SEARCH · PubMed Health

Results for “COPI complex”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,513 records · Page 84Linked to original sources

PubMed2002

Rst1 and Rst2 are required for the a/alpha diploid cell type in yeast.

In the budding yeast Saccharomyces cerevisiae, the preservation of the mating competent haploid (a or alpha) and the mating incompetent diploid (a/alpha) is necessary to prevent aneuploidy. Once haploid cells respond to pheromone, the mating-specific signal transduction pathway is activated, and the MAP kinase Fus3 phosphorylates two specific repressor proteins Rst1 and Rst2 (also known as Dig1 and Dig2) to promote Ste12-dependent transcription of mating-specific genes. In contrast, diploid cells cannot mate because genes that encode components of the mating pathway are repressed through the combined action of the Mata1-Matalpha2 and Matalpha2-Mcm1 repressors. Surprisingly, repression of Ste12 by Rst1 and Rst2 is essential for diploid sterility. Homozygous deletion of both RST1 and RST2 (rst-) causes a/alpha diploid cells constitutively to express a-specific genes and mate preferentially as a-cells. This phenotype is sensitive to Ste12 dosage, as removal of one copy of STE12 completely reduces the ectopic activation of a-specific genes. The Matalpha2-Mcm1 complex, which normally represses a-specific genes, is defective in rst- diploids because Matalpha2 is destabilized in rst- diploids, possibly as a consequence of its relocalization from the nucleus to the cytoplasm. This study finds that Rst1 and Rst2 are necessary for the a/alpha diploid cell type. Rst1 and Rst2 are required in order to prevent the amplification of a robust Ste12 transcriptional programme that appears to over-ride Matalpha2-dependent repression of haploid and a-specific genes.

Diploidy↗

PubMed2002

Mitochondrial diseases.

Mitochondrial disorders are caused by deficient respiratory chain function, resulting in a complex series of pathophysiological events. Genetic counselling is complicated because the respiratory chain subunits are encoded by both nuclear and mitochondrial DNA genes. Only a minority of the nuclear genes involved in mitochondrial function have been identified, and even fewer are associated with human mitochondrial disease. Mutations in mitochondrial DNA are particularly challenging because of the complexities of mitochondrial genetics: the mitochondrial DNA is strictly maternally inherited; there are 10(3)-10(4) copies of mitochondrial DNA in somatic cells; affected individuals often have a mixture of normal and mutated mitochondrial DNA (mitochondrial DNA heteroplasmy), the level of mutated mitochondrial DNA (the mitochondrial DNA mutation load) may vary widely between different maternally related individuals, between tissues and with time; a particular minimal threshold of mutated mitochondrial DNA is required to impair respiratory chain function; and there is not always a good correlation between mutant load and phenotype.

DNA, Mitochondrial↗

PubMed1990

Complete nucleotide sequence of an immunoglobulin heavy-chain gene and analysis of immunoglobulin gene organization in a primitive teleost species.

The immunoglobulin heavy-chain variable region (VH) locus in a phylogenetically primitive teleost (Elops saurus) has been characterized by a strategy that relied initially on cross-hybridization between genomic VH segments and a murine VH probe. Using a homologous (Elops) VH probe and DNA sequencing, this gene family has been shown to be complex and to contain overt pseudogenes. A homologous probe also has been used to isolate a full copy length cDNA containing constant (CH) as well as joining (JH) and VH regions. Genomic analyses using CH-, JH-, and VH-specific probes have demonstrated the presence of only a single hybridizing CH and several JH elements. JH-CH linkage is less than or equal to 3.6 kilobases (kb) and VH-CH linkage is less than or equal to 100 kb, as estimated by field-inversion gel electrophoresis. An additional VH family sharing less than 50% nucleotide identity with the prototype Elops VH sequence is described. Taken together, these results suggest that the immunoglobulin VH locus in a comparatively primitive teleost resembles the VH locus in mammals, but not that found in the more phylogenetically distant elasmobranchs. The evolutionary radiations of cartilaginous and bony fishes are associated with a dramatic change in the organization and, presumably, regulation of immunoglobulin genes. The origins of the modern VH gene locus can be traced to the primitive teleost fishes.

Amino Acid Sequence↗

PubMed1992

A 33-kDa polypeptide with homology to the laminin receptor: component of translation machinery.

A 33-kDa polypeptide (termed p40), which shares an antigenic determinant with a laminin receptor and is under translational control, is believed to serve as a precursor to the receptor and to be related to the neoplastic state. The present study of subcellular localization of this protein shows it to be a cytoplasmic component not associated with the plasma membrane. Most of the cellular p40 was found to be associated with polyribosomes as well as with 40S to 60S cytoplasmic particles. Conditions that lead to polysome disruption also caused release of the polysomal form of p40 as smaller particles, and polysome reconstitution was accompanied by uptake of p40 into these structures. Because of the large abundance of this protein in the cells (six to eight copies per ribosome), it is unlikely that it represents a factor that associates with the 40S preinitiation complex. The p40-containing particles appear to represent a newly discovered structure involved in the process of polysome formation.

Animals↗

PubMed1998

Differential transcriptional regulation of the human squalene synthase gene by sterol regulatory element-binding proteins (SREBP) 1a and 2 and involvement of 5' DNA sequence elements in the regulation.

Transcription of the human squalene synthase (HSS) gene is regulated by variations in the level of cellular cholesterol. Three regulatory elements in the HSS promoter region are known to be involved in the regulation: 1) a modified sterol regulatory element (SRE) 1 (HSS-SRE-1), 2) an inverted SRE-3 (Inv-SRE-3), 3) an inverted Y box (Inv-Y-Box). We report here the regulatory role of distinct cis-elements in the HSS promoter by using mutants of an HSS-luciferase promoter reporter. The activity of a wild-type promoter reporter transiently transfected into HepG-2 cells is increased by sterol depletion of the cells or by coexpression of mature forms of the SRE-binding proteins (SREBP) 1a and SREBP-2. Differential activation by SREBP-1a and SREBP-2 of the reporter gene mutated at various regions of the promoter is observed. Mutation of either the HSS-SRE-1 or the Inv-SRE-3 sequence diminished the activation by SREBP-1a and by sterol depletion but did not affect the activation by SREBP-2. Simultaneous mutations of both of these sequences almost completely abolished activation of the promoter by SREBP-1a or by sterol depletion, but activation by SREBP-2 was retained at 70%. Mutation of the Inv-Y-Box sequence element decreased the activity of the promoter by 50% or more, and if mutated together with both SREs, the activation was almost completely abolished. Mutation of any single GC box of the two located at -40 to -57 did not affect activity, whereas simultaneous mutation of the two decreased activation by SREBP-2 by 60%, by lipid depletion by 20%, and had no effect on the activation by SREBP-1a. A Y box motif at -159 to -166 and an SRE-like sequence element (SRE-1(8/10)) at position -101 to -108 are also involved in the sterol regulation. These results indicate that the complex sterol-mediated transcriptional regulation of the HSS gene is due to the presence of multiple copies of diverse cis elements in the HSS promoter. The differential activation of the HSS promoter may point to specific role of the SREBPs in cholesterogenesis.

CCAAT-Enhancer-Binding Proteins↗

PubMed2004

Disruption of the mechanism of long range activation within the human alpha-globin complex.

The human alpha-globin complex lies at the tip of the short arm of chromosome 16. It comprises three functional globin genes (5'-zeta2-alpha2-alpha1-3'), the expression of which is strictly dependent on a positive regulatory element located 40-kb upstream, HS-40. This DNase I-hypersensitive site is the only known regulatory element displaying strong erythroid-specific enhancer activity within the human alpha-globin complex. How this enhancer activity is shared among different erythroid genes present in the same cluster without affecting the ubiquitous genes present within and around the complex is poorly understood. To address this issue, we used hybrid murine erythroleukemia cells containing a single copy of human chromosome 16 and targeted the insertion of different sequences downstream of HS-40 by recombinase-mediated cassette exchange. We thus demonstrate that (i). HS-40-mediated erythroid-specific activation of the alpha-globin genes is impaired solely by the insertion of a promoter sequence and not a coding sequence, unless it is methylated, and that (ii). the degree of transcriptional repression observed seems to be related directly to the transcriptional rate of the inserted promoter. Taken together, these results emphasize the importance of promoter sequences as the main targets for the activation mechanism of the human alpha-globin genes by HS-40.

Animals↗

PubMed2006

Structural basis for the differential regulation of DNA by the methionine repressor MetJ.

The Met regulon in Escherichia coli encodes several proteins responsible for the biosynthesis of methionine. Regulation of the expression of most of these proteins is governed by the methionine repressor protein MetJ and its co-repressor, the methionine derivative S-adenosylmethionine. Genes controlled by MetJ contain from two to five sequential copies of a homologous 8-bp sequence called the metbox. A crystal structure for one of the complexes, the repressor tetramer bound to two metboxes, has been reported (Somers, W. S., and S. E. Phillips (1992) Nature 359, 387-393), but little structural work on the larger assemblies has been done presumably because of the difficulties in crystallization and the variability in the number and sequences of metboxes for the various genes. Small angle neutron scattering was used to study complexes of MetJ and S-adenosylmethionine with double-stranded DNA containing two, three, and five metboxes. Our results demonstrate that the crystal structure of the two-metbox complex is not the native solution conformation of the complex. Instead, the system adopts a less compact conformation in which there is decreased interaction between the adjacent MetJ dimers. Models built of the higher order complexes from the scattering data show that the three-metbox complex is organized much like the two-metbox complex. However, the five-metbox complex differs significantly from the smaller complexes, providing much closer packing of the adjacent MetJ dimers and allowing additional contacts not available in the crystal structure. The results suggest that there is a structural basis for the differences observed in the regulatory effectiveness of MetJ for the various genes of the Met regulon.

Crystallography, X-Ray↗

PubMed2006

Relationship between accuracy and organizational approach on the Rey-Osterrieth Complex Figure and the differential ability scales: a pilot investigation.

The present study was designed as an initial exploration of the relationship between global cognitive functioning and organizational and accuracy scores on the Rey-Osterrieth Complex Figure (ROCF) in a sample of children and adolescents. The relationship between ROCF accuracy scores at Copy and Delay as well as Organization and the Differential Ability Scales (DAS) was examined. Results indicate moderate correlations between Copy and Delay ROCF scores and various DAS indicators of nonverbal problem solving and visuospatial processing. Contrary to expectations, organizational scores were not significantly correlated with any of the DAS subscales or composite scales. Although further research is needed to explore the validity of this organizational scoring scheme with younger patients, these findings suggest that organization of the ROCF may be generally unrelated to global measures of cognitive ability or may assess processes associated with executive functioning untapped by the DAS.

Adolescent↗

PubMed2004

High-resolution analysis of DNA copy number using oligonucleotide microarrays.

Genomic copy number alterations are a feature of many human diseases including cancer. We have evaluated the effectiveness of an oligonucleotide array, originally designed to detect single-nucleotide polymorphisms, to assess DNA copy number. We first showed that fluorescent signal from the oligonucleotide array varies in proportion to both decreases and increases in copy number. Subsequently we applied the system to a series of 20 cancer cell lines. All of the putative homozygous deletions (10) and high-level amplifications (12; putative copy number >4) tested were confirmed by PCR (either qPCR or normal PCR) analysis. Low-level copy number changes for two of the lines under analysis were compared with BAC array CGH; 77% (n = 44) of the autosomal chromosomes used in the comparison showed consistent patterns of LOH (loss of heterozygosity) and low-level amplification. Of the remaining 10 comparisons that were discordant, eight were caused by low SNP densities and failed in both lines. The studies demonstrate that combining the genotype and copy number analyses gives greater insight into the underlying genetic alterations in cancer cells with identification of complex events including loss and reduplication of loci.

Cell Line↗

PubMed2004

Two functionally redundant isoforms of Drosophila melanogaster eukaryotic initiation factor 4B are involved in cap-dependent translation, cell survival, and proliferation.

Eukaryotic initiation factor (eIF) 4B is part of the protein complex involved in the recognition and binding of mRNA to the ribosome. DrosophilaeIF4B is a single-copy gene that encodes two isoforms, termed eIF4B-L (52.2 kDa) and eIF4B-S (44.2 kDa), generated as a result of the alternative recognition of two polyadeynlation signals during transcription termination and subsequent alternative splicing of the two pre-mRNAs. Both eIF4B mRNAs and proteins are expressed during the entire embryogenesis and life cycle. The proteins are cytoplasmic with polarized distribution. The two isoforms bind RNA with the same affinity. eIF4B-L and eIF4B-S preferentially enhance cap-dependent over IRES-dependent translation initiation in a Drosophila cell-free translation system. RNA interference experiments suggest that eIF4B is required for cell survival, although only a modest reduction in rate of protein synthesis is observed. Overexpression of eIF4B in Drosophila cells in culture and in developing eye imaginal discs promotes cell proliferation.

Amino Acid Sequence↗

PubMed2026

Transposable elements as modulators of homoeologous gene expression in bread wheat: lessons from the pan-transcriptome era.

Bread wheat (Triticum aestivum L.) is an allohexaploid (AABBDD) whose three ancestral subgenomes generate complex patterns of gene regulation. Most genes exist as homoeologous triads, and the relative expression balance among copies, homoeolog expression bias, is central to polyploid evolution and adaptation. Recent high-quality assemblies, long-read transcriptomics, and pan-transcriptome resources have uncovered extensive cultivar-specific transcriptional diversity. Because transposable elements (TEs) compose over 80% of the wheat genome, they are prime candidates for shaping subgenome asymmetry. We synthesize recent pan-genomic and transcriptomic evidence, including genome-wide associations between TE insertions and genome-specific expression, and propose a unifying framework in which TEs modulate homoeolog expression by donating cis-regulatory sequences, altering chromatin states, producing small RNAs, and driving structural variation. We discuss experimental and computational challenges for establishing causality, and outline future functional and translational strategies to leverage TE-associated regulatory diversity in wheat breeding.

Triticum↗

PubMed2000

TAS49--a dispersed repetitive sequence isolated from subtelomeric regions of Nicotiana tomentosiformis chromosomes.

We have isolated and characterized a new repetitive sequence, TAS49, from terminal restriction fragments of Nicotiana tomentosiformis genomic DNA by means of a modified vectorette approach. The TAS49 was found directly attached to telomeres of N. tabacum and one of its ancestors, N. tomentosiformis, and also at inner chromosome locations. No association with telomeres was detected neither in N. otophora nor in the second tobacco ancestor, N. sylvestris. PCR and Southern hybridization reveal similarities in the arrangement of TAS49 on the chromosomes of 9 species of the genus Nicotiana, implying its occurrence as a subunit of a conserved complex DNA repeat. TAS49 belongs to the family of dispersed repetitive sequences without features of transposons. The copy number of TAS49 varies widely in the genomes of 8 species analyzed being lowest in N. sylvestris, with 3300 copies per diploid genome. In N. tomentosiformis, TAS49 forms about 0.56% of the diploid genome, corresponding to 17400 copies. TAS49 units are about 460 bp long and show about 90% of mutual homology, but no significant homology to DNA sequences deposited in GenBank and EMBL. Although genomic clones of TAS49 contain an open reading frame encoding a proline-rich protein similar to plant extensins, no mRNA transcript was detected. TAS49 is extensively methylated at CpG and CpNpG sites and its chromatin forms nucleosomes phased with a 170 +/- 8 bp periodicity.

Base Sequence↗

PubMed2002

Functional cloning using pFB retroviral cDNA expression libraries.

Retroviral cDNA expression libraries allow the efficient introduction of complex cDNA libraries into virtually any mitotic cell type for screening based on gene function. The cDNA copy number per cell can be easily controlled by adjusting the multiplicity of infection, thus cell populations may be generated in which >90% of infected cells contain one to three cDNAs. We describe the isolation of two known oncogenes and one cell-surface receptor from a human Burkitt's lymphoma (Daudi) cDNA library inserted into the high-titer retroviral vector pFB.

3T3 Cells↗

PubMed1999

Screening of transgenic plants by amplification of unknown genomic DNA flanking T-DNA.

For the screening of transfer DNA (T-DNA) integration in transgenic plant material, we developed a method based on specific amplification of genomic plant DNA flanking T-DNA borders. This approach is possible because the length of the region flanking T-DNA extremity on a restriction fragment is specific to the integration locus. We have modified an adaptor ligation PCR technique developed for amplification of unknown DNA flanking known sequence. The PCR patterns obtained were specific and reproducible for different plants from a given transgenic line. Furthermore, the number of PCR products obtained could be considered a good estimation of the T-DNA copy number. When compared to Southern blot analysis, the PCR results give valuable complementary information about the complexity of the T-DNA integration pattern and also about the integrity of the T-DNA borders. We describe the applications of this approach to populations of transgenic Arabidopsis thaliana plants.

Arabidopsis↗

PubMed1992

[Quantitative analysis of eye movement during VDT work].

The point of fixation during visual display terminal (VDT) work was analyzed by using Eye Mark Recorder-NAC with their corneal reflexes. The subjects were categorized into 2 groups, expert VDT worker and non-expert with VDT work. As for the VDT task, Japanese sentences were loaded. On the other hand, ordinary desk work copying was loaded using the same Japanese sentences. The following results were obtained. VDT work needed more complex eye movements in both vertical and horizontal directions compared with desk work. The point of fixation was mainly located on the surface of the oscilloscope in the expert subjects, whereas, it was mainly located on the keyboard in non-expert subjects. In analyzing the velocity of eye movements during VDT work, the expert moved the eyes more slowly than the non-expert. These results suggested that the VDT experts can move their eyes more effectively and slowly.

Adult↗

PubMed1988

Clonal diversity of the Kirsten-ras oncogene during tumor progression in athymic nude mice: mechanisms of amplification and rearrangement.

Single-cell clones from primary and lung metastatic tumors have been evaluated for the state of the viral-Kirsten-ras oncogene (v-Ki-ras) by Southern blot analysis after injection of Kirsten sarcoma virus-transformed BALB/c 3T3 cells (KiMSV, with a replication-defective provirus) into athymic nude mice by four different injection routes. While all clones of early-passage KiMSV cells contained an EcoRI-generated 5.3-kilobase DNA fragment at high dosage level, most clones of late-passage cells had lost this v-Ki-ras fragment or had greatly diminished levels. However, all clones of all tumors (greater than 90 tested) obtained after injection of these late-passage cells contained a dosage of the 5.3-kilobase v-Ki-ras band similar to that of the early-passage KiMSV cells, suggesting either a very strong selection for v-Ki-ras-bearing cells of the early-passage type in tumor formation and/or the ability of a subset of late-passage cells to amplify this gene to some minimal dosage level. Both flow cytometric analyses for DNA content and quantitation of chromosomes showed that all primary and lung metastatic tumors had more than twice the number of chromosomes as the late-passage KiMSV cells; however, four of 80 late-passage cells had a chromosome count in the range of tumors, consistent with their importance in tumor generation and possibly amplification of the v-Ki-ras-bearing chromosome. Clonal analyses of lung micrometastatic tumors revealed a v-Ki-ras blot pattern identical to that of the s.c. primary tumors. However, two of five lung metastases from the footpad (as large rapidly growing nodules) and i.v. routes had multiple copies of v-Ki-ras in new sites; a second injection round led to even greater complexity in v-Ki-ras patterns in clones of lung tumors. Two assays were used to demonstrate that these new v-Ki-ras integrations were generated by superinfection with a "helper" retrovirus, not sarcomagenic by itself in the nude mice, that led to rescue/reinfection of tumor cells with the defective Kirsten sarcoma proviral genome--cellular transformation of 3T3 or C3H10T1/2 cells and RNA dot blot analyses for medium-secreted retrovirus specific for LTR or v-Ki-ras sequences. This "helper" retrovirus could not be detected in early- or late-passage KiMSV cells used for inoculation but could be detected in certain tissues of normal nude mice, demonstrating its in vivo origin.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1984

[Separation of rat thymocyte populations in a ficoll-paque gradient. IV. The genetic complexity of the cellular RNA of thymocyte subfractions].

The sequence complexity of the total cellular RNA was measured by RNA-driven hybridization to 125I-single copy DNA (sc-DNA). In the high density subfraction of thymocytes 4.5% of sc-DNA was saturated with cellular RNA. The sc-DNA probe was recovered from the DNA--RNA hybrids and rehybridized with homologous RNA and heterologous RNA from the cells with low density and middle density. Heterologous hybridization reactions with recycling sc-DNA probes revealed that 5.5% RNA sequences were specific of the cells from the high density subfraction and absent in both low and middle density subfractions. This is equivalent to expression of approximately 1100 additional structural genes in the high density subfraction of thymocytes.

Animals↗

PubMed1984

Organization and regulation of nitrogen fixation genes of Rhodopseudomonas capsulata.

The nitrogen fixation (nif) genes of Rhodopseudomonas capsulata appear to be much more widely dispersed than those of the well-studied Klebsiella pneumoniae. In both organisms the genes coding for the structural components of the nitrogenase complex, nifHDK, comprise a single unit of transcription. Only in the photosynthetic bacterium, however, are there multiple copies of these genes. The extra copies are normally silent but they can be activated by mutation, detected as nif+ pseudorevertants of nif- deletions of the expressed nifHDK genes. Glutamine is required for the repression of nif gene transcription in R. capsulata.

Chromosome Mapping↗