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Results for “regulatory element transcripts”

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PubMed1988

Conservation of histone H2A/H2B intergene regions: a role for the H2B specific element in divergent transcription.

The organization and function of potential regulatory elements associated with the promoters of chicken H2A and H2B genes pairs have been examined. The intergene regions of six dispersed and divergently-transcribed H2A/H2B gene pairs contain several extremely well conserved and spaced blocks of sequence homology. Adjacent coding regions are on average 342 base-pairs apart. Respective TATA boxes are separated by 180 base-pairs and within this confined region there are four CCAAT boxes and a previously identified 13 base-pair H2B-specific element (H2B-box) which has homology to the octamer motif present in a number of gene promoter/enhancer elements. Transcription of H2A and H2B genes from wild-type and mutant constructs was measured in transient assays by transfection into HeLa cells, and in permanently transformed clonal cell lines. In vitro separation of the two genes at a unique intergenic site significantly decreased transcription of each gene. This suggested that the H2A/H2B gene pairs contained overlapping promoters. Deletion or point mutagenesis of the H2B-specific element decreased the levels of H2B and the H2A transcripts indicating that this sequence is a common regulatory element of both genes in the divergent-pair configeration.

Animals↗

PubMed2006

Ets-1 and runx2 regulate transcription of a metastatic gene, osteopontin, in murine colorectal cancer cells.

Osteopontin (OPN) is a sialic acid-rich phosphoprotein secreted by a wide variety of cancers. We have shown previously that OPN is necessary for mediating hepatic metastasis in CT26 colorectal cancer cells. Although a variety of stimuli can induce OPN, the molecular mechanisms that regulate OPN gene transcription in colorectal cancer are unknown. We hypothesized that cis- and trans-regulatory elements determine OPN transcription in CT26 cells. OPN transcription was analyzed in CT26 cancer cells and compared with YAMC (young adult mouse colon) epithelial cells. Clonal deletion analysis of OPN promoter-luciferase constructs identified cis-regulatory regions. A specific promoter region, nucleotide (nt) -107 to -174, demonstrated a >8.0-fold increase in luciferase activity in CT26 compared with YAMC. Gel-shift assays sublocalized two cis-regulatory regions, nt -101 to -123 and nt -121 to -145, which specifically bind CT26 nuclear proteins. Competition with unlabeled mutant oligonucleotides revealed that the regions nt -115 to -118 and nt -129 to -134 were essential for protein binding. Subsequent supershift and chromatin immunoprecipitation assays confirmed the corresponding nuclear proteins to be Ets-1 and Runx2. Functional relevance was demonstrated through mutations in the Ets-1 and Runx2 consensus binding sites resulting in >60% decrease in OPN transcription. Ets-1 and Runx2 protein expression in CT26 was ablated using antisense oligonucleotides and resulted in a >7-fold decrease in OPN protein expression. Ets-1 and Runx2 are critical transcriptional regulators of OPN expression in CT26 colorectal cancer cells. Suppression of these transcription factors results in significant down-regulation of the OPN metastasis protein.

Animals↗

PubMed2002

Identification of regulatory elements in the human adipose most abundant gene transcript-1 ( apM-1) promoter: role of SP1/SP3 and TNF-alpha as regulatory pathways.

AIMS/HYPOTHESIS: The human adipocyte-specific apM-1 (adipose most abundant gene transcript-1) gene encodes for a secretory protein of the adipose tissue that seems to play a role in the pathogenesis of obesity-related insulin resistance and its expression is inhibited by TNF-alpha. Our aim was to characterize the tissue-specific regulation of the recently cloned apM-1 promoter and the mechanisms of TNF-alpha-induced downregulation of the apM-1 gene. METHODS: We characterised the apM-1 gene by electrophoretic mobility shift assays (EMSA) and luciferase reporter gene assays (LRA). RESULTS: Although several putative binding sites for transcription factors known to be involved in adipogenesis such as C/EBP and PPARgamma are present in the promoter, we could not detect any binding of these nuclear proteins from differentiated adipocytes. However, a proximal SP1 binding site specifically binds both, recombinant SP1 protein and SP1 derived from adipocyte nuclear extracts. Since the expression of SP1 during adipocyte differentiation has not yet been analysed, we could show by using EMSA, that binding activity of SP1 is increased during adipocyte differentiation. The stimulatory activity of SP1 was confirmed in LRA by cotransfection experiments in S2 Schneider cells lacking endogenous SP factors. An inhibitory activity of SP3 on the stimulatory effect of SP1 could be confirmed in LRA by contransfection experiments in adipocytes. Nuclear extracts from adipocytes incubated with TNF-alpha showed a reduced binding activity of SP1. CONCLUSION/INTERPRETATION: SP1 is expressed and its binding activity is enhanced during adipocyte differentiation. SP1 has stimulatory effects, SP3 has inhibitory effects on apM-1 promoter activity, mediated by a proximal SP1 binding site. The mechanism of TNF-alpha-induced inhibition of apM-1 gene expression is, at least in part, due to a decrease of transcriptional SP1 binding activity caused by TNF-alpha and thus provides a new mechanism of TNF-alpha-dependent signalling.

3T3 Cells↗

PubMed2000

Multiple mechanisms, independent of sterol regulatory element binding proteins, regulate low density lipoprotein gene transcription.

Transcription of the LDL receptor gene is markedly enhanced in the Jurkat T cell line by stimulation with the combination of the phorbol ester phorbol 12-myristate 13-acetate (PMA) and the protein synthesis inhibitor cycloheximide (CHX). The DNA sequences necessary for this response were identified by analysis of Jurkat T cells permanently transfected with reporter gene expression vectors containing fragments of the LDL receptor promoter extending from 68 bp to 1472 bp 5' of the major transcription start site. The magnitude of the response of this array of promoter fragments to stimulation with PMA and CHX was similar to that previously observed with a approximately 6.5 kb promoter fragment. However, the various promoter fragments differed with regard to the role of the sterol regulatory element-1 (SRE-1) sequence. Thus, whereas a 142 bp promoter mediated transcription stimulated by PMA and CHX independently of SRE-1, a shorter 115 bp promoter was absolutely dependent on SRE-1. Furthermore, internal deletion of promoter sequences from -142 bp to -113 bp from longer promoter constructs in which the SRE-1 was mutated prevented the induction of transcription by PMA and CHX. Electrophoretic mobility shift assays (EMSAs) demonstrated sequence-specific, stimulus-independent binding by Jurkat nuclear proteins to the novel response element mapped between -142 and -115. Even though the minimal 115 bp or 68 bp promoter fragment required an intact SRE-1 to respond to PMA and CHX, transcriptional induction persisted when nuclear levels of sterol regulatory element binding proteins (SREBPs) were made undetectable by culture in suppressive sterols. Taken together, these data indicate that non-sterol stimuli such as the combination of PMA and CHX induce LDL receptor gene transcription through at least two distinct promoter elements, neither of which requires the presence of SREBPs. However, the element proximal to the transcription start site is dependent on the SRE-1.

Base Sequence↗

PubMed1992

BLyF, a novel cell-type- and stage-specific regulator of the B-lymphocyte gene mb-1.

The mb-1 gene encodes an integral membrane protein that appears to be required for the surface expression and signalling function(s) of the immunoglobulin receptor on B lymphocytes. The gene is expressed in a lineage-restricted manner. It is activated early in B-cell ontogeny, continues to be expressed in mature B cells, but is turned off in terminally differentiated plasma cells. We have identified the mb-1 promoter and functionally tested its activity by transient transfections. A 737-bp promoter fragment preferentially stimulates accurately initiated transcription in mb-1-expressing B cells. Deletion analysis of the promoter suggests the presence of two functional domains, proximal and distal. Both domains independently activate transcription from a heterologous promoter. The distal domain functions in a cell-type- and stage-specific manner, activating transcription in B cells but not in T cells or plasma cells. A 25-bp element within this domain is necessary and sufficient for activity. This element is recognized by a novel cell-type- and stage-specific transcription factor termed BLyF. The binding of BLyF completely correlates with the ability of the regulatory element to stimulate transcription. Thus, BLyF appears to positively regulate transcription of the mb-1 gene. Our results also suggest that the inactivity of the mb-1 locus in plasma cells is not simply due to the loss of BLyF activity.

Animals↗

PubMed1992

Characterization and purification of a novel transcriptional repressor from HeLa cell nuclear extracts recognizing the negative regulatory element region of human immunodeficiency virus-1 long terminal repeat.

Cellular transcription factors play critical roles in regulating human immunodeficiency virus (HIV) gene transcription, although the precise mechanism(s) defining their roles are not well established. Primarily it has been suggested that sequence-specific interaction of trans-activating proteins with cis-acting DNA elements plays a crucial role in regulating the target genes. The negative regulatory element (NRE) of HIV-1 long terminal repeat (LTR) is one such defined region that has been reported to down-regulate LTR-directed HIV gene expression. Information regarding the role of this region in the regulation of HIV expression is lacking. Here we describe an attempt to further characterize the role of NRE cis-elements and define any sequence-specific interaction with cellular factors. Using gel mobility shift DNA-binding and Southwestern blot assays, we have mapped a distinct region of NRE (-290 to -260, a 30-base pair (bp) domain of NRE-A) sequences of HIV-1 LTR, which recognizes a specific DNA-binding protein from HeLa cell nuclear extracts. This factor is a 38-kDa polypeptide which can be affinity-purified to near homogeneity by this 30-bp specific oligonucleotide in affinity chromatography. The cellular factor from HeLa cell nuclear extract exhibits specific interaction only with the 30-bp NRE-A domain of HIV-1 LTR and acts as a strong transcriptional repressor/inhibitor molecule in the DNA-protein gel binding, as well as in vitro transcriptional studies with the nuclear extracts from cells with productive HIV-1 infection. To our knowledge, this is the first report of a factor recognizing a distinct segment within NRE that has been shown to exert an inhibitory effect on transcriptionally active DNA-protein "pre-initiation" complex formation, suggesting a possible role in HIV-1 gene regulation.

Base Sequence↗

PubMed2001

[Regulation of carbohydrate metabolism by insulin: role of transcription factor SREBP-1c in the hepatic transcriptional effects of the hormone].

A number of tissues such as the brain must be continuously provided with glucose to meet their energy demand. In contrast, carbohydrate absorption during meals is a discontinuous process. Thus, we must store glucose when its is provided, release it or spare it when it is less abundant. Insulin, secreted by the pancreatic beta-cell is a key hormone in the adaptations of metabolic pathways linked to glucose homeostasis. It inhibits hepatic glucose production, promotes glucose storage in the liver and glucose uptake and storage in muscles and adipose tissues. This is achieved through the modifications of the activity of existing proteins (enzymes, transporters) but also through the regulation of gene expression. In the liver, when the diet is rich in carbohydrates, insulin is secreted and stimulates the expression of genes involved in glucose utilization (glucokinase, L-pyruvate kinase, lipogenic enzymes) and inhibits genes involved in glucose production (phosphenolpyruvate carboxykinase). The mechanisms by which insulin controls the expression of these genes were poorly understood. Recently, the transcription factor Sterol Regulatory Element Binding Protein-1c (SREBP-1c) has been proposed as a key mediator of insulin transcriptional effects. Insulin increases the synthesis and nuclear abundance of this factor which when overexpressed in the liver mimics the effects of insulin on insulin-sensitive genes. This suggests that SREBP-1c could be involved in pathologies such as type 2 diabetes, obesity and more generally in insulin resistance syndromes.

Adipose Tissue↗

PubMed2003

The SREBP pathway--insights from Insigs and insects.

Animal cells coordinate lipid homeostasis by end-product feedback regulation of transcription. The control occurs through the proteolytic release of transcriptionally active sterol regulatory element binding proteins (SREBPs) from intracellular membranes. This feedback system has unexpected features that are found in all cells. Here, we consider recently discovered components of the regulatory machinery that govern SREBP processing, as well as studies in Drosophila that indicate an ancient role for the SREBP pathway in integrating membrane composition and lipid biosynthesis.

Animals↗

PubMed1990

Transcription of the T cell receptor beta-chain gene is controlled by multiple regulatory elements.

The cis-acting sequences regulating transcription of the beta-chain of the TCR have been analyzed and multiple elements identified. The minimum 5' upstream sequence displaying promoter activity is a fragment extending 85 bp upstream of the transcriptional start site. Deletion of an additional 43 bp from the 5' end of this fragment abolished promoter activity. The presence of the conserved TCR beta-chain decanucleotide motif, an AP-1 consensus sequence and an inverted repeat in the deleted region, suggests their role as targets for transacting factors regulating transcription of the beta chain gene. Sequences between -343 and -85 increase transcription from the -85 fragment in T cells. The promoter is active in both T cells and fibroblasts. The enhancer was capable of enhancing TCR V beta 2 promoter activity in both T cells and fibroblasts. Sequences further upstream of the V beta 2 promoter down regulate V beta 2 promoter activity in the absence of the enhancer but its repressive influence is overcome in the presence of the TCR beta-chain enhancer.

Animals↗

PubMed1990

Human erythropoietin gene expression in transgenic mice: multiple transcription initiation sites and cis-acting regulatory elements.

Erythropoietin (EPO) is the primary humoral regulator of mammalian erythropoiesis. The single-copy EPO gene is normally expressed in liver and kidney, and increased transcription is induced by anemia or cobalt chloride administration. To identify cis-acting DNA sequences responsible for regulated expression, transgenic mice were generated by microinjection of a 4-kilobase-pair (kb) (tgEPO4) or 10-kb (tgEPO10) cloned DNA fragment containing the human EPO gene, 0.7 kb of 3'-flanking sequence, and either 0.4 or 6 kb of 5'-flanking sequence, respectively. tgEPO4 mice expressed the transgene in liver, where expression was inducible by anemia or cobalt chloride, kidney, where expression was not inducible, and other tissues that do not normally express EPO. Human EPO RNA in tgEPO10 mice was detected only in liver of anemic or cobalt-treated mice. Both tgEPO4 and tgEPO10 mice were polycythemic, demonstrating that the human EPO RNA transcribed in liver is functional. These results suggest that (i) a liver inducibility element maps within 4 kb encompassing the gene, 0.4 kb of 5'-flanking sequence, and 0.7 kb of 3'-flanking sequence; (ii) a negative regulatory element is located between 0.4 and 6 kb 5' to the gene; and (iii) sequences required for inducible kidney expression are located greater than 6 kb 5' or 0.7 kb 3' to the gene. RNase protection analysis revealed that human EPO RNA in anemic transgenic mouse liver and hypoxic human hepatoma cells is initiated from several sites, only a subset of which is utilized in nonanemic transgenic liver and human fetal liver.

Animals↗

PubMed2004

Porcine adenovirus type 3 E1 transcriptional control region contains a bifunctional regulatory element.

We identified a bifunctional regulatory element located between nt 374 and 431 upstream of TATA box of porcine adenovirus (PAV) 3 E1A promoter. Deletion of the element dramatically reduced the steady-state level of E1A mRNA, but increased that of E1B, which lies immediately downstream of E1A. The mutant virus displayed defective replication at early times of infection, but replicated nearly as efficiently as wild-type PAV-3 at late times of infection. This defect was complemented with coinfecting wild-type virus in a mixed infection. The results indicated that the upstream activation sequences (UAS) of E1A overlap the upstream repression sequences (URS) of E1B, although both transcription units are transcribed from different promoters.

Adenovirus E1A Proteins↗

PubMed1997

The structure of the gene for murine CTP:phosphocholine cytidylyltransferase, Ctpct. Relationship of exon structure to functional domains and identification of transcriptional start sites and potential upstream regulatory elements.

Phosphatidylcholine (PC) is the most abundant eukaryotic phospholipid and serves critical structural and cell-signaling functions. CTP:phosphocholine cytidylyltransferase (CT) is the rate-limiting enzyme in the CDP-choline pathway of PC biosynthesis, which is utilized by all tissues and is the sole or major PC biosynthetic pathway in all non-hepatic cells. Herein, we present the complete structure of the murine CT (Ctpct) gene. One P1 genomic clone and six subsequent plasmid subclones were isolated and analyzed for the exon-intron organization of the Ctpct gene. The gene spans approximately 26 kilobases and is composed of 9 exons and 8 introns. The exons match the distinct functional domains of the CT enzyme: exon 1 is untranslated; exon 2 codes for the nuclear localization signal domain; exons 4-7 encompass the catalytic domain; exon 8 codes for the alpha-helical membrane-binding domain; and exon 9 includes the C-terminal phosphorylation domain. Two transcriptional initiation sites, spaced 35 nucleotides apart, were identified using 5'-rapid amplification of cDNA ends polymerase chain reaction. The 5' natural flanking region was found to lack TATA or CAAT boxes and to contain GC-rich regions, which are features typical of promoters of housekeeping genes. Several sites that have the potential to interact with transcription regulatory factors, such as Sp1, AP1, AP2, AP3, Y1, and TFIIIA, were identified in the 5'-region of the gene and found to be distributed in two distinct clusters. These data will provide the basis for future studies on the cis- and trans-acting factors involved in Ctpct gene transcription and for the creation of induced mutant mouse models of altered CT activity.

Animals↗

PubMed2005

The HIV-1 Tat protein enhances megakaryocytic commitment of K562 cells by facilitating CREB transcription factor coactivation by CBP.

The human immunodeficiency virus type 1 (HIV-1) Tat protein regulates transcription factor functions and alters cellular gene expression. Because hematopoietic progenitor cell (HPC) differentiation requires activation of lineage-specific transcription factors, Tat may affect hematopoiesis in HIV-1-infected micro-environments. We have monitored the molecular effects of Tat on megakaryocytic differentiation in the HPC line, K562. Flow cytometry analysis of CD61 indicated that phorbol myristate acetate (PMA) (16 nM) stimulated megakaryocytic commitment of K562 cells was increased (3- to 4-fold) following exposure to Tat (1-100 ng/ml). Activation of the megakaryocytic transcription factor cAMP regulatory element binding protein (CREB) and its coactivation by the CREB binding protein (CBP) was subsequently monitored. CREB phosphorylation and DNA binding were measured by Western immunodetection and electrophoretic mobility shift assays (EMSA), respectively. Within 2 hrs after stimulation, Tat increased both CREB phosphorylation and DNA binding by 7- to 10-fold. Transient cotransfection with CREB reporter and CBP expression plasmids demonstrated that Tat treatment increases (3- to 4-fold) both PMA-stimulated and CBP-mediated transcription via the cAMP regulatory element. Histone acetyl transferase (HAT) activity was increased (8- to 10-fold) in Tat-stimulated cells, which suggested increased chromosomal accessibility of transcription factors. Two-hybrid cotransfection assays using reporter plasmid containing the GAL4 DNA-binding domain and expression plasmid coding for the GAL4-CBP fusion protein, showed that Tat increases (2-fold) CBP-mediated coactivation of CREB. Both reverse transcription-polymerase chain reaction (RT-PCR) and Western blot analysis showed that Tat treatment increases CBP gene expression (7- to 9-fold) and protein levels (5- to 7-fold) within 6-12 hrs after stimulation. Our findings indicated that Tat treatment increases both CREB function and CREB coactivation by CBP, which may facilitate megakaryocytic commitment of K562 cells. Induction of this molecular signaling by HIV-1 Tat protein may have relevance in understanding the HIV-induced hematologic manifestations and possibly in regulation of viral infectivity parameters in progenitor cell reservoirs.

CREB-Binding Protein↗

PubMedDate not supplied

[Metabolism of cholesterol and fatty acids in nephrotic syndrome and its regulation by sterol regulatory element binding proteins (SREBP's). Effect of soy protein consumption].

Hyperlipidemia occurs during nephrotic syndrome (NS). It is known that cholesterol and fatty acid biosynthesis is controlled by the transcription factors sterol regulatory element binding proteins (SREBPs). Soy protein consumption reduces the concentration of these lipids, although its mechanism of action is not well known. The aim of the present study was to establish whether soy protein consumption reduces cholesterol and triglycerides levels by regulating of SREBPs. Male Wistar rats with experimental NS were studied for 64 days. The results showed that rats fed with soy protein had significantly lower plasma cholesterol and triglyceride concentrations as well as proteinuria than rats fed with casein diet. These decrements were associated with a decrease in the expression of SREBP-1 and fatty acid biosynthetic enzymes. In addition, Western blot analysis revealed that in nuclear extracts from hepatocytes of rats fed with soy protein, there was a lower concentration of SREBP-1 than in rats fed with casein. The results of this study indicate that consumption of a soy protein diet has beneficial effects on nephrotic syndrome.

Animals↗

PubMed2000

Transcription regulatory regions database (TRRD): its status in 2000.

Transcription Regulatory Regions Database (TRRD) has been developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry in TRRD corresponds to a particular gene and contains a description of structure-function features of its regulatory regions (transcription factor binding sites, promoters, enhancers, silencers, etc.) and gene expression regulation patterns. The current release, TRRD 4.2.5, comprises the description of 760 genes, 3403 expression patterns, and >4600 regulatory elements including 3604 transcription factor binding sites, 600 promoters and 152 enhancers. This information was obtained through annotation of 2537 scientific publications. TRRD 4.2.5 is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/

Databases, Factual↗

PubMed1987

Mutation of the c-fos gene dyad symmetry element inhibits serum inducibility of transcription in vivo and the nuclear regulatory factor binding in vitro.

In vitro mutagenesis of a 61-base-pair DNA sequence element that is necessary for induction of the c-fos proto-oncogene by growth factors revealed that a small region of dyad symmetry within the sequence element is critical for c-fos transcriptional activation. The same c-fos dyad symmetry element was found to bind a nuclear protein in vitro, causing a specific mobility shift of this c-fos regulatory sequence. An analysis of insertion and deletion mutants established a strict correlation between the ability of the dyad symmetry element to promote serum activation of c-fos transcription and in vitro nuclear protein binding. These experiments suggest that the DNA mobility shift assay detects a nuclear protein that mediates growth factor stimulation of c-fos expression. In vitro competition experiments indicate that the c-fos regulatory factor also binds to sequences within another growth factor-inducible gene, the beta-actin gene.

Animals↗

PubMed1999

Sterol regulatory element-binding proteins: activators of cholesterol and fatty acid biosynthesis.

A family of transcription factors designated sterol regulatory element-binding proteins (SREBPs) mediates the previously described end-product feedback regulation of cholesterol biosynthesis. In addition, SREBPs are emerging as important regulators of fatty acid synthesis. The current review focuses on the in-vivo regulation of SREBPs in liver and the coordinate regulation of SREBP-activated target genes.

Animals↗

PubMed1998

Isolation of cholesterol-requiring mutant Chinese hamster ovary cells with defects in cleavage of sterol regulatory element-binding proteins at site 1.

The synthesis and uptake of cholesterol requires transcription factors designated sterol regulatory element-binding proteins (SREBPs). SREBPs are bound to membranes in a hairpin orientation with their transcriptionally active NH2-terminal segments facing the cytosol. The NH2-terminal segments are released from membranes by two-step proteolysis initiated by site 1 protease (S1P), which cleaves in the luminal loop between two membrane-spanning segments. Next, site 2 protease (S2P) releases the NH2-terminal fragment of SREBP. The S2P gene was recently isolated by complementation cloning using Chinese hamster ovary cells that require cholesterol for growth, due to a mutation in the S2P gene. A similar approach cannot be used for S1P because all previous cholesterol auxotrophs manifest defects in S2P, which is encoded by a single copy gene. To circumvent this problem, in the current studies we transfected Chinese hamster ovary cells with the S2P cDNA, assuring multiple copies. We mutagenized the cells, selected for cholesterol auxotrophy, and identified two mutant cell lines (SRD-12A and -12B) that fail to cleave SREBPs at site 1. Complementation analysis demonstrated that the defects in both cell lines are recessive and noncomplementing, indicating a mutation in the same gene. These cells should now be useful for expression cloning of the sterol-regulated S1P gene.

Acetates↗