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At least 199 records · Page 11Linked to original sources
PubMed1981

Analysis of transcriptional regulatory signals of the HSV thymidine kinase gene: identification of an upstream control region.

We have identified a transcriptional control region of the herpes simplex virus tk gene. This finding results from in vivo transcription assays of specific deletion mutants constructed in vitro. A region located between 40 and 100 nucleotides upstream from the putative transcription start site of the tk gene can promote transcription by RNA polymerase form II in the complete absence of the mRNA-coding component of the gene. When the region is deleted enzymatically from a 5' direction, accurate transcriptional expression is reduced by a factor of 50. The small remaining level of accurate transcription is eliminated by deletion of sequences from 32 to 16 nucleotides upstream from the the structural gene. It appears that the sequences between 16 and 32 nucleotides upstream from the 5' terminus of the tk gene are required to specify the exact start site of transcription. Control of both the efficiency of transcription and rough specification of the position of initiation, however, depends on sequences 40--100 nucleotides upstream from the tk structural gene.

Animals↗
PubMed1986

A transcription terminator located upstream of the mouse rDNA initiation site affects rRNA synthesis.

Mouse ribosomal genes have a short sequence upstream of the transcription initiation site that is related in structure and function to the terminator boxes previously identified at the 3' end of the transcription unit. This upstream terminator recognizes the same protein factor as the 3'-terminal sites and is able to terminate RNA polymerase I transcription in vitro. S1 mapping and nucleolar run-on experiments reveal the presence of 5'-terminal spacer transcripts that are terminated at this site. These transcripts probably derive from spacer promoters, one of which has been identified approximately 2 kb upstream of the pre-rRNA start site. The interaction of a specific nuclear factor with the upstream terminator increases the efficiency of initiation, suggesting that transcription termination and initiation at the adjacent promoter work in an interrelated fashion.

Animals↗
PubMed1987

Defective distal regulatory element at the 5' upstream of rat prolactin gene of steroid-nonresponsive GH-subclone.

The prolactin-nonproducing (PRL-) GH cell strains (rat pituitary tumor cells in culture). GH12C1 and F1BGH12C1, do not respond to steroid hormones estradiol or hydrocortisone (HC). However, the stimulatory effect of estradiol and the inhibitory effect of hydrocortisone on prolactin synthesis can be demonstrated in the prolactin-producing GH cell strain, GH4C1. In this investigation we have examined the 5' end flanking region of rat prolactin (rat PRL) gene of steroid-responsive, GH4C1 cells to identify the positive and negative regulatory elements and to verify the status of these elements in steroid-nonresponsive F1BGH12C1 cells. Results presented in this report demonstrate that the basel level expression of the co-transferred Neo gene (neomycin phosphoribosyl transferase) is modulated by the distal upstream regulatory elements of rat PRL gene in response to steroid hormones. The expression of adjacent Neo gene is inhibited by dexamethasone and is stimulated by estradiol in transfectants carrying distal regulatory elements (SRE) of steroid-responsive cells. These responses are not observed in transfectants with the rat PRL upstream sequences derived from steroid-nonresponsive cells. The basal level expression of the host cell alpha-2 tubulin gene is not affected by dexamethasone. We report here the identification of the distal steroid regulatory element (SRE) located between 3.8 and 7.8 kb upstream of the transcription initiation site of rat PRL gene. Both the positive and the negative effects of steroid hormones can be identified within this upstream sequence. This distal SRE appears to be nonfunctional in steroid-nonresponsive cells. Though the proximal SRE is functional, the defect in the distal SRE makes the GH substrain nonresponsive to steroid hormones. These results suggest that both the proximal and the distal SREs are essential for the mediation of action of steroid hormones in GH cells.

Animals↗
PubMed1990

Potential binding sites of the trans-activator FIS are present upstream of all rRNA operons and of many but not all tRNA operons.

FIS, the Escherichia coli protein that stimulates the inversion of various DNA segments by binding to a recombinational enhancer, trans-activates a number of stable RNA operons and binds to the upstream activator sequence (UAS) of these operons (Nilsson et al. (1990) EMBO J. 9, 727). In a search for potential FIS-binding sites we have compared UASs of other stable RNA operons with a consensus FIS-binding sequence, compiled by comparing recombinational enhancers. Such sites can thus be recognized upstream of all rRNA and 13 tRNA operons. Matching with the consensus sequence varied, suggesting that the affinity of FIS for the sites differed. Accordingly, FIS binding to an upstream sequence of the metY(nusA) operon was found to be weaker than that to the UAS of the thrU(tufB) operon. No FIS binding sites were found upstream three tRNA operons.

Anticodon↗
PubMed1986

Estradiol-dependent transcription initiation upstream from the chicken apoVLDLII gene coding for the very-low-density apolipoprotein II.

We have investigated RNAs originating from the 5'-flanking region of the chicken very-low-density apolipoprotein II (apoVLDLII) gene. S1 nuclease mapping and primer extension experiments revealed two minor upstream transcription start points located 1105 and 1530 nucleotides in front of the apoVLDLII gene. Transcription starting at these points is dependent upon estradiol as is transcription from the major start points. The transcripts are polyadenylated, but are not detectable in polysomes. Run-on assays indicated that the low concentration of the upstream initiated transcripts is due both to low transcription levels and to low transcript stability. The sequence around the upstream start points does not show strong homologies with consensus sequences of promoters for eukaryotic protein encoding genes. Nevertheless, the upstream sequences are transcribed in vivo by RNA polymerase II.

Animals↗
PubMed1992

Analysis of the promoter for the gene encoding the testis-specific histone H1t in a somatic cell line: evidence for cell-cycle regulation and modulation by distant upstream sequences.

Gene H1t encodes a testis-specific variant of the H1 histone family expressed in pachytene spermatocytes during the meiotic phase of spermatogenesis. Fusions between various upstream fragments of the H1t gene and the chloramphenicol acetyltransferase-encoding reporter gene were analyzed in mouse L cells by both transient and permanent transfection. Expression of the minimal promoter [174 nucleotides (nt) upstream from the transcription start point] was enhanced by sequences extending to nt -693, but was reduced in constructs with kb of upstream sequence. Using synchronized cells, expression was at least twofold higher in growing than in inhibited cells. Thus, the H1t promoter is modulated both positively and negatively by distant upstream sequences, and it displays some of the S-phase-dependent character of a replication-dependent histone.

Animals↗
PubMed1995

Upstream promoter elements are sufficient for selenocysteine tRNA[Ser]Sec gene transcription and to determine the transcription start point.

The TATA box, located upstream at about nt -30, and the proximal sequence element, located at about nt -60, are both essential and sufficient for basal level transcription of the Xenopus laevis (Xl) selenocysteine (Sec) tRNA[Ser]Sec gene as demonstrated by its microinjection into Xl oocytes. Point mutations within either of these regions abolish transcription, while deletion of the internal boxA element or insertion of 13 nt within the internal boxB element does not impair transcription. The latter mutations (within the internal regions) affect processing of the 3'-trailer sequence. Replacement of the tRNA[Ser]Sec coding sequence with an Escherichia coli M1 RNA gene resulted in expression of the E. coli gene governed by the upstream tRNA[Ser]Sec promoter elements. These studies demonstrate unequivocally that the upstream promoter elements are sufficient for the basal level of tRNA[Ser]Sec gene transcription. Primer extension studies with spacer mutants show that the internal elements do not play a role in selecting the transcription start point (tsp), but that selection of the tsp is determined by the region upstream from the gene. Further, studies with spacer mutants show that the distance between the TATA box and the tsp is quite likely the critical factor in selecting the position of tsp.

Animals↗
PubMed1995

The upstream region of the SP-B gene: intrinsic promoter activity and glucocorticoid responsiveness related to a new DNA-binding protein.

We identified and cloned the rabbit SP-B gene, encoding the pulmonary surfactant-associated protein, and sequenced its upstream region from -2635 to +428, including a much larger fragment of the upstream region than has previously been reported for an SP-B for any species. Rabbit SP-B showed substantial homology to its human counterpart in the coding and noncoding regions immediately upstream from the TATAA box. Using a luciferase (Luc) reporter gene (luc) construct we measured promoter activity with a 212-bp fragment (SPB212) from nucleotides (nt) -41 to -252, inclusive. SPB212 functioned as an active promoter in this assay. Further, we identified, cloned and sequenced the cDNA encoding a unique DNA-binding protein, N, that bound SPB212 at approx. -195. When the N cDNA was cloned into the expression vector pKC4 and cotransfected with the luc reporter construct, N significantly enhanced Luc production, but only in the presence of dexamethasone. Therefore, we identified and sequenced a functional promoter region upstream from rabbit SP-B, and isolated and characterized a DNA-binding protein that confers enhanced glucocorticoid responsiveness on this promoter.

Amino Acid Sequence↗
PubMed2006

The 3'-UTR of the glutamine-synthetase gene interacts specifically with upstream regulatory elements, contains mRNA-instability elements and is involved in glutamine sensing.

Glutamine synthetase (GS) is expressed at various levels in a wide range of tissues, suggesting that a complex network of modules regulates its expression. We explored the interactions between the upstream enhancer, regulatory regions in the first intron, and the 3'-untranslated region and immediate downstream genomic sequences of the GS gene (the GS "tail"), and compared the results with those obtained previously in conjunction with the bovine growth hormone (bGH) tail. The statistical analysis of these interactions revealed that the GS tail was required for full enhancer activity of the combination of the upstream enhancer and either the middle or the 3'-intron element. The GS tail also prevented a productive interaction between the upstream enhancer and the 5'-intron element, whereas the bGH tail did not, suggesting that the 5'-intron element is a regulatory element that needs to be silenced for full GS expression. Using the CMV promoter/enhancer and transfection experiments, we established that the 2.8 kb GS mRNA polyadenylation signal is approximately 10-fold more efficient than the 1.4 kb mRNA signal. Because the steady-state levels of both mRNAs are similar, the intervening conserved elements destabilize the long mRNA. Indeed, one but not all constructs containing these elements had a shorter half life in FTO-2B cells. A construct containing only 300 bases before and 100 bases after the 2.8 kb mRNA polyadenylation site sufficed for maximal expression. A stretch of 21 adenines inside this fragment conferred, in conjunction with the upstream enhancer and the 3'-part of the first intron, sensitivity of GS expression to ambient glutamine.

3' Untranslated Regions↗
PubMed2006

Mitochondrial upstream promoter sequences modulate in vivo the transcription of a gene in yeast mitochondria.

An in vivo study of the importance of the length and/or structures of sequences upstream of a mitochondrial promoter was undertaken in Saccharomyces cerevisiae. Short tandem mtDNA repeats were introduced upstream of the COX2 gene. Our data show that its expression is modulated by the sequence located over 200 bp upstream of the promoter. A deletion decreases the level of transcripts to about 50%. The initial level can be recovered by a fill-in AT-rich sequence or partially by the presence of a long repeat tract; on the contrary, a smaller number of copies tends to intensify the effect of the deletion. These results show that the length and base composition upstream of mitochondrial promoter are involved in vivo in the modulation of the gene expression.

DNA, Mitochondrial↗
PubMed2006

Alterations in rdxA and frxA genes and their upstream regions in metronidazole-resistant Helicobacter pylori isolates.

Metronidazole resistance among Helicobacter pylori strains has been related to alterations in gene products having metronidazole nitroreductase activities. RdxA and FrxA proteins are the two major contributing factors. In this investigation, the rdxA and frxA genes and their upstream regions were analyzed in 19 H. pylori isolates, 8 of which were metronidazole-sensitive (MIC < or = 8 microg/mL) and 11 of which were metronidazole-resistant (MIC > or = 8 microg/mL), as determined by the E-test. Among the metronidazole-resistant isolates, three contained both RdxA and FrxA proteins with premature truncation caused by gene nonsense mutations or frameshift mutations, while three contained only stop mutations in FrxA and two only in RdxA. Substitutions of amino acids occurred in other RdxA (5/6) and FrxA (4/5) proteins from metronidazole resistant isolates as compared with those from metronidazole-sensitive ones. All metronidazole-resistant isolates had alterations in RdxA and/or FrxA proteins. Moreover, the upstream regions (-1 to -35) of rdxA and frxA genes in some metronidazole-resistant isolates varied by nucleotide insertion and/or deletion or substitution. The patterns of variation in both genes and their upstream regions were highly diversified. Alterations in rdxA and frxA genes and their upstream regions may be involved in the development of metronidazole resistance in H. pylori.

Amino Acid Sequence↗
PubMed2005

Characterization of an upstream regulatory element of adenovirus L1 poly (A) site.

The transition from early to late stage infection by adenovirus involves a change in mRNA expression from the adenovirus major late transcription unit (AdMLTU). This early to late switch centers around alternative selection of one of five poly (A) sites (L1-L5) that code for the major structural proteins of Adenovirus. During the early stage of infection, steady state mRNA is primarily derived from the L1 poly (A) site. During the late stage of infection, each of the MLTU poly (A) sites is represented in the steady state mRNA pool (Falck-Pedersen, E., Logan, J., 1989. Regulation of poly(A) site selection in adenovirus. J. Virol. 63 (2), 532-541.). Using transient transfection of a plasmid expressing Chloramphenicol Acetyl Transferase with a tandem poly (A) minigene system (L13) (DeZazzo, J.D., Falck-Pedersen, E., Imperiale, M.J., 1991. Sequences regulating temporal poly(A) site switching in the adenovirus major late transcription unit. Mol. Cell. Biol. 11 (12), 5977-5984; Prescott, J., Falck-Pedersen, E., 1994. Sequence elements upstream of the 3' cleavage site confer substrate strength to the adenovirus L1 and L3 polyadenylation sites. Mol. Cell. Biol. 14 (7), 4682-4693.), it has been demonstrated that the promoter-proximal L1 poly (A) site which is poorly recognized by the 3' end processing machinery, contains an upstream repressor element (URE) that influences steady state levels of mRNA (Prescott, J.C., Liu, L., Falck-Pedersen, E., 1997. Sequence-mediated regulation of adenovirus gene expression by repression of mRNA accumulation. Mol. Cell. Biol. 17 (4), 2207-2216.). In this study, we have further characterized the elements that mediate L1URE function. These studies indicate that the L1 upstream regulatory element (L1 URE) contains a complex RNA architecture that serves to repress gene expression through multiple sub-effectors. The L1URE functions when located upstream of a heterologous poly (A) site, and is able to strongly suppress steady state mRNA expression from the MLTU L3 poly (A) site or the murine beta-globin poly (A) site. In the tandem L13 mini-gene system, the L1URE is revealed to influence steady state mRNA stability, and subdomains within L1URE influence both gene expression and the steady state ratio of transcripts processed at proximal versus distal poly (A) sites. Transcript and gene repression mediated by the L1URE may provide a general strategy employed by adenovirus to block premature expression of late stage MLTU transcripts.

Adenoviridae↗
PubMed2007

Accumulation of immune cells and high expression of chemokines/chemokine receptors in the upstream shoulder of atherosclerotic carotid plaques.

The presence of immune cells is important for plaque destabilization. Disturbed flow conditions were shown to enhance the recruitment of circulating immune cells. Thus, we analyzed in 54 atherosclerotic carotid plaques the frequency of different immune cells, HLA-DR, chemokines, and chemokine receptors, comparing the upstream with the downstream plaque shoulder. The presence of neovascularization and intraplaque hemorrhages was investigated by CD34 immunostaining and Mallory's iron stain. Immunohistochemical analyses were performed to detect smooth muscle cells (SMC: actin), macrophages (CD68), T cells (CD3), dendritic cells (DC: fascin), mature DC (CD83), and the expression of HLA-DR, chemokine receptors (CCR-2, CCR-6), and chemokines (MCP-1, MIP-3alpha). Significantly more SMC were detected downstream than upstream (p<0.001). In contrast, significantly more macrophages (p=0.01), DC (p=0.03), mature DC (p=0.007), and a higher expression of HLA-DR (p=0.004), CCR-2 (p=0.002), CCR-6 (p<0.001), MCP-1 (p=0.04), and MIP-3alpha (p=NS) were observed upstream than downstream. Immune cells were strongly associated with neovascularization. The abundance of SMC downstream provides an explanation for distal plaque growth. Enhanced recruitment of immune cells through neovessels into the upstream shoulder might be contributing to plaque destabilization.

Aged↗
PubMed1990

Transcription initiation and nuclease-sensitive sites upstream of the epsilon-globin gene in K562 cells are related to poly (dA).poly (dT) sequences.

Previous studies have documented transcription initiation sites and nuclease hypersensitive sites upstream of the epsilon-globin canonical cap site in K562 cells. The upstream transcription initiation sites coincide with some of the nuclease hypersensitive sites. Comparison of the positions of the upstream transcription initiation and the nuclease hypersensitive sites with the nucleotide base order shows that these upstream sites fall significantly closer to poly (dA).poly (dT) tracts than can reasonably be accounted for by chance. It is concluded that these sites are related to the occurrence of poly (dA).poly (dT) tracts of at least five base pairs. Other studies have related some particular functional properties to poly (dA).poly (dT) tracts. Additionally, poly (dA).poly (dT) tracts have been shown to have unusual physical characteristics and to produce an intrinsic bending of the DNA molecules in which they are located. This study indicates that poly (dA).poly (dT) tracts can provide access to DNA for RNA polymerases and induce a DNA conformation recognized by DNase I or S1 nuclease.

Base Sequence↗
PubMed2002

Characterization of an upstream open reading frame in the 5' untranslated region of PR-39, a cathelicidin antimicrobial peptide.

Cathelicidins are antimicrobial peptides present in humans, and laboratory and domestic animals. These peptides are essential components of innate and acquired immune responses; however, little is known about cathelicidin gene regulation. To investigate the regulatory mechanisms of cathelicidin gene expression, we characterized the promoter of the PR-39 gene, a multifunctional cathelicidin. Deletion analysis identified a negative regulatory element in the 5'-flanking region of the gene located in the sequence from nt (nucleotide(s)) -69 to -63. Site-directed mutagenesis indicated that ATG and its vicinity nucleotides are critical for the repressive activity of this region. A primer extension assay identified a transcription start site upstream from the negative repressor ATG and 76 nt upstream from the major open reading frame (ORF). RT-PCR and 3'-RACE further demonstrated that cDNA of PR-39 and the cathelicidin porcine myeloid antimicrobal peptide (PMAP)-23, which share prepro sequence identity, start from nt -79. Sequencing of this region showed that the 5' untranslated region (UTR) of the gene contains an upstream translation start site and an upstream ORF that functions as a repressor of the PR-39 gene. These findings indicate extensive regulation of the PR-39 gene and suggest a mechanism for the tissue-specific and age-dependent repression of this cathelicidin gene.

5' Untranslated Regions↗
PubMed2002

The residue immediately upstream of the RNase P cleavage site is a positive determinant.

We have studied the importance of the residue at the position immediately upstream of the RNase P RNA cleavage site using model substrates that mimic the structure at and near the cleavage site of the tRNA(His) precursor. The various model substrates were studied with respect to cleavage site recognition as well as the kinetics of cleavage using M1 RNA, the catalytic subunit of Escherichia coli RNase P. Our studies showed that the identity of the residue immediately upstream of the cleavage site critically influences both these aspects. Among the ones tested, U is the preferred nucleotide at this position. Hence, these findings rationalize why most bacterial tRNA(His) genes/transcripts harbor a U immediately upstream of the RNase P cleavage site and extend our understanding of the cleavage site recognition process in general and the unusual cleavage of the tRNA(His) precursor in particular. Based on our as well as the data of others, we suggest that the nucleotide immediately upstream of the cleavage site is a positive determinant for cleavage by RNase P in general and the expression of tRNA genes is influenced by structural elements localized outside the promoter region i.e. in the leader and spacer regions of tRNA transcripts.

Adenosine Triphosphate↗
PubMed2001

Identification of negative and positive estrogen response elements in human GnRH upstream promoter in the placental JEG-3 cells.

Results from our previous studies have demonstrated regulatory effects of estradiol on human gonadotropin-releasing hormone (GnRH) gene expression in human placental cells. The present study was designed to determine the molecular mechanisms whereby estrogens regulate the human GnRH gene expression in the placenta. The effects of estradiol on human GnRH upstream promoter activity in JEG-3 cells depends on the amounts of estrogen receptor (ER) alpha expression vector co-transfected, with the maximal effect obtained at the amount of 1.0 microg of ER expression vector cotransfected. Estriol, an isoform of estradiol, also possesses a regulatory effect on the upstream promoter activity, while estrone, another isoform, does not. Serial deletion studies revealed two estrogen responsive elements in the GnRH upstream promoter region. One element (-987 to -968 bp, E4 element) confers a negative estradiol response, while another one (-827 to -730 bp) is responsible for a positive estradiol effect. Replacement of these two elements with unrelated DNA sequences could abolish the responsiveness to estradiol treatment. Furthermore, footprinting and gel shift assays demonstrated that nuclear protein from estradiol-treated JEG-3 cells, but not from control cells, could bind to a 41 bp DNA fragment (-824 to -784 bp) within the estrogen positive responsive element. Results of gel-shift assay demonstrated that other protein(s) might also be involved in interacting the E4 element to mediate the negative effect of estradiol on the hGnRH upstream promoter activity in JEG-3 cells.

Dose-Response Relationship, Drug↗
PubMed2001

The involvement of sex steroid hormones in downstream and upstream migratory behavior of masu salmon.

From May through July when masu salmon, Oncorhynchus masou, commence downstream migration under natural conditions, yearling precocious male masu salmon (resident form) showed higher GSI and plasma levels of testosterone (T) and 11-ketotestosterone (11-KT) in contrast to immature smolts (migratory form). From March through September coinciding with the upstream migration period, 2-year-old male and female adults also showed higher GSI and plasma levels of T, estradiol-17beta (E(2)) 11-KT, 17alpha-hydroxyprogesterone and 17alpha,20beta-dihydroxy-4-pregnene-3-one (DHP). In order to test the effects of steroid hormones on migratory behaviors, silascone tube capsules containing 500 microg of T, E(2), 11-KT, DHP, or a vehicle was implanted into smolts, castrated precocious males, or immature parr, and downstream and upstream behavior were observed in artificial raceways in spring and autumn. Downstream behavior of smolts was inhibited significantly by T, E(2) and 11-KT. Upstream behavior was stimulated by T and 11-KT in castrated precocious males and stimulated by T, E(2) and 11-KT in immature parr. These results indicate that T, E(2) and 11-KT are the factors regulating downstream and upstream migratory behavior. In particular, because of its changing patterns in plasma and significant effects, T, the common precursor hormone of E(2) (female) and 11-KT (male), is considered to play central roles in both types of behavior.

Animals↗