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Results for “regulatory element transcripts”

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PubMed1999

Antisilencing: myelin proteolipid protein gene expression in oligodendrocytes is regulated via derepression.

Antisilencer or antirepressor elements have been described, thus far, for only a few eukaryotic genes and were identified by their ability not to augment gene expression per se but to override repression mediated via negative transcription regulatory elements. Here we report the first case of antisilencing for a neural-specific gene, the myelin proteolipid protein (PLP) gene (Plp). PLP is the most abundant protein found in CNS myelin. The protein is synthesized in oligodendrocytes, and its expression is regulated developmentally. Previously we have shown that a PLP-lacZ transgene (which includes the entire sequence for Plp intron 1) is regulated in mice, in a manner consistent with the spatial and temporal expression of the endogenous Plp gene. In the present report, we demonstrate by transfection analyses, using various PLP-lacZ deletion constructs, that Plp intron 1 DNA contains multiple elements that collectively regulate Plp gene expression in oligodendrocytes. One of these regulatory elements functions as an antisilencer element, which acts to override repression mediated by at least two negative regulatory elements located elsewhere within Plp intron 1 DNA. The mechanism for antisilencing appears to be complex as the intragenic region that mediates this function binds multiple nuclear factors specifically.

Animals↗

PubMed1988

The human growth hormone gene contains both positive and negative control elements.

A subset of DNA sequences in the 5'-flanking DNA of the human growth hormone (hGH) gene was examined by protein-DNA binding and gene transfer-expression experiments. Two adjacent cis-acting elements (I and II) were identified between nucleotides -308/-235 of the hGH gene that modulated the expression of a linked reporter gene in transfected HeLa cells. Elements I and II repressed gene expression whereas element II alone activated it. HeLa whole cell extracts contain two factors that bind hGH DNA carrying elements I and II. Factor I binds to single-stranded DNA, and its binding is correlated with repression of gene expression. Factor II binds between nucleotides -275/-257 of the hGH gene. This region is homologous to the binding site for the adenovirus major late transcription factor, and factor II binding to hGH DNA is competed by adenovirus major late promoter DNA, indicating that the hGH and major late adenovirus promoters share a transcription regulatory element.

Animals↗

PubMed1992

Identification of a binding protein to the X gene promoter region of hepatitis B virus.

The X protein of hepatitis B virus (HBV) is a transactivator to homologous and heterologous viral and cellular transcriptional regulatory elements. One sequence-specific binding protein, whose binding site located from nt 1102 to nt 1117 of HBV DNA, was identified by mobility shift assay and DNase I foot-printing analysis. A CAT assay experiment demonstrated this 16-bp binding site to have a promoter activity in the X gene transcription. The 58-bp DNA fragment (nt 1085 to nt 1142), which contains the above binding site, could be enhanced by the HBV enhancer. Mobility shift assay using the mutated 58-bp DNA fragments as probes, showed that the mutation, which damaged the palindrome structure between nt 1105 and nt 1112, resulted in loss of the binding activity. This mutation also remarkably reduced the promoter activity. The binding site differed from the target sequences of known transcriptional factors. This factor was thus concluded to be a binding protein to the X gene promoter (X-PBP) of HBV. A homology search demonstrated the binding site to be highly homologous to the promoter elements of human laminin receptor (2H5epitope) and lipoprotein receptor-related protein (LRP) genes.

Base Sequence↗

PubMed1995

Genetic analysis of embryonic cis-acting regulatory elements of the Drosophila homeotic gene sex combs reduced.

The homeotic gene Sex combs reduced (Scr) of Drosophila melanogaster is expressed in the labial and prothoracic segments of the ectoderm, in parasegments two and three of the CNS, and in the visceral mesoderm of the anterior and posterior midgut. The mutationally defined function of Scr is to specify the identity of the labial and prothoracic segments and to control the development of the gastric caeca. The Scr locus occupies a chromosomal region of approximately 80 kb within the Antennapedia complex (ANT-C). To understand how Scr's spatiotemporal expression pattern is generated in the embryo, we have mapped its transcriptional regulatory elements using three approaches. First, we examined the expression pattern of Scr in embryos containing chromosomal rearrangements that remove potential Scr regulatory elements. Second, we made and analyzed a set of Scr minigene transformants. Third, we analyzed a set of Scr-lacZ enhancer tester constructs. Using more sensitive anti-SCR antisera, we discovered that Scr is expressed in tissues that were not previously thought to accumulate SCR: a stripe of ectodermal cells in the parasegment 2 region of stage 5 embryos, the embryonic salivary glands, and the dorsal ridge. Four DNA fragments that had previously been shown in an analysis of Scr-lacZ reporter constructs to contain putative Scr enhancer elements were found to have functional enhancers; similarly, another Scr fragment was found to contain a functional repressor. Our results suggest that regulation of Scr in the labial segment and the CNS requires the apparently synergistic action of multiple, widely spaced enhancer elements. Regulation in the prothorax also appears to be controlled by multiple enhancers:one complete pattern element and one subpattern element. In contrast, Scr regulation in the visceral mesoderm is controlled by an enhancer(s) located in only one DNA fragment.

Animals↗

PubMed2006

Regulation of cytokine transcription in the context of chromatin.

Understanding the transcriptional regulation of an important class of innate and adaptive immune system effector molecules, the cytokines, is increasingly important given the promise cytokine regulation holds for treating various autoimmune and inflammatory diseases. Studies defining the mechanisms regulating cytokine transcription initially focused on identifying the cis-acting elements and trans-acting factors that activate cytokine promoters and enhancers. In the past, these studies were largely completed in the absence of constraints instituted by cellular chromatin. Over the past decade it has become obvious that changes in chromatin accessibility critically control, rather than simply correlate with, the transcriptional activation of most genes, including cytokines. Hence candidate transcriptional activators are being re-evaluated for potency in the context of cellular chromatin. Several distinct mechanisms for manipulating the generally repressive context of chromatin have been identified for cytokine genes. Most recently, single nucleotide polymorphisms in cytokine transcriptional regulatory elements have been shown to play measurable roles in regulating cytokine levels in the context of naturally selected haplotypes. Overall, subtle differences in DNA sequence and nucleoprotein complex composition, including protein post-translational modification, come together in cell type-specific combinations to explain the normal variation in cytokine transcription throughout the human populace.

Animals↗

PubMed1990

Human poly(ADP-ribose) polymerase gene. Cloning of the promoter region.

The promoter region of the poly(ADP-ribose) polymerase gene has been isolated using a Sau3AI genomic library derived from human leukocyte. It lacks typical transcriptional regulatory elements such as TATA and CAAT boxes, but it contains two potential Sp1 binding sites and three putative AP-2 binding elements. The region up to nucleotide position-99 in relation to the predominant transcriptional initiation site exhibits promoter activity as judged by chloramphenicol acetyltransferase assay and the activity is enhanced both by cAMP and by phorbol ester. Northern blot and Western blot analyses have revealed that expression of the polymerase gene is also stimulated by both of these compounds in cultured HeLa cells. Southern blot hybridization of genomic DNA separately digested with various endonucleases gives a discrete single band in each case when the 5'-untranslated region of the polymerase cDNA is used as a probe. These results indicate that poly(ADP-ribose) polymerase is encoded by a unique gene whose expression is regulable by cAMP and by phorbol ester.

Amino Acid Sequence↗

PubMed2003

Introns in gene evolution.

Introns are integral elements of eukaryotic genomes that perform various important functions and actively participate in gene evolution. We review six distinct roles of spliceosomal introns: (1) sources of non-coding RNA; (2) carriers of transcription regulatory elements; (3) actors in alternative and trans-splicing; (4) enhancers of meiotic crossing over within coding sequences; (5) substrates for exon shuffling; and (6) signals for mRNA export from the nucleus and nonsense-mediated decay. We consider transposable capacities of introns and the current state of the long-lasting debate on the 'early-or-late' origin of introns. Cumulative data on known types of contemporary exon shuffling and the estimation of the size of the underlying exon universe are also discussed. We argue that the processes central to introns-early (exon shuffling) and introns-late (intron insertion) theories are entirely compatible. Each has provided insight: the latter through elucidating the transposon capabilities of introns, and the former through understanding the importance of introns in genomic recombination leading to gene rearrangements and evolution.

Alternative Splicing↗

PubMed2001

Transcriptional targeted gene therapy for hepatocellular carcinoma by adenovirus vector.

Hepatocellular carcinoma (HCC) is one of the most common malignancies with poor prognosis and is highly amenable to the development of novel therapeutic strategy. The human alpha-fetoprotein (AFP) gene is normally expressed in fetal liver and is transcriptionally silent in adult liver but overexpressed in HCC. In order to destroy AFP-producing HCC specifically, replication defective adenoviral vectors containing the transcriptional control elements of the AFP gene were designed. Expression of suicide genes by the AFP promoter/enhancer induced prodrug sensitivity in AFP (+) cells but not AFP (-) cells. The expression of suicide genes by ubiquitous promoter, however, showed no selectivity after prodrug treatment. Adenoviral vector transduced genes efficiently not only in vitro but also in vivo, and AFP-producing HCC xenografts regressed by transduction with transcriptionally targeted vectors and subsequent systemic administration of prodrug in animal model. Utilization of the transcriptional regulatory element to drive drug sensitive genes can be a promising strategy for cancer specific therapy.

Adenoviruses, Human↗

PubMedDate not supplied

NF-kappa B site-mediated negative regulation of the HIV-1 promoter by CCAAT/enhancer binding proteins in brain-derived cells.

Several transcription regulatory elements that interact with cellular DNA-binding proteins have been identified in the HIV-1 long terminal repeat (LTR). We have identified two sequence motifs in the U3 region of the LTR that are similar to the consensus 9-bp DNA-binding element of the CCAAT/enhancer-binding protein (C/EBP) family of transcription factors. One of the sequences (promoter-proximal) mapped immediately upstream of the NF-kappa B element, whereas the other (promoter-distal) completely overlapped the upstream stimulatory factor (USF) binding site. In this study, we investigated the role of the enhancer-proximal consensus C/EBP binding sequence in the expression of the HIV-1 LTR. In cotransfection assays we found that although this sequence is a functional C/EBP-responsive element, the regulation of the HIV promoter by C/EBP is very complex. C/EBP isoforms inhibited the phorbol 12-myristate 13-acetate (PMA)-stimulated HIV-1 promoter activity in human glioblastoma U138MG and neuroblastoma SHSY5Y cells, but not in HeLa epithelial cells, and this inhibition required the NF-kappa B element. C/EBP also downregulated the HIV NF-kappa B element-containing SV40 early promoter activity, regardless of the presence of the flanking C/EBP-binding sequences, in the two brain-derived cells. In electrophoretic mobility shift assays with nuclear extracts from HeLa and U138MG cells, purified C/EBP markedly increased the complex formation between endogenous proteins and the NF-kappa B DNA probe without detectable association with the complex. However, with extracts from U138MG cells but not from HeLa cells, a slow migrating complex was observed. Our data suggest that the C/EBP family of transcription factors can downregulate the HIV-1 promoter activity in CNS-derived cells through the NF-kappa B binding elements.

Animals↗

PubMed2000

Transcriptional activation of the cyclooxygenase-2 gene in endotoxin-treated RAW 264.7 macrophages.

Cyclooxygenase-2 (COX-2), the enzyme primarily responsible for induced prostaglandin synthesis, is an immediate early gene induced by endotoxin in macrophages. We investigated the cis-acting elements of the COX-2 5'-flanking sequence, the transcription factors and signaling pathways responsible for transcriptional activation of the COX-2 gene in endotoxin-treated murine RAW 264.7 macrophages. Luciferase reporter constructs with alterations in presumptive cis-acting transcriptional regulatory elements demonstrate that the cyclic AMP-response element and two nuclear factor interleukin-6 (CCAAT/enhancer-binding protein (C/EBP)) sites of the COX-2 promoter are required for optimal endotoxin-dependent induction. In contrast, the E-box and NF-kappaB sites are not required for endotoxin-dependent induction. Inhibition of endotoxin-induced NF-kappaB activation by expression of an inhibitor-kappaB alpha mutant does not block endotoxin-dependent COX-2 reporter activity. Overexpression of c-Jun, C/EBPbeta, and C/EBPdelta enhances induction of the COX-2 reporter, while overexpression of cyclic AMP-response element-binding protein or "dominant negative" C/EBPbeta represses COX-2 induction. In addition, endotoxin rapidly and transiently elicits c-Jun phosphorylation in RAW 264.7 macrophages. Cotransfection of the COX-2 reporter with dominant negative expression vectors shows that endotoxin-induced COX-2 gene expression requires signaling through a Ras-independent pathway involving the adapter protein ECSIT and the signaling kinases MEKK1 and JNK. In contrast, endotoxin-induced COX-2 reporter activity is not blocked by overexpression of dominant-negative forms of Raf-1, ERK1, or ERK2.

Adaptor Proteins, Signal Transducing↗

PubMed1996

Analysis of the promoter of the NAD+ dependent 11 beta-hydroxysteroid dehydrogenase (HSD11K) gene in JEG-3 human choriocarcinoma cells.

The NAD+ dependent (K or type 2) isozyme of 11 beta-hydroxysteroid dehydrogenase oxidizes glucocorticoids and thus prevents them from occupying mineralocorticoid receptors. Mutations in the HSD11K (HSD11B2) gene encoding this isozyme cause a genetic form of hypertension, the syndrome of apparent mineralocorticoid excess (AME). This isozyme is expressed at high levels in placenta and kidney but is undetectable in liver. We have now analyzed the proximal 1788 nucleotides (nt) of the 5' flanking region of the HSD11K gene to identify transcriptional regulatory elements that are active in JEG-3 human choriocarcinoma cells. Using luciferase reporter constructs, the region from -2 to -330 nt relative to the initial ATG codon was identified as an essential region for basal transcription of the HSD11K gene. Two segments in this region, -278 to -257 and -215 to -194. were protected in DNase 1 footprinting analysis. Both segments have consensus binding sites for the Spl transcription factor. Gel shift assays of these segments show several DNA-protein complexes using JEG-3 nuclear extract. Only the slowest migrating complex was competed by an antiserum to Spl. These results suggest that the two Spl sites, either alone or in combination, are essential for transcription of the HSD11K gene in JEG-3 cells.

11-beta-Hydroxysteroid Dehydrogenases↗

PubMed1999

Transcriptional regulation of mouse delta-opioid receptor gene.

Three major types of opioid receptors, mu (MOR), delta (DOR), and kappa (KOR), have been cloned and characterized. Each opioid receptor exhibits a distinct pharmacological profile as well as a distinct pattern of temporal and spatial expression in the brain, suggesting the critical role of transcription regulatory elements and their associated factors. Here, we report the identification of a minimum core promoter, in the 5'-flanking region of the mouse DOR gene, containing an E box and a GC box that are crucial for DOR promoter activity in NS20Y cells, a DOR-expressing mouse neuronal cell line. In vitro protein-DNA binding assays and in vivo transient transfection assays indicated that members of both the upstream stimulatory factor and Sp families of transcription factors bound to and trans-activated the DOR promoter via the E box and GC box, respectively. Furthermore, functional and physical interactions between these factors were critical for the basal as well as maximum promoter activity of the DOR gene. Thus, the distinct developmental emergence and brain regional distribution of the delta opioid receptor appear to be controlled, at least in part, by these two regulatory elements and their associated factors.

Animals↗

PubMed2004

Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer.

Transcriptional regulatory element X (Trex) is a positive control site within the Muscle creatine kinase (MCK) enhancer. Cell culture and transgenic studies indicate that the Trex site is important for MCK expression in skeletal and cardiac muscle. After selectively enriching for the Trex-binding factor (TrexBF) using magnetic beads coupled to oligonucleotides containing either wild-type or mutant Trex sites, quantitative proteomics was used to identify TrexBF as Six4, a homeodomain transcription factor of the Six/sine oculis family, from a background of approximately 900 copurifying proteins. Using gel shift assays and Six-specific antisera, we demonstrated that Six4 is TrexBF in mouse skeletal myocytes and embryonic day 10 chick skeletal and cardiac muscle, while Six5 is the major TrexBF in adult mouse heart. In cotransfection studies, Six4 transactivates the MCK enhancer as well as muscle-specific regulatory regions of Aldolase A and Cardiac troponin C via Trex/MEF3 sites. Our results are consistent with Six4 being a key regulator of muscle gene expression in adult skeletal muscle and in developing striated muscle. The Trex/MEF3 composite sequence ([C/A]ACC[C/T]GA) allowed us to identify novel putative Six-binding sites in six other muscle genes. Our proteomics strategy will be useful for identifying transcription factors from complex mixtures using only defined DNA fragments for purification.

Animals↗

PubMed2000

Interference of the simian virus 40 origin of replication by the cytomegalovirus immediate early gene enhancer: evidence for competition of active regulatory chromatin conformation in a single domain.

Replication origins are often found closely associated with transcription regulatory elements in both prokaryotic and eukaryotic cells. To examine the relationship between these two elements, we studied the effect of a strong promoter-enhancer on simian virus 40 (SV40) DNA replication. The human cytomegalovirus (CMV) immediate early gene enhancer-promoter was found to exert a strong inhibitory effect on SV40 origin-based plasmid replication in Cos-1 cells in a position- and dose-dependent manner. Deletion analysis indicated that the effect was exerted by sequences located in the enhancer portion of the CMV sequence, thus excluding the mechanism of origin occlusion by transcription. Insertion of extra copies of the SV40 origin only partially alleviated the inhibition. Analysis of nuclease-sensitive cleavage sites of chromatin containing the transfected plasmids indicate that the chromatin was cleaved at one of the regulatory sites in the plasmids containing more than one regulatory site, suggesting that only one nuclease-hypersensitive site existed per chromatin. A positive correlation was found between the degree of inhibition of DNA replication and the decrease of P1 cleavage frequency at the SV40 origin. The CMV enhancer was also found to exhibit an inhibitory effect on the CMV enhancer-promoter driving chloramphenicol acetyltransferase expression in a dose-dependent manner. Together these results suggest that inhibition of SV40 origin-based DNA replication by the CMV enhancer is due to intramolecular competition for the formation of active chromatin structure.

Animals↗

PubMed2000

Expression of HSD11K (NAD+ dependent 11beta-hydroxysteroid dehydrogenase) promoter constructs in renal cell lines.

The kidney (11-HSD2 or 11-HSDK) isozyme of 11beta-hydroxysteroid dehydrogenase confers specificity for aldosterone on mineralocorticoid receptors in target tissues. In rodent kidney, this isozyme is expressed mainly in cortical collecting ducts and is undetectable in proximal tubules. Using mouse M-1 and rabbit RCD cortical collecting duct cells, we analyzed the 5'-flanking region of the human HSD11K gene encoding this enzyme in an attempt to identify transcriptional regulatory elements responsible for gene expression in the kidney. M-1 and RCD cells had high levels of NAD+ dependent 11-HSD activity with corticosterone as the substrate. Luciferase reporter constructs containing 1785 or 327 nucleotides (nt) upstream of the initiator ATG codon were expressed at similar levels in each cell line, but deletion to 167 nt almost completely abolished expression in both cell types. This region is GC-rich and contain Sp1 binding sites. Electrophoretic mobility shift assays of the region containing the putative Sp1 sites showed several DNA-protein complexes in both the cell types. Mutations of the Sp1 sites decreased transcriptional activity in M-1 cells; however, these mutations had a marginal effect in the RCD cells. These results suggest that elements controlling renal cell type expression are located in the proximal 327 nucleotides of the 5' flanking region of HSD11K.

11-beta-Hydroxysteroid Dehydrogenases↗

PubMed1991

A short, novel promoter sequence confers the expression of human leukosialin, a major sialoglycoprotein on leukocytes.

Human leukosialin (CD43) is a major sialoglycoprotein expressed on leukocytes and platelets. In order to investigate the transcriptional regulation of this gene, we have isolated a genomic DNA of 12 kilobases in size that includes the 5'-flanking sequence. Comparison of the genomic and cDNA sequences revealed that the leukosialin gene consists of two exons, and that its entire translation product is encoded in the second exon. The transcriptional start site was determined by primer extension analysis in human T-cell line Jurkat. No canonical TATA or CAAT boxes were found in the prospected upstream region, but a guanine-rich region was observed on the sense strand. To localize the transcriptional regulatory region of this gene, various regions of 5' sequences were fused to the chloramphenicol acetyltransferase (CAT) gene, and transient expression assays were conducted in Jurkat cells. We employed the polymerase chain reaction to generate a series of clones containing 5' sequences of the leukosialin gene using primer sequences based on the genomic sequence. This strategy enabled us to narrow the search for a transcriptional regulatory element. In addition, we introduced site-directed mutations in the regulatory region by polymerase chain reaction to define it in detail. These studies showed that the sequence from -53 to -40 base pairs 5' to the transcriptional start site is critically involved in leukosialin expression. This sequence, 5'GGGTGGGTGGAGCC3', represents a novel promoter sequence which has not been reported in the promoters for other molecules expressed in T-lymphocytes.

Amino Acid Sequence↗

PubMed1992

Organization of immunoglobulin heavy chain constant and joining region genes in the channel catfish.

A channel catfish genomic lambda library was screened with CH and JH probes which were derived from our earlier sequence analyses on different full-length heavy chain cDNA clones. One clone, designated C7, contained a genomic insert of about 18 kb and hybridized with specific probes for each of the four domains of the known C region gene as well as with different oligonucleotides specific for JH gene segments. Southern blot hybridization analysis identified a cluster of JH gene segments which are closely linked to the CH gene. Sequence analysis of the CH-proximal JH element, located about 1.9 kb upstream from the CH1 domain, showed that this element contains 5'-recombination signals typical of JH elements defined in higher vertebrates, i.e. a nonamer, a 24 bp spacer, and a heptamer. The coding region of this JH element was identical to that contained in the variable region sequence of a cDNA clone previously reported. Sequence analysis of the catfish JH-CH intron suggests that several sequences are present which appear similar to important transcriptional regulatory elements found within JH-CH introns of higher vertebrates. These features include sequences similar to higher vertebrate enhancer elements and regulatory octamers. An additional feature reminiscent of some higher vertebrate heavy chain switch regions is a repetitive sequence area composed of tandemly repeated simple sequences. Lastly, several restriction length polymorphisms were identified and mapped within a 1 kb region located immediately upstream from the JH cluster. This finding suggests that polymorphisms within the IgH locus should be useful in the analyses of channel catfish populations. These combined studies provide further evidence that the genomic organization of heavy chain genes in bony fish shares common organizational features with those known from higher vertebrates.

Amino Acid Sequence↗

PubMed2006

WPRE-mediated enhancement of gene expression is promoter and cell line specific.

The success of gene therapy approaches relies on sufficiently high levels of expression of the therapeutic gene. However, if tissue specific or tumour specific gene expression is desired, a lower level of transgene expression usually has to be accepted due to the weakness of the majority of available tissue or tumour specific promoters. This obstacle can in part be overcome by the insertion of viral cis-acting elements that enhance gene expression in various expression vector contexts regardless of the respective promoter. We designed a series of murine leukaemia virus (MLV)-based retroviral promoter conversion (ProCon) vectors that contain the woodchuck hepatitis post-transcriptional regulatory element (WPRE) and evaluated its use by measuring enhanced green fluorescent protein (EGFP) levels and viral titres. In viral vector packaging cells, when the EGFP encoding gene was transcribed from the MLV promoter, incorporation of the WPRE resulted in a marked improvement of the vectors in terms of EGFP expression and virus titres. However, in infected cells after promoter conversion had taken place, the effect of the WPRE became promoter and cell line dependent. When the EGFP gene was transcribed from the heterologous mouse mammary tumour virus (MMTV) promoter the same beneficial role of the WPRE on transgene expression was observed in all eight cell lines tested. In contrast, when EGFP gene expression was driven by the murine whey acidic protein (WAP) promoter, the positive effect of the WPRE could only be observed in two cell lines whereas expression was actually reduced in the six other cell lines tested. This decrease of EGFP expression was not only demonstrated at the protein level but also manifested on the RNA level.

Animals↗