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Results for “regulatory element transcripts”

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PubMed2004

Patterning the forebrain: FoxA4a/Pintallavis and Xvent2 determine the posterior limit of Xanf1 expression in the neural plate.

During early development of the nervous system in vertebrates, expression of the homeobox gene Anf/Hesx1/Rpx is restricted to the anterior neural plate subdomain corresponding to the presumptive forebrain. This expression is essential for normal forebrain development and ectopic expression of Xenopus Anf, Xanf1 (also known as Xanf-1), results in severe forebrain abnormalities. By use of transgenic embryos and a novel bi-colour reporter technique, we have identified a cis-regulatory element responsible for transcriptional repression of Xanf1 that defines its posterior expression limit within the neural plate. Using this element as the target in a yeast one-hybrid system, we identified two transcription factors, FoxA4a/Pintallavis and Xvent2 (also known as Xvent-2), which are normally expressed posterior to Xanf1. Overexpression of normal and dominant-negative versions of these factors, as well as inhibition of their mRNA translation by antisense morpholinos, show that they actually function as transcriptional repressors of Xanf1 just behind its posterior expression limit. The extremely high similarity of the identified Anf cis-regulatory sequences in Xenopus, chick and human, indicates that the mechanism restricting posterior expression of Anf in Xenopus is shared among vertebrates. Our findings support Nieuwkoop's activation-transformation model for neural patterning, according to which the entire neurectoderm is initially specified towards an anterior fate, which is later suppressed posteriorly as part of the trunk formation process.

Animals↗

PubMed1992

Transactivation of the major capsid protein gene of herpes simplex virus type 1 requires a cellular transcription factor.

The purpose of this investigation was to identify and characterize the regulatory elements involved in the transcriptional activation of the beta gamma (leaky-late or gamma 1) genes of herpes simplex virus type 1 (HSV-1) by using the major capsid protein (VP5 or ICP5) gene as model. Gel mobility shift assays with nuclear extracts from uninfected and infected HeLa cells enabled us to identify two major protein-DNA complexes involving the VP5 promoter. The mobilities of these two complexes remained unaltered, and no unique complexes were observed when infected cell nuclear extracts were used. DNase I and orthophenanthroline-Cu+ footprint analyses revealed that the two complexes involve a single binding site, GGCCATCTTGAA, located between -64 and -75 bp relative to the VP5 cap site. To determine the function of this leaky-late binding site (LBS) in VP5 gene activation, we tested the effect of mutations in this region by using transient expression of a cis-linked chloramphenicol acetyltransferase gene. Deletion of the above sequence resulted in a seven- to eightfold reduction in the level of transactivation of the chloramphenicol acetyltransferase gene by superinfection with HSV-1 or by cotransfection of HSV-1 immediate-early genes. From these results, we conclude that the LBS sequence and a cellular factor(s) are involved in the transactivation of the VP5 gene. A search of published gene sequences revealed that sequences related to the LBS exist in a number of other HSV-1, cytomegalovirus, retrovirus, and cellular promoters. Sequence homologies of binding sites and results of unpublished competition binding studies suggest that this leaky-late binding factor may be related to, or the same as, a ubiquitous cellular transcriptional factor called YY1 or common factor-1 (also known as NF-E1, delta, and UCRBP).

Base Sequence↗

PubMed1992

Discordant regulation of human type I collagen genes by prostaglandin E2.

We examined the expression of type I collagen genes in prostaglandin E2 (PGE2)-treated human lung fibroblast cultures. Addition of PGE2 to fibroblast cultures inhibited alpha 1(I) mRNA levels by approx. 25% after 6 h and 60% after 24 h. Further studies showed that dibutyryl cAMP did not inhibit alpha 1(I) mRNA levels and that cycloheximide blocked the inhibitory effect of PGE2. In contrast, PGE2 treatment with or without cycloheximide did not affect alpha 2(I) mRNA levels. Moreover, in vitro translation of RNA derived from untreated and PGE2-treated cells yielded similar amounts of alpha 2(I) collagen peptides. Taken together, these results suggest that PGE2 induces a protein which inhibits alpha 1(I) transcription through distinct regulatory elements not under the control of cAMP and provide further evidence that the type I collagen genes can be discordantly regulated.

Blotting, Northern↗

PubMed2006

Mechanisms of sterol regulatory element-binding protein-2 (SREBP-2) regulation of human prostasin gene expression.

Prostasin is a glycosylphosphatidylinositol (GPI)-anchored serine protease and a suppressor of tumor cell invasion. We recently reported that the human prostasin gene is up-regulated by the transcription factor sterol regulatory element-binding protein-2 (SREBP-2). In the present study, we identified multiple SREBP-2 binding sites, known as sterol regulatory elements (SREs), located at positions -897, -538, +8, +71, and +98 (named SRE-897, SRE-538, SRE+8, SRE+71, and SRE+98) in the human prostasin gene promoter. Prostasin promoter-reporter constructs, representing serial deletions of the 5'-flanking region of the human prostasin gene, were transiently transfected into HEK-293 cells for evaluation of promoter activities. The region defined by nucleotides -17 to +232 of the prostasin gene promoter was shown to be essential for the basal transcriptional activity of the human prostasin gene. Mutagenesis of the five SREs was carried out for evaluation of their roles in SREBP-2 up-regulation. SRE+98, a novel functional sterol regulatory element, was found to be the major site for the stimulatory response of prostasin gene expression to SREBP-2.

5' Flanking Region↗

PubMed1991

Organization, promoter analysis and transcriptional regulation of the Staphylococcus xylosus xylose utilization operon.

The Staphylococcus xylosus xyl genes were cloned in Staphylococcus carnosus by complementation to xylose utilization. Xylose isomerase assays under inducing (xylose present) and non-inducing (xylose absent) conditions indicated the presence of a regulated xylA gene on the recombinant plasmid. The nucleotide sequence (4520 bases) revealed three open reading frames with the same polarity. They were identified by sequence homologies as xylR, encoding the Xyl repressor, xylA, encoding xylose isomerase and xylB, encoding xylulokinase. Primer extension analyses indicated constitutive transcription of xylR and xylose-inducible transcription of xylA. Promoter consensus sequences were found upstream of both transcriptional start sites. A transcriptional terminator between xylR and xylA separates the different transcriptional units. Potential regulatory elements were identified by sequence analysis and suggest a repressor-operator mechanism for the regulation of xylAB expression.

Aldose-Ketose Isomerases↗

PubMed1987

Heat shock loci 93D of Drosophila melanogaster and 48B of Drosophila hydei exhibit a common structural and transcriptional pattern.

A comparison of gene structure, sequence, and transcription pattern of heat shock loci 93D of Drosophila melanogaster and 48B of Drosophila hydei has been performed. Both heat shock loci consist of an unique region that is flanked by an internally repetitive element. Different members of these elements are highly conserved, repeat unit length, however, and primary sequence diverged totally. Whereas the overall gene structure in both species is substantially related, sequence conservation is only observed at very few sites in the unique region. These represent primarily sequences that are identified as regulatory elements for faithful transcription and processing. The number and size of transcripts obtained from heat shock locus 48B in third instar larvae closely resembles the pattern of heat shock locus 93D. Thus their quite alike structure and transcription pattern suggest strongly a conserved hitherto unknown function.

Animals↗

PubMed2002

Distribution and characterization of regulatory elements in the human genome.

The regulation of transcription and subsequent gene splicing are crucial to correct gene expression. Although a number of regulatory sequences involved in both processes are known, it is not clear how general their functions are in the genomic context, nor how the regulatory regions are distributed throughout the genome. Here we study the distribution of known mutagenic elements within human introns and exons to deduce the properties of regions essential for splicing and transcription. We show that intronic splicing regulators are generally found close to the splice sites, but may be found as far as 200 nucleotides away from the splice junctions. Similarly, sequences important for splicing may be located as far as 125 nucleotides away from the junctions, within exons. We characterize several types of simple repetitive sequences and low-complexity regions that are overrepresented close to both intron ends and are likely to play important roles in the splicing process. We show that the first introns within most genes play a particularly important regulatory role that is most likely, however, to be involved in transcription control. We also study the distribution of two known regulatory motifs, the GGG trinucleotide and the CpG dinucleotide, and deduce their respective importance to splicing and transcription regulation.

Base Composition↗

PubMed1995

Antagonism of COUP-TF and PPAR alpha/RXR alpha on the activation of the malic enzyme gene promoter: modulation by 9-cis RA.

We previously demonstrated that heterodimers of the Peroxisome Proliferator Activated Receptor alpha (PPAR alpha) and the Retinoid X Receptor alpha (RXR alpha) stimulate malic enzyme gene transcription through a regulatory element in the promoter region (ME-PPRE). In this report, we show that the orphan nuclear receptor COUP-TF also displays affinity for the ME-PPRE and competes with PPAR alpha/RXR alpha for binding to this element. In transient transfections of a reporter driven by the MRE-PPRE in a heterologous or in the homologous promoter context, COUP-TF strongly antagonizes the transactivation by PPAR alpha RXR alpha in the absence of exogenously added ligands. Although 9-cis RA did not further enhance the transcriptional effects of the heterodimers activated by ciprofibrate, it greatly impaired the suppressive effects of COUP-TF on the ciprofibrate activated PPAR alpha/RXR alpha. We conclude that the antagonism by COUP-TF uncovers differential activation states of PPAR alpha/RXR alpha heterodimers in the absence and in the presence of 9-cis RA.

Animals↗

PubMed2006

Identification of degenerate motifs using position restricted selection and hybrid ranking combination.

The identification of regulatory elements recognized by transcription factors and chromatin remodeling factors is essential to studying the regulation of gene expression. When no auxiliary data, such as orthologous sequences or expression profiles, are used, the accuracy of most tools for motif discovery is strongly influenced by the motif degeneracy and the lengths of sequence. Since suitable auxiliary data may not always be available, more work must be conducted to enhance tool performance to identify transcription elements in the metazoan. A non-alignment-based algorithm, MotifSeeker, is proposed to enhance the accuracy of discovering degenerate motifs. MotifSeeker utilizes the property that variable sites of transcription elements are usually position-specific to reduce exposure to noise. Consequently, the efficiency and accuracy of motif identification are improved. Using data fusion, the ranking process integrates two measures of motif significance, resulting in a more robust significance measure. Testing results for the synthetic data reveal that the accuracy of MotifSeeker is less sensitive to the motif degeneracy and the length of input sequences. Furthermore, MotifSeeker has been tested on a well-known benchmark [M. Tompa, N. Li, T.L. Bailey, G.M. Church, B. De Moor, E. Eskin, A.V. Favorov, M.C. Frith, Y. Fu, W.J. Kent, et al. (2005) Nat. Biotechnol., 23, 137-144], yielding a correlation coefficient of 0.262, which compares favorably with those of other tools. The high applicability of MotifSeeker to biological data is further demonstrated experimentally on regulons of Saccharomyces cerevisiae and liver-specific genes with experimentally verified regulatory elements.

Algorithms↗

PubMed2004

A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel.

Consolidation of long-term memory (LTM) is a complex process requiring synthesis of new mRNAs and proteins. Many studies have characterized the requirement for de novo mRNA and protein synthesis; however, few studies have comprehensively identified genes regulated during LTM consolidation. We show that consolidation of long-term contextual memory in the hippocampus triggers altered expression of numerous genes encompassing many aspects of neuronal function. Like contextual memory formation, this altered gene expression required NMDA receptor activation and was specific for situations in which the animal formed an association between a physical context and a sensory stimulus. Using a bioinformatics approach, we found that regulatory elements for several transcription factors are over-represented in the upstream region of genes regulated during consolidation of LTM. Using a knock-out mouse, we found that c-rel, one of the transcription factors identified in our bioinformatics study, is necessary for hippocampus-dependent long-term memory formation.

Animals↗

PubMed1978

The relationship between function and DNA sequence in an intercistronic regulatory region in phage lambda.

rho factor-mediated transcription termination at the tr1 terminator site of bacteriophage lambda is examined. Mutations affecting the termination event are characterised. These mutations define features of the site which seem to be important to terminator function. In addition, other related transcriptional and translational regulatory elements are defined within the region surrounding the termination site. The potential molecular interactions and structural overlaps of these control signals apparently couple the regulation of the decision between lytic and lysogenic growth patterns by phage lambda.

Base Sequence↗

PubMed2004

Molecular evidence supporting the portal theory: a causative link between visceral adiposity and hepatic insulin resistance.

The mechanism by which increased central adiposity causes hepatic insulin resistance is unclear. The "portal hypothesis" implicates increased lipolytic activity in the visceral fat and therefore increased delivery of free fatty acids (FFA) to the liver, ultimately leading to liver insulin resistance. To test the portal hypothesis at the transcriptional level, we studied expression of several genes involved in glucose and lipid metabolism in the fat-fed dog model with visceral adiposity vs. controls (n = 6). Tissue samples were obtained from dogs after 12 wk of either moderate fat (42% calories from fat; n = 6) or control diet (35% calories from fat). Northern blot analysis revealed an increase in the ratio of visceral to subcutaneous (v/s ratio) mRNA expression of both lipoprotein lipase (LPL) and peroxisome proliferator-activated receptor-gamma (PPARgamma). In addition, the ratio for sterol regulatory element-binding transcription factor-1 (SREBP-1) tended to be higher in fat-fed dogs, suggesting enhanced lipid accumulation in the visceral fat depot. The v/s ratio of hormone-sensitive lipase (HSL) increased significantly, implicating a higher rate of lipolysis in visceral adipose despite hyperinsulinemia in obese dogs. In fat-fed dogs, liver SREBP-1 expression was increased significantly, with a tendency for increased fatty acid-binding protein (FABP) expression. In addition, glucose-6-phosphatase (G-6-Pase) and phosphoenolpyruvate carboxykinase (PEPCK) increased significantly, consistent with enhanced gluconeogenesis. Liver triglyceride content was elevated 45% in fat-fed animals vs. controls. Moreover, insulin receptor binding was 50% lower in fat-fed dogs. Increased gene expression promoting lipid accumulation and lipolysis in visceral fat, as well as elevated rate-limiting gluconeogenic enzyme expression in the liver, is consistent with the portal theory. Further studies will need to be performed to determine whether FFA are involved directly in this pathway and whether other signals (either humoral and/or neural) may contribute to the development of hepatic insulin resistance observed with visceral obesity.

Adipose Tissue↗

PubMed1997

Signaling from G protein-coupled receptors to the c-jun promoter involves the MEF2 transcription factor. Evidence for a novel c-jun amino-terminal kinase-independent pathway.

The c-Jun amino-terminal kinases (JNKs) are a subfamily of mitogen-activated protein kinases that phosphorylate c-Jun and ATF2, and it has been postulated that phosphorylated c-Jun enhances its own expression through AP-1 sites on the c-jun promoter. In this study, we asked whether signals activating JNK regulate the c-jun promoter. Using NIH 3T3 cells expressing G protein-coupled m1 acetylcholine receptors as an experimental model, we have recently shown that the cholinergic agonist carbachol, but not platelet-derived growth factor, potently elevates JNK activity. Consistent with these findings, carbachol, but not platelet-derived growth factor, increased the activity of a c-jun promoter-driven reporter gene (for chloramphenicol acetyltransferase). However, coexpression of JNK kinase kinase (MEKK) effectively increased JNK activity, but resulted in surprisingly limited induction of the c-jun promoter. This raised the possibility that pathway(s) distinct from JNK control the c-jun promoter, and prompted us to explore which of its regulatory elements participate in transcriptional control. We observed that deletion of the 3' AP-1 site diminished chloramphenicol acetyltransferase activity in response to carbachol, but only to a limited extent. In contrast, deletion of a MEF2 site dramatically reduced expression, and deletion of both the MEF2 and 3' AP-1 sites abolished induction. Furthermore, cotransfection with MEF2C and MEF2D cDNAs potently enhanced the activity of the c-jun promoter in response to carbachol, and stimulation of m1 receptors, but not direct JNK activation, induced expression of a MEF2-responsive plasmid. Taken together, these data strongly suggest that MEF2 mediates c-jun promoter expression by G protein-coupled receptors through a yet to be identified pathway, distinct from that of JNK.

3T3 Cells↗

PubMed2006

Transcription promoter activity of the human S100A7 gene in oral squamous cell carcinoma cell lines.

The S100A7 (psoriasin) gene has been shown to be markedly over-expressed in squamous cell carcinomas (SCCs) as well as in psoriasis. We herein examined the S100A7 gene promoter activity in human oral SCC cell lines to identify the putative SCC-specific regulatory regions for the S100A7 transcription. Functional deletion assays of 5'-flanking region demonstrated that the segments, (-1513 to -988), (-1954 to -1513) and (-3040 to -2578), play important roles in the transcription activity in the oral SCCs. The internal deletion of the short segments, (-1248 to -1110), (-1109 to -988) and (-1248 to -988), decreased this activity. These segments cloned upstream of the heterologous promoter increased the promoter activity in oral SCC cell line. Electrophoretic mobility shift assays, using the sequence segmental probes, (-1248 to -1110) and (-1109 to -988), showed different DNA-protein complex patterns depending on the types of used cell lines. One of the complexes was only observed in the oral SCCs. These data suggested that the segment from -1513 to -988 contains up-regulatory elements for the transcription activity of the S100A7 gene in oral SCCs.

Calcium-Binding Proteins↗

PubMed1997

Ultraspiracle, a Drosophila retinoic X receptor alpha homologue, can mobilize the human thyroid hormone receptor to transactivate a human promoter.

We have analyzed the functional domains of the Drosophila orphan receptor Ultraspiracle (usp), a homologue of the vertebrate retinoic X receptor alpha, as well as the ability of heterodimers between usp and the thyroid hormone receptor beta (T3Rbeta) to transactivate the human apolipoprotein A-II (apoA-II) promoter. DNA binding assays demonstrated that heterodimers of usp and the human T3Rbeta can bind to the hormone response element (HRE) of the regulatory element AIIJ (-734 to -716) of the human apoA-II promoter. Cotransfection experiments have shown that the combination of usp and T3Rbeta can transactivate the human apoA-II promoter in COS-1 cells 7-8-fold in the presence of thyroid hormone (T3). The observed transactivation was not affected by the deletion of the amino-terminal residues 1-85 of usp, which represent a putative transactivation domain, suggesting that the function of usp is to recruit T3Rbeta. Furthermore, a mutant usp, with impaired DNA binding properties, can form heterodimers with T3Rbeta in vitro but has reduced ability to transactivate the human apoA-II promoter. A minimal thymidine kinase (tk) promoter driven by four AIIJ regulatory elements is repressed to 20% of its original activity by T3Rbeta and the repression is relieved by usp/T3Rbeta heterodimers. Deletion analysis demonstrated that factors bound to the regulatory elements AIIJ, AIIAB, and AIIH participate in the usp/T3Rbeta-mediated transactivation of the human apoA-II promoter. Similarly to element AIIJ, element AIIAB binds usp/T3Rbeta heterodimers, whereas element AIIH binds a COS-1 nuclear activity that is supershifted with anti-hepatic nuclear factor 1 antibodies. The findings suggest that optimal transactivation of the apoA-II promoter by usp/T3Rbeta heterodimers requires complex interactions between these heterodimers and factors bound to other regulatory elements. The observed transcriptional activation through heterodimer formation between nuclear receptors from species as divergent in the evolutionary scale as insects and mammals indicates that the functional domains of these proteins have been highly conserved.

Animals↗

PubMed2002

RNA structure analysis assisted by capillary electrophoresis.

Although most capillary electrophoresis (CE) applications in the nucleic acid field performed so far address DNA analysis, various RNA assays by CE have also been done. Both natural and synthetic RNAs have been examined to evaluate their quantities, sizes and interactions. In this report, we show a novel application of CE in RNA research for the analysis of RNA stable conformers. First, we present a successful adaptation of two different enzymatic methods for the 3'-end labeling of RNAs with commercially available fluorescent probes. Then, we show the high performance of CE with laser-induced fluorescence detection (CE-LIF) assisting the structural studies of transcripts. Using the example of regulatory elements present in the breast cancer gene transcript BRCA1, we demonstrate-by direct comparisons-the advantages of CE-LIF over the traditional slab-gel electrophoresis. These include a better and more reproducible separation of conformers, shorter analysis time and higher detection sensitivity.

BRCA1 Protein↗

PubMed1999

The role of oxysterols in cholesterol homeostasis.

Cholesterol biosynthesis is regulated by transcription factors named steroid regulatory element-binding proteins. A newly discovered transcription factor, LXR, regulates the catabolic degradation of cholesterol by activation of the gene controlling cholesterol 7 alpha-hydroxylase, the rate-limiting enzyme in the formation of bile acids. Excessive dietary cholesterol leads to increased oxysterol formation. Oxysterol binds to LXR and thereby induces transcription of cholesterol 7 alpha-hydroxylase, thus increasing the removal of cholesterol as bile acids.

Animals↗

PubMed1990

Regulation of mouse serum amyloid A gene expression in transfected hepatoma cells.

Expression of mouse serum amyloid A (SAA1, -2, and -3) mRNAs can be induced up to 1,000-fold in the liver in response to acute inflammation. This large increase is primarily the result of a 200-fold increase in the rates of SAA gene transcription. To analyze the cis-acting regulatory element(s) responsible for regulating transcription, we fused 306 base pairs of the mouse SAA3 promoter to a reporter gene, the chloramphenicol acetyltransferase (CAT) gene, and transfected this chimeric DNA into cultured cells. In transient expression assays, this 5' sequence was sufficient to confer cell-specific expression: CAT activity was readily detectable when the construct was transfected into liver-derived cells but was not detectable in nonliver cells. Furthermore, when liver cells transfected with this construct were treated with conditioned media prepared from activated mixed lymphocyte cultures or with recombinant interleukin-1, a 10- to 15-fold increase in CAT activity was detected. Deletion analyses showed two regions of interest: a proximal region that enhanced CAT expression in a cell-specific manner and a distal region that conferred responsiveness to both conditioned media and recombinant interleukin-1. This distal responsive element had properties of an inducible transcriptional enhancer, and deletion of the proximal cell-specific region rendered the distal element responsive to stimulation by conditioned media in nonliver cells.

Animals↗