1 and Piendo1 showed that there is a putative core promoter element encompassing the TSS (-2 to +5) that has high sequence and functional homology to a known core promoter element present in other eukaryotes, the initiator element (Inr). Downstream and flanking the Inr is a highly conserved oomycete promoter region (+7 to +15), hereafter referred to as FPR (flanking promoter region), which is also important for promoter function. The importance of the 19-nt core promoter region (Inr and FPR) in Piexo1 and Piendo1 was further investigated through electrophoretic mobility shift assays (EMSA). The EMSA studies showed that (i) both core promoters were able to specifically bind a protein or protein complex in a P. infestans whole-cell protein extract and (ii) the same mutations that reduced binding of the EMSA complex also reduced beta-glucuronidase (GUS) levels in transient expression assays. The consistency of results obtained using two different assays (GUS transient assays [in vivo] and EMSA studies [in vitro]) supports a convergence of inference about the relative importance of specific nucleotides within the 19-nt core promoter region.
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Affiliation(s)
- Adele McLeod
- Department of Plant Pathology, Cornell University, Ithaca, New York 14853, USA
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19
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Zhou GP, Wong C, Su R, Crable SC, Anderson KP, Gallagher PG. Human potassium chloride cotransporter 1 (SLC12A4) promoter is regulated by AP-2 and contains a functional downstream promoter element. Blood 2004; 103:4302-9. [PMID: 14976052 DOI: 10.1182/blood-2003-01-0107] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Most K-Cl cotransport in the erythrocyte is attributed to potassium chloride cotransporter 1 (KCC1). K-Cl cotransport is elevated in sickle erythrocytes, and the KCC1 gene has been proposed as a modifier gene in sickle cell disease. To provide insight into our understanding of the regulation of the human KCC1 gene, we mapped the 5' end of the KCC1 cDNA, cloned the corresponding genomic DNA, and identified the KCC1 gene promoter. The core promoter lacks a TATA box and is composed of an initiator element (InR) and a downstream promoter element (DPE), a combination found primarily in Drosophila gene promoters and rarely observed in mammalian gene promoters. Mutational analyses demonstrated that both the InR and DPE sites were critical for full promoter activity. In vitro DNase I footprinting, electrophoretic mobility shift assays, and reporter gene assays identified functional AP-2 and Sp1 sites in this region. The KCC1 promoter was transactivated by forced expression of AP-2 in heterologous cells. Sequences encoding the InR, DPE, AP-2, and Sp1 sites were 100% conserved between human and murine KCC1 genes. In vivo studies using chromatin immunoprecipitation assays with antihistone H3 and antihistone H4 antibodies demonstrated hyperacetylation of this core promoter region.
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Affiliation(s)
- Guo-Ping Zhou
- Department of Pediatrics, Yale University School of Medicine, PO Box 208064, 333 Cedar St, New Haven, CT 06520-8064, USA
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20
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Kim SY, Choi SY, Chao W, Volsky DJ. Transcriptional regulation of human excitatory amino acid transporter 1 (EAAT1): cloning of the EAAT1 promoter and characterization of its basal and inducible activity in human astrocytes. J Neurochem 2004; 87:1485-98. [PMID: 14713304 DOI: 10.1046/j.1471-4159.2003.02128.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Excitatory amino acid transporter 1 (EAAT1) is one of the two glial glutamate transporters that clear the extracellular glutamate generated during neuronal signal transmission. Here, we cloned and characterized a 2.1-kb promoter region of human EAAT1 and investigated its function in the transcriptional regulation of the EAAT1 gene in human primary astrocytes. The full-length promoter region lacked TATA and CCAAT boxes and an initiator element, it contained several potential transcription factor-binding sites and it exhibited promoter activity in primary astrocytes and in several types of transformed cells. Consecutive 5'-deletion analysis of the EAAT1 promoter indicated the presence of negative and positive regulatory regions and a putative core promoter between -57 bp and +20 bp relative to the transcription start site (TSS). The core promoter contained a single GC-box in position -52/-39 and one E-box near the TSS and the GC-box site that was responsible for 90% of the basal promoter activity as determined by mutational analysis. Electrophoretic mobility shift, supershift and competition assays demonstrated binding of stimulating proteins (Sp) 1 and 3 to the GC-box and upstream stimulating factor (USF) 1 to the E-box. Treatment of primary human astrocytes with cellular modulators 8-bromo cyclic AMP and epidermal growth factor increased EAAT1 promoter activity in transient transfection assays and increased cellular EAAT1 mRNA expression and glutamate uptake by astrocytes. Conversely, tumor necrosis factor-alpha reduced both EAAT promoter activity and cellular EAAT1 mRNA expression. These results enable studies of transcriptional regulation of EAAT1 gene at the promoter level.
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Affiliation(s)
- Seon-Young Kim
- Molecular Virology Division, St. Luke's-Roosevelt Hospital Center and Columbia University, New York, USA
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21
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Hulzink RJM, Weerdesteyn H, Croes AF, Gerats T, van Herpen MMA, van Helden J. In silico identification of putative regulatory sequence elements in the 5'-untranslated region of genes that are expressed during male gametogenesis. PLANT PHYSIOLOGY 2003; 132:75-83. [PMID: 12746513 PMCID: PMC166953 DOI: 10.1104/pp.102.014894] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2002] [Revised: 11/28/2002] [Accepted: 01/02/2003] [Indexed: 05/19/2023]
Abstract
During pollen development, transcription of a large number of genes results in the appearance of distinct sets of transcripts. Similar mRNA sets are present in pollen of both mono- and dicotyledonous plant species, which indicates an evolutionary conservation of genetic programs that determine pollen gene expression. In pollen, regulation of gene expression occurs at the transcriptional and posttranscriptional level. The 5'-untranslated region (UTR) of several pollen transcripts has been shown to be important for regulation of pollen gene expression. The important regulatory role of 5'-UTR sequences and the evolutionary conservation of genetic programs in pollen led to the hypothesis that the 5'-UTRs of pollen-expressed genes share regulatory sequence elements. In an attempt to identify these pollen 5'-UTR elements, a statistical analysis was performed using 5'-UTR sequences of pollen- and sporophytic-expressed genes. The analysis revealed the presence of several pollen-specific 5'-UTR sequence elements. Assembly of the pollen 5'-UTR elements led to the identification of various consensus sequences, including those that previously have been demonstrated to play a role in the regulation of pollen gene expression. Several pollen 5'-UTR elements were found to be preferentially associated to genes from dicots, wet-type stigma plants, or plants containing bicellular pollen. Moreover, three sequence elements exhibited a preferential association to the 5'-UTR of pollen-expressed genes from Arabidopsis and Brassica napus. Functional implications of these observations are discussed.
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22
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Vallejo AN, Bryl E, Klarskov K, Naylor S, Weyand CM, Goronzy JJ. Molecular basis for the loss of CD28 expression in senescent T cells. J Biol Chem 2002; 277:46940-9. [PMID: 12324461 DOI: 10.1074/jbc.m207352200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
CD28(null) T cells are the most consistent biological indicator of the aging immune system in humans and are predictors of immunoincompetence in the elderly. The loss of CD28 is the result of an inoperative transcriptional initiator (INR), which consists of two nonoverlapping alpha and beta motifs that have distinct protein binding profiles but function as a unit. In CD28(null) T cells, there is a coordinate loss of alpha-/beta-bound complexes, hence the alphabeta-INR is inactive. In the present work therefore, studies were conducted to identify the components of such complexes that may account for the trans-activation of the alphabeta-INR. By affinity chromatography and tandem mass spectrometry, two proteins, namely, nucleolin and the A isoform of heterogeneous nuclear ribonucleoprotein-D0 (hnRNP-D0A), were identified to be among the key components of the site alpha complex. In DNA binding assays, specific antibodies indicated their antigenic presence in alpha-bound complexes. Transcription assays showed that they are both required in the trans-activation of alphabeta-INR-driven DNA templates. Because CD28 is T cell-restricted, and nucleolin and hnRNP-D0A are ubiquitous proteins, these results support the notion that cell-specific functions can be regulated by commonly expressed proteins. The present data also provide evidence for INR-regulated transcription that is independent of the known components of the basal transcription complex.
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Affiliation(s)
- Abbe N Vallejo
- Department of Medicine and Immunology, Mayo Clinic, Rochester, Minnesota 55905, USA.
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23
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Suzuki Y, Taira H, Tsunoda T, Mizushima-Sugano J, Sese J, Hata H, Ota T, Isogai T, Tanaka T, Morishita S, Okubo K, Sakaki Y, Nakamura Y, Suyama A, Sugano S. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep 2001; 2:388-93. [PMID: 11375929 PMCID: PMC1083880 DOI: 10.1093/embo-reports/kve085] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The 'oligo-capping' method enabled us to introduce a sequence tag to the first base of an mRNA by replacing the cap structure of the mRNA. Using cDNA libraries made from oligo-capped mRNAs, we could identify the transcriptional start site of an individual mRNA just by sequencing the 5'-end of the cDNA. The fine mapping of transcriptional start sites was performed for 5880 mRNAs in 276 human genes. Contrary to our expectations, the majority of the genes showed a diverse distribution of transcriptional start sites. They were distributed over 61.7 bp with a standard deviation of 19.5. Our finding may reflect the dynamic nature of transcriptional initiation events of human genes in vivo.
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Affiliation(s)
- Y Suzuki
- Department of Virology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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24
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Zhou T, Chiang CM. The intronless and TATA-less human TAF(II)55 gene contains a functional initiator and a downstream promoter element. J Biol Chem 2001; 276:25503-11. [PMID: 11340078 DOI: 10.1074/jbc.m102875200] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human TAF(II)55 (hTAF(II)55) is a component of the multisubunit general transcription factor TFIID and has been shown to mediate the functions of many transcriptional activators via direct protein-protein interactions. To uncover the regulatory properties of the general transcription machinery, we have isolated the hTAF(II)55 gene and dissected the regulatory elements and the core promoter responsible for hTAF(II)55 gene expression. Surprisingly, the hTAF(II)55 gene has a single uninterrupted open reading frame and is the only intronless general transcription factor identified so far. Its expression is driven by a TATA-less promoter that contains a functional initiator and a downstream promoter element, as illustrated by both transfection assays and mutational analyses. Moreover, this core promoter can mediate the activity of a transcriptional activator that is artificially recruited to the promoter in a heterologous context. Interestingly, in the promoter-proximal region there are multiple Sp1-binding sites juxtaposed to a single AP2-binding site, indicating that Sp1 and AP2 may regulate the core promoter activity of the hTAF(II)55 gene. These findings indicate that a combinatorial regulation of a general transcription factor-encoding gene can be conferred by both ubiquitous and cell type-specific transcriptional regulators.
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Affiliation(s)
- T Zhou
- Department of Biochemistry, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106-4935, USA
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25
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Nicolás M, Noé V, Jensen KB, Ciudad CJ. Cloning and characterization of the 5'-flanking region of the human transcription factor Sp1 gene. J Biol Chem 2001; 276:22126-32. [PMID: 11294852 DOI: 10.1074/jbc.m010740200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 5'-flanking region of the human Sp1 gene was cloned and characterized. Sequence analysis of this region showed the absence of both CAAT and TATA boxes and an initiator element. The proximal promoter of the Sp1 gene is a GC-rich region that contains multiple GC boxes and Ap2 binding sites. The major transcription start site is located 63 base pairs upstream of the translation start site. Transfection experiments demonstrate that all the elements necessary to achieve significant basal transcription activity are located between positions -443 and -20 relative to the translational start. Sp1 and Sp3 proteins bind to the downstream GC box located in the proximal promoter of Sp1. Furthermore, we demonstrate that the Sp1 protein activates Sp1 transcription activity; thus the Sp1 gene is autoregulated.
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Affiliation(s)
- M Nicolás
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
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26
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Suzuki Y, Tsunoda T, Sese J, Taira H, Mizushima-Sugano J, Hata H, Ota T, Isogai T, Tanaka T, Nakamura Y, Suyama A, Sakaki Y, Morishita S, Okubo K, Sugano S. Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes. Genome Res 2001. [DOI: 10.1101/gr.164001] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the “oligo-capping” method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA+/Inr+PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and theTM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.[The nucleotide sequences described in this paper have been deposited in the DDBJ, EMBL, and GenBank data libraries under accession nos.AU098358–AU100608.]
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27
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Ferrigno O, Virolle T, Djabari Z, Ortonne JP, White RJ, Aberdam D. Transposable B2 SINE elements can provide mobile RNA polymerase II promoters. Nat Genet 2001; 28:77-81. [PMID: 11326281 DOI: 10.1038/ng0501-77] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Short interspersed elements (SINEs) are highly abundant components of mammalian genomes that are propagated by retrotransposition. SINEs are recognized as a causal agent of human disease and must also have had a profound influence in shaping eukaryotic genomes. The B2 SINE family constitutes approximately 0.7% of total mouse genomic DNA (ref. 2) and is also found at low abundance in humans. It resembles the Alu family in several respects, such as its mechanism of propagation. B2 SINEs are derived from tRNA and are transcribed by RNA polymerase (pol) III to generate short transcripts that are not translated. We find here, however, that one B2 SINE also carries an active pol II promoter located outside the tRNA region. Indeed, a B2 element is responsible for the production of a mouse Lama3 transcript. The B2 pol II promoters can be bound and stimulated by the transcription factor USF (for upstream stimulatory factor), as shown by transient transfection experiments. Moreover, this pol II activity does not preclude the pol III transcription necessary for retrotransposition. Dispersal of B2 SINEs by retrotransposition may therefore have provided numerous opportunities for creating regulated pol II transcription at novel genomic sites. This mechanism may have allowed the evolution of new transcription units and new genes.
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Affiliation(s)
- O Ferrigno
- U385 INSERM, Faculté de Médecine, Nice, France
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28
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Abstract
Nerve growth factor (NGF) and retinoic acid (RA) exert important actions on PC12 cells. We have previously shown that incubation with NGF induces retinoic acid receptor beta (RARbeta) binding to a hormone response element in PC12 cells. In this study we show that NGF increases RARbeta protein levels by enhancing basal RARbeta2 promoter activity, and potentiates stimulation by RA in transient transfection assays. The effect of RA is mediated by a RA response element (RARE) located at -37/-53 and mutation of this element abolishes activation by the retinoid, as well as cooperation with NGF. However, the action of NGF is independent of the RARE and is mediated by sequences overlapping the TATA box and the INR comprising nucleotides -59 to +14. NGF produces a strong decrease in some of the complexes that bind to the INR. These results suggest that the RARbeta2 gene could be in a basal repressed state and NGF could increase RARbeta2 transcription by inducing the release of some inhibitory factors from the INR. Functional Ras is required for RARbeta2 promoter activation by NGF because expression of oncogenic Ras increases promoter activity and a dominant inhibitory Ras mutant blocks the effect of NGF. Oncogenic Raf also mimics the effect of NGF on the promoter. Other ligands of tyrosine kinase receptors that stimulate Ras also cause RARbeta2 promoter activation and act cooperatively with RA. These results indicate the existence of cross-coupling of the Ras-Raf signal transduction pathway with retinoid receptor pathways which could increase sensitivity to RA and be important for PC12 cell function.
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Affiliation(s)
- J M Cosgaya
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
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29
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Vallejo AN, Weyand CM, Goronzy JJ. Functional disruption of the CD28 gene transcriptional initiator in senescent T cells. J Biol Chem 2001; 276:2565-70. [PMID: 11069899 DOI: 10.1074/jbc.m005503200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We recently reported that aging is accompanied by the emergence of CD4(+)CD28(null) T cells, a functionally aberrant lymphocyte subset rarely seen in individuals younger than 40 years. Here, we directly examined whether the lack of CD28 expression is due to a defect at the level of transcriptional initiation. Molecular studies reveal that CD28 gene transcription is controlled by two sequence motifs, sites alpha and beta. In vitro transcription assays using initiator-dependent DNA templates revealed that reversed polarity or the deletion of either motif inhibited transcription, indicating that alpha/beta sequences constitute a composite initiator. Moreover, nuclear extracts from CD28(null) cells failed to activate transcription of alphabeta-initiator DNA templates. Transcription of such templates was, however, restored with the addition of extracts from CD28(+) cells. Although previously described initiator elements have been defined by a consensus sequence, the alphabeta-initiator has no homology to such sequence. These studies demonstrate that initiators have functions other than positioning elements for the basal transcription complex. Rather, initiators can have a direct role in regulating the expression of specific genes. The gain or loss of initiator activity can be an important determinant of cell phenotypes.
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Affiliation(s)
- A N Vallejo
- Departments of Medicine and Immunology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA.
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30
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Abstract
Many viral genes contain core promoters with two basal control elements, the TATA box and the pyrimidine-rich initiator (Inr). However, the molecular mechanisms involved in transcription initiation from composite core promoters (TATA(+) Inr(+)) containing Inr elements are unclear. The Rous sarcoma virus (RSV) long terminal repeat (LTR) contains a transcriptionally potent enhancer and core promoter composed of a TATA box and an Inr-like sequence, termed the transcription start site core (TSSC). Previously we demonstrated that the TSSC binds the multifunctional Inr-binding protein YY1. Here we present evidence that the TSSC also binds the multifunctional transcription factor TFII-I and that both TFII-I and YY1 are required for RSV LTR transcriptional activity. Gel shift assays using anti-TFII-I antibody show that TFII-I is present in a protein complex that specifically binds to the TSSC. Mutations in the TSSC that reduce TFII-I binding also reduce RSV LTR enhancer and promoter activity. Transient-transfection assays demonstrate that TFII-I transactivates the RSV LTR from ca. fourfold (basal) to ca. sevenfold (enhanced) in both human and natural host cell lines. Importantly, the activity of the TSSC element can be attributed to the binding activity of TFII-I and the YY1 protein, since mutation of each of these binding sites within the TSSC element abolishes all viral expression as demonstrated by transient-transfection assays. Taken together, these data demonstrate that expression of RSV viral mRNA is dependent on both TFII-I and YY1.
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Affiliation(s)
- C M Mobley
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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31
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Galdemard C, Yamagata H, Brison O, Lavialle C. Regulation of FGF-3 gene expression in tumorigenic and non-tumorigenic clones of a human colon carcinoma cell line. J Biol Chem 2000; 275:17364-73. [PMID: 10749884 DOI: 10.1074/jbc.m909316199] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The FGF-3 gene is constitutively expressed in tumorigenic clones from the SW613-S human colon carcinoma cell line but is silent in non-tumorigenic clones. We have investigated the transcriptional mechanisms responsible for this differential expression. Mapping of DNase I-hypersensitive sites throughout the FGF-3 gene and the region extending 15 kilobases upstream disclosed differences in the patterns obtained between tumorigenic and non-tumorigenic cells. Transient expression assays carried out with a reporter gene driven by FGF-3 promoter fragments of various lengths (0.143 to 11 kilobases) did not reproduce the differential regulation of the resident gene between the two cell types. The same constructs did exhibit a differential activity in stable transfectants, suggesting the involvement of a chromatin-based mechanism in this regulation. Under these conditions, even the 143-base pair minimal promoter fragment was able to drive the differential expression of the reporter gene. During the course of these analyses, several transcriptional modulatory elements (mainly activators) were identified in the FGF-3 upstream region and were found to colocalize with DNase I-hypersensitive sites. Moreover, a putative new promoter was discovered 6 kilobases upstream of FGF-3. Altogether, these data provide a basis for the elucidation of the complex regulation of the human FGF-3 gene.
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Affiliation(s)
- C Galdemard
- Laboratoire de Génétique Oncologique, CNRS UMR 1599, Institut Gustave-Roussy, 94805 Villejuif, France
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32
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Funke-Kaiser H, Bolbrinker J, Theis S, Lemmer J, Richter CM, Paul M, Orzechowski HD. Characterization of the c-specific promoter of the gene encoding human endothelin-converting enzyme-1 (ECE-1). FEBS Lett 2000; 466:310-6. [PMID: 10682850 DOI: 10.1016/s0014-5793(00)01086-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Human ECE-1 is expressed in four isoforms with different tissue distribution and its mRNA and protein levels are altered under certain pathophysiological conditions. To investigate the transcriptional regulation of ECE-1, we studied the regulatory region of ECE-1c, the major ECE-1 isoform. A genomic clone comprising the complete human ECE-1 gene including the putative ECE-1c-specific promoter was obtained. Up to 968 bp upstream of the putative c-specific translation initiation start codon and several serial deletion mutants were subcloned into a reporter vector and transfected into endothelial (BAEC, EA.hy926, ECV304) and epithelial (MDA MB435S, MCF7) cells, showing very strong promoter activity in comparison to the SV40 promoter and to the previously described ECE-1a and 1b promoters. Transfection of serial deletion mutants indicated two positive regulatory regions within the promoter (-142/-240 and -240/490) likely involved in binding GATA and ETS transcription factors. RNase protection assay (RPA) and 5'-RACE revealed multiple transcriptional start sites located at about -110, -140 and -350 bp. Site-directed mutagenesis demonstrated a crucial role for the E2F cis-element for basal ECE-1c promoter activity. Additionally, we found a correlation between isoform-specific ECE-1 mRNA levels and corresponding ECE-1a, 1b, 1c promoter activities.
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Affiliation(s)
- H Funke-Kaiser
- Institute of Clinical Pharmacology and Toxicology, Benjamin Franklin Medical Center, Freie Universität, Berlin, Germany
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33
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McKay LM, Carpenter B, Roberts SG. Regulation of the Wilms' tumour suppressor protein transcriptional activation domain. Oncogene 1999; 18:6546-54. [PMID: 10597258 DOI: 10.1038/sj.onc.1203046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Wilms' tumour suppressor protein WT1 contains a transcriptional regulatory domain that can either activate or repress transcription depending upon its cellular environment. The mechanistic basis for this dichotomy is unclear however. Here, we dissect the transcriptional regulatory domains of WT1. We find that a region within the domain of WT1 attributed to transcriptional repression is a potent suppressor of the activation domain at several promoters and in different cell types. In vitro transcription analysis suggests that the mechanism of suppression of the activation domain occurs at the level of transcription initiation. Furthermore we find that the WT1 suppression domain is able to inhibit a heterologous activation domain when fused in cis. Dissection of this domain resulted in the delineation of a 30 amino acid region that was sufficient to confer suppression of a transcriptional activation domain both in vivo and in vitro. Additionally, we find that the WT1 transcriptional activation domain interacts with the general transcription factor TFIIB and that this interaction is not affected by the suppression domain. Taken together, these studies suggest that the suppression domain of WT1 interacts with a cosuppressor protein to mediate inhibition of the WT1 transcriptional activation domain.
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Affiliation(s)
- L M McKay
- Department of Biochemistry, University of Dundee, UK
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34
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Abstract
Progress in diverse scientific fields has been realized partly by the continued refinement of mammalian gene expression vectors. A growing understanding of biological processes now allows the design of vector components to meet specific objectives. Thus, gene expression in a tissue-selective or ubiquitous manner may be accomplished by selecting appropriate promoter/enhancer elements; stabilization of labile mRNAs may be effected through removal of 3' untranslated regions or fusion to heterologous stabilizing sequences; protein targeting to selected tissues or different organelles is carried out using specific signal sequences; fusion moieties effect the detection, enhanced yield, surface expression, prolongation of half-life, and facile purification of recombinant proteins; and careful tailoring of the codon content of heterologous genes enhances protein production from poorly translated transcripts. The use of viral as well as nonviral genetic elements in vectors allows the stable replication of episomal elements without the need for chromosomal integration. The development of baculovirus vectors for both transient and stable gene expression in mammalian cells has expanded the utility of such vectors for a broad range of cell types. Internal ribosome entry sites are now widely used in many applications that require coexpression of different genes. Progress in gene targeting techniques is likely to transform gene expression and amplification in mammalian cells into a considerably less labor-intensive operation. Future progress in the elucidation of eukaryotic protein degradation pathways holds promise for developing methods to minimize proteolysis of specific recombinant proteins in mammalian cells and tissues.
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Affiliation(s)
- S C Makrides
- EIC Laboratories, Inc., Norwood, Massachusetts, 02062, USA
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35
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Transcriptional elongation of the rat apolipoprotein A-I gene: identification and mapping of two arrest sites and their signals. J Lipid Res 1999. [DOI: 10.1016/s0022-2275(20)33485-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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36
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Crawley E, Kay R, Sillibourne J, Patel P, Hutchinson I, Woo P. Polymorphic haplotypes of the interleukin-10 5' flanking region determine variable interleukin-10 transcription and are associated with particular phenotypes of juvenile rheumatoid arthritis. ARTHRITIS AND RHEUMATISM 1999; 42:1101-8. [PMID: 10366102 DOI: 10.1002/1529-0131(199906)42:6<1101::aid-anr6>3.0.co;2-y] [Citation(s) in RCA: 412] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To determine the distribution of the interleukin-10 (IL-10) 5' flanking region haplotypes in children with arthritis and in controls, and to investigate the functional significance of each haplotype. METHODS Sequence-specific oligonucleotide probing was used to determine haplotype frequency. Transient transfection studies were used to investigate the transcription of reporter genes driven by each haplotype. Whole blood cultures were performed to assess IL-10 production by each genotype. RESULTS Patients with arthritis involving >4 joints were more likely to have a genotype with an ATA haplotype than those whose arthritis remained restricted to <4 joints. This ATA haplotype was associated with lower transcriptional activity than the GCC haplotype (P = 0.02), and the ATA/ATA genotype was associated with lower IL-10 production under lipopolysaccharide stimulation than other genotypes (P < 0.02). CONCLUSION The results of this study demonstrate the functional significance of the ATA haplotype and reveal a significant association of genotypes containing this haplotype with extended oligoarthritis.
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Affiliation(s)
- E Crawley
- University College , London Medical School, UK
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37
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Ohishi-Shofuda T, Suzuki Y, Yano K, Sakurai H, Fukasawa T. Transcription initiation mediated by initiator binding protein in Saccharomyces cerevisiae. Biochem Biophys Res Commun 1999; 255:157-63. [PMID: 10082672 DOI: 10.1006/bbrc.1999.0157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many instances of the initiator element in the core promoter of protein-coding genes have been reported in mammalian cells and their viruses, but only one has been reported in the yeast Saccharomyces cerevisiae at the GAL80 gene. The initiator element of GAL80 directs transcription by itself and interacts with a nuclear protein designated yeast initiator binding factor (yIF). Here we show that yIF in a partially purified sample binds the sequence from -18 to +10 of GAL80. By employing a selected and amplified binding procedure, we have determined the preferred sequence for yIF binding to be -2 CACTN +3 (N indicates any nucleotide). Binding affinity of selected sequences to yIF correlated with their initiator-directed transcription in vivo, suggesting that the yIF-initiator interaction mediates transcription from the initiator in yeast. We also suggest that sequences flanking the preferred sequence affect both yIF binding and initiator activity.
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Affiliation(s)
- T Ohishi-Shofuda
- Institute for Advanced Medical Research, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
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38
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Wu Y, Patterson C. The human KDR/flk-1 gene contains a functional initiator element that is bound and transactivated by TFII-I. J Biol Chem 1999; 274:3207-14. [PMID: 9915861 DOI: 10.1074/jbc.274.5.3207] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
KDR/flk-1, the receptor for vascular endothelial growth factor, is required for normal vascular development. KDR/flk-1 is a TATA-less gene, containing four upstream Sp1 sites and a single transcription start site, although analysis of the start site sequence discloses only weak similarities with the consensus initiator element (Inr) sequence. In vitro transcription assays, however, demonstrate that the region from -10 to +10 relative to the start site contains Inr activity that is orientation- and position-dependent, and mutagenesis of the KDR/flk-1 Inr reduces promoter activity to 28% of the wild-type promoter in transient transfection assays. Gel shift assays confirm that nuclear proteins specifically bind the Inr, and competition experiments demonstrate that TFII-I, a multifunctional Inr-binding nuclear protein, is a component of these DNA-protein complexes. TFII-I transactivates the wild-type KDR/flk-1 promoter, but not a promoter containing a mutated Inr, in transient transfection assays. Immunodepletion of TFII-I from nuclear extracts prior to in vitro transcription assays abolishes transcription from the KDR/flk-1 Inr, an effect that can be rescued by adding back purified TFII-I, reflecting the importance of TFII-I in KDR/flk-1 Inr activity. These experiments demonstrate that the KDR/flk-1 gene contains a functional Inr that is bound by TFII-I and that both the functional Inr and TFII-I activity are essential for transcription.
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Affiliation(s)
- Y Wu
- University of Texas Medical Branch, Division of Cardiology and Sealy Center for Molecular Cardiology, Galveston, Texas 77555-1064, USA
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39
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Reuter I, Werner T, Wingender E. Computer-assisted methods for the identification and characterization of polymerase II promoters. GENETIC ENGINEERING 1998; 20:25-40. [PMID: 9705623 DOI: 10.1007/978-1-4899-1739-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- I Reuter
- Gesellschaft f ur Biotechnologische Forschung, Mascheroder Weg 1, D-38124 Braunschweig, Germany
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40
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Cheriyath V, Novina CD, Roy AL. TFII-I regulates Vbeta promoter activity through an initiator element. Mol Cell Biol 1998; 18:4444-54. [PMID: 9671454 PMCID: PMC109030 DOI: 10.1128/mcb.18.8.4444] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In our effort to understand the transcriptional regulation of naturally occurring TATA-less but initiator (Inr)-containing genes, we have employed the murine T-cell receptor Vbeta 5.2 promoter as a model. Here we show by transient-transfection assays that the Inr binding transcription factor TFII-I is required for efficient expression of the Vbeta promoter in vivo. Mutations in the Inr element that reduced binding of TFII-I also abolished the Vbeta promoter activity by ectopic TFII-I. We further biochemically identified a protease-resistant N-terminal DNA binding fragment of TFII-I, p70. When ectopically expressed, recombinant p70 bound to the Vbeta Inr element with a specificity similar to that of wild-type TFII-I. More importantly, p70, which lacks independent activation functions, behaved as a dominant negative mutant that inhibited Inr-specific function of wild-type TFII-I. However, the activation functions of p70 were restored when fused to the heterologous activation domain of the yeast activator protein GAL4. Taken together, these data suggest that TFII-I functions in vivo require an intact Inr element and that the Inr-specific transcriptional functions of TFII-I are solely dictated by its N-terminal DNA binding domain and do not require its own C-terminal activation domain.
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Affiliation(s)
- V Cheriyath
- Department of Pathology and Program in Immunology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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41
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Leung KK, Ng LJ, Ho KK, Tam PP, Cheah KS. Different cis-regulatory DNA elements mediate developmental stage- and tissue-specific expression of the human COL2A1 gene in transgenic mice. J Biophys Biochem Cytol 1998; 141:1291-300. [PMID: 9628886 PMCID: PMC2132792 DOI: 10.1083/jcb.141.6.1291] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Expression of the type II collagen gene (human COL2A1, mouse Col2a1) heralds the differentiation of chondrocytes. It is also expressed in progenitor cells of some nonchondrogenic tissues during embryogenesis. DNA sequences in the 5' flanking region and intron 1 are known to control tissue-specific expression in vitro, but the regulation of COL2A1 expression in vivo is not clearly understood. We have tested the regulatory activity of DNA sequences from COL2A1 on the expression of a lacZ reporter gene in transgenic mice. We have found that type II collagen characteristic expression of the transgene requires the enhancer activity of a 309-bp fragment (+2, 388 to +2,696) in intron 1 in conjunction with 6.1-kb 5' sequences. Different regulatory elements were found in the 1.6-kb region (+701 to +2,387) of intron 1 which only needs 90-bp 5' sequences for tissue-specific expression in different components of the developing cartilaginous skeleton. Distinct positive and negative regulatory elements act together to control tissue-specific transgene expression in the developing midbrain neuroepithelium. Positive elements affecting expression in the midbrain were found in the region from -90 to -1,500 and from +701 to +2,387, whereas negatively acting elements were detected in the regions from -1,500 to -6,100 and +2,388 to +2,855.
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Affiliation(s)
- K K Leung
- Department of Biochemistry, The University of Hong Kong, Hong Kong
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42
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Dode L, De Greef C, Mountian I, Attard M, Town MM, Casteels R, Wuytack F. Structure of the human sarco/endoplasmic reticulum Ca2+-ATPase 3 gene. Promoter analysis and alternative splicing of the SERCA3 pre-mRNA. J Biol Chem 1998; 273:13982-94. [PMID: 9593748 DOI: 10.1074/jbc.273.22.13982] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human chromosome 17-specific genomic clones extending over 90 kilobases (kb) of DNA and coding for sarco/endoplasmic reticulum Ca2+-ATPase 3 (SERCA3) were isolated. The presence of the D17S1828 genetic marker in the cosmid contig enabled us to map the SERCA3 gene (ATP2A3) 11 centimorgans from the top of the short arm p of chromosome 17, in the vicinity of the cystinosis gene locus. The SERCA3 gene contains 22 exons spread over 50 kb of genomic DNA. The exon/intron boundaries are well conserved between human SERCA3 and SERCA1 genes, except for the junction between exons 8 and 9 which is found in the SERCA1 gene but not in SERCA3 and SERCA2 genes. The transcription start site (+1) is located 152 nucleotides (nt) upstream of the AUG codon. The 5'-flanking region, including exon 1, is embedded in a 1.5-kb CpG island and is characterized by the absence of a TATA box and by the presence of 14 putative Sp1 sites, 11 CACCC boxes, 5 AP-2-binding motifs, 3 GGCTGGGG motifs, 3 CANNTG boxes, a GATA motif, as well as single sites for Ets-1, c-Myc, and TFIIIc. Functional promoter analysis indicated that the GC-rich region (87% G + C) from -135 to -31 is of critical importance in initiating SERCA3 gene transcription in Jurkat cells. Exon 21 (human, 101 base pairs; mouse, 86 base pairs) can be alternatively excluded, partially included, or totally included, thus generating, respectively, SERCA3a (human and mouse, 999 amino acids (aa)), SERCA3b (human, 1043 aa; mouse, 1038 aa), or SERCA3c (human, 1024 aa; mouse, 1021 aa) isoforms with different C termini. Expression of the mouse SERCA3 isoforms in COS-1 cells demonstrated their ability to function as active pumps, although with different apparent affinities for Ca2+.
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Affiliation(s)
- L Dode
- Laboratorium voor Fysiologie, Katholieke Universiteit Leuven, Campus Gasthuisberg, Herestraat 49, B-3000, Leuven, Belgium.
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43
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Cao Y, Stafforini DM, Zimmerman GA, McIntyre TM, Prescott SM. Expression of plasma platelet-activating factor acetylhydrolase is transcriptionally regulated by mediators of inflammation. J Biol Chem 1998; 273:4012-20. [PMID: 9461591 DOI: 10.1074/jbc.273.7.4012] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Platelet-activating factor (PAF) is a potent phospholipid with diverse physiological and pathological actions, and it is inactivated by PAF acetylhydrolase. In this study, we analyzed the tissue distribution of the plasma PAF acetylhydrolase mRNA in humans. We isolated a 3.5-kilobase fragment containing the 5' genomic sequence of the plasma PAF acetylhydrolase gene and further characterized the promoter activity. We determined the transcriptional initiation site by primer extension. We then prepared constructs containing various lengths of 5' genomic fragments fused to a luciferase reporter gene and transfected these constructs into COS-7 cells. We found that there is more than one region in the 1.3-kilobase 5' genomic sequence conferring promoter activity and that a very short 5'-flanking region (72 base pairs) is sufficient for more than 65% of the basal activity. In parallel, we examined the regulation of expression of the PAF acetylhydrolase gene. We found that interferon-gamma (IFNgamma) and lipopolysaccharide (LPS) significantly inhibited synthesis of PAF acetylhydrolase, whereas other cytokines, including IFNalpha, interleukin (IL) 1alpha, IL4, IL6, tumor necrosis factor-alpha, granulocyte/macrophage colony-stimulating factor, and macrophage colony-stimulating factor, had a smaller or no effect in human monocyte-derived macrophages. Furthermore, transfection of the promoter/reporter construct into macrophage RAW264.7 cells revealed that IFNgamma and LPS decreased the promoter activity by 35% and 50%, respectively, whereas PAF stimulated it by 52% via its receptor. The promoter activity was much lower in monocytic U937 cells compared with the basal level in COS-7 cells, while the activities in P388D1 and RAW264.7 macrophagic cells were considerably higher than the basal level in COS-7 cells. There are multiple regions in the PAF acetylhydrolase promoter that contain responsive elements for signal transducer and activators of transcription-related proteins, and also for myeloid-specific transcription factors. Our data indicate that the opposite of mRNA expression in monocytes versus macrophages is due to inhibition of the promoter activity in the former and activation in the latter cells.
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Affiliation(s)
- Y Cao
- Program in Human Molecular Biology and Genetics, the Huntsman Cancer Institute, Salt Lake City, Utah 84112, USA
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44
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Di Matteo G, Salerno M, Guarguaglini G, Di Fiore B, Palitti F, Lavia P. Interactions with single-stranded and double-stranded DNA-binding factors and alternative promoter conformation upon transcriptional activation of the Htf9-a/RanBP1 and Htf9-c genes. J Biol Chem 1998; 273:495-505. [PMID: 9417108 DOI: 10.1074/jbc.273.1.495] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The murine Htf9-a/RanBP1 and Htf9-c genes are divergently transcribed from a shared TATA-less promoter. Transcription of both genes is initiated on complementary DNA strands and is controlled by cell cycle-dependent mechanisms. The bidirectional promoter harbors a genomic footprint flanking the major transcription start site of both genes. Transient promoter assays showed that the footprinted element is important for transcription of both genes. Protein-binding experiments and antibody assays indicated that members of the retinoid X receptor family interact with the double-stranded site. In addition, distinct factors interact with single DNA strands of the element. Double-stranded binding factors were highly expressed in liver cells, in which neither gene is transcribed, while single-stranded binding proteins were abundant in cycling cells, in which transcription of both genes is efficient. In vivo S1 analysis of the promoter depicted an S1-sensitive organization in cells in which transcription of both genes is active; S1 sensitivity was not detected in conditions of transcriptional repression. Thus, the same element is a target for either retinoid X receptor factors, or for single-stranded binding proteins, and form distinct complexes in different cellular conditions depending on the DNA conformation in the binding site.
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Affiliation(s)
- G Di Matteo
- CNR Centre of Evolutionary Genetics, c/o Department of Genetics and Molecular Biology, University "La Sapienza," Rome 00185, Italy
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45
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Connelly MA, Zhang H, Kieleczawa J, Anderson CW. The promoters for human DNA-PKcs (PRKDC) and MCM4: divergently transcribed genes located at chromosome 8 band q11. Genomics 1998; 47:71-83. [PMID: 9465298 DOI: 10.1006/geno.1997.5076] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A 30-kb genomic segment containing the promoter and first 9 exons of PRKDC, the gene encoding the catalytic subunit (DNA-PKcs) of the human DNA-activated protein kinase, DNA-PK, was isolated and partially sequenced. Sequence comparison with the NCBI nonredundant database revealed the locations of the first 13 exons of the upstream gene, MCM4. MCM4 is an essential component of a protein complex that prevents DNA from being replicated more than once per cell cycle. The MCM4 and DNA-PKcs promoters are in CpG islands separated by approximately 700 bp, and transcription from each initiates at multiple, closely spaced sites. Both promoters lack TATA boxes, and the MCM4 promoter also lacks an initiator (Inr) element but has an inverted CCAAT box. The DNA-PKcs promoter has an Inr-like sequence as well as a downstream MED-1 element. The two promoters appear to function independently, as sequences required for core promoter activity do not overlap, and sequences extending into the 5' region of each gene had little or no effect on transcription of the other gene, as shown in transient transfection assays. The arrangement of the PRKDC/MCM4 gene pair is similar to that of the ATM/E14(NPAT) gene pair. ATM, the product of the gene mutated in ataxia telangiectasia, and DNA-PKcs function in pathways that detect or repair DNA damage and are members of a family of large, serine/threonine kinases that are closely related to phosphatidylinositol 3 kinases.
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Affiliation(s)
- M A Connelly
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
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46
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Luján HD, Mowatt MR, Nash TE. Mechanisms of Giardia lamblia differentiation into cysts. Microbiol Mol Biol Rev 1997; 61:294-304. [PMID: 9293183 PMCID: PMC232612 DOI: 10.1128/mmbr.61.3.294-304.1997] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Microbiologists have long been intrigued by the ability of parasitic organisms to adapt to changes in the environment. Since most parasites occupy several niches during their journey between vectors and hosts, they have developed adaptive responses which allow them to survive under adverse conditions. Therefore, the life cycles of protozoan and helminthic parasites are excellent models with which to study numerous mechanisms involved in cell differentiation, such as the regulation of gene expression, signal transduction pathways, and organelle biogenesis. Unfortunately, many of these studies are very difficult because the conditions needed to elicit developmental changes in parasites remain undetermined in most cases. Recently, several interesting findings were reported on the process of differentiation of Giardia lamblia trophozoites into cysts. G. lamblia is a flagellated protozoan that inhabits the upper small intestine of its vertebrate host and is a major cause of enteric disease worldwide. It belongs to the earliest identified lineage among eukaryotes and therefore offers a unique insight into the progression from primitive to more complex eukaryotic cells. The discovery of a specific stimulus that induces trophozoites to differentiate into cysts, the identification and characterization of encystation-specific molecules, the elucidation of novel biochemical pathways, and the development of useful reagents and techniques have made this parasite an excellent model with which to study differentiation in eukaryotic cells. In this review, we summarize the most recent fundings on several aspects of Giardia differentiation and discuss the significance of these findings within the context of current knowledge in the field.
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Affiliation(s)
- H D Luján
- Department of Biological Chemistry, School of Medicine, National University of Córdoba, Argentina
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47
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Rauch U, Meyer H, Brakebusch C, Seidenbecher C, Gundelfinger ED, Beier DR, Fässler R. Sequence and chromosomal localization of the mouse brevican gene. Genomics 1997; 44:15-21. [PMID: 9286696 DOI: 10.1006/geno.1997.4853] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Brevican is a brain-specific proteoglycan belonging to the aggrecan family. Phage clones containing the complete mouse brevican open reading frame of 2649 bp and the complete 3'-untranslated region of 341 bp were isolated from a mouse brain cDNA library, and cosmid clones containing the mouse brevican gene were isolated from a genomic library using a PCR-generated DNA fragment as probe. The obtained genomic sequence of 13,700 nucleotides revealed that the murine gene has a size of approximately 13 kb and contains the sequence of the mRNA for the secreted brevican isoform on 14 exons. The exon-intron structure reflected the structural organization of the multidomain protein brevican. No consensus TATA sequence was found upstream of the first exon, and RNase protection experiments revealed multiple transcriptional start sites for the brevican gene. The first part of the sequence of intron 8 corresponded to an alternative brevican cDNA, coding for a GPI-linked isoform. Single strand conformation polymorphism analysis mapped the brevican gene (Bcan) to chromosome 3 between the microsatellite markers D3Mit22 and D3Mit11.
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Affiliation(s)
- U Rauch
- Max-Planck-Institut für Biochemie, Martinsried, Germany
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48
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Wei Z, Angerer LM, Angerer RC. Multiple positive cis elements regulate the asymmetric expression of the SpHE gene along the sea urchin embryo animal-vegetal axis. Dev Biol 1997; 187:71-8. [PMID: 9224675 DOI: 10.1006/dbio.1997.8603] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The mechanism that establishes the maternally determined animal-vegetal axis of sea urchin embryos is unknown. We have analyzed the cis-regulatory elements of the SpHE gene of Strongylocentrotus purpuratus, which is asymmetrically expressed along this axis, in an effort to identify components of maternal positional information. Previously, we defined a regulatory region that is sufficient to provide correct nonvegetal expression of a beta-galactosidase reporter gene (Wei, Z., Angerer, L. M., Gagnon, M. L., and Angerer, R. C., Dev. Biol. 171, 195-211, 1995). We have now analyzed this region intensively in order to determine if the spatial pattern is controlled by nonvegetal-positive activities or by vegetal-negative activities. The regulatory sequences, except the basal promoter, were mutated by either deletion or sequence replacement. None of these mutations resulted in ectopic beta-gal expression in vegetal cells, showing that no single negative cis element is responsible for the lack of vegetal SpHE transcription. Surprisingly, even short segments of the regulatory region containing only several identified cis elements also direct nonvegetal expression. Furthermore, the SpHE basal promoter functions effectively in vegetal cells in combination with cis-acting elements derived from the PMC-specific gene, SM50. We conclude that the spatial pattern of SpHE transcription is achieved by multiple positive activities concentrated in nonvegetal cells. The vegetal expression of SM50 also is regulated only by positive activities (Makabe, K. W., Kirchhamer, C. V., Britten, R. J., and Davidson, E. H., Development 121, 1957-1970, 1995). A chimeric promoter containing both SpHE and SM50 regulatory sequences is active ubiquitously, suggesting that these regulators are not reciprocally repressive. These observations suggest a model in which the SpHE and SM50 genes are activated by separate sets of positive maternal activities concentrated, respectively, in nonvegetal and vegetal domains of the early embryo.
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Affiliation(s)
- Z Wei
- Department of Biology, University of Rochester, New York 14627, USA
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49
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Garrity DB, Chang MJ, Blissard GW. Late promoter selection in the baculovirus gp64 envelope fusion protein gene. Virology 1997; 231:167-81. [PMID: 9168879 DOI: 10.1006/viro.1997.8540] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The upstream promoter region of the Autographa californica multicapsid nuclear polyhedrosis virus (AcMNPV) gp64 gene contains five copies of TAAG, the conserved sequence found at the transcriptional initiation sites of almost all baculovirus late genes. In AcMNPV-infected Sf9 cells, late transcription initiation is detected from only two upstream TAAG sites and not from three downstream TAAG sites. To examine several models for preferential TAAG site utilization, we constructed a series of recombinant AcMNPV baculoviruses that contain promoter region sequences from the gp64 gene fused to a chloramphenicol acetyl transferase reporter gene. Promoter-reporter constructs were inserted in the polyhedrin locus. To test a scanning model in which TAAG sites are sequentially selected according to their location in the region, we generated recombinant viruses in which the highly transcribed sites were inactivated by point mutations. Transcription from the mutant promoter constructs was compared qualitatively and quantitatively to transcription from the wild-type gp64 promoter. Inactivation of the upstream TAAG sites did not result in increased transcription from the downstream TAAG sites, suggesting that immediate context, rather than position, determines promoter utilization. To test this hypothesis, we made a series of minimal promoter constructs containing decreasing quantities of the sequences immediately flanking one of the active gp64 TAAG sites. Reporter constructs containing a gp64 TAAG site and > or = 12 bp of flanking sequence on both sides were transcribed at near wild-type levels. Constructs with less flanking sequence (9 or 6 bp of flanking sequence) were accurately transcribed, but at substantially lower levels, and transcription was not detected from constructs containing only 3 bp of flanking sequence. These results suggest that nucleotides immediately flanking the TAAG site (4-6 bp) are necessary for basal promoter activity while additional flanking sequences (> or = 12 bp) are required for late promoter activation and regulation. To further examine late promoter selection, we constructed recombinant AcMNPV baculoviruses that contain heterologous late promoters from the gp64 gene of the related virus Orgyia pseudotsugata MNPV (OpMNPV). TAAG sites that serve as functional late promoters in OpMNPV were found to mediate transcription initiation at only basal levels in the context of the AcMNPV genome, suggesting that late promoter activation may be virus specific within the family Baculoviridae.
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Affiliation(s)
- D B Garrity
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
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50
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Meisel L, Lam E. Switching of gene expression: analysis of the factors that spatially and temporally regulate plant gene expression. GENETIC ENGINEERING 1997; 19:183-99. [PMID: 9193109 DOI: 10.1007/978-1-4615-5925-2_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this chapter, we have reviewed the present research and understanding of several families of transcription factors in plants. From this information, it appears there is good conservation between the types of transcription factors in plants and animals. However, there are several types of factors which have been isolated in plants that remain to be documented in animals (e.g., HD-Zip and GT). These as well as the presence of two types of TATA-binding proteins (TBPs) in plants suggest that although transcription in eukaryotes is highly conserved, fundamental differences may exist. Despite the differences, the modes of regulating transcription are well conserved. Figure 3 summarizes these modes of regulation. In recent years, the role of chromatin structure as well as subcellular localization have been the focus of a vast amount of research in mammals, Drosophila and yeast. However, very little research in these areas has been done in plants. Isolation of genes such as Curly leaf suggest a conservation of genes that influence the formation of heterochromatin-like structures. Whether or not this gene influences chromatin/heterochromatin structure in plants, however, remains to be tested. The study of nuclear localization of factors such as COP1 and KN1 is now leading to models for regulating nuclear transport as well as intercellular transport of transcription factors. Further study of the inter- and intracellular movement of these and other transcription factors may provide information on new modes of regulating transcription. In addition to understanding the role chromatin structure and subcellular localization of transcription factors may have on transcription initiation, the biological role of many plant transcription factors remains to be identified. Several approaches may be taken to understand the mechanisms by which transcription factors influence biochemical and physiological processes in the plant. These steps include 1) identification of the DNA-binding sites of the factors as well as the promoter regions which contain these sites. Presently, this approach is limiting in that not many non-coding regions have been sequenced and characterized in detail. Furthermore, the presence of a putative binding site within a promoter does not necessarily indicate that the factor will bind to the site in vivo. 2) Analysis of the binding affinity for a particular factor to a binding site in comparison to other related factors, via in vitro competition assays and quantitative titrations. This will provide information on how strongly these factors are binding to the sites, but without knowledge of all the factors present in a single cell it is difficult to recreate the in vivo conditions. 3) Generation of transgenic plants or microinjection of DNA/RNA to express a particular factor ectopically, reduce expression of the factor via antisense expression, and creation of dominant negative mutants by overexpression of key dimerization domains may provide information concerning what biological pathways these factors influence. 4) Isolation of mutations in particular transcription factors has been extremely informative in floral development. However, this approach usually entails isolation of a mutant due to a phenotype and eventual mutated locus. The cloning of the locus may or may not involve a transcription factor. 5) Many plant transcription factors have been isolated via sequence similarity to other previously identified and/or characterized transcription factors. However, the biological role of may of these factors is not known. In addition to ectopic expression of these factors by creating transgenic plants, isolation of a loss-of-function mutation may provide valuable information concerning the role of this factor in vivo. Many loss-of-function mutations in MADS box genes have led to a better understanding of how the MADS domain proteins interact with one another as well as how they influence floral development. (ABSTRACT TRUNCATED)
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Affiliation(s)
- L Meisel
- AgBio Tech Center, Rutgers, Cook College, New Brunswick, New Jersey 08903-0231, USA
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