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At least 1,135 records · Page 63Linked to original sources
PubMed2000

Cloning and functional characterization of the 5'-regulatory region of the human CD86 gene.

The induction of CD86 expression by IFN-gamma on the surface of various antigen presenting cells has been previously reported. In order to understand the mechanisms by which the expression of the CD86 gene is regulated by IFN-gamma at the transcriptional level, we have cloned and characterized the 5'-flanking region of the human CD86 gene. To functionally analyze the upstream regulatory region of the CD86 gene, a series of luciferase reporter gene constructs were prepared and used for transfection of cells from the monocytic line U937 and Raji B cell line. Under basal conditions, functional activity of these constructs was detected in Raji cells, which show high constitutive expression of the CD86 molecule, but not in U937 cells, which show low expression of CD86 in non-activated state. Induction of CD86 expression by stimulation of U937 cells with IFN-gamma revealed the presence of two functional GAS (gamma-interferon activation site) elements. Gel mobility shift assays showed that these two GAS elements specifically bind an IFN-gamma-induced transcriptional complex. The DNA-protein complex was supershifted by antibody to Stat1 alpha (signal transducer and activator of transcription), but not by antibodies to Stat 2, Stat 3 and Sp1, indicating that GAS elements interact with Stat1 alpha. Point mutations in the GAS elements prevented the formation of DNA-protein complex and significantly reduced the responsiveness of the reporter gene to IFN-gamma. These findings suggest that two functional GAS elements within the human CD86 promoter play an important role in the induction of CD86 gene by binding to IFN-gamma-induced Stat1 alpha.

Antigens, CD↗
PubMed2003

Somatic mobility of the maize element Ac and its utility for gene tagging in aspen.

We have investigated the somatic activity of the maize Activator (Ac) element in aspen with the objective of developing an efficient transposon-based system for gene isolation in a model tree species. The analysis of the new insertion sites revealed the exact reconstitution of the Ac, however, aberrant transposition events were also found. Characterization of the genomic sequences flanking the Ac insertions showed that about one third (22/75) of the sequences were significantly similar to sequences represented in public databases and might correspond to genes. The frequency of Ac landing into coding regions was about two-fold higher when compared to the frequency of T-DNA hitting the predicted genes (5/32) in the aspen genome. Thus, Ac is demonstrated to be a potentially useful heterologous transposon tag in a tree species. This is the first report on transposon-based gene tagging in a tree species describing the excision and reinsertion of transposable element into new genomic positions. We also suggest a heterologous transposon tagging strategy that can be used in aspen somatic cells to obtain dominant gain-of-function mutants and recessive loss-of-function mutants overcoming the regeneration time barrier of a long-lived tree species.

Base Sequence↗
PubMed2000

Identification of two regulatory elements within the high mobility group box transcription factor XTCF-4.

Some members of the Wnt family of extracellular glycoproteins regulate target gene expression by inducing stabilization and nuclear accumulation of beta-catenin, which functions as a transcriptional activator after binding to transcription factors of the T-cell factor/lymphoid enhancer factor (TCF/LEF) family. Three different members of this family have been identified in Xenopus laevis thus far that differ in their ability to influence mesodermal differentiation and to activate expression of the Wnt target gene fibronectin. Here we report on the isolation and characterization of additional variants of XTCF-4. We show that the differential ability of these proteins and other members of the TCF family to activate target genes is neither due to preferential interaction with transcriptional cofactors of the groucho family or SMAD4 nor to different DNA binding affinities. Expression of these proteins in an epithelial cell line reveals differences in their ability to form a ternary complex with DNA and beta-catenin. Interestingly, formation of this ternary complex was not sufficient to activate target gene expression as previously thought. Our experiments identify two amino acid sequence motifs, LVPQ and SFLSS, in the central domain of XTCF-4 that regulate the formation of the DNA-TCF-beta-catenin complex or activation of target genes, respectively. Biochemical studies reveal that the phosphorylation state of these XTCF-4 variants correlates with their ability to form a ternary complex with beta-catenin and DNA but not to activate target gene expression. The described variants of XTFC-4 with their different properties in complex formation provide strong evidence that in addition to the regulation of beta-catenin stability the isoforms of TCF/LEF transcription factors and their posttranslational modifications define the cellular response of a Wnt/wingless signal.

Amino Acid Sequence↗
PubMed2001

The influence of biosolids treatment files on the mobility of metal trace elements.

The production of sludge in France is estimated to be about 900,000 metric tons dry matter per year and 60% of this is recycled onto agricultural land. At present, the long term future of this procedure is open to question and among the different arguments being put forward are the levels of metallic trace elements and the risk of accumulation in soils. This study presents the behaviour of metallic trace elements in sludges from three different treatment procedures: thickened liquid sludges, dewatered sludges and dried sludges. These biosolids are mixed with a clay soil and then placed in a temperature and humidity controlled glasshouse. Several containers are seeded with ryegrass and compared with controls. For the three harvests, covering all the amendments studied (including non-amended soil), the differences are not really representative. Absorption by the ryegrass is low in all cases. For the cadmium, the chromium, the nickel and the lead, the roots are 5 to 10 times more concentrated than the leaves. The majority of these elements stay absorbed in the roots, regardless of the amendment used. The addition of the sludges has considerably reduced the uptake of water in ryegrass throughout its growth cycle. Quite apart from their fertilizing qualities, wastewater treatment plant sludges could offer important implications for irrigation.

Absorption↗
PubMed2005

[Alu family and its biological significance].

The Alu family of short (approximately 300bp)interspersed elements (SINEs) is one of the most successful mobile genetic elements, having arisen to a copy number in excess of 500,000 within primate genomes in the last 65 million years. The proliferation of these elements had a significant impact on the architecture of primate genomes. Now the functions of Alu elements are still unclear. It is speculated that Alu elements are involved in aspects of gene regulation, e.g. gene rearrangement, CpG methylation, alternative splicing of hnRNA, binding sites of transcription factors and hormone receptors, etc. At the same time, Alu family is an important research method in human population genetics, forensic, oncology, etc. Additionally, Alu insertion, deletion and recombination led to many ancestor genetic diseases and cancers.

Alu Elements↗
PubMed1982

Mobile dispersed repeated DNA elements in the Drosophila genome.

The molecular and cytogenetic organizations of 19 nonhomologous dispersed repeated sequence families were studied in 15 different laboratory strains of Drosophila melanogaster. Elements from each of the families appear to undergo transposition within the Drosophila genome, because there were striking differences in both the number and chromosomal locations of these elements between strains. A significant fraction (greater than 1%) of Drosophila DNA therefore has an unstable genomic organization. Each middle repetitive family exhibited similar variations in the chromosomal distribution of elements between the strains. Although the movements of these elements are not limited to a small number of genomic sites, there are chromosomal regions where elements from the different dispersed repeated DNA families appear to be clustered. The locations of such preferred integration sites are different in each of the D. melanogaster strains examined.

Base Sequence↗
PubMed1990

Structural and functional characterization of tnpI, a recombinase locus in Tn21 and related beta-lactamase transposons.

A novel discrete mobile DNA element from Tn21 from the plasmid R100.1 is described, and its mobilization function was confirmed experimentally. In addition, the element behaves as a recombinase-active locus (tnpI) which facilitates insertions of antibiotic resistance genes as modules or cassettes at defined hot spots or integration sites. A similar tnpI sequence was detected by DNA hybridization in a series of beta-lactamase transposons and plasmids and localized on their physical maps. The genetic function of the locus cloned from Tn21 into pACYC184 was tested for conduction and integration into the plasmids R388 and pOX38Km, and the results suggested recombinase-integrase activity and recA independence. DNA sequence analysis of the tnpI locus revealed no inverted or direct terminal repeats or transposition features of class I and class II transposons. The coding capacity revealed three putative open reading frames encoding 131, 134, and 337 amino acids. Orf3 encoded a putative polypeptide product of 337 amino acids that shared highly significant identity with the carboxyl region of integrase proteins. A comparison and an alignment of the tnpI locus from Tn21 and its flanking sequences identified similar sequences in plasmids and in transposons. The alignment revealed discrete nucleotide changes in these tnpI-like loci and a conserved 3' and 5' GTTA/G hot spot as a duplicated target site. Our data confirm the remarkable ubiquity of tnpI associated with antibiotic resistance genes. We present a model of transposon modular evolution into more complex multiresistant units via tnpI and site-specific insertions, deletions, and DNA rearrangements at this locus.

Amino Acid Sequence↗
PubMed1997

The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression.

The goal of the fungal mitochondrial genome project (FMGP) is to sequence complete mitochondrial genomes for a representative sample of the major fungal lineages; to analyze the genome structure, gene content, and conserved sequence elements of these sequences; and to study the evolution of gene expression in fungal mitochondria. By using our new sequence data for evolutionary studies, we were able to construct phylogenetic trees that provide further solid evidence that animals and fungi share a common ancestor to the exclusion of chlorophytes and protists. With a database comprising multiple mitochondrial gene sequences, the level of support for our mitochondrial phylogenies is unprecedented, in comparison to trees inferred with nuclear ribosomal RNA sequences. We also found several new molecular features in the mitochondrial genomes of lower fungi, including: (1) tRNA editing, which is the same type as that found in the mitochondria of the amoeboid protozoan Acanthamoeba castellanii; (2) two novel types of putative mobile DNA elements, one encoding a site-specific endonuclease that confers mobility on the element, and the other constituting a class of highly compact, structured elements; and (3) a large number of introns, which provide insights into intron origins and evolution. Here, we present an overview of these results, and discuss examples of the diversity of structures found in the fungal mitochondrial genome.

Base Sequence↗
PubMed2003

IS Rm31, a new insertion sequence of the IS 66 family in Sinorhizobium meliloti.

Sinorhizobium meliloti natural populations show a high level of genetic polymorphism possibly due to the presence of mobile genetic elements such as insertion sequences (IS), transposons, and bacterial mobile introns. The analysis of the DNA sequence polymorphism of the nod region of S. meliloti p SymA megaplasmid in an Italian isolate led to the discovery of a new insertion sequence, IS Rm31. IS Rm31 is 2,803 bp long and has 22-bp-long terminal inverted repeat sequences, 8-bp direct repeat sequences generated by transposition, and three ORFs (A, B, C) coding for proteins of 124, 115, and 541 amino acids, respectively. ORF A and ORF C are significantly similar to members of the transposase family. Amino acid and nucleotide sequences indicate that IS Rm31 is a member of the IS 66 family. IS Rm31 sequences were found in 30.5% of the Italian strains analyzed, and were also present in several collection strains of the Rhizobiaceae family, including S. meliloti strain 1021. Alignment of targets sites in the genome of strains carrying IS Rm31 suggested that IS Rm31 inserts randomly into S. meliloti genomes. Moreover, analysis of IS Rm31 insertion sites revealed DNA sequences not present in the recently sequenced S. meliloti strain 1021 genome. In fact, IS Rm31 was in some cases linked to DNA fragments homologous to sequences found in other rhizobia species.

Base Composition↗
PubMed2003

Diverse sequences within Tlr elements target programmed DNA elimination in Tetrahymena thermophila.

Tlr elements are a novel family of approximately 30 putative mobile genetic elements that are confined to the germ line micronuclear genome in Tetrahymena thermophila. Thousands of diverse germ line-limited sequences, including the Tlr elements, are specifically eliminated from the differentiating somatic macronucleus. Macronucleus-retained sequences flanking deleted regions are known to contain cis-acting signals that delineate elimination boundaries. It is unclear whether sequences within deleted DNA also play a regulatory role in the elimination process. In the current study, an in vivo DNA rearrangement assay was used to identify internal sequences required in cis for the elimination of Tlr elements. Multiple, nonoverlapping regions from the approximately 23-kb Tlr elements were independently sufficient to stimulate developmentally regulated DNA elimination when placed within the context of flanking sequences from the most thoroughly characterized family member, Tlr1. Replacement of element DNA with macronuclear or foreign DNA abolished elimination activity. Thus, diverse sequences dispersed throughout Tlr DNA contain cis-acting signals that target these elements for programmed elimination. Surprisingly, Tlr DNA was also efficiently deleted when Tlr1 flanking sequences were replaced with DNA from a region of the genome that is not normally associated with rearrangement, suggesting that specific flanking sequences are not required for the elimination of Tlr element DNA.

Animals↗
PubMed2004

Contrasting mammalian parathyroid hormone (PTH) promoters: nuclear factor-Y binds to a deoxyribonucleic acid element unique to the human PTH promoter and acts as a transcriptional enhancer.

The identification of a highly conserved specificity protein 1 (Sp1) DNA element in mammalian PTH promoters was recently reported. However, the presence of a novel DNA-binding complex was subsequently observed exclusively with the human PTH (hPTH) Sp1 element in mobility shift studies. Point mutations in the hPTH Sp1 element revealed the factor recognized a CAAT-like sequence resulting from a single nucleotide difference unique to the human sequence relative to other mammalian promoters. A consensus nuclear factor Y (NF-Y) element was able to specifically compete for formation of the novel complex, whereas antiserum directed against the B-subunit of NF-Y supershifted the complex without disturbing binding by the Sp3/Sp1 proteins. Moreover, immunocytochemistry confirmed the nuclear localization of NF-Y in parathyroid gland cells. Transient expression of a dominant negative form of NF-Y impaired basal hPTH promoter activity in opossum kidney cells. Studies in Drosophila SL2 cells revealed that an intact NF-Y complex was required to strongly activate transcription from the hPTH promoter, and mutational analysis confirmed the identity of the NF-Y and Sp1 DNA elements. Finally, coexpression studies in SL2 cells indicated that NF-Y and Sp1 competed for binding to their adjoining sites in the hPTH promoter. In summary, an NF-Y enhancer DNA element has been identified that is uniquely positioned in the hPTH promoter and partially overlaps with the species-conserved Sp1 element. Binding appears to be mutually exclusive by the two transcription factors to this site and suggests that separate signaling pathways may be using this DNA locus to enhance transcription of the hPTH gene.

Animals↗
PubMed1995

U.S. screening mammography services with mobile units: results from the National Survey of Mammography Facilities.

PURPOSE: To investigate elements of mobile facilities for mammography in the United States. MATERIALS AND METHODS: The prevalence and performance of mobile facilities for mammography in the United States were studied with regard to cost, price, quality assurance, and access. Data were acquired from the National Cancer Institute's National Survey of Mammography Facilities, conducted in 1992. RESULTS: Of the 1,057 facilities surveyed, 2.4% were identified as mobile and accounted for 3% of mammography examinations performed. All mobile facilities reported accreditation by the American College of Radiology, and 92% were in Statistically Metropolitan Areas. Most were affiliated with community hospitals or private radiology practice and were more likely to be associated with lower fees, convenient operating hours, batch interpretation, and computerized reporting than were their stationary counterparts. CONCLUSION: Mobile mammography facilities compare favorably with stationary facilities. The use of these mobile units in the United States, however, has been limited.

Accreditation↗
PubMed2000

Double-hairpin elements in the mitochondrial DNA of allomyces: evidence for mobility.

The mitochondrial DNA (mtDNA) of the chytridiomycete fungus Allomyces macrogynus contains 81 G+C-rich sequence elements that are 26-79 bases long and can be folded into a unique secondary structure consisting of two stem-loops. At the primary sequence level, the conservation of these double-hairpin elements (DHEs) is variable, ranging from marginal to complete identity. Forty of these DHEs are inserted in intergenic regions, 35 in introns, and 6 in variable regions of rRNA genes. Ten DHEs are inserted into other DHE elements (twins); two even form triplets. A comparison of DHE sequences shows that loop regions contain more sequence variation than helical regions and that the latter often contain compensatory base changes. This suggests a functional importance of the DHE secondary structure. We further identified nine DHEs in a 4-kb region of Allomyces arbusculus, a close relative of A. macrogynus. Eight of these DHEs are highly similar in sequence (90%-100%) to those in A. macrogynus, but only five are inserted at the same positions as in A. macrogynus. Interestingly, DHEs are also found in the mtDNAs of other chytridiomycetes, as well as certain zygomycete and ascomycete fungi. The overall distribution pattern of DHEs in fungal mtDNAs suggests that they are mobile elements.

Base Sequence↗
PubMed2003

Structure and expression of mobile ETnII retroelements and their coding-competent MusD relatives in the mouse.

ETnII elements are mobile members of the repetitive early transposon family of mouse long terminal repeat (LTR) retroelements and have caused a number of mutations by inserting into genes. ETnII sequences lack retroviral genes, but the recent discovery of related MusD retroviral elements with regions similar to gag, pro, and pol suggests that MusD provides the proteins necessary for ETnII transposition in trans. For this study, we analyzed all ETnII elements in the draft sequence of the C57BL/6J genome and classified them into three subtypes (alpha, beta, and gamma) based on structural differences. We then used database searches and quantitative real-time PCR to determine the copy number and expression of ETnII and MusD elements in various mouse strains. In 7.5-day-old embryos of a mouse strain in which two mutations due to ETnII-beta insertions have been identified (SELH/Bc), we detected a three- to sixfold higher level of ETnII-beta and MusD transcripts than in control strains (C57BL/6J and LM/Bc). The increased ETnII transcription level can in part be attributed to a higher number of ETnII-beta elements, but 70% of the MusD transcripts appear to have been derived from one or a few MusD elements that are not detectable in C57BL/6J mice. This element belongs to a young MusD subgroup with intact open reading frames and identical LTRs, suggesting that the overexpressed element(s) in SELH/Bc mice might provide the proteins for the retrotransposition of ETnII and MusD elements. We also show that ETnII is expressed up to 30-fold more than MusD, which could explain why only ETnII, but not MusD, elements have been positively identified as new insertions.

Animals↗