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PubMed1997

Localization of silencer and enhancer elements in the human type X collagen gene.

Collagen type X is a short, network-forming collagen expressed temporally and spatially tightly controlled in hypertrophic chondrocytes during endochondral ossification. Studies on chicken chondrocytes indicate that the regulation of type X collagen gene expression is regulated at the transcriptional level. In this study, we have analyzed the regulatory elements of the human type X collagen (Col10a1) by reporter gene constructs and transient transfections in chondrogenic and nonchondrogenic cells. Four different promoter fragments covering up to 2,864 bp of 5'-flanking sequences, either including or lacking the first intron, were linked to luciferase reporter gene and transfected into 3T3 fibroblasts, HT1080 fibrosarcoma cells, prehypertrophic chondrocytes from the resting zone, hypertrophic chondrocytes, and chondrogenic cell lines. The results indicated the presence of three regulatory elements in the human Col10a1 gene besides the proximal promoter. First, a negative regulatory element located between 2.4 and 2.8 kb upstream of the transcription initiation site was active in all nonchondrogenic cells and in prehypertrophic chondrocytes. Second, a positive, but also non-tissue-specific positive regulatory element was present in the first intron. Third, a cell-type-specific enhancer element active only in hypertrophic chondrocytes was located between -2.4 and -0.9 kb confirming a previous report by Thomas et al. [(1995): Gene 160:291-296]. The enhancing effect, however, was observed only when calcium phosphate was either used for transfection or included in the culture medium after lipofection. These findings demonstrate that the rigid control of human Col10a1 gene expression is achieved by both positive and negative regulatory elements in the gene and provide the basis for the identification of factors binding to those elements.

Animals↗
PubMed1994

Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster.

A combination of cytogenetic and molecular analyses has shown that several different transposable elements are involved in the restructuring of Drosophila chromosomes. Two kinds of elements, P and hobo, are especially prone to induce chromosome rearrangements. The mechanistic details of this process are unclear, but, at least some of the time, it seems to involve ectopic recombination between elements inserted at different chromosomal sites; the available data suggest that these ectopic recombination events are much more likely to occur between elements in the same chromosome than between elements in different chromosomes. Other Drosophila transposons also appear to mediate chromosome restructuring by ectopic recombination; these include the retrotransposons BEL, roo, Doc and I and the foldback element FB. In addition, two retrotransposons, HeT-A and TART, have been found to be associated specifically with the ends of Drosophila chromosomes. Very limited data indicate that transposon-mediated chromosome restructuring is occurring in natural populations of Drosophila. This suggests that transposable elements may help to shape the structure of the Drosophila genome and implies that they may have a similar role in other organisms.

Animals↗
PubMed1988

A cis-acting element and associated binding factor required for CNS expression of the Drosophila melanogaster dopa decarboxylase gene.

A cis-acting sequence from the Drosophila melanogaster dopa decarboxylase (Ddc) gene is selectively required for Ddc expression in the central nervous system. We analyze several parameters influencing the function of the sequence element and describe a factor which interacts with it and mediates CNS expression of Ddc. The element, element I, can function in vivo when included on a synthetic oligonucleotide inserted near its normal location, or closer to the RNA startpoint. It displays partial activity when inverted. Two different 2-bp mutations in element I abolish its ability to stimulate neuronal Ddc expression in the CNS. A factor present in embryonic nuclear extracts specifically protects element I in DNase I footprinting assays. The binding affinity of this factor is reduced by each alteration of element I that inhibits neuronal expression, indicating a role in mediating CNS expression of Ddc. Element I alone has no detectable activity when placed adjacent to a heterologous promoter, although 2.2 kb of 5' Ddc sequences direct correct cell-specific expression of a heterologous promoter.

Animals↗
PubMed1996

The heme-responsive element of the mouse heme oxygenase-1 gene is an extended AP-1 binding site that resembles the recognition sequences for MAF and NF-E2 transcription factors.

Jun and Fos (AP-1) transcription factors were recently proposed to mediate induction of the mouse heme oxygenase-1 gene by different agents including heme and cadmium. In this report we show that the AP-1 binding sequence, TGAGTCA, is necessary but insufficient for gene activation in response to heme or cadmium. The minimal heme response element was identified as an extended AP-1 binding site, (T/C)GCTGAGTCA. In addition to the AP-1 heptad, this element also contains an interdigitated antioxidant response element, GCnnnGTCA. Specific antioxidant response elements from the NAD(P)H:quinone oxidoreductase-1 and the glutathione S-transferase Ya subunit genes were in fact responsive to heme but not all sequences that conform to the consensus antioxidant response element were activated by this agent. The heme response element resembles the consensus binding sites for the product of the maf oncogene and for the transcription factor NF-E2. The potential role of these and related transcription factors and the implication of the composite heme response element in heme oxygenase-1 gene regulation are discussed.

Animals↗
PubMed1999

The 5'-flanking sequence and regulatory elements of the cystatin S gene.

The gene encoding rat cystatin S (Cys S), a salivary gland-specific secretory protein, has CAAT and TATA boxes upstream of the inititation codon (Cox and Shaw, 1992), and contains regions that resemble those of other hormonally responsive eukaryotic genes. The 5'-flanking sequence of the rat Cys S gene has a potential CREB/AP-1 binding site (Rupp et al., 1990; Trejo et al., 1992), two potential glucocorticoid responsive elements (GREs, Drouin et al., 1989), and a possible GR/PR (glucocorticoid/progesterone) responsive element (Forman and Samuels, 1990). One of these potential GREs is adjacent to a potential AP-2 binding site, and another is typical of the glucocorticoid and progesterone receptor binding site. In this report, we have identified three regions in the 5'-flanking region of the Cys S gene that are found in salivary gland-specific genes (Ting et al., 1992) with a GT-rich region located between conserved elements II and III. Transfection experiments described in this paper suggest that a 281-bp DNA fragment from the Cys S gene promoter region with conserved elements II and III, the GT-rich region, and a possible GR/PR responsive element contains a negative regulatory element. In addition, our experiments suggest that the GT-rich region by itself is acting as a positive regulatory element.

Animals↗
PubMed1999

Identification of a mineralocorticoid/glucocorticoid response element in the human Na/K ATPase alpha1 gene promoter.

Sodium-potassium ATPase (Na/K ATPase) is a major target of mineralocorticoids. Both aldosterone and glucocorticoids activate the human Na/K ATPase alpha1 and beta1 genes transcriptionally. The mineralocorticoid receptor (MR) and the glucocorticoid receptor (GR) have been shown to bind the glucocorticoid response element (GRE); however, a specific element responsible for the activation of the MR is not known. Sequence analysis of the putative regulatory region of the Na/K ATPase alpha1 gene revealed the presence of a hormone response element that allows the MR to interact with it, at least as well as if not better than the GR. This response element is designated MRE/GRE. In this investigation, we demonstrated the MR and GR induced gene expression in COS-1 cells by cotransfecting with respective expression plasmids (RshMR and RshGR) along with a luciferase reporter. The synthetic MRE/GRE linked to a neutral promoter was activated by MR (6-fold); however, the GR induced a lower level of expression (3.8-fold), suggesting that the element may be preferably MR responsive. Mutations in the synthetic MRE/GRE could not induce the expression with MR, whereas GR had a small effect. Electrophoretic mobility shift analyses demonstrated a direct interaction of MR and GR with the MRE/GRE that was supershifted by an antiMR antibody and the complex was partially cleared by an antiGR antibody, respectively, whereas nonimmune serum had no effect. Footprinting analyses of the promoter region showed that a portion of the DNA containing this element is protected by recombinant MR and GR. Thus these data confirm that this MRE/GRE interacts with both MR and GR but interaction with receptors may be more MR-responsive than response elements previously described.

Adrenal Cortex Hormones↗
PubMed1993

Functional dissection of two promoters that control sense and antisense transcription of Drosophila melanogaster F elements.

Drosophila melanogaster F elements are members of the super-family of LINEs, mobile repeated DNA sequences that lack LTRs and propagate by the reverse transcription of unit-length RNA intermediates. The F 5' end region harbours two promoters (F(in) and F(out)) that transcribe in a convergent manner. Each promoter has been functionally dissected by assaying in D. melanogaster cultured cells templates carrying base substitutions and/or deletions across the +1 to +245 region of the element F12. F(in), that likely controls the synthesis of gene products and transposition intermediates, is internal to the transcribed region. Two elements play a major role in F-sense transcription. The proximal element spans the interval +6 to +14 and includes a major RNA start site. Heterologous DNA featuring a nearly identical purine-pyrimidine sequence can functionally replace the initiator-like module only when properly spaced from downstream F sequences. The distal element is within the interval +18 to +46 and may correspond to a motif (AGACGTTT, +34 to +41) conserved in other Drosophila LINEs. F(out) is a TATA-less promoter that directs transcription predominantly from three nearby sites (a to c). F(out) expression is influenced by multiple elements located upstream of residue -68 relative to site a as +1 within a region (alpha) shown to stimulate the D. melanogaster hsp70 promoter in an orientation and position-independent fashion. Changes within the -43 to +24 interval may suppress or stimulate transcription from sites a and c. Initiation from a site approximately 30 nucleotides upstream of site a is enhanced by alterations of the interval -43 to -5. The expression of the two F promoters, determined by the interaction of the transcriptional machinery with distinct DNA sequences, is influenced by a common element within the alpha region.

Animals↗
PubMed1997

Multiple downstream promoter modules regulate the transcription of the Drosophila melanogaster I, Doc and F elements.

The basal promoters of three Drosophila long interspersed nuclear elements (LINEs), the I factor and the F and Doc elements, have the same architecture. In each, transcription is directed by an initiator which is faithfully and efficiently recognized only when flanked 3' by a DNA segment approximately 20 bp in length called the B region. The B regions of the three promoters are interchangeable and have a complex structure, comprising three functionally distinct elements: de1, de2 and de3. While de2 is relatively conserved, fitting the consensus RGACGTGY, de1 and de3 vary among the three promoters. At different levels, each downstream element is able to ensure accurate recognition of the initiator. The de2 domain stimulates transcription of the F, I and Doc promoters to the same extent. In contrast, the I de1 domain stimulates transcription much more efficiently than the corresponding domains of the F and Doc elements. The finding that de2 is selectively required in order to detect full activity of enhancer sequences found in the F element suggests that de1 and de2 interact with different proteins. The B regions can be replaced by and synergize with a TATA element, can functionally substitute for downstream promoter sequences in the Drosophila hsp70 gene, and significantly activate the mouse terminal deoxynucleotidyl transferase initiator. Our data suggest that the B regions stimulate transcription by providing sites of interaction for the TFIID complex. Sequences homologous to the del to de3 array are found downstream from the transcription start site(s) both in TATA-less and TATA-containing promoters.

Animals↗
PubMed1994

IS1237, a repetitive chromosomal element from Clavibacter xyli subsp. cynodontis, is related to insertion sequences from gram-negative and gram-positive bacteria.

We describe here a repetitive chromosomal element, which appears to be an insertion sequence, isolated from Clavibacter xyli subsp. cynodontis, a gram-positive plant-associated bacterium. The element, IS1237, is 905 bp in size, is bounded by 19-bp perfect inverted repeats and 3-bp direct repeats, and appears at least 16 times in the genome. It contains three open reading frames which show similarity to open reading frames from various other insertion sequences. We have found that there are two groups of related mobile elements: one in which two open reading frames are read separately and the other in which these two open reading frames are fused together to give one predicted protein product. Using one of these open reading frames to search amino acid sequence databases, we found two instances in which similar reading frames flank genes carried on plasmids. We believe therefore that these plasmid-borne genes may be parts of previously unidentified mobile elements. For IS1237, a frameshift in two of the open reading frames and a stop codon in the third may indicate that this particular copy of the element is no longer active in transposition. The similarity of IS1237 to other elements from both gram-negative and gram-positive bacteria provides further evidence that mobile elements have been transferred between these two bacterial groups.

Actinomycetales↗
PubMed2000

A novel IS-like element frequently inserted in a putative virulence regulator in bovine mastitis isolates of Streptococcus dysgalactiae.

Streptococcus dysgalactiae, a Lancefield group C streptococcus, is commonly isolated from bovine mastitis. We recently identified a putative regulon in two S. dysgalactiae strains, 8215 and Epi9, consisting of two consecutive genes, dmg and dem, coding for a possible regulatory protein and an M-like protein with fibrinogen- and IgG-binding-properties, respectively. During these studies a short sequence homologous to an IS element was found to be inserted in the dmg gene of strain 8215. The present investigation describes the complete sequence of this IS-like element, named ISSdy1, which consists of 1218 bp and contains two ORFs, flanked by imperfect repeats. The nucleotide sequence of the IS-like element shows 82% identity to the previously reported sequence of IS199 from Streptococcus mutans V403. The deduced amino acid sequences of the ORFs also revealed high homology to transposases from IS elements in Enterococcus faecium, Escherichia coli, and Shigella dysenteriae, all belonging to the IS3 family. We studied the distribution of ISSdy1 in 57 S. dysgalactiae isolates using PCR analysis with specific primers derived from the IS element. Ninety-eight percent of the isolates contained the ISSdy1 element. Surprisingly, in the majority of studied strains a copy of the IS-like element was found to be inserted in the dmg gene, a putative virulence regulator.

Amino Acid Sequence↗
PubMed1993

Acrylamide disrupts elemental composition and water content of rat tibial nerve. III. Recovery.

We have previously demonstrated that subacute and subchronic acrylamide (ACR) intoxication are associated with a loss of subcellular elemental regulation in myelinated axons and Schwann cells of rat tibial nerve (LoPachin et al., Toxicol. Appl. Pharmacol. 115, 21-34, 1992; LoPachin et al., Toxicol. Appl. Pharmacol. 115, 35-43, 1992). In the present study, rats were allowed to recover partially from subchronic oral ACR intoxication (2.8 mM in drinking water for approximately 30 days). Elemental composition and water content of tibial nerve myelinated axons and Schwann cells were measured by electron probe X-ray microanalysis. Results show that K and Cl concentrations in larger tibial nerve axons were shifted toward normal values or above. For the most part, small axons also exhibited elemental changes that reflected recovery from ACR intoxication. Mitochondria displayed elemental changes that were similar to corresponding axoplasm. Schwann cells in tibial nerve of recovering animals had altered Na, P, Cl, K, and Mg concentrations that were similar in magnitude and extent to those occurring during ACR intoxication. In contrast, myelin displayed few changes. These results suggest that the recovery process following ACR intoxication is associated with characteristic changes in subaxonal elemental composition that might be related to repair mechanisms. That recovery-related elemental changes differ from those associated with intoxication provides additional support for the hypothesis (LoPachin et al., Toxicol. Appl. Pharmacol. 115, 21-34, 1992) that perturbation of elemental regulation is a specific component of ACR neurotoxicity. The observation of persistent Schwann cell disruption during recovery might reflect either long-term secondary consequences or delayed recovery from direct injury. Further studies are necessary to resolve this issue.

Acrylamide↗
PubMed1994

Disruption of the murine p53 gene by insertion of an endogenous retrovirus-like element (ETn) in a cell line from radiation-induced osteosarcoma.

The mammalian genome harbors a large number of endogenous retroviruses and retrovirus-like elements. Increasing evidence is found that such elements can be activated and act as insertional mutagens. The activation of endogenous retroviral elements can be induced by a variety of environmental factors including irradiation. We have observed the insertion of a murine endogenous retrovirus-like ETn element into intro 4 of the p53 gene in an osteosarcoma cell line derived from a radiation-induced osteosarcoma. The insertion resulted in a p53-ETn-p53 fusion mRNA, a novel form of p53 mutation. This is the first report on insertion of an endogenous retroviral element into the p53 tumor suppressor gene. The data suggest that activated endogenous retroviruses and retrovirus-like elements might pose an enhanced risk for individuals exposed to noxae, which activate endogenous retroviral elements.

Animals↗
PubMed1996

A 68 bp element of the beta-phaseolin promoter functions as a seed-specific enhancer.

In beans, expression of the beta-phaseolin gene (phas), encoding the major seed storage protein of bean (Phaseolus vulgaris) is confined to the cotyledons of developing embryos. Phaseolin has not been detected in the endosperm, which remains liquid and is lost early in development. However, fusion constructs between the phas promoter and the gus-coding region yield expression in both embryo and endosperm of developing seeds from transgenic tobacco (Nicotiana tabacum) plants. Although elements extending 1470 bp upstream of the transcription start site are known to modulate phas expression, the proximal 295 bp (p295) are sufficient to drive high levels of seed-specific GUS activity. This region was dissected into three elements: a 68 bp element (seed specific enhancer, SSE: -295 to -227), a middle region (-227 to -109) and a basal phas promoter (-109 to +20: p109). Different promoter constructs containing the SSE or middle region upstream of p109 or a CaMV 35S basal promoter (-64 to +6) were fused to gus. Each construct was expressed in seed, but not in vegetative tissues. Use of the various phas promoter regions yielded notable differences in relative GUS activity in embryo or endosperm. Addition of both the SSE and middle region resulted in higher activity than the sum of adding either element alone to p109, indicating synergistic interaction between these elements. Seeds from plants transformed with the proximal 227 bp of promoter (p227) showed embryo-specific GUS activity. In contrast, constructs containing two copies of the SSE element were preferentially expressed in the endosperm. These results illustrate the modular nature of the proximal phas promoter, where distinct elements contribute to high levels of expression in different parts of the seed.

Base Sequence↗
PubMed1996

Functional dissection of a napin gene promoter: identification of promoter elements required for embryo and endosperm-specific transcription.

The promoter region (-309 to +44) of the Brassica napus storage protein gene napA was studied in transgenic tobacco by successive 5' as well as internal deletions fused to the reporter gene GUS (beta-glucuronidase). The expression in the two main tissues of the seed, the endosperm and the embryo, was shown to be differentially regulated. This tissue-specific regulation within the seed was found to affect the developmental expression during seed development. The region between -309 to -152, which has a large effect on quantitative expression, was shown to harbour four elements regulating embryo and one regulating endosperm expression. This region also displayed enhancer activity. Deletion of eight bp from position -152 to position -144 totally abolished the activity of the napA promoter. This deletion disrupted a cis element with similarity to an ABA-responsive element (ABRE) overlapping with an E-box, demonstrating its crucial importance for quantitative expression. An internal deletion of the region -133 to -120, resulted in increased activity in both leaves and endosperm and a decreased activity in the embryo. Within this region, a cis element similar to the (CA)n element, found in other storage protein promoters, was identified. This suggest that the (CA)n element is important for conferring seed specificity by serving both as an activator and a repressor element.

2S Albumins, Plant↗
PubMed1996

Pegasus, a small terminal inverted repeat transposable element found in the white gene of Anopheles gambiae.

Pegasus, a novel transposable element, was discovered as a length polymorphism in the white gene of Anopheles gambiae. Sequence analysis revealed that this 535 bp element was flanked by 8 bp target site duplications and 8 bp perfect terminal inverted repeats similar to those found in many members of the Tc1 family. Its small size and lack of long open reading frames preclude protein coding capacity. Southern analysis and in situ hybridization to polytene chromosomes demonstrated that Pegasus occurs in approximately 30 copies in the genomes of An. gambiae and its sibling species and is homogenous in structure but polymorphic in chromosomal location. Characterization of five additional elements by sequencing revealed nucleotide identities of 95% to 99%. Of 30 Pegasus-containing phage clones examined by PCR, only one contained an element exceeding 535 bp in length, due to the insertion of another transposable element-like sequence. Thus, the majority, if not all, extant Pegasus elements may be defective copies of a complete element whose contemporary existence in An. gambiae is uncertain. No Pegasus-hybridizing sequences were detected in nine other anophelines and three culicines examined, suggesting a very limited taxonomic distribution.

Animals↗
PubMed1990

Chromosomal rearrangements caused by the aberrant transposition of double Ds elements are formed by Ds and adjacent non-Ds sequences.

The Ds-induced unstable sh-m6258 allele is caused by the insertion of at least 45 kb of non-sh DNA. Genomic clones spanning the two junctions of sh sequences with insert sequences were isolated and analysed. The long insert in the sh-m6258 allele is bordered by Ds sequences on either side. A 3 kb double Ds structure which consists of one complete Ds element of approximately 2 kb and one half Ds element of approximately 1 kb was found in the sh-m6258 allele at the junction between the 3' region of the sh locus and the insert. At the junction between the 5' region of the sh locus and the insert a half Ds element is present. This truncated Ds element was probably left behind after the excision of a 2 kb Ds element from a 3 kb double Ds structure similar to that found at the 3' junction. Sequence analysis of the insert sequences beyond the Ds elements demonstrated that the long inserts in both the sh-m6258 and the sh-m5933 alleles originated from the same contiguous chromosomal segment in their common progenitor strain. One revertant derivative of the sh-m6258 allele was investigated. In the revertant strain, which displays a normal non-shrunken phenotype, a 2 kb Ds element is present at the site of the 45 kb insert in the mutant allele. This 2 kb insertion, which is located in the last but one intervening sequence of the Sh gene, does not inhibit expression of the gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed1993

Functional cis-element sequence requirements for suppression of gene expression by the TNPA protein of the Zea mays transposon En/Spm.

TNPA, one of the two transposition proteins encoded by the En/Spm transposable elements of Zea mays, suppresses the expression of genes that contain an appropriate cis element. Suppression can be monitored in tobacco protoplasts in a transient expression assay as follows. The plant promoter-driven expression of the Escherichia coli-glucuronidase (GUS)-encoding gene, uidA, is repressed in the presence of TNPA if the GUS gene contains a functional cis element in the untranslated RNA leader sequence. Earlier, we found that the minimal cis element is composed of two 12 bp sequences in a tail-to-tail inverted orientation. Each 12 bp sequence is sufficient to bind TNPA in vitro and can be thought of as a half-site in the cis element. Here, we investigated the sequence requirements of the minimal cis element. Our observations support our expectations that a functional cis element must provide a template to which two TNPA molecules can bind in the correct orientation. Sequences within the half-sites can be altered as long as the eight bases that make up the consensus binding sites are not changed. However, we found the following unexpected sequence specificities. Firstly, some changes to the consensus binding sequence can be tolerated in one half-site, as long as the other site matches the consensus. Secondly, although the region between the half-sites can vary in sequence and in length between two and four bases, a thymidine residue is not tolerated directly 5' preceding the second half-site.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1995

The transposable element impala, a fungal member of the Tc1-mariner superfamily.

A new transposable element has been isolated from an unstable niaD mutant of the fungus Fusarium oxysporum. This element, called impala, is 1280 nucleotides long and has inverted repeats of 27 bp. Impala inserts into a TA site and leaves behind a "foot-print" when it excises. The inserted element, impala-160, is cis-active, but is probably trans-defective owing to several stop codons and frameshifts. Similarities exist between the inverted repeats of impala and those of transposons belonging to the widely dispersed mariner and Tc1 families. Moreover, translation of the open reading frame revealed three regions showing high similarities with Tc1 from Caenorhabditis elegans and with the mariner element of Drosophila mauritiana. The overall comparison shows that impala occupies an intermediate position between the mariner and Tc1-like elements, suggesting that all these elements belong to the same superfamily. The degree of relatedness observed between these elements, described in different kingdoms, raises the question of their origin and evolution.

Amino Acid Sequence↗