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PubMed1996

A cytokine mRNA-destabilizing element that is structurally and functionally distinct from A+U-rich elements.

The control of mRNA stability is crucial to the regulation of cytokine expression. We describe here a novel, potent destabilizing element found in the 3' untranslated region of granulocyte colony-stimulating factor mRNA. This element, which appears to require at least one stem-loop structure, we term the stem-loop destabilizing element (SLDE). Functionally equivalent elements appear to also exist in the interleukin 2 and interleukin 6 mRNAs. The SLDE is functionally distinct from the A+U-rich elements, which are also present in these and other cytokine mRNAs, because it destabilizes a chimeric mRNA in a tumor cell line in which A+U-rich elements do not function. In addition, the effect of the SLDE is insensitive to calcium ionophore and is therefore regulated independently of A+U destabilizing elements. The existence of two distinct mRNA-destabilizing elements provides an additional mechanism for the differential regulation of cytokine expression.

3T3 Cells↗
PubMed1994

Site-specific mutagenesis of the nodule-infected cell expression (NICE) element and the AT-rich element ATRE-BS2* of the Sesbania rostrata leghemoglobin glb3 promoter.

Sesbania rostrata leghemoglobin glb3 (Srglb3) promoter sequences responsible for expression in infected cells of transgenic Lotus corniculatus nodules were delimited to a 78-bp Dral-Hinfl fragment. This region, which is located between coordinates -194 to -116 relative to the start codon of the Srglb3 gene, was named the nodule-infected cell expression (NICE) element. Insertion of the NICE element into the truncated nopaline synthase promoter was found to confer a nodule-specific expression pattern on this normally root-enhanced promoter. Within the NICE element, three distinct motifs ([A]AAAGAT, TTGTCTCTT, and CACCC[T]) were identified; they are highly conserved in the promoter regions of a variety of plant (leg)hemoglobin genes. The NICE element and the adjacent AT-rich element (ATRE-BS2*) were subjected to site-directed mutagenesis. The expression patterns of nine selected Srglb3 promoter fragments carrying mutations in ATRE-BS2* and 19 with mutations in the NICE element were examined. Mutations in ATRE-BS2* had varying effects on Srglb3 promoter activity, ranging from a two- to threefold reduction to a slight stimulation of activity. Mutations in the highly conserved (A)AAAGAT motif of the NICE element reduced Srglb3 promoter activity two- to fourfold, whereas mutations in the TCTT portion of the TTGTCTCTT motif virtually abolished promoter activity, demonstrating the essential nature of these motifs for Srglb3 gene expression. An A-to-T substitution in the CACCC(T) motif of the NICE element also abolished Srglb3 promoter activity, while a C-to-T mutation at position 4 resulted in a threefold reduction of promoter strength. The latter phenotypes resemble the effect of similar mutations in the conserved CACCC motif located in the promoter region of mammalian beta-globin genes. The possible analogies between these two systems will be discussed.

Base Sequence↗
PubMed1994

Cis-acting elements reinforcing the activity of the estrogen-response element in the very-low-density apolipoprotein II gene promoter.

The gene coding for chicken very low density apolipoprotein II (apoVLDLII) is expressed exclusively in liver in response to estrogen. Previous work in our laboratory identified several protein binding sites, identified by the letters A to F, and their cognate factors within the first 300 bp flanking the gene. Here we present an extensive functional analysis of the apoVLDLII promoter by gene transfer experiments using a chicken hepatoma cell line and cultured non-hepatic cells. Deletion analysis revealed that the -301 to -163-bp promoter region, comprising elements E1, E2 and F, is sufficient for strong estrogen-dependent expression. Mutation analysis demonstrated that efficient transcription requires the interplay of the major estrogen response element E1 with several other cis-acting elements. Analysis of individual protein binding sites showed that element E1 is sufficient by itself to confer weak estrogen-induced transcription from the apoVLDLII promoter, and that additional promoter elements are required for full estrogen-responsiveness. Elements F and B1 were capable of strongly potentiating the activity of element E1. In general, the activity of certain cis-acting elements appeared to be strongly promoter-context dependent. Cultured non-liver cells expressed transfected VLDL-CAT reporter plasmids in the presence of cotransfected estrogen receptor expression vector in a hormone-dependent way, indicating that for the control of tissue specificity the 5'-proximal promoter region is not sufficient.

Animals↗
PubMed1999

Analysis of a ubiquitous promoter element in a primitive eukaryote: early evolution of the initiator element.

Typical metazoan core promoter elements, such as TATA boxes and Inr motifs, have yet to be identified in early-evolving eukaryotes, underscoring the extensive divergence of these organisms. Towards the identification of core promoters in protists, we have studied transcription of protein-encoding genes in one of the earliest-diverging lineages of Eukaryota, that represented by the parasitic protist Trichomonas vaginalis. A highly conserved element, comprised of a motif similar to a metazoan initiator (Inr) element, surrounds the start site of transcription in all examined T. vaginalis genes. In contrast, a metazoan-like TATA element appears to be absent in trichomonad promoters. We demonstrate that the conserved motif found in T. vaginalis protein-encoding genes is an Inr promoter element. This trichomonad Inr is essential for transcription, responsible for accurate start site selection, and interchangeable between genes, demonstrating its role as a core promoter element. The sequence requirements of the trichomonad Inr are similar to metazoan Inrs and can be replaced by a mammalian Inr. These studies show that the Inr is a ubiquitous, core promoter element for protein-encoding genes in an early-evolving eukaryote. Functional and structural similarities between this protist Inr and the metazoan Inr strongly indicate that the Inr promoter element evolved early in eukaryotic evolution.

Adenosine↗
PubMed2003

The new RENT family of repetitive elements in Nicotiana species harbors gene regulatory elements related to the tCUP cryptic promoter.

The tCUP cryptic constitutive promoter was discovered in the tobacco genome by T-DNA (transfer DNA) tagging with a promoterless GUS-nos gene. Here, we show that the portion of the tCUP sequence containing a variety of cryptic gene regulatory elements is related to a new family of moderately repetitive sequences (10(2) copies), the RENT (repetitive element from Nicotiana tabacum) family. The RENT family is found only in certain Nicotiana species. Five RENT elements were cloned and sequenced. The RENT elements are a minimum of 5 kb in length and share 80-90% sequence similarity throughout their length. The 5' termini are the same in the isolated RENT family members and are characterized by a conserved border sequence (TGTTGA(T or C)ACCCAATTTT(T or C)). The 3' ends of RENT sequence similarity vary in location and sequence. The tCUP cryptic promoter originated from a unique truncated RENT element that interrupts a phytochelatin synthase-like gene that may have undergone rearrangements prior to or resulting from T-DNA insertion. No evidence was found for expressed coding regions within the RENT elements; however, like the cryptic gene regulatory elements within the tCUP sequence, the isolated RENT elements possess promoter activity and translational enhancer activity.

Base Sequence↗
PubMed1992

Identification of positive and negative placenta-specific basal elements and a cyclic adenosine 3',5'-monophosphate response element in the human gene for P450scc.

The chronic regulation of steroiodgenesis is mediated principally by transcriptional regulation of the genes encoding the various steroidogenic enzymes. The cholesterol side-chain cleavage enzyme, P450scc, is rate limiting and hormonally regulated in a tissue-specific fashion. Human placental steroidogenesis is regulated by LH and hCG through increased intracellular cAMP, and forskolin and 8-bromo-cAMP increase the abundance of human P450scc mRNA in human JEG-3 choriocarcinoma cells. We transfected JEG-3 cells with 24 promoter/reporter constructions to examine the tissue-specific and hormonally induced transcription of the human P450scc gene in these cells. A reporter construction containing only bases -79 to +49 of the human P450scc gene was expressed in JEG-3 cells. This basal expression was increased by four elements, especially by a powerful element between -152 to -142. Adding DNA sequences to -177 suppressed the basal expression seen with the -152 construction, indicating that a repressor element lies between -177 and -152. Thus, basal expression of the human P450scc gene in JEG-3 cells is mediated by the interplay of several separate cis-acting DNA elements. Forskolin induction was conferred by sequences between -108 and -89. The mechanism for cAMP induction appears to be direct, as this induction is rapid and is not blocked by inhibiting protein synthesis with cycloheximide. Gel mobility shift experiments identified six specific DNA-protein complexes. Five of these complexes correlate closely with the basal transcription activities identified by the reporter assays. The powerful basal element, the repressor element, and the cAMP element differ from those identified by similar experiments in mouse adrenal Y1 cells, suggesting that the human P450scc gene is regulated by the tissue-specific use of different regulatory elements.

8-Bromo Cyclic Adenosine Monophosphate↗
PubMed1990

A cis-acting element located between the cAMP response elements and CCAAT box augments cell-specific expression of the glycoprotein hormone alpha subunit gene.

Several cis-acting elements interact through their cognate trans-acting factors to confer placenta-specific expression to the alpha subunit gene of glycoprotein hormones. These elements include two tandemly arranged cAMP response elements (CREs, located between base pairs (bp) -146 and -111 relative to the transcription start site), an upstream regulatory element (URE, located between -180 and -150), and a CCAAT box (located between bp -100 and -80). Here, we identify a new regulatory region, junctional regulatory element (JRE), with critical nucleotides located between the CREs and CCAAT box (bp -120 to -100). Although the binding site of the JRE abuts the 3' CRE, methylation interference assays indicate that no overlap occurs between the contact points of the proteins that bind to the JRE and CRE. This new regulatory element is highly conserved across species and contains a palindromic binding site for a 50-kDa nuclear factor(s) which is distinct from the factors that bind the URE, CRE, and CCAAT box of the alpha subunit gene. Finally, gene transfer studies suggest that, although JRE binding activity is found in several cell types, this element acts relatively cell-specifically. We conclude that this element and its cognate trans-acting factor act in conjunction with the complexes formed over the URE, CREs, and CCAAT box to enhance the placenta-specific activity of the alpha subunit promoter.

Base Sequence↗
PubMed2005

Transposition of Regulatory Elements by P-Element-Mediated Rearrangements in Drosophila melanogaster.

Previously we described highly unstable mutations in the yellow locus, induced by the chimeric element and consisting of sequences from a distally located 1A unique genomic region, flanked by identical copies of an internally deleted 1.2-kb P element. Here we show that a sequence, which is part of the yellow 1A region, can be transmitted to the AS-C by successive inversion and reinversion generated by yellow- and AS-C-located P elements. The chimeric element contains a regulatory element from the 1A region that specifically blocks yellow wing and body enhancers and simultaneously stimulates yellow expression in bristles. These results suggest that P-element-generated chimeric elements may play a certain role in rapid changes of regulatory regions of genes during evolution.

Alleles↗
PubMed1987

The estrogen-responsive element as an inducible enhancer: DNA sequence requirements and conversion to a glucocorticoid-responsive element.

The estrogen-responsive element (ERE) present in the 5'-flanking region of the Xenopus laevis vitellogenin (vit) gene B1 has been characterized by transient expression analysis of chimeric vit-tk-CAT (chloramphenicol acetyltransferase) gene constructs transfected into the human estrogen-responsive MCF-7 cell line. The vit B1 ERE behaves like an inducible enhancer, since it is able to confer estrogen inducibility to the heterologous HSV thymidine kinase (tk) promoter in a relative position- and orientation-independent manner. In this assay, the minimal B1 ERE is 33 bp long and consists of two 13 bp imperfect palindromic elements both of which are required for the enhancer activity. A third imperfect palindromic element is present further upstream within the 5'-flanking region of the gene but is unable to confer hormone responsiveness by itself. Similarly, neither element forming the B1 ERE can alone confer estrogen inducibility to the tk promoter. However, in combinations of two, all three imperfect palindromes can act cooperatively to form a functional ERE. In contrast a single 13 bp perfect palindromic element, GGTCACTGTGACC, such as the one found upstream of the vit gene A2, is itself sufficient to act as a fully active ERE. Single point mutations within this element abolish estrogen inducibility, while a defined combination of two mutations converts this ERE into a glucocorticoid-responsive element.

Acetyltransferases↗
PubMed1988

Elements required for transcription initiation of the human U2 snRNA gene coincide with elements required for snRNA 3' end formation.

Formation of the human U1 and U2 snRNA 3' ends requires both a conserved sequence, the 3' box, located downstream of the snRNA termini and sequences within the snRNA promoter regions. Indeed, replacement of the U1 snRNA promoter by mRNA promoters inhibits U1 3' end formation. We have now mutated the 5' flanking region of the human U2 gene and assayed the effects on initiation of transcription and 3' end formation. The 5' flanking region of the U2 gene contains two major promoter elements, a previously characterized distal element that enhances the efficiency of transcription and a proximal element, which our analysis localizes between positions -59 and -43 in a segment conserved in vertebrate snRNA genes. The 5' flanking region does not contain an element required solely for 3' end formation. However, when enhancer elements from an mRNA-encoding gene are introduced into a U2 promoter lacking its distal element, 3' end formation is inhibited. Together, these results suggest that the U2 promoter elements themselves are involved in 3' end formation, presumably by directing the formation of a unique transcription complex which is compatible with 3' end formation at the 3' box. Alteration of the composition of this transcription complex results in increased read-through at the 3' box.

DNA Mutational Analysis↗
PubMed1992

Transposable DNA elements and life history traits. I. Transposition of P DNA elements in somatic cells reduces the lifespan of Drosophila melanogaster.

As an initial study of the influence of transposable DNA elements on life history traits, and as a model system for estimating the impact of somatic genetic damage on longevity, the effect of P DNA element movement in somatic cells on adult lifespan was measured in Drosophila melanogaster males. Lifespan was significantly reduced in males that contained the somatically active P[ry+ delta 2-3](99B) element and 17, 4, 3, but not just a single P element. Furthermore, there appears to be a direct correlation between the number of transposing P elements and the amount of lifespan reduction. This reduction in lifespan observed in males with somatically active P elements is probably due to genetic damage in embryos, larvae and pupae from P-element excisions and insertions, leading to changes in gene structure and regulation, chromosome breakage, and subsequent cell death in adults. This hypothesis is supported in this study by a significant increase in recessive sex-linked lethal mutations in the same males that had reduced lifespans and by the previous observation of chromosome breakage in somatic cells of similar males. The evolutionary implications of these results are discussed, including the possible influence of somatic DNA transpositions on fitness and other life history traits.

Animals↗
PubMed1991

Newly activated germinal Uq elements in maize are clustered on one linkage group independently of the standard Uq element.

Allelism tests between the standard Uq element (Uq1) and five newly activated germinal Uq elements (Uq2, Uq3, UQ4, Uq5, and Uq6) demonstrate that these new Uq elements are independent of Uq1. Gametes that either contain one Uq or various combinations of two different and phenotypically distinguishable Uq elements, have been constructed either with or without the a-ruq reporter allele. Genetic analyses of the progenies of the gametes (using the standard a-ruq tested line as the other parent) have indicated that (i) each Uq element, when present alone, has the capacity to express full activity except when a secondary transposition or loss of activity has occurred; (ii) all five new Uq elements are independent of Uq1 with respect to transposition activity; and (iii) these newly originated Uqs are clustered on one linkage group. Uq2 is allelic to Uq4, and Uq3 is allelic to Uq5, whereas Uq6 is linked to both allelic pairs. A putative linkage map of these Uq elements is presented. In reciprocal crosses there is a striking difference in phenotypic segregation of Uq; when transmitted via the male parent Uq loses full expression capacity.

Alleles↗
PubMed1988

Regulation of Mu element copy number in maize lines with an active or inactive Mutator transposable element system.

In the progeny of an active Mutator plant, the number of Mu elements increases on self-pollination and maintains the average parental Mu content on outcrossing to a non-Mutator line; both patterns of transmission require an increase in the absolute number of Mu elements from one generation to the next. The same average copy number of Mu elements is transmitted through the male and female, but there is wide variation in the absolute copy number among the progeny. In inactive Mutator plants-defined both by the loss of somatic instability at a reporter gene (bronze2-mu1) and by modification of the HinfI sites in the terminal inverted repeat sequences of Mu elements - the absolute copy number of Mu elements is fixed in the parent. Thus, in outcrosses Mu element number is halved, and on self-pollination Mu copy number is constant. Reactivation of somatic mutability at cryptic bz2-mu1 alleles in inactive individuals by crossing to an active line seems not to involve an increase in Mu element copy number transmitted by the inactive individual. These and other results suggest that increases in Mu copy number occur late in plant development or in the gametophyte rather than after fertilization.

DNA Transposable Elements↗
PubMed1989

Mapping of insertion elements IS1, IS2 and IS3 on the Escherichia coli K-12 chromosome. Role of the insertion elements in formation of Hfrs and F' factors and in rearrangement of bacterial chromosomes.

The chromosome of an Escherichia coli K-12 strain W3110 contains seven copies of insertion element IS1, 12 copies of IS2 and six copies of IS3. We determined the approximate locations of six copies of IS1 (named is1A to is1F), ten copies of IS2 (named is2A to is2J), and five copies of IS3 (named is3A to is3E) on the W3110 chromosome by plaque hybridization using the "mini-set" of the lambda phage library that includes 476 clones carrying chromosomal segments that cover the W3110 chromosome almost entirely. Cleavage maps of the W3110 chromosome and cleavage analysis of phage DNAs carrying insertion elements allowed us to assign more precise locations to most of the insertion elements and to determine their orientations. Insertion elements were distributed randomly along the W3110 chromosome in one or other orientation. Several of these were located at the same positions on the chromosome of another E. coli K-12 strain, JE5519, and they were assumed to be the original complement of insertion elements in E. coli K-12 wild-type. Locations and orientations of such insertion elements were correlated well with Hfr points of origin and with crossover points for excision of some F' factors derived from several Hfrs. Insertion elements may be involved also in rearrangement of bacterial chromosomes.

Chromosomes, Bacterial↗
PubMed2004

Serum trace element levels and the complexity of inter-element relations in patients with Parkinson's disease.

Trace elements have been postulated to play a role in Parkinson's disease (PD). In order to elucidate whether changes in the serum levels of trace elements reflect the progression of PD, we assessed serum levels of 12 elements (Na, K, Fe, Al, Cu, Zn, Ca, Mg, Mn, Si, P and S) in early PD, severe PD and normal subjects, using inductively coupled plasma atomic emission spectrometry. The concentrations in micromol/ml, the relative mole percentage distribution and inter-element relations were computed. Statistical analysis of these data showed a definite pattern of variation among certain elements in early and severe PD compared to controls. In both early and severe PD serum, Al and S concentrations were significantly decreased (p<0.05) compared to the controls. Fe (p<0.01) and Zn (p<0.05) concentrations were significantly lower in severe PD, while K, Mg, Cu (p < 0.01) and P (p < 0.05) concentrations were higher in early and severe PD compared to the controls. The data revealed an imbalance in the inter-element relations in both early and severe PD serum compared to controls, as shown by the direct and inverse correlations. These results suggest a disturbance in the element homeostasis during the progression of PD.

Acute Disease↗
PubMed2005

Laser ablation ICP-MS profiling and semiquantitative determination of trace element concentrations in desert tortoise shells: documenting the uptake of elemental toxicants.

The outer keratin layer (scute) of desert tortoise shells consists of incrementally grown laminae in which various bioaccumulated trace elements are sequestered during scute deposition. Laser ablation ICP-MS examination of laminae in scutes of dead tortoises revealed patterns of trace elemental distribution from which the chronology of elemental uptake can be inferred. These patterns may be of pathologic significance in the case of elemental toxicants such as arsenic, which has been linked to both shell and respiratory diseases. Laser ablation transects, performed along the lateral surfaces of sectioned scutes, offered the most successful means of avoiding exogenous contamination that was present on the scute exterior. Semiquantitative determination of elemental concentrations was achieved using sulfur, a keratin matrix element, as an internal standard. The results presented here highlight the potential of laser ablation ICP-MS as a diagnostic tool for investigating toxic element uptake as it pertains to tortoise morbidity and mortality.

Animals↗
PubMed2000

Finite element estimates of interface stress in the trans-tibial prosthesis using gap elements are different from those using automated contact.

When compared with automated contact methods of finite element (FE) analyses, gap elements have certain inherent disadvantages in simulating large slip of compliant materials on stiff surfaces. However, automated contact has found limited use in the biomechanical literature. A non-linear, three-dimensional, geometrically accurate, FE analysis of the trans-tibial limb-socket prosthetic system was used to compare an automated contact interface model with a gap element model, and to evaluate the sensitivity of automated contact to interfacial coefficient of friction (COF). Peak normal stresses and resultant shear stresses were higher in the gap element model than in the automated contact model, while the maximum axial slip was less. Under proximally directed load, compared with automated contact, gap elements predicted larger areas of stress concentration that were located more distally. Gap elements did not predict any relative slip at the distal end, and also transmitted a larger proportion of axial load as shear stress. Both models demonstrated non -linear sensitivity to COF, with larger variation at lower magnitudes of COF. By imposing physical connections between interface surfaces, gap elements distort the interface stress distributions under large slip. Automated contact methods offer an attractive alternative in applications such as prosthetic FE modeling, where the initial position of the limb in the socket is not known, where local geometric features have high design significance, and where large slip occurs under load.

Artificial Limbs↗
PubMed2001

Human placenta as a 'dual' biomarker for monitoring fetal and maternal environment with special reference to potentially toxic trace elements. Part 2: essential minor, trace and other (non-essential) elements in human placenta.

A survey of elemental composition of the human placenta was undertaken to evaluate reference values for minor and trace elements (essential and non-essential). The new data collection was narrowed down to results generated between the period of 1975-2000, since analytical methodology was becoming increasingly reliable with time for many elements. The search revealed the following results (microg/g, based on wet weight): Ca = 770; Cl = 1900; K = 1685; Mg = 100; Na = 360; P = 1700; and S = 350. However, Na, P and S need further confirmation. For a group of essential trace elements following average values were evaluated (microg/g, based on wet weight): Co = 0.007; Cr = 0.03; Cu = 0.9; Fe = 69; I = 0.005; Mn = 0.08; Mo = 0.02; Se = 0.2; and Zn = 10. However, the iodine value needs further confirmation. In addition, information values have been identified for a number of so-called non-essential elements such as Ag, Au, B, Ba, Br, Cs, F, La, Rb, Sb, Sc, Si, Sn, Sr, Ti, V and W. The survey results for toxic trace elements As, Cd, Hg, Ni and Pb are discussed in part 3 of this paper along with placenta as a biomonitor for toxic trace elements.

Adult↗