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At least 199 records · Page 11Linked to original sources
PubMed1993

The hobo transposable element of Drosophila can be cross-mobilized in houseflies and excises like the Ac element of maize.

The hobo transposable element from Drosophila melanogaster was found to be capable of excision, resulting in donor sites unlike those reported for any other transposable element currently known in animals. These empty sites most closely resemble those left by the transposable elements Ac and Tam3 in Zea mays and Antirrhinum majus, respectively. Like Ac and Tam3, the hobo element was found to function in a distantly related species, in this case the housefly Musca domestica. Hobo excision in M. domestica was found not to require the expression of hobo-encoded transposase but instead appears to be driven by an endogenous hobo transposase-like activity. DNA sequences displaying high homology to the hobo transposase gene were isolated from the genome of M. domestica and appear to be part of a mobile-element system related to hobo, Ac, and Tam3.

Animals↗
PubMed1996

Sterol regulatory element binding protein binds to a cis element in the promoter of the farnesyl diphosphate synthase gene.

Sterol-regulated transcription of the gene for rat farnesyl diphosphate (FPP) synthase (geranyl-diphosphate:isopentenyl-diphosphate geranyltranstransferase, EC 2.5.1.10) is dependent in part on the binding of the ubiquitous transcription factor NF-Y to a 6-bp element within the proximal promoter. Current studies identify a second element in this promoter that is also required for sterol-regulated transcription in vivo. Mutation of three nucleotides (CAC) within this element blocks the 8-fold induction of FPP synthase promoter-reporter genes that normally occurs when the transfected cells are incubated in medium deprived of sterols. Gel mobility-shift assays demonstrate that the transcriptionally active 68-kDa fragment of the sterol regulatory element (SRE-1)-binding protein assays (SREBP-1) binds to an oligonucleotide containing the wild-type sequence but not to an oligonucleotide in which the CAC has been mutated. DNase 1 protection pattern (footprint) analysis indicates that SREBP-1 binds to nucleotides that include the CAC. Both the in vivo and in vitro assays are affected by mutagenesis of nucleotides adjacent to the CAC. Coexpression of SREBP with a wild-type FPP synthase promoter-reporter gene in CV-1 cells results in very high levels of reporter activity that is sterol-independent. In contrast, the reporter activity remained low when the promoter contained a mutation in the CAC trinucleotide. We conclude that sterol-regulated transcription of FPP synthase is controlled in part by the interaction of SREBP with a binding site that we have termed SRE-3. Identification of this element may prove useful in the identification of other genes that are both regulated by SREBP and involved in lipid biosynthesis.

Alkyl and Aryl Transferases↗
PubMedDate not supplied

Edge-element based finite element analysis of microwave hyperthermia treatments for superficial tumours on the chest wall.

Several three-dimensional hyperthermia treatment planning systems for deep regional hyperthermia have been successfully utilized for improving the performance of applicators such as the BSD Sigma 60. Treatment planning systems for superficial heating in contrast have been less utilized. This paper presents a study of the applicability of the finite element method that has been developed for modelling hyperthermia treatments of recurrent chest wall cancer using a patient geometry. The patient model was created by reconstructing the tissue geometry of a patient using a series of axial CT scans. Tetrahedral grids were generated from this geometry for use in finite element simulations of the SAR profile using edge-elements and in finite element simulations of the steady-state temperature profile using scalar elements. The predicted temperature profile was well correlated with thermometry readings taken after 30 min of heating during a hyperthermia treatment. The model predicted the presence of hot-spots in regions that were not monitored. Simulations also showed that the hot-spots can be manipulated by rotating the applicator by 90 degrees. This study demonstrates the ability of the model to provide detailed and accurate heating profiles in a patient specific model for superficial microwave hyperthermia of the chest wall.

Computer Simulation↗
PubMed1997

Chromatin insulator elements block the silencing of a target gene by the Drosophila polycomb response element (PRE) but allow trans interactions between PREs on different chromosomes.

Polycomb response elements (PREs) can establish a silenced state that affects the expression of genes over considerable distances. We have tested the ability of insulator or boundary elements to block the repression of the miniwhite gene by the Ubx PRE. The gypsy element and the scs element interposed between PRE and miniwhite gene protect it against silencing but the scs' is only weakly effective. When the PRE-miniwhite gene construct is insulated from flanking chromosomal sequences by gypsy elements at both ends, it can still establish efficient silencing in some lines but not others. We show that this can be caused by interactions in trans with PREs at other sites. PRE-containing transposons inserted at different sites or even on different chromosomes can interact, resulting in enhanced silencing. These trans interactions are not blocked by the gypsy insulator and reveal the importance of nonhomologous associations between different regions of the genome for both silencing and activation of genes. The similarity between the behavior of PREs and enhancers suggests a model for their long-distance action.

Animals↗
PubMed1998

P-Element insertion at the polyhomeotic gene leads to formation of a novel chimeric protein that negatively regulates yellow gene expression in P-element-induced alleles of Drosophila melanogaster.

Polyhomeotic is a member of the Polycomb group (Pc-G) of homeotic repressors. The proteins encoded by the Pc-G genes form repressive complexes on the polycomb group response element sites. The phP1 mutation was induced by insertion of a 1.2-kb P element into the 5' transcribed nontranslated region of the proximal polyhomeotic gene. The phP1 allele confers no mutant phenotype, but represses transcription of P-element-induced alleles at the yellow locus. The phP1 allele encodes a chimeric P-PH protein, consisting of the DNA-binding domain of the P element and the PH protein lacking 12 amino-terminal amino acids. The P-PH, Polycomb (PC), and Posterior sex combs (PSC) proteins were immunohistochemically detected on polytene chromosomes in the regions of P-element insertions.

Animals↗
PubMed1999

Serum response elements activate and cAMP responsive elements inhibit expression of transcription factor Egr-1 in synovial fibroblasts of rheumatoid arthritis patients.

Analyzing the induction kinetics and promoter elements regulating the expression of the transcription factor Egr-1, we found elevated levels of Egr-1-encoding mRNA in synovial fibroblasts of rheumatoid arthritis (RA) patients when compared to controls. By contrast, synovial lymphocytes and macrophages do not show an elevated Egr-1 transcription. Therefore, the overexpression of Egr-1 may serve as a diagnostic marker to characterize synovial fibroblasts of RA patients. To study the regulatory mechanisms controlling Egr-1 expression we analyzed the function of transcription factor binding sites located in the Egr-1 promoter. Individual transcription factor binding sites within the Egr-1 promoter were specifically mutated and Egr-1 promoter activity was tested using reporter gene constructs. Our experiments demonstrate that serum response elements are the main positive regulators and binding to a cAMP responsive element represents the major negative regulator for Egr-1 expression in synovial fibroblasts. In addition, we functionally defined a new element, which was not yet described in the human Egr-1 promoter and which serves as a second negative regulatory element for Egr-1 expression. Therefore increased serum response factor activity or failure of Egr-1 repressing signals may account for Egr-1 overexpression in RA synovial fibroblasts.

Arthritis, Rheumatoid↗
PubMed1989

Site-specific ribosomal DNA insertion elements in Anopheles gambiae and A. arabiensis: nucleotide sequence of gene-element boundaries.

The nucleotide sequence of the junctions between the 28S ribosomal gene and site-specific insertion elements from two sibling mosquito species, Anopheles gambiae and A. arabiensis, is reported. In both species, elements insert at the same point within the 28S gene, but this site is 634 basepairs (bp) 3' of the R1 (Type I) insertion site in Drosophila melanogaster. The two mosquito elements each have poly A tails and a polyadenylation signal, but the extreme 3' and 5' ends show no other similarity to each other or to any other insertion element. In both mosquito species, identical target site duplications of 17 bp are generated. The sequence TNTCCCTNT found in this duplication is also found in the 14 bp target site duplications that flank R1 elements in D. melanogaster. Another sequence in this duplication, GGGATAACT, is very similar to the sequence GGGAGTAACT found in the 24 base sequence required by the Bombyx mori R2 endonuclease.

Animals↗
PubMed1998

Embryo deadenylation element-dependent deadenylation is enhanced by a cis element containing AUU repeats.

The deadenylation of maternal mRNAs in the Xenopus embryo is a sequence-specific process. One cis element that targets maternal mRNAs for deadenylation after fertilization is the embryo deadenylation element (EDEN). This element, composed of U/R repeats, is specifically bound by a protein, EDEN-BP. In the present study we show that the rate at which an RNA containing an EDEN is deadenylated can be increased by the presence of an additional cis element composed of three AUU repeats. This effect was observed for a natural EDEN (c-mos) and two synthetic EDENs. Hence, the enhancement of EDEN-dependent deadenylation conferred by the (AUU)3 motif is not due to an interaction with a particular EDEN sequence. Mutation of the (AUU)3 motif abrogated the enhancement of EDEN-dependent deadenylation. These data indicate that the rate at which a specific maternal mRNA is deadenylated in Xenopus embryos is probably defined by a cross talk between multiple cis elements.

Animals↗
PubMed2000

A double-strand break in a chromosomal LINE element can be repaired by gene conversion with various endogenous LINE elements in mouse cells.

A double-strand break (DSB) in the mammalian genome has been shown to be a very potent signal for the cell to activate repair processes. Two different types of repair have been identified in mammalian cells. Broken ends can be rejoined with or without loss or addition of DNA or, alternatively, a homologous template can be used to repair the break. For most genomic sequences the latter event would involve allelic sequences present on the sister chromatid or homologous chromosome. However, since more than 30% of our genome consists of repetitive sequences, these would have the option of using nonallelic sequences for homologous repair. This could have an impact on the evolution of these sequences and of the genome itself. We have designed an assay to look at the repair of DSBs in LINE-1 (L1) elements which number 10(5) copies distributed throughout the genome of all mammals. We introduced into the genome of mouse epithelial cells an L1 element with an I-SceI endonuclease site. We induced DSBs at the I-SceI site and determined their mechanism of repair. We found that in over 95% of cases, the DSBs were repaired by an end-joining process. However, in almost 1% of cases, we found strong evidence for repair involving gene conversion with various endogenous L1 elements, with some being used preferentially. In particular, the T(F) family and the L1Md-A2 subfamily, which are the most active in retrotransposition, appeared to be contributing the most in this process. The degree of homology did not seem to be a determining factor in the selection of the endogenous elements used for repair but may be based instead on accessibility. Considering their abundance and dispersion, gene conversion between repetitive elements may be occurring frequently enough to be playing a role in their evolution.

Animals↗
PubMed1987

Ingi, a 5.2-kb dispersed sequence element from Trypanosoma brucei that carries half of a smaller mobile element at either end and has homology with mammalian LINEs.

A dispersed repetitive element named ingi, which is present in the genome of the protozoan parasite Trypanosoma brucei, is described. One complete 5.2-kilobase element and the ends of two others were sequenced. There were no direct or inverted terminal repeats. Rather, the ends consisted of two halves of a previously described 512-base-pair transposable element (G. Hasan, M.J. Turner, and J.S. Cordingley, Cell 37:333-341, 1984). Oligo(dA) tails and possible insertion site duplications suggested that ingi is a retroposon. The sequenced element appears to be a pseudogene copy of an original retroposon with one or more open reading frames occupying most of its length. Significant homologies of the encoded amino acid sequences with reverse transcriptases and mammalian long interpersed nuclear element sequences suggest a remote evolutionary origin for this kind of retroposon.

Animals↗
PubMed2006

A convenient scheme for coupling a finite element curvilinear mesh to a finite element voxel mesh: application to the heart.

BACKGROUND: In some cases, it may be necessary to combine distinct finite element meshes into a single system. The present work describes a scheme for coupling a finite element mesh, which may have curvilinear elements, to a voxel based finite element mesh. METHODS: The method is described with reference to a sample problem that involves combining a heart, which is defined by a curvilinear mesh, with a voxel based torso mesh. The method involves the creation of a temporary (scaffolding) mesh that couples the outer surface of the heart mesh to a voxel based torso mesh. The inner surface of the scaffolding mesh is the outer heart surface, and the outer surface of the scaffolding mesh is defined by the nodes in the torso mesh that are nearest (but outside of) the heart. The finite element stiffness matrix for the scaffolding mesh is then computed. This stiffness matrix includes extraneous nodes that are then removed, leaving a coupling matrix that couples the original outer heart surface nodes to adjacent nodes in the torso voxel mesh. Finally, a complete system matrix is assembled from the pre-existing heart stiffness matrix, the heart/torso coupling matrix, and the torso stiffness matrix. RESULTS: Realistic body surface electrocardiograms were generated. In a test involving a dipole embedded in a spherical shell, relative error of the scheme rapidly converged to slightly over 4%, although convergence thereafter was relatively slow. CONCLUSION: The described method produces reasonably accurate results and may be best suited for problems where computational speed and convenience have a higher priority than very high levels of accuracy.

Algorithms↗
PubMed1999

Transcriptional regulation of the gonadotropin-releasing hormone receptor gene is mediated in part by a putative repressor element and by the cyclic adenosine 3',5'-monophosphate response element.

The levels of the GnRH receptor (GnRHR) and its messenger RNA depend on the pattern of administration of GnRH. In this study, internal deletion mutants in a luciferase reporter gene vector (GnRHR-pXP2) containing a 1226-bp promoter fragment of mouse GnRHR gene were used to examine the regulation of GnRHR gene transcription in GGH3 cells. Our results indicate that the mouse GnRHR promoter contains one putative repressor element located at position -343/-335. When this sequence was deleted, the GnRHR promoter activity was significantly increased in both basal and GnRH agonist (Buserelin)-, phorbol ester-, and forskolin-stimulated cells. Gel mobility shift assay showed that the sequence -343/-335 is capable of binding GGH3 nuclear proteins. With deletion of the cAMP response element (-107/-100), basal and Buserelin-stimulated transcription was decreased. The same response was observed after stimulation with forskolin. Stimulation with (Bu)2cAMP did not alter transcription above basal levels. The stimulation with phorbol ester resulted in an attenuated increase in transcriptional activity, suggesting that this sequence of the GnRHR promoter is a cAMP response element. These results suggest that the transcriptional activity of the GnRHR gene is mediated in part by a putative repressor element and by the cAMP response element.

Animals↗
PubMed2004

Age-related changes of elements and relationships among elements in the common bile and pancreatic ducts.

To elucidate compositional changes of the common bile and main pancreatic ducts with aging, the authors investigated age-related changes of element contents in the common bile and pancreatic ducts by inductively coupled plasma-atomic emission spectrometry. After ordinary dissection by medical students was finished, the common bile ducts and main pancreatic ducts (pancreatic ducts) were resected and the element contents were determined. The Mg content increased significantly only in the pancreatic duct with aging, but the other element contents did not change significantly in both the common bile and pancreatic ducts with aging. Regarding the relationships among the elements, significant direct correlations were found among the contents of Ca, P, S, and Mg in the common bile ducts, with some exceptions between P and either S or Mg contents. In the pancreatic ducts, significant direct correlations were found between S and Mg contents and between P and Na contents. The relationships in the elements between the common bile and pancreatic ducts were examined. It was found that there were significant direct correlations in the Ca, Mg, and Fe contents between the common bile and pancreatic ducts; that is, as Ca, Mg, and Fe increased in the common bile duct, they increased simultaneously in the pancreatic duct.

Aged↗
PubMed1998

Sp1 and Sp3 transactivate the human lipoprotein lipase gene promoter through binding to a CT element: synergy with the sterol regulatory element binding protein and reduced transactivation of a naturally occurring promoter variant.

Lipoprotein lipase (LPL) is a key enzyme in lipoprotein and energy metabolism and, therefore, regulation of its expression could have an important bearing on these processes. We have identified an evolutionarily conserved 5'-CCTCCCCCC-3' motif (from -91 to -83, CT element) in the human LPL gene promoter, deletion or mutation of which caused approximately 70-80% decrease in promoter activity. We found that Sp1 and Sp3 in THP-1 nuclear protein extracts bind specifically to this element. Co-transfection with Sp1 and Sp3 expression plasmids transactivated the LPL promoter via the CT element in Drosophila SL2 cells devoid of Sp proteins. Sp3 moderately repressed Sp1-mediated LPL promoter activation when both were co-expressed in SL2 cells. Furthermore, co-expression of an active sterol regulatory element binding protein (SREBP-1), with Sp1, but not with Sp3, synergistically activated the LPL promoter in SL2 cells. We previously reported a naturally occurring T-->G substitution at position -93 of the human LPL promoter which reduces promoter activity by 40-50% in transient transfection assays. In this study, we showed that this substitution results in reduced binding affinity to Sp1/Sp3 and in diminished transactivation by Sp1/Sp3 alone and by the synergistic action of Spl and SREBP-1 In conclusion, recruitment of Sp1/Sp3 by the CT element may play an important role in expression of the human lipoprotein lipase gene. Synergistic transcriptional activation by Sp1 and SREBP-1 may provide a mechanism for cross-talk between cholesterol and triglyceride metabolic pathways.

Base Sequence↗
PubMed2000

A novel Pax-6 binding site in rodent B1 repetitive elements: coevolution between developmental regulation and repeated elements?

Pax-6 encodes a transcription factor that is important in the development of eye and CNS. Identification of Pax-6 target genes is crucial for understanding the gene regulatory network in these developmental processes. Using an in-vitro approach of cyclic amplification of the protein binding sequences (CAPBS), we isolated a PAX6 binding sequence from a human single-copy (sc) DNA library. Characterization of this PAX6 binding sequence revealed a 15bp region (hGCalpha1BLs5) that is sufficient for PAX6 specific binding. From a homology search in the GenBank, we found that an hGCalpha1BLs5-like Pax-6 binding site exists in 21 genes (16 from rodent), 15 of which were shown to be able to bind Pax-6 in vitro. Interestingly, some of these sites occur in B1 repetitive elements. Although hGCalpha1BLs5 is highly similar to a region in B1 repetitive elements, PAX6 does not bind to the consensus sequence in B1. However, a single-step mutation in some B1 elements can lead to a gain of function for PAX6 binding. This experimental evidence and phylogenetic analysis raise an interesting speculation for the coevolution between PAX6 regulation and repeat elements. Since a (Pax-6-binding) null B1 element can be re-activated by even a single-step mutation, it has the potential to recruit gene targets for Pax-6 if it is inserted into the regulatory region, and therefore may play a role for evolutionary modification of Pax-6 regulation.

Animals↗
PubMed2000

Identification of a C-rich element as a novel cytoplasmic polyadenylation element in Xenopus embryos.

During Xenopus early development, the length of the poly(A) tail of maternal mRNAs is a key element of translational control. Several sequence elements (cytoplasmic polyadenylation elements) localized in 3' untranslated regions have been shown to be responsible for the cytoplasmic polyadenylation of certain maternal mRNAs. Here, we demonstrate that the mRNA encoding the catalytic subunit of phosphatase 2A is polyadenylated after fertilization of Xenopus eggs. This polyadenylation is mediated by the additive effects of two cis elements, one being similar to already described cytoplasmic polyadenylation elements and the other consisting of a polycytosine motif. Finally, a candidate specificity factor for polycytosine-mediated cytoplasmic polyadenylation has been purified and identified as the Xenopus homologue of human alpha-CP2.

3' Untranslated Regions↗
PubMed1998

A proximal element within the human alpha 2(I) collagen (COL1A2) promoter, distinct from the tumor necrosis factor-alpha response element, mediates transcriptional repression by interferon-gamma.

Previous studies have shown that interferon-gamma (IFN-gamma) inhibits type I collagen gene expression through both transcriptional and post-transcriptional mechanisms (Kahäri et al., 1990). In the present study, using transient cell transfections of human dermal fibroblast cultures with a series of 5' deletion promoter/CAT reporter gene constructs, we have identified the IFN-gamma-response element of the human alpha 2(I) collagen gene (COL1A2) promoter. Specifically, we have identified a segment of the proximal promoter region, located between nucleotides -161 and -125 relative to the transcription start site, as critical for down-regulation of COL1A2 promoter activity by IFN-gamma. This IFN-gamma response element (IgRE) is clearly distinct from the previously described tumor necrosis factor-alpha response element (TaRE) located between nucleotides -265 and -241 of the COL1A2 promoter, a difference which is likely to explain the additive inhibitory effect of these two cytokines. The inhibitory effect of IFN-gamma was dose-dependent and rapidly induced, requiring less than 5 min exposure of fibroblast cultures. Gel mobility shift assays indicated that a highly specific nuclear protein complex bound to this 37-base pair region of promoter. Competition experiments with oligonucleotides spanning discrete segments of this promoter region mapped the binding element within a distinctive pyrimidine-rich sequence. Point mutations within the latter revealed that this element plays a crucial role not only in the IFN-gamma response, but also in the basal activity of the proximal promoter. Substitution mutations within the IgRE of the -161/CAT construct attenuated the promoter response to IFN-gamma, as measured in transient cell transfections, and eliminated specific DNA/protein complex formation, as measured by gel mobility shift assay. UV-crosslinking experiments indicated that two DNA/protein complexes were formed with the IgRE, with molecular weights around 55 kDa and 30 kDa, corresponding to proteins of approximately 30 kDa and approximately 6 kDa, respectively. Our results further clarify the molecular mechanisms involved in the regulation of type I collagen gene expression by IFN-gamma.

Binding, Competitive↗
PubMed1996

Tissue-specific expression of the vasoactive intestinal peptide gene requires both an upstream tissue specifier element and the 5' proximal cyclic AMP-responsive element.

An upstream enhancer element [tissue specifier element (TSE)] located between 4.66 and 4.02 kb from the transcription start site is important for cell type-specific expression and phorbol ester induction of the vasoactive intestinal peptide (VIP) gene. An element located within 100 bases of the VIP promoter [the VIP cyclic AMP-responsive element (VIP-CRE)] confers cyclic AMP and phorbol ester responsiveness to heterologous promoters. The possibility that these two regions of the VIP gene function cooperatively to determine tissue-specific and second messenger-dependent expression of the VIP gene was addressed by assaying transcription from a VIP-luciferase reporter gene with progressive deletions from the 5' flanking sequence of the gene, with or without inactivation of the proximal VIP-CRE. Basal expression of the reporter gene in both SH-EP and SK-N-SH human neuroblastoma cells, which express endogenous VIP mRNA, was absolutely dependent on the presence of the upstream TSE. Full constitutive expression was also dependent on the intact VIP-CRE. Forskolin-mediated induction of the reporter gene in SH-EP and SK-N-SH cells was completely abolished by mutations in the VIP-CRE but not by deletion of the upstream sequence, indicating that the VIP-CRE alone determines cyclic AMP responsiveness. In contrast to reports that the VIP-CRE imparts 12-O-tetradecanoylphorbol 13-acetate (phorbol 12-myristate 13-acetate; PMA) responsiveness to heterologous promoters, PMA stimulation in SK-N-SH cells was independent of an intact VIP-CRE but dependent on a region between -2.5 kb and the VIP-CRE. Sequencing of the entire 5.2-kb VIP 5' flank revealed a consensus PMA-responsive element (TGACTCA) 2.25 kb upstream of the transcription start site that may represent the site imparting PMA responsiveness to the VIP gene.

Animals↗