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Published: 10 December 2022
Last updated: 30 January 2023

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1

Takahashi, Takayuki, Charanjeet Guron, Sheetal Shetty, Hideo Matsui, and Rajendra Raghow. "A Minimal MurineMsx-1Gene Promoter." Journal of Biological Chemistry 272, no. 36 (September 5, 1997): 22667–78. http://dx.doi.org/10.1074/jbc.272.36.22667.

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2

Chan, Shuheng, Dan Shen, Yatong Sang, Saisai Wang, Yali Wang, Cai Chen, Bo Gao, and Chengyi Song. "Development of enhancer-trapping and -detection vectors mediated by the Tol2 transposon in zebrafish." PeerJ 7 (April 30, 2019): e6862. http://dx.doi.org/10.7717/peerj.6862.

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Enhancers are key transcriptional drivers of gene expression. The identification of enhancers in the genome is central for understanding gene-expression programs. Although transposon-mediated enhancer trapping (ET) is a powerful approach to the identification of enhancers in zebrafish, its efficiency varies considerably. To improve the ET efficiency, we constructed Tol2-mediated ET vectors with a reporter gene (mCherry) expression box driven by four minimal promoters (Gata, Myc, Krt4 and Oct4), respectively. The ET efficiency and expression background were compared among the four promoters by zebrafish embryo injection at the one-cell stage. The results showed that the Gata minimal promoter yielded the lowest basic expression and the second-highest trapping efficiency (44.6% at 12 hpf (hour post-fertilization) and 23.1% at 72 hpf, n = 305 and n = 307). The Krt4 promoter had the highest trapping efficiency (64% at 12 hpf and 67.1% at 72 hpf, n = 302 and n = 301) and the strongest basic expression. To detect enhancer activity, chicken 5′HS4 double insulators were cloned into the two ET vectors with the Gata or Krt4 minimal promoter, flanking the mCherry expression box. The resulting detection vectors were injected into zebrafish embryos. mCherry expression driven by the Gata promoter (about 5%, n = 301) was decreased significantly compared with that observed for embryos injected with the ET vectors (23% at 72 hpf, n = 308). These results suggest that the insulators block the genome-position effects and that this vector is fit for enhancer-activity evaluation. To assess the compatibility between the enhancers and the minimal promoters, four enhancers (CNS1, Z48, Hand2 and Hs769) were cloned upstream of the Gata or Beta-globin minimal promoter in the enhancer-activity-detection vectors. The resulting recombinant vectors were assayed by zebrafish embryo injection. We found that Z48 and CNS1 responded to the Gata minimal promoter, and that Hand2 only responded to the Beta-globin minimal promoter. In contrast, Hs769 did not respond to either the Gata or Beta-globin minimal promoters. These results suggest the existence of compatibility between enhancers and minimal promoters. This study represents a systematic approach to the discovery of optional ET and enhancer-detection vectors. We are eager to provide a superior tool for understanding functional genomics.
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3

Thompson, AA, WJ Jr Wood, MJ Gilly, MA Damore, SA Omori, and R. Wall. "The promoter and 5' flanking sequences controlling human B29 gene expression." Blood 87, no. 2 (January 15, 1996): 666–73. http://dx.doi.org/10.1182/blood.v87.2.666.bloodjournal872666.

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The product of the B-cell-specific B29 gene (B29, Ig beta, CD79b) is essential for Ig-mediated B-cell activation via the B-cell antigen receptor complex (BCR) on human and murine B lymphocytes. To better understand the regulation of this pivotal gene, we have analyzed the human genomic DNA sequence upstream of the B29 ATG start codon for transcriptional control activity. The human B29 gene lacks either a TATA or a CAAT box and transcription is initiated at multiple sites. The minimal promoter of the human B29 gene is contained within a 193-bp region 5′ of these multiple start sites. This minimal promoter exhibits B-cell-specific activity and contains SP1, ETS, OCT, and IKAROS/LYF-1 transcription factor motifs. All these motifs are strikingly conserved in sequence and placement relative to the previously characterized murine B29 promoter. Additional upstream gene segments dramatically affected B29 minimal promoter activity. A newly identified motif called the B29 conserved sequence (BCS), found upstream of both human and murine B29 promoters, appears to stimulate B29 transcription through a novel mechanism. A single BCS had little effect either on the minimal B29 promoter or on a heterologous promoter. Instead, the BCS stimulated transcription by counteracting 5′ negative regulatory DNA sequences that block the activity of the B29 minimal promoter in its absence. These findings indicate that B29 gene expression is controlled by the complex interplay of positive and negative regulatory elements.
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4

Adami, G., and L. E. Babiss. "Evidence that USF can interact with only a single general transcription complex at one time." Molecular and Cellular Biology 12, no. 4 (April 1992): 1630–38. http://dx.doi.org/10.1128/mcb.12.4.1630-1638.1992.

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By in vitro analysis, the major late promoter (MLP) of adenovirus has been shown to be a simple promoter requiring two elements for efficient transcription: a minimal promoter element (MPE), where the general transcription factor-polymerase II complex binds, and a single functional upstream promoter element (UPE) which interacts with USF. Two hundred bases upstream of the MLP cap site and divergently oriented is the IVa2 promoter. This promoter has its own MPE but shares the MLP UPE, suggesting the possibility that these promoters are coordinately regulated. To determine mechanistically how this might function, we replaced the weak IVa2 minimal promoter with a strong MPE (from the viral E1A gene) and observed mutual inhibition of both promoters and unstable transcription factor binding. Only by duplication of the UPE could this inhibition be relieved. When tested independently, both promoters were shown to require the USF site for maximal activity. These results are compatible with a model in which USF can stably interact with only one transcription complex at a time. When two divergently oriented general transcription complexes compete efficiently for binding of USF, transcription is reduced to the same levels as if the USF site were absent.
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5

Adami, G., and L. E. Babiss. "Evidence that USF can interact with only a single general transcription complex at one time." Molecular and Cellular Biology 12, no. 4 (April 1992): 1630–38. http://dx.doi.org/10.1128/mcb.12.4.1630.

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By in vitro analysis, the major late promoter (MLP) of adenovirus has been shown to be a simple promoter requiring two elements for efficient transcription: a minimal promoter element (MPE), where the general transcription factor-polymerase II complex binds, and a single functional upstream promoter element (UPE) which interacts with USF. Two hundred bases upstream of the MLP cap site and divergently oriented is the IVa2 promoter. This promoter has its own MPE but shares the MLP UPE, suggesting the possibility that these promoters are coordinately regulated. To determine mechanistically how this might function, we replaced the weak IVa2 minimal promoter with a strong MPE (from the viral E1A gene) and observed mutual inhibition of both promoters and unstable transcription factor binding. Only by duplication of the UPE could this inhibition be relieved. When tested independently, both promoters were shown to require the USF site for maximal activity. These results are compatible with a model in which USF can stably interact with only one transcription complex at a time. When two divergently oriented general transcription complexes compete efficiently for binding of USF, transcription is reduced to the same levels as if the USF site were absent.
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6

Kiss, I., Z. Bösze, P. Szabó, R. Altanchimeg, E. Barta, and F. Deák. "Identification of positive and negative regulatory regions controlling expression of the cartilage matrix protein gene." Molecular and Cellular Biology 10, no. 5 (May 1990): 2432–36. http://dx.doi.org/10.1128/mcb.10.5.2432-2436.1990.

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A complex pattern of regulation of the cartilage matrix protein gene was revealed by transient expression experiments. A minimal promoter from positions -15 to +64 functioned in chondrocytes and fibroblasts. An enhancer located in the first intron exerted chondrocyte-specific stimulation on the minimal promoter activity. The same fragment, however, had a negative effect in fibroblasts. Between -334 and -15, a silencer was found which inhibited the gene expression driven from its homologous as well as heterologous promoters both in chondrocytes and fibroblasts. Additional positive and negative control regions were mapped further upstream of the promoter.
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7

Kiss, I., Z. Bösze, P. Szabó, R. Altanchimeg, E. Barta, and F. Deák. "Identification of positive and negative regulatory regions controlling expression of the cartilage matrix protein gene." Molecular and Cellular Biology 10, no. 5 (May 1990): 2432–36. http://dx.doi.org/10.1128/mcb.10.5.2432.

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A complex pattern of regulation of the cartilage matrix protein gene was revealed by transient expression experiments. A minimal promoter from positions -15 to +64 functioned in chondrocytes and fibroblasts. An enhancer located in the first intron exerted chondrocyte-specific stimulation on the minimal promoter activity. The same fragment, however, had a negative effect in fibroblasts. Between -334 and -15, a silencer was found which inhibited the gene expression driven from its homologous as well as heterologous promoters both in chondrocytes and fibroblasts. Additional positive and negative control regions were mapped further upstream of the promoter.
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8

Koev, Gennadiy, and W. Allen Miller. "A Positive-Strand RNA Virus with Three Very Different Subgenomic RNA Promoters." Journal of Virology 74, no. 13 (July 1, 2000): 5988–96. http://dx.doi.org/10.1128/jvi.74.13.5988-5996.2000.

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ABSTRACT Numerous RNA viruses generate subgenomic mRNAs (sgRNAs) for expression of their 3′-proximal genes. A major step in control of viral gene expression is the regulation of sgRNA synthesis by specific promoter elements. We used barley yellow dwarf virus (BYDV) as a model system to study transcriptional control in a virus with multiple sgRNAs. BYDV generates three sgRNAs during infection. The sgRNA1 promoter has been mapped previously to a 98-nucleotide (nt) region which forms two stem-loop structures. It was determined that sgRNA1 is not required for BYDV RNA replication in oat protoplasts. In this study, we show that neither sgRNA2 nor sgRNA3 is required for BYDV RNA replication. The promoters for sgRNA2 and sgRNA3 synthesis were mapped by using deletion mutagenesis. The minimal sgRNA2 promoter is approximately 143 nt long (nt 4810 to 4952) and is located immediately downstream of the putative sgRNA2 start site (nt 4809). The minimal sgRNA3 core promoter is 44 nt long (nt 5345 to 5388), with most of the sequence located downstream of sgRNA3 start site (nt 5348). For both promoters, additional sequences upstream of the start site enhanced sgRNA promoter activity. These promoters contrast to the sgRNA1 promoter, in which almost all of the promoter is located upstream of the transcription initiation site. Comparison of RNA sequences and computer-predicted secondary structures revealed little or no homology between the three sgRNA promoter elements. Thus, a small RNA virus with multiple sgRNAs can have very different subgenomic promoters, which implies a complex system for promoter recognition and regulation of subgenomic RNA synthesis.
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9

Kiran, Manjot, Erin Maloney, Hava Lofton, Ashwini Chauhan, Rasmus Jensen, Renata Dziedzic, Murty Madiraju, and Malini Rajagopalan. "Mycobacterium tuberculosis ftsZ expression and minimal promoter activity." Tuberculosis 89 (December 2009): S60—S64. http://dx.doi.org/10.1016/s1472-9792(09)70014-9.

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10

Zhang, Min, Brian C. Thomas, and Joseph L. Napoli. "Gene structure and minimal promoter of mouse rdh1." Gene 305, no. 1 (February 2003): 121–31. http://dx.doi.org/10.1016/s0378-1119(02)01236-2.

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11

Fandl, J. P., L. K. Thorner, and S. W. Artz. "Mutations that affect transcription and cyclic AMP-CRP regulation of the adenylate cyclase gene (cya) of Salmonella typhimurium." Genetics 125, no. 4 (August 1, 1990): 719–27. http://dx.doi.org/10.1093/genetics/125.4.719.

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Abstract We studied the expression of the cya promoter(s) in cya-lac fusion strains of Salmonella typhimurium and demonstrated cAMP receptor protein (CRP)-dependent repression by cAMP. Expression of cya was reduced about fourfold in cultures grown in acetate minimal medium as compared to cultures grown in glucose-6-phosphate minimal medium. Expression of cya was also reduced about fourfold by addition of 5 mM cAMP to cultures grown in glucose minimal medium. We constructed in vitro deletion and insertion mutations altering a major cya promoter (P2) and a putative CRP binding site overlapping P2. These mutations were recombined into the chromosome by allele replacement with M13mp::cya recombinant phages and the regulation of the mutant promoters was analyzed. A 4-bp deletion of the CRP binding site and a 4-bp insertion in this site nearly eliminated repression by cAMP. A mutant with the P2 promoter and the CRP binding site both deleted exhibited an 80% reduction in cya expression; the 20% residual expression was insensitive to cAMP repression. This mutant retained a Cya+ phenotype. Taken together, the results establish that the cya gene is transcribed from multiple promoters one of which, P2, is negatively regulated by the cAMP-CRP complex. Correction for the contribution to transcription by the cAMP-CRP nonregulated cya promoters indicates that the P2 promoter is repressed at least eightfold by cAMP-CRP.
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12

Cai, Yao-Min, Kalyani Kallam, Henry Tidd, Giovanni Gendarini, Amanda Salzman, and Nicola J. Patron. "Rational design of minimal synthetic promoters for plants." Nucleic Acids Research 48, no. 21 (August 28, 2020): 11845–56. http://dx.doi.org/10.1093/nar/gkaa682.

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Abstract Promoters serve a critical role in establishing baseline transcriptional capacity through the recruitment of proteins, including transcription factors. Previously, a paucity of data for cis-regulatory elements in plants meant that it was challenging to determine which sequence elements in plant promoter sequences contributed to transcriptional function. In this study, we have identified functional elements in the promoters of plant genes and plant pathogens that utilize plant transcriptional machinery for gene expression. We have established a quantitative experimental system to investigate transcriptional function, investigating how identity, density and position contribute to regulatory function. We then identified permissive architectures for minimal synthetic plant promoters enabling the computational design of a suite of synthetic promoters of different strengths. These have been used to regulate the relative expression of output genes in simple genetic devices.
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13

Buermeyer, A. B., N. E. Thompson, L. A. Strasheim, R. R. Burgess, and P. J. Farnham. "The HIP1 initiator element plays a role in determining the in vitro requirement of the dihydrofolate reductase gene promoter for the C-terminal domain of RNA polymerase II." Molecular and Cellular Biology 12, no. 5 (May 1992): 2250–59. http://dx.doi.org/10.1128/mcb.12.5.2250-2259.1992.

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We examined the ability of purified RNA polymerase (RNAP) II lacking the carboxy-terminal heptapeptide repeat domain (CTD), called RNAP IIB, to transcribe a variety of promoters in HeLa extracts in which endogenous RNAP II activity was inhibited with anti-CTD monoclonal antibodies. Not all promoters were efficiently transcribed by RNAP IIB, and transcription did not correlate with the in vitro strength of the promoter or with the presence of a consensus TATA box. This was best illustrated by the GC-rich, non-TATA box promoters of the bidirectional dihydrofolate reductase (DHFR)-REP-encoding locus. Whereas the REP promoter was transcribed by RNAP IIB, the DHFR promoter remained inactive after addition of RNAP IIB to the antibody-inhibited reactions. However, both promoters were efficiently transcribed when purified RNAP with an intact CTD was added. We analyzed a series of promoter deletions to identify which cis elements determine the requirement for the CTD of RNAP II. All of the promoter deletions of both DHFR and REP retained the characteristics of their respective full-length promoters, suggesting that the information necessary to specify the requirement for the CTD is contained within approximately 65 bp near the initiation site. Furthermore, a synthetic minimal promoter of DHFR, consisting of a single binding site for Sp1 and a binding site for the HIP1 initiator cloned into a bacterial vector sequence, required RNAP II with an intact CTD for activity in vitro. Since the synthetic minimal promoter of DHFR and the smallest REP promoter deletion are both activated by Sp1, the differential response in this assay does not result from upstream activators. However, the sequences around the start sites of DHFR and REP are not similar and our data suggest that they bind different proteins. Therefore, we propose that specific initiator elements are important for determination of the requirement of some promoters for the CTD.
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14

Buermeyer, A. B., N. E. Thompson, L. A. Strasheim, R. R. Burgess, and P. J. Farnham. "The HIP1 initiator element plays a role in determining the in vitro requirement of the dihydrofolate reductase gene promoter for the C-terminal domain of RNA polymerase II." Molecular and Cellular Biology 12, no. 5 (May 1992): 2250–59. http://dx.doi.org/10.1128/mcb.12.5.2250.

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We examined the ability of purified RNA polymerase (RNAP) II lacking the carboxy-terminal heptapeptide repeat domain (CTD), called RNAP IIB, to transcribe a variety of promoters in HeLa extracts in which endogenous RNAP II activity was inhibited with anti-CTD monoclonal antibodies. Not all promoters were efficiently transcribed by RNAP IIB, and transcription did not correlate with the in vitro strength of the promoter or with the presence of a consensus TATA box. This was best illustrated by the GC-rich, non-TATA box promoters of the bidirectional dihydrofolate reductase (DHFR)-REP-encoding locus. Whereas the REP promoter was transcribed by RNAP IIB, the DHFR promoter remained inactive after addition of RNAP IIB to the antibody-inhibited reactions. However, both promoters were efficiently transcribed when purified RNAP with an intact CTD was added. We analyzed a series of promoter deletions to identify which cis elements determine the requirement for the CTD of RNAP II. All of the promoter deletions of both DHFR and REP retained the characteristics of their respective full-length promoters, suggesting that the information necessary to specify the requirement for the CTD is contained within approximately 65 bp near the initiation site. Furthermore, a synthetic minimal promoter of DHFR, consisting of a single binding site for Sp1 and a binding site for the HIP1 initiator cloned into a bacterial vector sequence, required RNAP II with an intact CTD for activity in vitro. Since the synthetic minimal promoter of DHFR and the smallest REP promoter deletion are both activated by Sp1, the differential response in this assay does not result from upstream activators. However, the sequences around the start sites of DHFR and REP are not similar and our data suggest that they bind different proteins. Therefore, we propose that specific initiator elements are important for determination of the requirement of some promoters for the CTD.
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15

Reidling, Jack C., and Hamid M. Said. "In vitro and in vivo characterization of the minimal promoter region of the human thiamin transporter SLC19A2." American Journal of Physiology-Cell Physiology 285, no. 3 (September 2003): C633—C641. http://dx.doi.org/10.1152/ajpcell.00076.2003.

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The molecular mechanisms involved in the regulation of thiamin transport in mammalian cells are poorly understood. Previous studies established that a human thiamin transporter, SLC19A2, plays a role in thiamin uptake in human tissues. We cloned the 5′ regulatory region of the SLC19A2 gene, identified the minimal promoter required for basal activity, and located multiple putative cis elements. To further characterize the SLC19A2 promoter, we investigated, in the present study, the role of the putative cis elements in regulating the activity of the SLC19A2 promoter in vitro and confirmed the activity of the SLC19A2 promoter in vivo. In vitro studies demonstrated that mutation of specific cis elements in the SLC19A2 minimal promoter [Gut-enriched Krupple-like factor (GKLF), nuclear factor-1 (NF-1), and stimulating protein-1 (SP-1)] led to a decrease in activity. Using electrophoretic mobility shift assays, four specific DNA/protein complexes were identified. The interacting factors were determined by oligonucleotide competition and antibody supershift analysis and shown to be GKLF, NF-1, and SP-1. Cotransfection studies of the SLC19A2 promoter with an SP-1 containing vector in Drosophila SL2 cells further confirmed a role for SP-1 in regulating SLC19A2 promoter activity. In vivo studies using transgenic mice established the functionality of the full-length and minimal SLC19A2 promoters. Furthermore, our studies revealed that the pattern of expression of the SLC19A2 promoter-Luciferase constructs in transgenic mice was similar to the reported SLC19A2 RNA expression pattern in native human tissues. The results demonstrate the importance of GKLF, NF-1, and SP-1 in regulating the activity of the SLC19A2 promoter and provide direct in vivo confirmation of promoter activity.
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16

MARTIN, Karen M., Peter D. ELLIS, James C. METCALFE, and Paul R. KEMP. "Selective modulation of the SM22α promoter by the binding of BTEB3 (basal transcription element-binding protein 3) to TGGG repeats." Biochemical Journal 375, no. 2 (October 15, 2003): 457–63. http://dx.doi.org/10.1042/bj20030870.

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We have previously identified a C2H2 zinc-finger transcription factor [BTEB3 (basal transcription element-binding protein 3)/KLF13 (Krüppel-like factor 13)] that activates the minimal promoter for the smooth muscle-specific SM22α gene in other types of cell. We show that recombinant BTEB3 binds to three TGGG motifs in the minimal SM22α promoter. By mutation analysis, only one of these boxes is required for BTEB3-dependent promoter activation in P19 cells and BTEB3 activates or inhibits reporter gene expression depending on the TGGG box to which it binds. Transient transfection experiments show that BTEB3 also activates reporter gene expression from the SM22α promoter in VSMCs (vascular smooth muscle cells). Similar studies showed that BTEB3 did not activate expression from the promoter regions of the smooth muscle myosin heavy chain or smooth muscle α-actin promoters, which contain similar sequences, implying that promoter activation by BTEB3 is selective. The expression of BTEB3 is readily detectable in VSMCs in vitro and is modulated in response to injury in vivo.
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17

Nabokina, Svetlana M., and Hamid M. Said. "Characterization of the 5′-regulatory region of the human thiamin transporter SLC19A3: in vitro and in vivo studies." American Journal of Physiology-Gastrointestinal and Liver Physiology 287, no. 4 (October 2004): G822—G829. http://dx.doi.org/10.1152/ajpgi.00234.2004.

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Transcriptional regulation of expression of the human thiamin transporter-2 (the product of the SLC19A3 gene) is unknown. In this study, we cloned the 5′-regulatory region of the human SLC19A3 gene (2,016 bp), identified the minimal promoter region required for basal activity, demonstrated a critical role for specific cis-regulatory elements in determining the promoter activity, and confirmed activity and physiological relevance of the cloned SLC19A3 promoter in vivo. With the use of transiently transfected human intestinal epithelial Caco-2 cells and 5′-deletion analysis, the minimal promoter region required for basal activity of the SLC19A3 promoter was found to be encoded in a sequence between −77 and +59 by using the start of transcription initiation as position 1. This minimal region was found to contain a number of putative cis-regulatory elements, with a critical role for a stimulating protein-1 (SP1)/GC-box binding site (at position −48/−45 bp) established by means of mutational analysis. With the use of EMSA and supershift assays, the binding of SP1 and SP3 to the minimal promoter region was also demonstrated. In transiently transfected Drosophila SL2 cells, both SP1 and SP3 transactivated the SLC19A3 minimal promoter in a dose-dependent manner and in combination demonstrated an additive stimulatory effect. Functionality of the full-length SLC19A3 promoter was confirmed in vivo in transgenic mice expressing the promoter-luciferase reporter gene. These studies report the first characterization of the SLC19A3 promoter in vitro and in vivo and demonstrate the importance of an SP1 cis-regulatory element in regulating promoter activity of this important human gene.
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18

Ferrer-Martínez, Andreu, Celia García-Martínez, and Anna M. Gómez-Foix. "Use of Adenoviral Vectors with a Minimal Cytomegalovirus Promoter." BioTechniques 34, no. 3 (March 2003): 600–602. http://dx.doi.org/10.2144/03343dd02.

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19

Soutto, Mohammed, Feng Zhang, Ben Enerson, Yingkai Tong, Mark Boothby, and Thomas M. Aune. "A Minimal IFN-γ Promoter Confers Th1 Selective Expression." Journal of Immunology 169, no. 8 (October 15, 2002): 4205–12. http://dx.doi.org/10.4049/jimmunol.169.8.4205.

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20

Gaspard, Gerard J., Jessica MacLean, Danielle Rioux, and Kishore B. S. Pasumarthi. "A novel β-adrenergic response element regulates both basal and agonist-induced expression of cyclin-dependent kinase 1 gene in cardiac fibroblasts." American Journal of Physiology-Cell Physiology 306, no. 6 (March 15, 2014): C540—C550. http://dx.doi.org/10.1152/ajpcell.00206.2013.

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Cardiac fibrosis, a known risk factor for heart disease, is typically caused by uncontrolled proliferation of fibroblasts and excessive deposition of extracellular matrix proteins in the myocardium. Cyclin-dependent kinase 1 (CDK1) is involved in the control of G2/M transit phase of the cell cycle. Here, we showed that isoproterenol (ISO)-induced cardiac fibrosis is associated with increased levels of CDK1 exclusively in fibroblasts in the adult mouse heart. Treatment of primary embryonic ventricular cell cultures with ISO (a nonselective β-adrenergic receptor agonist) increased CDK1 protein expression in fibroblasts and promoted their cell cycle activity. Quantitative PCR analysis confirmed that ISO increases CDK1 transcription in a transient manner. Further, the ISO-responsive element was mapped to the proximal −100-bp sequence of the CDK1 promoter region using various 5′-flanking sequence deletion constructs. Sequence analysis of the −100-bp CDK1 minimal promoter region revealed two putative nuclear factor-Y (NF-Y) binding elements. Overexpression of the NF-YA subunit in primary ventricular cultures significantly increased the basal activation of the −100-bp CDK1 promoter construct but not the ISO-induced transcription of the minimal promoter construct. In contrast, dominant negative NF-YA expression decreased the basal activity of the minimal promoter construct and ISO treatment fully rescued the dominant negative effects. Furthermore, site-directed mutagenesis of the distal NF-Y binding site in the −100-bp CDK1 promoter region completely abolished both basal and ISO-induced promoter activation of the CDK1 gene. Collectively, our results raise an exciting possibility that targeting CDK1 or NF-Y in the diseased heart may inhibit fibrosis and subsequently confer cardioprotection.
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21

Galvagni, F., M. Lestingi, E. Cartocci, and S. Oliviero. "Serum response factor and protein-mediated DNA bending contribute to transcription of the dystrophin muscle-specific promoter." Molecular and Cellular Biology 17, no. 3 (March 1997): 1731–43. http://dx.doi.org/10.1128/mcb.17.3.1731.

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The minimal muscle-specific dystrophin promoter contains the consensus sequence CC(A/T)6GG, or the CArG element, which can be found in serum-inducible or muscle-specific promoters. The serum response factor (SRF), which mediates the transcriptional activation of the c-fos gene in response to serum stimulation, can bind to different CArG box elements, suggesting that it could be involved in muscle-constitutive transcription. Here we show that SRF binds to the dystrophin promoter and regulates its muscle-specific transcription. In transient transfections, an altered-binding-specificity SRF mutant restores the muscle-constitutive transcription of a dystrophin promoter with a mutation in its CArG box element. The muscle-constitutive transcription of the dystrophin promoter also requires the sequence GAAACC immediately downstream of the CArG box. This sequence is recognized by a novel DNA bending factor which was named dystrophin promoter-bending factor (DPBF). Mutations of the CArG flanking sequence abolish both DPBF binding and the promoter activity in muscle cells. Its replacement with a p62/ternary complex factor binding site changes the promoter specificity from muscle constitutive to serum responsive. These results show that, on the dystrophin promoter, the transcriptional activation induced by SRF requires the DNA bending induced by DPBF. The bending, next to the CArG box, could promote interactions between SRF and other proteins in the transcriptional complex.
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22

Burns, LJ, JF Waring, JJ Reuter, MF Stinski, and GD Ginder. "Only the HLA class I gene minimal promoter elements are required for transactivation by human cytomegalovirus immediate early genes." Blood 81, no. 6 (March 15, 1993): 1558–66. http://dx.doi.org/10.1182/blood.v81.6.1558.1558.

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Abstract The immediate early (IE) genes of human cytomegalovirus (HCMV) are expressed in lymphocytes and are known to transactivate both viral and cellular promoters. The mechanism by which IE gene products of HCMV transactivate expression of the HLA A2 gene promoter in Jurkat cells, a T-lymphocyte cell line, was investigated. Transient expression assays were performed using plasmids containing the HLA A2 promoter-regulatory region linked to the bacterial chloramphenicol acetyltransferase (CAT) gene and a plasmid expressing the CMV IE genes. The upregulation of the HLA A2 promoter by HCVM IE gene products was shown not to be secondary to either interferon-gamma or -alpha. Previously described MHC class I regulatory or enhancer elements such as the interferon-stimulated response element (ISRE), NF-kappa B and H2TF1 binding sequences, and the interferon consensus sequence (ICS) were not required for transactivation of the A2 promoter. Rather, the only known regulatory elements in the HLA A2 promoter necessary for both basal expression and transactivation by HCVM IE gene products are the CCAAT box and TATA box motifs. These results support a model in which HCVM IE gene products act through the minimal HLA A2 promoter elements to increase gene expression.
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23

Burns, LJ, JF Waring, JJ Reuter, MF Stinski, and GD Ginder. "Only the HLA class I gene minimal promoter elements are required for transactivation by human cytomegalovirus immediate early genes." Blood 81, no. 6 (March 15, 1993): 1558–66. http://dx.doi.org/10.1182/blood.v81.6.1558.bloodjournal8161558.

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The immediate early (IE) genes of human cytomegalovirus (HCMV) are expressed in lymphocytes and are known to transactivate both viral and cellular promoters. The mechanism by which IE gene products of HCMV transactivate expression of the HLA A2 gene promoter in Jurkat cells, a T-lymphocyte cell line, was investigated. Transient expression assays were performed using plasmids containing the HLA A2 promoter-regulatory region linked to the bacterial chloramphenicol acetyltransferase (CAT) gene and a plasmid expressing the CMV IE genes. The upregulation of the HLA A2 promoter by HCVM IE gene products was shown not to be secondary to either interferon-gamma or -alpha. Previously described MHC class I regulatory or enhancer elements such as the interferon-stimulated response element (ISRE), NF-kappa B and H2TF1 binding sequences, and the interferon consensus sequence (ICS) were not required for transactivation of the A2 promoter. Rather, the only known regulatory elements in the HLA A2 promoter necessary for both basal expression and transactivation by HCVM IE gene products are the CCAAT box and TATA box motifs. These results support a model in which HCVM IE gene products act through the minimal HLA A2 promoter elements to increase gene expression.
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24

Hua, Ping, Hua Xu, Jennifer K. Uno, Maciej A. Lipko, Jiali Dong, Pawel R. Kiela, and Fayez K. Ghishan. "Sp1 and Sp3 mediate NHE2 gene transcription in the intestinal epithelial cells." American Journal of Physiology-Gastrointestinal and Liver Physiology 293, no. 1 (July 2007): G146—G153. http://dx.doi.org/10.1152/ajpgi.00443.2006.

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Our previous studies have identified a minimal Sp1-driven promoter region (nt −36/+116) directing NHE2 expression in mouse renal epithelial cells. However, this minimal promoter region was not sufficient to support active transcription of NHE2 gene in the intestinal epithelial cells, suggesting the need for additional upstream regulatory elements. In the present study, we used nontransformed rat intestinal epithelial (RIE) cells as a model to identify the minimal promoter region and transcription factors necessary for the basal transcription of rat NHE2 gene in the intestinal epithelial cells. We identified a region within the rat NHE2 gene promoter located within nt −67/−43 upstream of transcription initiation site as indispensable for the promoter function in intestinal epithelial cells. Mutations at nt −56/−51 not only abolished the DNA-protein interaction in this region, but also completely abolished NHE2 gene promoter activity in RIE cells. Supershift assays revealed that Sp1 and Sp3 interact with this promoter region, but, contrary to the minimal promoter indispensable for renal expression of NHE2, both transcription factors expressed individually in Drosophila SL2 cells activated rat NHE2 gene promoter. Moreover, Sp1 was a weaker transactivator and when coexpressed in SL2 cells it reduced Sp3-mediated NHE2 basal promoter activity. Furthermore, DNase I footprinting confirmed that nt −58/−51 is protected by nuclear protein from RIE cells. We conclude that the mechanism of basal control of rat NHE2 gene promoter activity is different in the renal and intestinal epithelium, with Sp3 being the major transcriptional activator of NHE2 gene transcription in the intestinal epithelial cells.
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25

Hunter, Donald A., and Lyn M. Watson. "The harvest-responsive region of the Asparagus officinalis sparagine synthetase promoter reveals complexity in the regulation of the harvest response." Functional Plant Biology 35, no. 12 (2008): 1212. http://dx.doi.org/10.1071/fp08161.

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The activity of a 1915-bp asparagine synthetase (AS) promoter of Asparagus officinalis L. was induced in mature leaves of transgenic Arabidopsis thaliana (L.) Heynh. plants when the leaves were detached and held in water for 24 h. To understand this induction by harvest, variants of the AS promoter were linked to the β-glucuronidase GUS reporter gene. Harvest induction in the leaves required detachment and was not simply a wound response. Two regions in the AS promoter (Region A, –640 to –523; Region B, –524 to –383) were independently able to confer harvest response to the otherwise unresponsive –383AS (minimal) promoter. Region A was studied in further detail. Various truncations, deletions, or nucleotide substitutions of Region A affected activity and fold induction of the minimal promoter. However, no harvest-inducible cis-acting element within Region A was identified. Although the minimal promoter contained a dehydration-responsive element and ACGT elements similar to ABA-responsive regulatory motifs these were not needed by the upstream regulatory regions for directing harvest response. When four copies of Region A were linked to the minimal promoter it became highly active in leaves before harvest. Deletions within Region A showed that it required its complete 117 bp for driving harvest response, yet the region cannot simply be thought of as a harvest-responsive module, since its concatemerisation led to constitutive expression.
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26

Hettiarachchi, G. H. C. M. "Light-mediated regulation defines a minimal promoter region of TOP2." Nucleic Acids Research 31, no. 18 (September 15, 2003): 5256–65. http://dx.doi.org/10.1093/nar/gkg744.

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27

Terzano, Susanna, Adriano Flora, Francesco Clementi, and Diego Fornasari. "The Minimal Promoter of the Human α3Nicotinic Receptor Subunit Gene." Journal of Biological Chemistry 275, no. 52 (October 3, 2000): 41495–503. http://dx.doi.org/10.1074/jbc.m006197200.

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28

Young, B. A. "Minimal Machinery of RNA Polymerase Holoenzyme Sufficient for Promoter Melting." Science 303, no. 5662 (February 27, 2004): 1382–84. http://dx.doi.org/10.1126/science.1092462.

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29

Geldermann, U., G. Langen, and K. H. Kogel. "Promoter studies of chemically induced BCI-genes in the pathosystem barley – powdery mildew." Plant Protection Science 38, SI 2 - 6th Conf EFPP 2002 (December 31, 2017): 487–88. http://dx.doi.org/10.17221/10531-pps.

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Chemical resistance inducers like BTH (S-methyl benzo (1,2,3)-thiadiazole-7-carbothiate) and DCINA (2,6-dichloro isonicotinic acid) activate resistance in barley against powdery mildew (Blumeria graminis f.sp. hordei). Nine BTH induced genes (Bci, barley chemically induced) have been identified in barley (BESSER et al. 2000) which are not responsive to pathogens in contrast to PR-proteins. From two Bci-genes (Bci3: similar to vsp, Bci4: Ca<sup>2+</sup>-binding EF-hand protein), the promoters were isolated. In transient transformation assays using promoter::GFP and promoter::GUS-constructs the functionality of these chemically induced promoters were studied. To identify the minimal promoter and regions with regulatory elements 5’-deletion constructs were used. Additionally, gel mobility shift assays were performed.
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30

YANG, Hsin-Sheng, Mark JOHNSON, and Mulchand S. PATEL. "Roles of an Ets motif and a novel CACGAC direct repeat in transcription of the murine dihydrolipoamide dehydrogenase (Dld) gene." Biochemical Journal 338, no. 3 (March 8, 1999): 667–75. http://dx.doi.org/10.1042/bj3380667.

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The 5´-flanking region of the murine dihydrolipoamide dehydrogenase (Dld) gene was characterized for its promoter activity. DNase I footprinting analysis of the promoter region (-545 bp to +41 bp) revealed six major protein-binding domains (termed P1 to P6) that were protected by NIH3T3 fibroblast nuclear extracts. Transient transfection assays, using a series of nested deletions of the 2.5 kb 5´-flanking region ligated to the chloramphenicol acetyltransferase reporter gene, identified that the -42-bp to +41-bp region, which harbours the P1, P2, and P3 domains, had minimal transcriptional activity. When the 5´-flanking region was extended from -42 bp to -82 bp, there was an approx. 5-fold increase in promoter activity. To identify further the cis elements involved in transcription of the Dld gene (-82 bp to +41 bp), a series of mutations were introduced into this region and evaluated for functional effects using transient transfection and electrophoretic mobility shift assays. Mutation or deletion of the CACGAC direct repeat, located from -61 bp to -46 bp, resulted in minimal promoter activity. Mutation of the Ets motif, located from -37 bp to -32 bp, reduced the minimal promoter activity by approx. 50%, whereas the deletion of this motif almost abolished the promoter activity. These results indicate that: (i) the Ets motif is required for the minimal promoter activity and (ii) the CACGAC direct repeat enhances promoter activity. Database searches failed to identify the direct repeat with the CACGAC motif and hence the CACGAC sequence may represent a novel motif. The requirement of both the Ets motif and the direct repeat element for optimal promoter activity represents a unique combination for gene transcription.
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31

Saiardi, A., P. Falasca, and D. Civitareale. "Synergistic transcriptional activation of the thyrotropin receptor promoter by cyclic AMP-responsive-element-binding protein and thyroid transcription factor 1." Biochemical Journal 310, no. 2 (September 1, 1995): 491–96. http://dx.doi.org/10.1042/bj3100491.

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In this study we have investigated the molecular mechanisms involved in hormonal induction of thyroid-specific transcription of the thyrotropin receptor (TSHr). A cyclic AMP-responsive element (CRE) has been characterized in the minimal TSHr promoter, and promoter activity shown to be also induced by thyroid transcription factor 1 (TTF-1). We here describe a cooperative effect between TTF-1 and CRE-binding protein on the TSHr promoter. Moreover we have identified a second TTF-1-binding site in the minimal promoter, which does not activate TSHr promoter activity but is required for the co-operative activation of the promoter. This report describes a new aspect of thyroid-specific gene expression, namely, how a generic extracellular signal can be interpreted in a thyroid-specific way.
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32

George, C. P., L. M. Lira-DeVito, S. L. Wampler, and J. T. Kadonaga. "A spectrum of mechanisms for the assembly of the RNA polymerase II transcription preinitiation complex." Molecular and Cellular Biology 15, no. 2 (February 1995): 1049–59. http://dx.doi.org/10.1128/mcb.15.2.1049.

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To explore the diversity in the mechanisms of basal transcription by RNA polymerase II, we have employed a novel biochemical approach that involves perturbation of the transcription reaction with exogenously added TFIIB or TATA box-binding protein (TBP). Under these conditions, we observe promoter-selective inhibition of transcription by excess TFIIB or excess TBP. This inhibition occurs at the level of basal transcription, because it is observed with minimal promoters that comprise only the TATA box and initiation site sequences as well as with preparations of basal transcription factors that have been purified to greater than 90% homogeneity. In addition, the excess basal factors inhibit the assembly of a functional preinitiation complex but do not inhibit transcription initiation from preassembled preinitiation complexes. A study of several promoters revealed a reciprocal trend in the promoter specificity of inhibition by excess TFIIB versus that by excess TBP. At opposite ends of this spectrum, promoters are strongly inhibited by excess TFIIB but not excess TBP and vice versa. These results reveal the existence of a spectrum of mechanisms for preinitiation complex assembly at different promoters. The mechanistic preference appears to be specified by the aggregate of basal promoter elements rather than by an individual component, such as the TATA box or initiation site sequence. This spectrum provides a new parameter by which differences in the function of minimal class II promoters can be analyzed in the context of both basal and regulated transcription.
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33

Ghosal, Abhisek, Subrata Sabui, and Hamid M. Said. "Identification and characterization of the minimal 5′-regulatory region of the human riboflavin transporter-3 (SLC52A3) in intestinal epithelial cells." American Journal of Physiology-Cell Physiology 308, no. 2 (January 15, 2015): C189—C196. http://dx.doi.org/10.1152/ajpcell.00342.2014.

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The human riboflavin (RF) transporter-3 (product of the SLC52A3 gene) plays an important role in intestinal RF absorption. Our aims in this study were to identify the minimal 5′-regulatory region of the SLC52A3 gene and the regulatory element(s) involved in its activity in intestinal epithelial cells, as well as to confirm promoter activity and establish physiological relevance in vivo in transgenic mice. With the use of transiently transfected human intestinal epithelial HuTu 80 cells and 5′-deletion analysis, the minimal SLC52A3 promoter was found to be encoded between −199 and +8 bp (using the start of the transcription start site as position 1). Although several putative cis-regulatory elements were predicted in this region, only the stimulating protein-1 (Sp1) binding site (at position −74/−71 bp) was found to play a role in promoter activity, as indicated by mutational analysis. Binding of Sp1 to the minimal SLC52A3 promoter was demonstrated by means of EMSA and supershift assays and by chromatin immunoprecipitation analysis. Studies with Drosophila SL2 cells (which lack Sp activity) confirmed the importance of Sp1 in driving the activity of the SLC52A3 minimal promoter; they further showed that Sp3 can also do the activation. Finally, with the use of luciferase gene fusions, the activity of the cloned SLC52A3 promoter was confirmed in vivo in transgenic mice. These studies report, for the first time, on the identification and characterization of the SLC52A3 promoter and also demonstrate the importance of Sp1 in regulating its activity in intestinal epithelial cells.
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34

Dunn, S. M., R. A. Keough, G. E. Rogers, and B. C. Powell. "Regulation of a hair follicle keratin intermediate filament gene promoter." Journal of Cell Science 111, no. 23 (December 1, 1998): 3487–96. http://dx.doi.org/10.1242/jcs.111.23.3487.

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During hair growth, cortical cells emerging from the proliferative follicle bulb rapidly undergo a differentiation program and synthesise large amounts of hair keratin proteins. To identify some of the controls that specify expression of hair genes we have defined the minimal promoter of the wool keratin intermediate filament gene K2.10. The region of this gene spanning nucleotides −350 to +53 was sufficient to direct expression of the lacZ gene to the follicle cortex of transgenic mice but deletion of nucleotides −350 to −150 led to a complete loss of promoter activity. When a four base substitution mutation was introduced into the minimal functional promoter at the binding site for lymphoid enhancer factor 1 (LEF-1), promoter activity in transgenic mice was decreased but specificity was not affected. To investigate the interaction of trans-acting factors within the minimal K2.10 promoter we performed DNase I footprinting analyses and electrophoretic mobility shift assays. In addition to LEF-1, Sp1, AP2-like and NF1-like proteins bound to the promoter. The Sp1 and AP2-like proteins bound sequences flanking the LEF-1 binding site whereas the NF1-like proteins bound closer to the transcription start site. We conclude that the LEF-1 binding site is an enhancer element of the K2.10 promoter in the hair follicle cortex and that factors other than LEF-1 regulate promoter tissue- and differentiation-specificity.
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35

POPPLETON, Helen M., and Rajendra RAGHOW. "Transcriptional activation of the minimal human Proα1(I) collagen promoter: obligatory requirement for Sp1." Biochemical Journal 323, no. 1 (April 1, 1997): 225–31. http://dx.doi.org/10.1042/bj3230225.

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A construct containing human Proα1(I) collagen gene promoter/enhancer-driven chloramphenicol acetyltransferase (CAT), pCOL-KT, failed to be expressed significantly in Sp1-deficient Schneider Drosophila line 2 (SL2) cells. However, CAT expression was induced 200-fold in SL2 cells co-transfected with pCOL-KT and pPACSp1, an Sp1-expression vector driven by the Drosophila actin 5C promoter. Elimination of the four potential Sp1-binding sites from pCOL-KT (pCOL-KTΔI), by removal of the first intron, did not abrogate Sp1-mediated induction of CAT. Even more significantly, a minimal Proα1(I) collagen promoter (-100 to +117 bp), containing a TATA box (-28 to -25 bp) and one putative Sp1-binding site (-87 to -82 bp), elicited strong Sp1-induced transactivation. Furthermore, mutation of the Sp1 motif in the minimal Proα1(I) collagen promoter-CAT construct abolished Sp1-induced expression of the reporter gene. Purified Sp1 protein bound specifically to DNA fragments of the Proα1(I) minimal promoter encompassing the putative Sp1-binding site; Sp1 binding could be competed out by a double-stranded oligonucleotide containing the wild-type Sp1 sequence, while an oligonucleotide containing a mutated Sp1 site failed to compete. Based on these results, we postulate that Sp1 plays an obligatory role in the transcriptional activation of the human Proα1(I) collagen gene. Additionally, we propose that a bona fide Sp1 motif, located most proximal to the TATA box, is necessary and sufficient for Sp1-mediated activation of the minimal Proα1(I) collagen promoter.
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36

Baliga, Nitin S., and Shiladitya DasSarma. "Saturation Mutagenesis of the TATA Box and Upstream Activator Sequence in the Haloarchaeal bop Gene Promoter." Journal of Bacteriology 181, no. 8 (April 15, 1999): 2513–18. http://dx.doi.org/10.1128/jb.181.8.2513-2518.1999.

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ABSTRACT Degenerate oligonucleotides were used to randomize 21 bp of the 53-bp minimal bop promoter in three 7-bp segments, including the putative TATA box and the upstream activator sequence (UAS). The mutagenized bop promoter and the wild-type structural gene and transcriptional terminator were inserted into a shuttle plasmid capable of replication in the halophilic archaeonHalobacterium sp. strain S9. Active promoters were isolated by screening transformants of an orange (Pum− bop) Halobacterium mutant for purple (Pum+ bop +) colonies on agar plates and analyzed for bop mRNA and/or bacteriorhodopsin content. Sequence analysis yielded the consensus sequence 5′-tyT(T/a)Ta-3′, corresponding to the promoter TATA box element 30 to 25 bp 5′ of the transcription start site. A putative UAS, 5′-ACCcnactagTTnG-3′, located 52 to 39 bp 5′ of the transcription start site was found to be conserved in active promoters. This study provides direct evidence for the requirement of the TATA box and UAS for bop promoter activity.
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37

Smith, R. L., D. L. Traul, J. Schaack, G. H. Clayton, K. J. Staley, and C. L. Wilcox. "Characterization of Promoter Function and Cell-Type-Specific Expression from Viral Vectors in the Nervous System." Journal of Virology 74, no. 23 (December 1, 2000): 11254–61. http://dx.doi.org/10.1128/jvi.74.23.11254-11261.2000.

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ABSTRACT Viral vectors have become important tools to effectively transfer genes into terminally differentiated cells, including neurons. However, the rational for selection of the promoter for use in viral vectors remains poorly understood. Comparison of promoters has been complicated by the use of different viral backgrounds, transgenes, and target tissues. Adenoviral vectors were constructed in the same vector background to directly compare three viral promoters, the human cytomegalovirus (CMV) immediate-early promoter, the Rous sarcoma virus (RSV) long terminal repeat, and the adenoviral E1A promoter, driving expression of the Escherichia coli lacZ gene or the gene for the enhanced green fluorescent protein. The temporal patterns, levels of expression, and cytotoxicity from the vectors were analyzed. In sensory neuronal cultures, the CMV promoter produced the highest levels of expression, the RSV promoter produced lower levels, and the E1A promoter produced limited expression. There was no evidence of cytotoxicity produced by the viral vectors. In vivo analyses following stereotaxic injection of the vector into the rat hippocampus demonstrated differences in the cell-type-specific expression from the CMV promoter versus the RSV promoter. In acutely prepared hippocampal brain slices, marked differences in the cell type specificity of expression from the promoters were confirmed. The CMV promoter produced expression in hilar regions and pyramidal neurons, with minimal expression in the dentate gyrus. The RSV promoter produced expression in dentate gyrus neurons. These results demonstrate that the selection of the promoter is critical for the success of the viral vector to express a transgene in specific cell types.
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38

Chen, Chien, and Thomas P. Yang. "Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of theHPRT Promoter." Molecular and Cellular Biology 21, no. 22 (November 15, 2001): 7682–95. http://dx.doi.org/10.1128/mcb.21.22.7682-7695.2001.

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ABSTRACT Differential chromatin structure is one of the hallmarks distinguishing active and inactive genes. For the X-linked human hypoxanthine phosphoribosyltransferase gene (HPRT), this difference in chromatin structure is evident in the differential general DNase I sensitivity and hypersensitivity of the promoter regions on active versus inactive X chromosomes. Here we characterize the nucleosomal organization responsible for the differential chromatin structure of the active and inactive HPRT promoters. The micrococcal nuclease digestion pattern of chromatin from the active allele in permeabilized cells reveals an ordered array of translationally positioned nucleosomes in the promoter region except over a 350-bp region that is either nucleosome free or contains structurally altered nucleosomes. This 350-bp region includes the entire minimal promoter and all of the multiple transcription initiation sites of the HPRT gene. It also encompasses all of the transcription factor binding sites identified by either dimethyl sulfate or DNase I in vivo footprinting of the active allele. In contrast, analysis of the inactive HPRT promoter reveals no hypersensitivity to either DNase I or a micrococcal nuclease and no translational positioning of nucleosomes. Although nucleosomes on the inactive promoter are not translationally positioned, high-resolution DNase I cleavage analysis of permeabilized cells indicates that nucleosomes are rotationally positioned over a region of at least 210 bp on the inactive promoter, which coincides with the 350-bp nuclease-hypersensitive region on the active allele, including the entire minimal promoter. This rotational positioning of nucleosomes is not observed on the active promoter. These results suggest a model in which the silencing of the HPRT promoter during X chromosome inactivation involves remodeling a transcriptionally competent, translationally positioned nucleosomal array into a transcriptionally repressed architecture consisting of rotationally but not translationally positioned nucleosomal arrays.
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39

Zhao-Emonet, Jing Chao, Olivier Boyer, José L. Cohen, and David Klatzmann. "Deletional and mutational analyses of the human CD4 gene promoter: characterization of a minimal tissue-specific promoter." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1442, no. 2-3 (November 1998): 109–19. http://dx.doi.org/10.1016/s0167-4781(98)00154-7.

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40

Gunther, M., T. Frebourg, M. Laithier, N. Fossar, M. Bouziane-Ouartini, C. Lavialle, and O. Brison. "An Sp1 binding site and the minimal promoter contribute to overexpression of the cytokeratin 18 gene in tumorigenic clones relative to that in nontumorigenic clones of a human carcinoma cell line." Molecular and Cellular Biology 15, no. 5 (May 1995): 2490–99. http://dx.doi.org/10.1128/mcb.15.5.2490.

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Clones of cells tumorigenic or nontumorigenic in nude mice have been previously isolated from the SW613-S human colon carcinoma cell line. We have already reported that tumorigenic cells overexpress the cytokeratin 18 (K18) gene in comparison with nontumorigenic cells and that this difference is mainly due to a transcriptional regulation. We now report that a 2,532-bp cloned human K18 gene promoter drives the differential expression of a reporter gene in a transient assay. A 62-bp minimal K18 promoter (TATA box and initiation site) has a low but differential activity. Analysis of deletion and substitution mutants as well as hybrid SV40-K18 promoters and reconstructed K18 promoters indicated that an important element for the activity of the K18 promoter is a high-affinity binding site for transcription factor Sp1 located just upstream of the TATA box. This Sp1 binding element, as well as the intron 1 enhancer element, stimulates the basal activity of the minimal promoter through mechanisms that maintain the differential activity. Gel shift assays and the use of an anti-Sp1 antibody have shown that both tumorigenic and nontumorigenic SW613-S cells contain three factors able to bind to the Sp1 binding element site and that one of them is Sp1. A hybrid GAL4-Sp1 protein transactivated to comparable extents in tumorigenic and nontumorigenic cells a reconstructed K18 promoter containing GAL4 binding sites and therefore without altering its differential behavior. These results indicate that the Sp1 transcription factor is involved in the overexpression of the K18 gene in tumorigenic SW613-S cells through its interaction with a component of the basal transcription machinery.
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41

Tokusumi, Yumiko, Sharleen Zhou, and Shinako Takada. "Nuclear Respiratory Factor 1 Plays an Essential Role in Transcriptional Initiation from the Hepatitis B Virus X Gene Promoter." Journal of Virology 78, no. 20 (October 15, 2004): 10856–64. http://dx.doi.org/10.1128/jvi.78.20.10856-10864.2004.

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ABSTRACT The X gene of hepatitis B virus (HBV) is one of the major factors in HBV-induced hepatocarcinogenesis and is essential for the establishment of productive HBV replication in vivo. Recent studies have shown that the X gene product targets mitochondria and induces calcium flux, thereby activating Ca+-dependent signal transduction pathways. However, regulatory mechanisms of X gene expression have remained unclear. Previous studies had localized a minimal promoter activity to a 21-bp GC-rich sequence located 130 bp upstream of the X protein coding region and showed that there was a cellular protein bound to this DNA. Interestingly, the 21-bp sequence identified as an X gene minimal promoter does not contain any previously identified core promoter elements, such as a TATA box. To better understand the mechanisms of transcriptional initiation of the X gene, we set out to biochemically purify the binding protein(s) for the 21-bp DNA. We report here the identification of the X gene minimal promoter-binding activity as nuclear respiratory factor 1 (NRF1), a previously known transcription factor that activates the majority of nucleus-encoded mitochondrial genes and various housekeeping genes. Primer extension analyses of the X mRNAs show that mutations at the binding site specifically inactivate transcription from this promoter and that a dominant-negative NRF1 mutant and short interfering RNAs inhibit transcription from this promoter. Therefore, NRF1 specifically binds the 21-bp minimal promoter and positively contributes to transcription of the X gene. Simultaneous activation of the X gene and mitochondrial genes by NRF1 may allow the X protein to target mitochondria most efficiently.
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42

Jiang, Lingling, Jiafang Wang, R. Sergio Solorzano-Vargas, Hugh V. Tsai, Edgar M. Gutierrez, Luis O. Ontiveros, Pawel R. Kiela, S. Vincent Wu, and Martín G. Martín. "Characterization of the rat intestinal Fc receptor (FcRn) promoter: transcriptional regulation of FcRn gene by the Sp family of transcription factors." American Journal of Physiology-Gastrointestinal and Liver Physiology 286, no. 6 (June 2004): G922—G931. http://dx.doi.org/10.1152/ajpgi.00131.2003.

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The regulatory elements that control the transcriptional regulation of the intestinal Fc receptor ( FcRn) have not been elucidated. The objective of this study was to characterize the core promoter region of the rat FcRn gene. Chimeric clones that contained various regions of the promoter located upstream of the luciferase reporter were transiently transfected into either IEC-6 or Caco-2 cell lines and nuclear extracts were used to perform DNase I footprint and DNA binding assays (EMSA). Transfection of chimeric upstream nested deletions-luciferase reporter clones into either of these cell lines supported robust reporter activity and identified the location of the minimal promoter at −157/+135. DNase I footprint analysis revealed two complexes located within the gene's core promoter region, and site-directed mutagenesis identified two regions that were critical to maintain basal expression. EMSA identified the presence of five Sp elements within the immediate promoter region that are capable of binding members of the Sp family of proteins. Among the five Sp elements, one element appears to not bind Sp1, Sp2, or Sp3 while influencing the interaction of Sp proteins with an adjacent Sp site. Overexpression of either Sp1 or Sp3 augments activity of the minimal promoter in Sp-deficient Drosophila SL2 cells. In summary, we report on the characterization of the rat FcRn minimal promoter, including the characterization of five Sp elements within this region that interact with members of the Sp family of transcriptional factors and drive promoter activity in intestinal cell lines.
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43

Treutlein, Barbara, Adam Muschielok, Joanna Andrecka, Anass Jawhari, Claudia Buchen, Dirk Kostrewa, Friederike Hög, Patrick Cramer, and Jens Michaelis. "Dynamic Architecture of a Minimal RNA Polymerase II Open Promoter Complex." Molecular Cell 46, no. 2 (April 2012): 136–46. http://dx.doi.org/10.1016/j.molcel.2012.02.008.

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44

Xia, C. L., I. G. Cowell, K. H. Dixon, S. E. Pemble, B. Ketterer, and J. B. Taylor. "Glutathione transferase π its minimal promoter and downstream cis-acting element." Biochemical and Biophysical Research Communications 176, no. 1 (April 1991): 233–40. http://dx.doi.org/10.1016/0006-291x(91)90914-s.

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45

Sandri, M. I., R. J. Isaacs, W. M. Ongkeko, A. L. Harris, I. D. Hickson, M. Broggini, and F. Vikhanskaya. "p53 Regulates the Minimal Promoter of the Human Topoisomerase II Gene." Nucleic Acids Research 24, no. 22 (November 1, 1996): 4464–70. http://dx.doi.org/10.1093/nar/24.22.4464.

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46

Sugiura, Takeyuki, Gertrud Hötten, and Shinji Kawai. "Minimal Promoter Components of the Human Growth/Differentiation Factor-5 Gene." Biochemical and Biophysical Research Communications 263, no. 3 (October 1999): 707–13. http://dx.doi.org/10.1006/bbrc.1999.1445.

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47

Wang, Lei, Yuli Guo, and Jay D. Gralla. "Regulation of Sigma 54-Dependent Transcription by Core Promoter Sequences: Role of −12 Region Nucleotides." Journal of Bacteriology 181, no. 24 (December 15, 1999): 7558–65. http://dx.doi.org/10.1128/jb.181.24.7558-7565.1999.

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ABSTRACT The tetranucleotide core recognition sequence (TTGC) of the sigma 54 promoter −12 recognition element was altered by random substitution. The resulting promoter mutants were characterized in vivo and in vitro. Deregulated promoters were identified, implying that this core element can mediate the response to enhancer-binding proteins. These promoters had in common a substitution at position −12 (consensus C), indicating its importance for keeping basal transcription in check. In another screen, nonfunctional promoters were identified. Their analysis indicated that positions −13 (consensus G) and −15 (consensus T) are important to maintain minimal promoter function. In vitro studies showed that the −13 and −15 positions contribute to closed-complex formation, whereas the −12 position has a stronger effect on recognition of the fork junction intermediate created during open-complex formation. Overall the data indicate that the −12 region core contains specific subsequences that direct the diverse RNA polymerase interactions required both to produce RNA and to restrict this RNA synthesis in the absence of activation.
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48

PASCALL, John C., and Kenneth D. BROWN. "Identification of a minimal promoter element of the mouse epidermal growth factor gene." Biochemical Journal 324, no. 3 (June 15, 1997): 869–75. http://dx.doi.org/10.1042/bj3240869.

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Abstract:
We have previously generated a transgenic mouse line (EGF/Tag) in which simian virus 40 (SV40) T-antigen expression is directed by the mouse epidermal growth factor (EGF) gene promoter. In these mice, cellular hyperproliferation is observed in the submaxillary gland associated with SV40 T-antigen expression. In addition, SV40 T-antigen-expressing tumours of prostatic origin are seen. We have now derived immortalized cell lines from these tissues and have used the cells to perform a functional analysis of the EGF gene promoter. Cells were transfected with EGF promoter/reporter constructs, and an element located between 51 and 35 bases upstream of the EGF mRNA start site required for basal activity of the promoter was identified. Electrophoretic mobility-shift analysis suggests that three proteins bind to this region, one of which is either Sp1 or a closely related protein.
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49

Jeong, Joseph, James Papin, and Dirk Dittmer. "Differential Regulation of the Overlapping Kaposi's Sarcoma-Associated Herpesvirus vGCR (orf74) and LANA (orf73) Promoters." Journal of Virology 75, no. 4 (February 15, 2001): 1798–807. http://dx.doi.org/10.1128/jvi.75.4.1798-1807.2001.

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ABSTRACT Similar to that of other herpesviruses, Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) lytic replication destroys the host cell, while the virus can persist in a latent state in synchrony with the host. During latency only a few genes are transcribed, and the question becomes one of what determines latent versus lytic gene expression. Here we undertake a detailed analysis of the latency-associated nuclear antigen (LANA [orf73]) promoter (LANAp). We characterized a minimal region that is necessary and sufficient to maintain high-level transcription in all tissues tested, including primary endothelial cells and B cells, which are the suspected natural host for KSHV. We show that in transient-transfection assays LANAp mimics the expression pattern observed for the authentic promoter in the context of the KSHV episome. Unlike other KSHV promoters tested thus far, LANAp is not affected by tetradecanoyl phorbol acetate or viral lytic cycle functions. It is, however, subject to control by LANA itself and cellular regulatory factors, such as p53. This is in contrast to the K14/vGCR (orf74) promoter, which overlaps LANAp and directs transcription on the opposite strand. We isolated a minimal cis-regulatory region sufficient for K14/vGCR promoter activity and show that it, too, mimics the regulation observed for the authentic viral promoter. In particular, we demonstrate that its activity is absolutely dependent on the immediate-early transactivator orf50, the KSHV homolog of the Epstein-Barr virus Rta transactivator.
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50

Smith, Aiping F., Robert M. Bigsby, R. Ann Word, and B. Paul Herring. "A 310-bp minimal promoter mediates smooth muscle cell-specific expression of telokin." American Journal of Physiology-Cell Physiology 274, no. 5 (May 1, 1998): C1188—C1195. http://dx.doi.org/10.1152/ajpcell.1998.274.5.c1188.

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Abstract:
A cell-specific promoter located in an intron of the smooth muscle myosin light chain kinase gene directs transcription of telokin exclusively in smooth muscle cells. Transgenic mice were generated in which a 310-bp rabbit telokin promoter fragment, extending from −163 to +147, was used to drive expression of simian virus 40 large T antigen. Smooth muscle-specific expression of the T-antigen transgene paralleled that of the endogenous telokin gene in all smooth muscle tissues except uterus. The 310-bp promoter fragment resulted in very low levels of transgene expression in uterus; in contrast, a transgene driven by a 2.4-kb fragment (−2250 to +147) resulted in high levels of transgene expression in uterine smooth muscle. Telokin expression levels correlate with the estrogen status of human myometrial tissues, suggesting that deletion of an estrogen response element (ERE) may account for the low levels of transgene expression driven by the 310-bp rabbit telokin promoter in uterine smooth muscle. Experiments in A10 smooth muscle cells directly showed that reporter gene expression driven by the 2.4-kb, but not 310-bp, promoter fragment could be stimulated two- to threefold by estrogen. This stimulation was mediated through an ERE located between −1447 and −1474. Addition of the ERE to the 310-bp fragment restored estrogen responsiveness in A10 cells. These data demonstrate that in addition to a minimal 310-bp proximal promoter at least one distal cis-acting regulatory element is required for telokin expression in uterine smooth muscle. The distal element may include an ERE between −1447 and −1474.
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