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1.  TRANSCRIPTIONAL REGULATION OF MOUSE L-SELECTIN 
Biochimica et biophysica acta  2008;1789(2):146-152.
L-selectin mediates the initial tethering and rolling of lymphocytes in high endothelial venules. To study the transcriptional regulation of mouse L-selectin, we cloned 4.5 kb 5’-flanking sequences of the mouse sell. Luciferase analysis of serial 5’-deletion mutants showed that the first 285 bp was sufficient to drive high promoter activity in EL4 cells, but not in Sell-negative HeLa cells, suggesting that this fragment harbors the minimal mouse sell promoter and contains cis-elements for lymphocyte-specific expression. Site-directed mutagenesis and chromatin immunoprecipitation showed that Mzf1, Klf2, Sp1, Ets1, and Irf1 bind to and activate the mouse sell promoter. Over expression of these transcription factors in EL4 cells increased expression of sell mRNA. Silencing the expression of Sp1 by siRNA significantly decreased sell promoter activity in EL4 cells. We conclude that sell transcription is regulated by Mzf1, Klf2, Sp1, Ets1, and Irf1.
doi:10.1016/j.bbagrm.2008.10.004
PMCID: PMC2650851  PMID: 19041738
L-selectin; promoter; gene regulation; Sp1; Mzf-1; Irf1; Klf2; Ets-1
2.  Myelin basic protein gene contains separate enhancers for oligodendrocyte and Schwann cell expression 
The Journal of Cell Biology  1992;119(3):605-616.
The DNA sequence between position +36 and -1907 of the murine myelin basic protein gene contains the enhancer and promoter elements necessary for abundant and cell specific expression in transgenic mice. Surprisingly, the pattern of expression promoted by this DNA fragment is a subset of that exhibited by the endogenous myelin basic protein (MBP) gene. Fusion genes prepared with this promoter/enhancer and a Lac Z reporter gene are expressed only in oligodendrocytes and not in Schwann cells, whereas the endogenous MBP gene is expressed in both cell types. The level of transgene expression measured by nuclear run- on experiments is very substantial and rivals that of the endogenous MBP gene. Furthermore, this 1.9-kb DNA fragment directs transcription on the same (or very similar) developmental schedule as the endogenous gene. These results indicate that the MBP promoter/enhancer sequences are at least tripartite: a core promoter, the oligodendrocyte enhancer elements, and a third component that either expands the specificity of the oligodendrocyte enhancer to include Schwann cells or acts independently to specifically stimulate transcription in Schwann cells.
PMCID: PMC2289674  PMID: 1383235
3.  Conditional cell ablation by stringent tetracycline-dependent regulation of barnase in mammalian cells 
Nucleic Acids Research  2001;29(16):e76.
Conditional expression of suicide genes in vivo has a wide range of applications in biological research and requires a minimal basal promoter activity in the uninduced state. To reduce basal activity of tetracycline (tc)-inducible target promoters we combined synthetic tet operators in varying numbers with a core promoter derived from the plant viral 35S promoter. An optimized promoter, PTF, was found to exert a stringent regulation of luciferase in combination with tTA and rtTA in different mammalian cell lines. We linked PTF to the barnase gene, coding for a highly active RNase from Bacillus amyloliquefaciens. Stable cell clones expressing barnase under control of tTA exerted cell death only after tc withdrawal, correlating with a 10-fold induction of barnase mRNA expression. Directing tTA expression through a neuron-specific enolase promoter (PNSE) leads to barnase expression and cell death in neuronal cells after tc withdrawal. Taken together, our data demonstrate that a stringent control of barnase expression in the uninduced state improves cell ablation studies, as high frequencies of transgene propagation in both cell lines and in transgenic mice are observed.
PMCID: PMC55860  PMID: 11504884
4.  Transcriptional Activation of REST by Sp1 in Huntington's Disease Models 
PLoS ONE  2010;5(12):e14311.
In Huntington's disease (HD), mutant huntingtin (mHtt) disrupts the normal transcriptional program of disease neurons by altering the function of several gene expression regulators such as Sp1. REST (Repressor Element-1 Silencing Transcription Factor), a key regulator of neuronal differentiation, is also aberrantly activated in HD by a mechanism that remains unclear. Here, we show that the level of REST mRNA is increased in HD mice and in NG108 cells differentiated into neuronal-like cells and expressing a toxic mHtt fragment. Using luciferase reporter gene assay, we delimited the REST promoter regions essential for mHtt-mediated REST upregulation and found that they contain Sp factor binding sites. We provide evidence that Sp1 and Sp3 bind REST promoter and interplay to fine-tune REST transcription. In undifferentiated NG108 cells, Sp1 and Sp3 have antagonistic effect, Sp1 acting as an activator and Sp3 as a repressor. Upon neuronal differentiation, we show that the amount and ratio of Sp1/Sp3 proteins decline, as does REST expression, and that the transcriptional role of Sp3 shifts toward a weak activator. Therefore, our results provide new molecular information to the transcriptional regulation of REST during neuronal differentiation. Importantly, specific knockdown of Sp1 abolishes REST upregulation in NG108 neuronal-like cells expressing mHtt. Our data together with earlier reports suggest that mHtt triggers a pathogenic cascade involving Sp1 activation, which leads to REST upregulation and repression of neuronal genes.
doi:10.1371/journal.pone.0014311
PMCID: PMC3001865  PMID: 21179468
5.  HNF4α and NF-E2 are key transcriptional regulators of the murine Abcc6 gene expression 
Biochimica et biophysica acta  2006;1759(8-9):426-436.
SUMMARY
Mutations in an ABC transporter gene called ABCC6 are responsible for pseudoxanthoma elasticum (PXE), a rare heritable disease characterized by elastic fiber calcification in skin, ocular and vascular tissues. The presumed function of this ABC transporter is to export metabolites from polarized cells. However, the endogenous substrate(s) are unknown and the exact relationship with elastic fibers is unclear. As ABCC6 is expressed at high level only in liver and kidneys, tissues seemingly unrelated to the PXE phenotype, we explored the transcriptional regulation of the murine Abcc6 gene to define transcriptional regulation conferring tissue specificity and to gather clues on its possible biological function. We cloned 2.9 kb of the mAbcc6 5′-flanking region and several deletion constructs linked to a luciferase reporter gene. We delineated a proximal promoter and a liver-specific enhancer region. We also demonstrated that the proximal region is a TATA-less promoter requiring an intact CCAAT-box and Sp1 binding for its basal activity. By using reporter assays and chromatin immunoprecipitations, we showed that HNF4α and surprinsingly, NF-E2, enhanced the mAbcc6 promoter activity. The involvement of both HNF4α and NF-E2 in the mAbcc6 gene regulation suggests that Abcc6 might be involved in a detoxification processes related to hemoglobin or heme.
doi:10.1016/j.bbaexp.2006.08.002
PMCID: PMC1876778  PMID: 16997394
Abcc6; ABC transporter; pseudoxanthoma elasticum; transcriptional regulation; reporter gene analysis
6.  The developmental activation of the chicken lysozyme locus in transgenic mice requires the interaction of a subset of enhancer elements with the promoter. 
Nucleic Acids Research  1997;25(15):2992-3000.
The complete chicken lysozyme locus is expressed in a position independent fashion in macrophages of transgenic mice and forms the identical chromatin structure as observed with the endogenous gene in chicken cells. Individual lysozyme cis -regulatory elements reorganize their chromatin structure at different developmental stages. Accordingly, their activities are developmentally regulated, indicating a differential role of these elements in locus activation. We have shown previously that a subset of enhancer elements and the promoter are sufficient to activate transcription of the chicken lysozyme gene at the correct developmental stage. Here, we analyzed to which grade the developmentally controlled chromatin reorganizing capacity of cis -regulatory elements in the 5'-region of the chicken lysozyme locus is dependent on promoter elements, and we examined whether the lysozyme locus carries a dominant chromatin reorganizing element. To this end we generated transgenic mouse lines carrying constructs with a deletion of the lysozyme promoter. Expression of the transgene in macrophages is abolished, however, the chromatin reorganizing ability of the cis -regulatory elements is differentially impaired. Some cis -elements require the interaction with the promoter to stabilize transcription factor complexes detectable as DNase I hypersensitive sites in chromatin, whereas other elements reorganize their chromatin structure autonomously.
PMCID: PMC146846  PMID: 9224598
7.  The transcription of bradyzoite genes in Toxoplasma gondii is controlled by autonomous promoter elements 
Molecular Microbiology  2008;68(6):1502-1518.
Experimental evidence suggests that apicomplexan parasites possess bipartite promoters with basal and regulated cis-elements similar to other eukaryotes. Using a dual luciferase model adapted for recombinational cloning and use in Toxoplasma gondii, we show that genomic regions flanking 16 parasite genes, which encompass examples of constitutive and tachyzoite- and bradyzoite-specific genes, are able to reproduce the appropriate developmental stage expression in a transient luciferase assay. Mapping of cis-acting elements in several bradyzoite promoters led to the identification of short sequence spans that are involved in control of bradyzoite gene expression in multiple strains and under different bradyzoite induction conditions. Promoters that regulate the heat shock protein BAG1 and a novel bradyzoite-specific NTPase during bradyzoite development were fine mapped to a 6–8 bp resolution and these minimal cis-elements were capable of converting a constitutive promoter to one that is induced by bradyzoite conditions. Gel-shift experiments show that mapped cis-elements are bound by parasite protein factors with the appropriate functional sequence specificity. These studies are the first to identify the minimal sequence elements that are required and sufficient for bradyzoite gene expression and to show that bradyzoite promoters are maintained in a ‘poised’ chromatin state throughout the intermediate host life cycle in low passage strains. Together, these data demonstrate that conventional eukaryotic promoter mechanisms work with epigenetic processes to regulate developmental gene expression during tissue cyst formation.
doi:10.1111/j.1365-2958.2008.06249.x
PMCID: PMC2440561  PMID: 18433450
8.  Expression vectors for the use of eukaryotic luciferases as bacterial markers with different colors of luminescence. 
An easy way to identify microorganisms is to provide them with gene markers that confer a unique phenotype. Several genetic constructions were developed to use eukaryotic luciferase genes for bacterial tagging. The firefly and click bettle luciferase genes, luc and lucOR, respectively, were cloned under constitutive control and regulated control from different transcriptional units driven by P1, lambda PR, and Ptrc promoters. Comparison of the expression of each gene in Escherichia coli cells from identical promoters showed that bioluminescence produced by luc could be detected luminometrically in a more sensitive manner. In contrast, luminescence from intact lucOR-expressing cells was much more stable and resistant to high temperatures than that from luc-expressing cells. To analyze the behavior of these constructions in other gram-negative bacteria, gene fusions with luc genes were cloned on broad-host-range vectors. Measurements of light emission from Rhizobium meliloti, Agrobacterium tumefaciens, and Pseudomonas putida cells indicated that both luciferases were poorly expressed from P1 in most bacterial hosts. In contrast, the lambda promoter PR yielded constitutively high levels of luciferase expression in all bacterial species tested. PR activity was not regulated by temperature when the thermosensitive repressor cI857 was present in the bacterial species tested, except for E. coli. In contrast, the regulated lacIq-Ptrc::lucOR fusion expression system behaved in a manner similar to that observed in E. coli cells. After IPTG (isopropyl-beta-D-thiogalactopyranoside) induction, this system produced the highest levels of lucOR expression in all bacterial species tested.(ABSTRACT TRUNCATED AT 250 WORDS)
PMCID: PMC167327  PMID: 7574604
9.  The Samd9L Gene: Transcriptional Regulation and Tissue-Specific Expression in Mouse Development 
Normophosphatemic familial tumoral calcinosis (NFTC) is caused by mutations in the SAMD9 gene. This gene is absent in mouse while there is a murine paralogue, SamD9-like (Samd9L). To clarify the relationships of SAMD9 and SAMD9L, we investigated the transcriptional regulation and the expression pattern of mouse Samd9L. An ~1.5-kb mouse Samd9L promoter fragment was cloned, and a series of 5’ deletion constructs were linked to a luciferase reporter gene. All constructs displayed significant activity in transfected epithelial cells and mouse fibroblasts, and the presence of regulatory cis-elements as close as 87 bp upstream of the transcription start site were identified. Ras-responsive element binding protein (Rreb-1) was identified in this region by protein-DNA binding array. The expression of Samd9L was up-regulated by calcitonin, and this was preceded by a significant increase in the expression of Rreb-1 mRNA. qRT-PCR analysis of Samd9L revealed near-ubiquitous expression, with the highest level in the kidney. Tissue-specific expression was also confirmed both by in situ β-gal staining and quantitative enzymatic activity assay in a novel transgenic Samd9L+/− mouse in which the LacZ gene replaced exon 2 in the Samd9L gene. These findings assist in understanding the regulation of Samd9L in the context of its paralogous gene, SAMD9, which harbors mutations in NFTC.
doi:10.1038/jid.2011.61
PMCID: PMC3173943  PMID: 21412262
familial tumoral calcinosis; Samd9L gene expression; calcitonin regulation; Rasresponsive element binding protein
10.  E2F2 and CREB cooperatively regulate transcriptional activity of cell cycle genes 
Nucleic Acids Research  2013;41(22):10185-10198.
E2F2 is essential for the maintenance of T lymphocyte quiescence. To identify the full set of E2F2 target genes, and to gain further understanding of the role of E2F2 in transcriptional regulation, we have performed ChIP-chip analyses across the genome of lymph node–derived T lymphocytes. Here we show that during quiescence, E2F2 binds the promoters of a large number of genes involved in DNA metabolism and cell cycle regulation, concomitant with their transcriptional silencing. A comparison of ChIP-chip data with expression profiling data on resting E2f2−/− T lymphocytes identified a subset of 51 E2F2-specific target genes, most of which are upregulated on E2F2 loss. Luciferase reporter assays showed a retinoblastoma-independent role for E2F2 in the negative regulation of these target genes. Importantly, we show that the DNA binding activity of the transcription factor CREB contributes to E2F2-mediated repression of Mcm5 and Chk1 promoters. siRNA-mediated CREB knockdown, expression of a dominant negative KCREB mutant or disruption of CREB binding by mutating a CRE motif on Mcm5 promoter, relieved E2F2-mediated transcriptional repression. Taken together, our data uncover a new regulatory mechanism for E2F-mediated transcriptional control, whereby E2F2 and CREB cooperate in the transcriptional repression of a subset of E2F2 target genes.
doi:10.1093/nar/gkt821
PMCID: PMC3905855  PMID: 24038359
11.  Regulation of the Dlx3 Homeobox Gene upon Differentiation of Mouse Keratinocytes 
The Journal of biological chemistry  1999;274(37):26599-26608.
The Distalless Dlx3 homeodomain gene is expressed in terminally differentiated murine epidermal cells, and there is evidence to support an essential role as a transcriptional regulator of the terminal differentiation process in these cells. In an attempt to determine the factors that induce Dlx3 gene expression, we have cloned the 1.2-kilobase pair proximal region of murine gene and analyzed its cis-regulatory elements and potential trans-acting factors. The proximal region of the Dlx3 gene has a canonical TATA box and CCAAT box, and the transcription start site was located 205 base pairs upstream from the initiation of translation site. Serial deletion analysis showed that the region between −84 and −34 confers the maximal promoter activity both in undifferentiated and differentiated primary mouse keratinocytes. Gel retardation assays and mutational analysis demonstrated that the transcriptional regulator NF-Y (also referred to as CBF) binds to a CCAAT box motif within this region and is responsible for the majority of the Dlx3 promoter activity. In addition, an Sp1-binding site was located immediately upstream of transcription start site that acts as a positive regulatory element of the Dlx3 promoter, independent of the CCAAT box motif. Importantly, elements residing between +30 to +60 of the Dlx3 gene are responsible for the Ca2+-dependent induction of Dlx3 during keratinocyte differentiation.
PMCID: PMC1317293  PMID: 10473625
12.  Transcriptional regulation of the human soluble epoxide hydrolase gene EPHX2 
Biochimica et biophysica acta  2007;1779(1):17-27.
Soluble epoxide hydrolase (sEH) is a multifunctional protein encoded by the EPHX2 gene. The biological functions and enzyme kinetics of sEH have been extensively investigated, however, little is known about its transcriptional regulation and mechanisms of tissue specific expression. Here, a luciferase gene based reporter assay was used to identify the minimal promoter and cis regulatory elements of EPHX2. The minimal promoter was identified as a GC-rich region between nts −374 to +28 with respect to the putative transcriptional start site. A reporter plasmid carrying this minimal promoter showed higher or similar activities in comparison to a reporter plasmid carrying nts −5,974 to +28 of EPHX2 in 9 human cell lines that were tested. Sp1 binding sites that are involved in augmenting the minimal promoter activity of EPHX2 were identified by nested deletion analysis, site-specific mutation, electrophoretic mobility shift assay, and chromatin immunoprecipitation assay.
doi:10.1016/j.bbagrm.2007.11.005
PMCID: PMC2699939  PMID: 18078836
epoxide hydrolase; EPHX2; promoter; transcription
13.  An adenoviral vector for probing promoter activity in primary immune cells 
Journal of immunological methods  2006;311(1-2):19-30.
Functional analysis of the DNA regulatory regions that control gene expression has largely been performed through transient transfection of promoter–reporter constructs into transformed cells. However, transformed cells are often poor models of primary cells. To directly analyze DNA regulatory regions in primary cells, we generated a novel adenoviral luciferase reporter vector, pShuttle-luciferase-GFP (pSLUG) that contains a promoterless luciferase cassette (with an upstream cloning site) for probing promoter activity, and a GFP expression cassette that allows for the identification of transduced cells. Recombinant adenoviruses generated from this vector can transduce a wide range of primary immune cells with high efficiency, including human macrophages, dendritic cells and T cells; and mouse T cells transgenic for the coxsackie and adenoviral receptor (CAR). In primary T cells, we show inducible nuclear factor of activated T cells (NF-AT) activity using a recombinant pSLUG adenovirus containing a consensus NF-AT promoter. We further show inducible IL-12/23 p40 promoter activity in primary macrophages and dendritic cells using a recombinant pSLUG adenovirus containing the proximal human IL-12/23 p40 promoter. The pSLUG system promises to be a powerful tool for the analysis of DNA regulatory regions in diverse types of primary immune cells.
doi:10.1016/j.jim.2006.01.009
PMCID: PMC2964867  PMID: 16563424
T cell; Macrophage; Dendritic cell; Transcription; Promoter
14.  A gastrin transcript expressed in gastrointestinal cancer cells contains an internal ribosome entry site 
British Journal of Cancer  2008;98(10):1696-1703.
As the hormone gastrin promotes gastrointestinal (GI) cancer progression by triggering survival pathways, regulation of gastrin expression at the translational level was explored. Sequence within the 5′ untranslated region of a gastrin transcript expressed in GI cancer cells was investigated, then cloned into a bicistronic vector upstream of firefly luciferase and transfected into a series of GI cancer cell lines. Firefly luciferase activity was measured relative to that of a cap-dependent Renilla luciferase. A gastrin transcript that was different from that described in Ensembl was expressed in GI cancer cells. Its transcription appears to be initiated within the region designated as the gene's first intron. In GI cancer cells transfected with the bicistronic construct, firefly luciferase activity increased 8–15-fold compared with the control vector, and there was a further induction of the signal (up to 25-fold) following exposure of the cells to genotoxic stress or hypoxia, suggesting that the sequence acts as an internal ribosome entry site. These data suggest that the gastrin transcript within GI cancer cells contains an internal ribosome entry site that may allow continued expression of gastrin peptides when normal translational mechanisms are inactive, such as in hypoxia, thereby promoting cancer cell survival.
doi:10.1038/sj.bjc.6604326
PMCID: PMC2391123  PMID: 18392051
gastrin; translation; gastrointestinal; internal ribosome entry
15.  Analysis of promoters and CREB/AP-1 binding sites of the human TMEM174 gene 
Transmembrane protein 174 (TMEM174) is a type III transmembrane protein with no clear signal peptide. The N and C terminals are located inside the cell. Our previous study demonstrated high expression of TMEM174 in the kidney and its potential involvement in renal cancer based on its capacity to stimulate cell proliferation. However, the mechanism by which TMEM174 promotes proliferation at the transcriptional level remains to be elucidated. In the present study, the TMEM174 promoter region was amplified from whole blood DNA. Six different regions of the regulatory sequences of the TMEM174 promoter region including ~2.5 kb of the upstream region were cloned into the dual luciferase expression vector pGL3-basic. Comparison of the activity of these fragments in dual luciferase reporter assays revealed higher levels of activity for the fragments spanning −186 to +674, −700 to +674, −1,000 to +674 and −2,500 to +1 bp. Lower levels of activity were detected for the fragments spanning −466 to +674 and −890 to +674 bp. The highest activity was detected for the fragment spanning −186 to +674 bp. Electrophoretic mobility shift assay (EMSA) was performed to determine effective transcription factor binding sites. Specific binding of the cyclic-AMP response element binding (CREB) within the TMEM174 gene promoter region was demonstrated, although binding of the activator protein-1 (AP-1) was also detected in this region. In conclusion, these results suggest that the core promoter region of the human TMEM174 gene is located within the region spanning −186 to +674 bp and that the transcription factors CREB and AP-1 are involved in the transcriptional regulation of this gene.
doi:10.3892/etm.2013.1275
PMCID: PMC3820833  PMID: 24223660
activator protein-1; core promoter; cyclic-AMP response element binding protein; transmembrane protein 174 gene; transcriptional regulation; luciferase
16.  Transcriptional and posttranscriptional mechanisms regulate murine thymidine kinase gene expression in serum-stimulated cells. 
Molecular and Cellular Biology  1988;8(12):5280-5291.
We previously isolated and characterized the structure of murine thymidine kinase (tk) genomic and cDNA sequences to begin a study designed to identify regions of the tk gene important for regulated expression during the transition of cells from G0 to a proliferating state. In this report, we describe the stable transfection of the cloned gene into L-M(TK-) cells and show that both thymidine kinase (TK) enzyme activity and DNA synthesis increase in parallel when transfectants in G0 arrest are stimulated by serum. To define promoter and regulatory regions more precisely, we have constructed a series of tk minigenes and have examined their expression in stable transfectants after serum stimulation. We have identified a 291-base-pair DNA fragment at the 5' end of the tk gene that has promoter function, and we have determined its sequence. In addition, we have found that DNA sequences which mediate serum-induced expression of TK are transcribed, since expression of the murine tk cDNA, fused to a promoter from either the murine tk gene, the simian virus 40 early region, or the herpes simplex virus tk gene, is stimulated by serum. Our constructs also reveal that the murine tk polyadenylation signal is not required for regulation, nor is most of the 3' untranslated region. RNA dot blot analysis indicates that murine cytoplasmic tk mRNA levels always parallel TK enzyme activity. Nuclear runon transcription assays show less than a 2-fold increase in transcription from the cloned tk gene in serum-stimulated transfectants, but an 11-fold increase in mouse L929 cells, which are inherently TK+. These results taken together suggest that the murine tk gene is controlled in serum-stimulated cells by a transcriptional mechanism influenced by DNA sequences that flank tk and also by a posttranscriptional system linked to gene sequences that are transcribed.
Images
PMCID: PMC365630  PMID: 3244356
17.  The Transcriptional Repressor REST Determines the Cell-Specific Expression of the Human MAPK8IP1 Gene Encoding IB1 (JIP-1) 
Molecular and Cellular Biology  2001;21(21):7256-7267.
Islet-brain 1 (IB1) is the human and rat homologue of JIP-1, a scaffold protein interacting with the c-Jun amino-terminal kinase (JNK). IB1 expression is mostly restricted to the endocrine pancreas and to the central nervous system. Herein, we explored the transcriptional mechanism responsible for this preferential islet and neuronal expression of IB1. A 731-bp fragment of the 5′ regulatory region of the human MAPK8IP1 gene was isolated from a human BAC library and cloned upstream of a luciferase reporter gene. This construct drove high transcriptional activity in both insulin-secreting and neuron-like cells but not in unrelated cell lines. Sequence analysis of this promoter region revealed the presence of a neuron-restrictive silencer element (NRSE) known to bind repressor zinc finger protein REST. This factor is not expressed in insulin-secreting and neuron-like cells. By mobility shift assay, we confirmed that REST binds to the NRSE present in the IB1 promoter. Once transiently transfected in β-cell lines, the expression vector encoding REST repressed IB1 transcriptional activity. The introduction of a mutated NRSE in the 5′ regulating region of the IB1 gene abolished the repression activity driven by REST in insulin-secreting β cells and relieved the low transcriptional activity of IB1 observed in unrelated cells. Moreover, transfection in non-β and nonneuronal cell lines of an expression vector encoding REST lacking its transcriptional repression domain relieved IB1 promoter activity. Last, the REST-mediated repression of IB1 could be abolished by trichostatin A, indicating that deacetylase activity is required to allow REST repression. Taken together, these data establish a critical role for REST in the control of the tissue-specific expression of the human IB1 gene.
doi:10.1128/MCB.21.21.7256-7267.2001
PMCID: PMC99900  PMID: 11585908
18.  Cell cycle regulation of the murine cyclin E gene depends on an E2F binding site in the promoter. 
Molecular and Cellular Biology  1996;16(7):3401-3409.
Cyclin E controls progression through the G1 phase of the cell cycle in mammalian fibroblasts and potentially in many other cell types. Cyclin E is a rate-limiting activator of cdk2 kinase in late G1. The abundance of cyclin E is controlled by phase-specific fluctuations in the mRNA level; in mammalian fibroblasts, mRNA is not detected under conditions of serum starvation and is accumulated upon serum stimulation, with expression starting in mid-G1. Here, we report the cloning of the murine cyclin E promoter. We isolated a 3.8-kb genomic fragment that contains several transcriptional start sites and confers cell cycle regulation on a luciferase reporter gene. This fragment also supports transcriptional activation by adenovirus E1A, a known upstream regulator of cyclin E gene expression. An E2F binding site which is required for G1-specific activation of the cyclin E promoter in synchronized NIH 3T3 cells was identified in this fragment.
PMCID: PMC231334  PMID: 8668155
19.  Ets factors and a newly identified polymorphism regulate Fli1 promoter activity in lymphocytes 
Molecular immunology  2007;45(1):1-12.
Fli1 is an Ets family member that is essential for embryonic development. Increasing evidence suggests modulating Fli1 gene expression impacts lymphocyte development/function and is an important mediator in the autoimmune disease lupus. Fli1 is over-expressed in splenic lymphocytes in lupus prone mouse strains and in PBMCs of lupus patients. Presently, it is unknown how Fli1 gene expression is controlled in lymphocytes or how it becomes over-expressed in lupus. Therefore, we examined Fli1 regulation in a murine B cell line and T cell line and identified several cis-regulatory elements within a 230 bp region that contribute to Fli1 promoter activity. Ets factors Elf1, Tel and Fli1 bind in vitro to this region and increase endogenous Fli1 expression when over-expressed in a T cell line. In addition, we determined that a microsatellite located adjacent to the region containing these cis-regulatory elements is polymorphic in three lupus prone mouse strains and that the length of the microsatellite is inversely correlated with promoter activity in a T cell line. These results suggest that several Ets factors, including Fli1 itself, are involved in the transcriptional regulation of Fli1 in lymphocytes. Furthermore, the presence of a polymorphic microsatellite in the Fli1 promoter may contribute to increased Fli1 expression in T cells during lupus disease progression.
doi:10.1016/j.molimm.2007.05.018
PMCID: PMC2045641  PMID: 17606295
transcription; gene regulation; transcription factors; Ets; B cells; T cells; systemic lupus erythematosus
20.  Characterization of the 5′-Flanking Region and Regulation of Expression of Human Anion Exchanger SLC26A6 
Journal of cellular biochemistry  2008;105(2):454-466.
SLC26A6 (putative anion transporter 1, PAT1) has been shown to play an important role in mediating the luminal Cl−/OH−(HCO3−) exchange process in the intestine. Very little is known about the molecular mechanisms involved in the transcriptional regulation of intestinal SLC26A6 gene expression in the intestine. Current studies were, therefore, designed to clone and characterize the 5′-regulatory region of the human SLC26A6 gene and determine the mechanisms involved in its regulation. A 1,120 bp (p−964/+156) SLC26A6 promoter fragment cloned upstream to the luciferase reporter gene in pGL2-basic exhibited high promoter activity when transfected in Caco2 cells. Progressive deletions of the 5′-flanking region demonstrated that −214/−44 region of the promoter harbors cis-acting elements important for maximal SLC26A6 promoter activity. Since, diarrhea associated with inflammatory bowel diseases is attributed to increased secretion of pro-inflammatory cytokines, we examined the effects of IFNγ (30 ng/ml, 24 h) on SLC26A6 function, expression and promoter activity. IFNγ decreased both SLC26A6 mRNA and function and repressed SLC26A6 promoter activity. Deletion analysis indicated that IFNγ response element is located between −414/−214 region and sequence analysis of this region revealed the presence of potential Interferon Stimulated Responsive Element (ISRE), a binding site (−318/−300 bp) for interferon regulatory factor-1 transcription factor (IRF-1). Mutations in the potential ISRE site abrogated the inhibitory effects of IFNγ. These studies provided novel evidence for the involvement of IRF-1 in the regulation of SLC26A6 gene expression by IFNγ in the human intestine.
doi:10.1002/jcb.21842
PMCID: PMC2705132  PMID: 18655181
PUTATIVE ANION TRANSPORTER 1 (PAT1) PROMOTER; IRF-1; IFNγ; HUMAN INTESTINE AND CHLORIDE ABSORPTION
21.  Sp1 and Sp3 regulate basal transcription of the human APOBEC3G gene 
Nucleic Acids Research  2007;35(11):3784-3796.
APOBEC3G (A3G), a member of the recently discovered family of human cytidine deaminases, is expressed in peripheral blood lymphocytes and has been shown to be active against HIV-1 and other retroviruses. To gain new insights into the transcriptional regulation of this restriction factor, we cloned and characterized the promoter region of A3G. Transcriptional start sites were identified by 5′-rapid amplification of cDNA ends analysis. Luciferase reporter assays demonstrated that a 1025 bp A3G promoter sequence (from −959 to +66 relative to the major transcriptional start site) displayed constitutive promoter activity. In T cells, the A3G promoter was not inducible by mitogenic stimulation, interferon treatment or expression of HIV-1 proteins. Using a series of 5′ deletion promoter constructs in luciferase reporter assays, we identified a 180 bp region that was sufficient for full promoter activity. Transcriptional activity of this A3G core promoter was dependent on a GC-box (located at position −87/−78 relative to the major transcriptional start site) and was abolished after mutation of this DNA element. Electrophoretic mobility shift assays and chromatin immunoprecipitation assays demonstrated that the identified GC-box represented a binding site for the ubiquitous transcription factors specificity protein (Sp) 1 and Sp3.
doi:10.1093/nar/gkm340
PMCID: PMC1920263  PMID: 17517765
22.  Epigenetic regulation of CD133/PROM1 expression in glioma stem cells by Sp1/myc and promoter methylation 
Oncogene  2012;32(26):10.1038/onc.2012.331.
Tumor stem cells, postulated to be the source cells for malignancies, have been identified in several cancers using cell-surface expression of markers including CD133, a pentaspan membrane protein. CD133+ve cells form neurospheres, exhibit self-renewal and differentiation, and are tumorigenic. However, despite its association with stem cells, a causal relationship of CD133 to tumorigenesis remains to be defined. Hypothesizing that specific epigenetic and transcription factors implicated in driving the stem cell state may concurrently regulate CD133 expression in stem cells, we analyzed the structure and regulation of CD133 promoter in glioma stem cells and glioma cell lines. Initially, a minimal promoter region was identified by analyzing the activity of CD133 promoter-driven luciferase-expressing 5’-and 3’-deletion-constructs upstream of the transcription start site. This region contained a CpG island that was hypermethylated in CD133−ve glioma stem cells (GSC) and glioma cells but unmethylated in CD133+ve ones. Of several predicted TF-binding sites in this region, the role of tandem Sp1 (−242 and −221) and two Myc (−541 and −25)-binding sites were examined. Overexpression of Sp1 or Myc increased CD133 minimal promoter-driven luciferase activity and CD133 levels in GSC and in glioma cell line. Mithramycin, a Sp1 inhibitor, decreased minimal promoter activity and downregulated CD133 levels in GSC. Gel-shift assays demonstrated direct binding of Sp1 to their predicted sites that was competitively inhibited by oligonucleotide-binding-site sequences and supershifted by anti-Sp1 confirming the interaction. Sp1 and Myc-antibody chromatin immunoprecipitation (ChIP) analysis in GSC showed enrichment of regions with Sp1 and Myc-binding sites. In CD133−ve cells, ChIP analysis showed binding of the methyl-DNA-binding proteins, MBD1, MBD2 and MeCP2 to the methylated CpG island and repression of transcription. These results demonstrate that Sp1 and Myc regulate CD133 transcription in GSC and that promoter methylation and methyl-DNA-binding proteins cause repression of CD133 by excluding transcription-factor binding.
doi:10.1038/onc.2012.331
PMCID: PMC3820114  PMID: 22945648
CD133; glioma Stem Cell; Sp1; Myc; promoter methylation; epigenetic regulation
23.  Glucocorticoid and estrogen regulation of a rat T-kininogen gene. 
Nucleic Acids Research  1989;17(7):2835-2848.
We have examined the regulation of a rat T-kininogen gene by glucocorticoid and estrogen. Expression of the endogenous gene in a rat hepatoma cell line is increased 5-fold and 2-fold in response to dexamethasone and 17 beta-estradiol-3-benzoate, respectively. Various deletion constructs of the 5' region of an isolated T-kininogen gene were fused to a chloramphenicol acetyltransferase (CAT) gene and introduced into the hepatoma cells by electroporation. Analysis of the CAT activity in cell extracts after treatment with glucocorticoid or estrogen revealed that a fragment from -167 to +52 is sufficient to confer full induction. An additional deletion in this region was unresponsive, while a larger fragment (-612 to -100) linked to a heterologous promoter did result in regulated expression. These results suggested that the sequence responsible for the hormonal response was located at -167 to -100 from the transcription start site. This 67 bp region contains a consensus for the core sequence of the glucocorticoid responsive element (GRE) and the estrogen responsive element (ERE). Interestingly these elements are located within 7 bp of each other and both sequences overlap a 16 bp palindrome that may be important in hormone receptor-DNA recognition.
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PMCID: PMC317660  PMID: 2541413
24.  Cloning the human SUMO1 promoter 
Molecular biology reports  2009;37(3):1155-1163.
Regulation of the sumoylation system at the level of gene expression has not yet been explored. To begin to define transcriptional regulatory features, the promoter region for the SUMO1 gene was cloned from human genomic DNA and characterized. Initially, a 532 base pair fragment upstream of and including the predicted SUMO1 transcription start site (TSS) was cloned and shown to possess promoter activity. Subsequent deletion analysis showed that a smaller fragment containing 158 bp upstream of the TSS region exhibited basal promoter activity in both human and rodent cell lines. Within this basal promoter fragment, there were predicted binding sites for numerous transcription factors, including the nude mouse gene product, Whn (FoxN1). Electrophoretic mobility shift assays showed that Whn could bind to an ACGC motif adjacent to the TSR, and in transfection studies Whn stimulated a 3-fold increase in transcription from this cloned promoter in keratinocytes (HaCaT cells). Mutation of the ACGC motif abrogated both Whn binding and transcriptional activation, indicating that the Whn effect is likely due to direct interaction with this promoter element. Consistent with these observations on the cloned promoter region, Whn also modestly stimulated transcription from the endogenous, genomic SUMO1 promoter in HaCaT cells, consistent with Whn potentially playing a regulatory role for SUMO1 transcription in keratinocytes.
doi:10.1007/s11033-009-9476-8
PMCID: PMC3083827  PMID: 19242820
Sumoylation; Differentiation; Keratinocytes
25.  Two lck transcripts containing different 5' untranslated regions are present in T cells. 
Molecular and Cellular Biology  1987;7(12):4407-4413.
p56lck is a new member of the src family of cellular tyrosine protein kinases. It is expressed constitutively at a low level in normal T cells and at an elevated level in the LSTRA and Thy19 Moloney murine leukemia virus-induced thymoma cell lines. It is possible that the expression of p56lck at an elevated level contributes to the transformation of these thymoma cells. The structure of the mRNAs encoding p56lck was examined by using an RNase protection assay. Both a chimeric lck mRNA containing the 5' untranslated region of Moloney virus mRNA and a normal lck mRNA were found in Thy19 and LSTRA cells. The chimeric lck transcript was 4- to 10-fold more abundant than the normal transcript. Transcription arising from a viral promoter is therefore responsible for the elevated levels of lck mRNA in these two cell lines. Surprisingly, uninfected murine T cells were also found to contain lck transcripts with differing 5' untranslated regions. One species of mRNA was colinear with the region of the chromosome just upstream of the initiation codon for p56lck. The other appeared to arise through splicing of an unidentified 5' untranslated exon to a sometimes cryptic splice acceptor just upstream of the region encoding p56lck. These data suggest that lck is expressed through the use of at least two different promoters. The promoters could be subject to different forms of regulation.
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PMCID: PMC368124  PMID: 3501824

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