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At least 847 records · Page 47Linked to original sources
PubMed2001

Local action of long-range repressors in the Drosophila embryo.

Previous studies have identified two corepressors in the early Drosophila embryo: Groucho and dCTBP: Both proteins are recruited to the DNA template by interacting with short peptide motifs conserved in a variety of sequence-specific transcriptional repressors. Once bound to DNA, Groucho appears to mediate long-range repression, while dCtBP directs short-range repression. The short-range Krüppel repressor was converted into a long-range repressor by replacing the dCtBP interaction motif (PxDLSxH) with a Groucho motif (WRPW). The resulting chimeric repressor causes a different mutant phenotype from that of the native Krüppel protein when misexpressed in transgenic embryos. The different patterning activities can be explained on the basis of long-range silencing within the hairy 5' regulatory region. The analysis of a variety of synthetic transgenes provides evidence that Groucho-dependent long-range repressors do not always cause the dominant silencing of linked enhancers within a complex cis-regulatory region. We suggest a "hot chromatin" model, whereby repressors require activators to bind DNA.

Alcohol Oxidoreductases↗
PubMed1977

Screening for autosomal aberrations.

A method of screening for autosomal aberrations is important as an indication for chromosome analysis such as that used in sex-chromatin examination for sex chromosome aberrations. In our clinic, malformed patients with mental retardation and abnormal dermatoglyphic patterns are strong suspects for autosomal aberrations. Abnormal dermatoglyphic patterns are separated into two categories: (1) Absolutely abnormal--radial loop of 1st finger, radial loop of 4th finger, radial loop of 5th finger, arch over 6 fingers, arch tibial, loop tibial, and arch fibular; (2) Borderline abnormalities--high axial triradius (t' and t"), simian crease, interdigital loop, and single crease of 5th finger. Of 416 cases showing malformation, retardation, and abnormal dermatoglyphics, 308 had autosomal aberrations, while 108 had normal karyotypes. In the group with autosomal aberrations, 279 patients (90.6%) had absolutely abnormal dermatoglyphics. In the group with normal karyotypes only 8 patients (7.4%) had absolutely normal dermatoglyphics, while most had abnormal dermatoglyphics in the borderline category. These clinical manifestations: absolutely abnormal dermatoglyphics, mental retardation, and malformations are therefore very useful in screening for autosomal aberrations.

Abnormalities, Multiple↗
PubMed2004

Orphan nuclear receptor small heterodimer partner represses hepatocyte nuclear factor 3/Foxa transactivation via inhibition of its DNA binding.

Small heterodimer partner (SHP; NR0B2) is an atypical orphan nuclear receptor and acts as a coregulator of various nuclear receptors. Herein, we examined a novel cross talk between SHP and a forkhead transcription factor HNF3 (hepatocyte nuclear factor 3/Foxa. Transient transfection assay demonstrated that SHP inhibited the transcriptional activity of all three isoforms of HNF3, HNF3alpha, beta, and gamma. In vivo and in vitro protein interaction studies showed that SHP physically interacted with HNF3. Adenovirus-mediated overexpression of SHP significantly decreased the mRNA levels of glucose-6-phosphase (G6Pase), cholesterol 7-alpha-hydroxylase (CYP7A1), and phosphoenolpyruvate carboxykinase (PEPCK) in HepG2 cells and rat primary hepatocytes. Moreover, the mRNA level of G6Pase was notably increased by down-regulation of SHP with small interfering RNA. Interestingly, HNF3 transactivity was still repressed by SHPDelta128-139 that fails to repress nuclear receptors. Mapping of interaction domain revealed that SHP interacted with forkhead DNA binding domain of HNF3alpha. Gel mobility shift and chromatin immunoprecipitation assays demonstrated that SHP inhibits DNA binding of HNF3. These results suggest that SHP is involved in the regulation of G6Pase, CYP7A1, and PEPCK gene expression via novel mechanism of inhibition of HNF3 activity and expand the role of SHP as a coregulator of other family of transcription factors in addition to nuclear receptors.

Binding, Competitive↗
PubMed1993

Mutational analysis of the Saccharomyces cerevisiae general regulatory factor CP1.

The Saccharomyces cerevisiae general regulatory factor CP1, a helix-loop-helix protein that binds the centromere DNA element I (CDEI) of yeast centromeres, is required in yeast for optimal centromere function and for methionine prototrophy. Mutant alleles of CEP1, the gene encoding CP1, were generated by linker insertion, 5'- and 3'-deletion, and random mutagenesis and assayed for DNA binding activity and their ability to confer CP1 function when expressed in yeast. A heterologous CDEI-binding protein, TFEB, was also tested for CP1 function. The results suggested that DNA binding is required for both biological functions of CP1 but is not sufficient. A direct and quantitative correlation was observed between the chromosome loss and nutritional (i.e., Met) phenotypes of strains carrying loss of function alleles, but qualitatively the chromosome loss phenotype was more sensitive to decreased CP1 expression. The data are consistent with a model in which CP1 performs the same general chromatin-related function at centromeres and MET gene promoters and is normally present in functional excess.

Alleles↗
PubMed2002

Basic helix-loop-helix transcription factor epicardin/capsulin/Pod-1 suppresses differentiation by negative regulation of transcription.

Epicardin/capsulin/Pod-1, expressed in skeletal myoblasts within brachial arches and in the condensing mesenchyme, is a member of the basic helix-loop-helix (bHLH) transcription factor family that is involved in various cell differentiation processes. In this study, we examined the functional properties of epicardin/capsulin/Pod-1 in differentiation. The yeast and mammalian two-hybrid systems showed physical associations between epicardin/capsulin/Pod-1 and E2A, both of which were present in the nuclei. The bHLH domains mediated this association. Ectopic expression of epicardin/capsulin/Pod-1 inhibited E2A-dependent activation of the exogenous and endogenous expression of the cyclin-dependent kinase inhibitor, p21(WAF1/Cip1) gene, and the muscle creatine kinase gene that encodes the predominant creatine kinase isoform expressed in mammalian skeletal muscle. Transfection with epicardin/capsulin/Pod-1 small interfering RNA abolished the epicardin/capsulin/Pod-1-mediated suppression of E12-dependent activation of the p21 promoter. Chromatin immunoprecipitation assay showed that epicardin/capsulin/Pod-1 was physically associated with the muscle creatine kinase promoter in vivo. Moreover, terminal differentiation of C2C12 myoblasts was inhibited by exogenous introduction of epicardin/capsulin/Pod-1. These inhibitory functions of epicardin/capsulin/Pod-1 closely resemble those of the bHLH inhibitor Twist protein. These results indicate that epicardin/capsulin/Pod-1 functions as a negative regulator of differentiation of myoblasts through transcription in at least two distinct steps, cell growth arrest and lineage-specific differentiation.

Animals↗
PubMed1991

Trypsin-induced changes in cell shape and chromatin structure result in radiosensitization of monolayer Chinese hamster V79 cells.

Trypsin is the enzyme commonly used to prepare single cell suspensions from monolayer and spheroid cultures, both to determine survival and to assay DNA damage. Trypsin induces rounding, dissociation and radiosensitization of anchorage-dependent cells. Radiosensitivity and chromatin structure were compared between trypsin-treated (0.05%) round V79 cells from monolayers and spheroids vs. untreated spread monolayer cells in situ. The fluorescent halo technique was used to measure the changes in DNA supercoiling in nucleoids isolated from control and irradiated round and spread cells. Maximal halo diameters, the amount of initial and residual radiation-induced DNA damage (estimated from nucleoid halo diameter changes), and the radiosensitivity were higher in round cells than in spread monolayer V79 cells. The effects on cellular radiosensitivity and maximal halo diameter of other agents which also round and dissociate cells, e.g. 0.25% trypsin, pronase E and a non-enzymatic cell-dissociation solution, were similar to those of 0.05% trypsin. In LY-S cells, which are anchorage-independent, DNA loop size, the initial amount of DNA damage and radiosensitivity were not affected by trypsin. We suggest that the higher radiosensitivity of anchorage-dependent cells under immediate trypsinization and plating conditions, compared to cells with postirradiation in situ repair incubation, is due to correlated changes in cell shape and chromatin structure.

Animals↗
PubMed2005

Upstream stimulating factors: highly versatile stress-responsive transcription factors.

Upstream stimulating factors (USF), USF-1 and USF-2, are members of the eucaryotic evolutionary conserved basic-Helix-Loop-Helix-Leucine Zipper transcription factor family. They interact with high affinity to cognate E-box regulatory elements (CANNTG), which are largely represented across the whole genome in eucaryotes. The ubiquitously expressed USF-transcription factors participate in distinct transcriptional processes, mediating recruitment of chromatin remodelling enzymes and interacting with co-activators and members of the transcription pre-initiation complex. Results obtained from both cell lines and knock-out mice indicates that USF factors are key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism, and in melanocytes USF-1 has been implicated as a key UV-activated regulator of genes associated with pigmentation. This review will focus on general characteristics of the USF-transcription factors and their place in some regulatory networks.

Animals↗
PubMed2003

Rationally designed insulator-like elements can block enhancer action in vitro.

Insulators are DNA sequences that are likely to be involved in formation of chromatin domains, functional units of gene expression in eukaryotes. Insulators can form domain boundaries and block inappropriate action of regulatory elements (such as transcriptional enhancers) in eukaryotic nuclei. Using an in vitro system supporting enhancer action over a large distance, the enhancer-blocking insulator activity has been recapitulated in a highly purified system. The insulator-like element was constructed using a sequence-specific DNA-binding protein making stable DNA loops (lac repressor). The insulation was entirely dependent on formation of a DNA loop that topologically isolates the enhancer from the promoter. This rationally designed, inducible insulator-like element recapitulates many key properties of eukaryotic insulators observed in vivo. The data suggest novel mechanisms of enhancer and insulator action.

Base Sequence↗
PubMed2001

The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains.

We have investigated the major Escherichia coli histone-like proteins (H-NS, HU, FIS, and IHF) as putative factors involved in the maintenance of the overall DNA looped arrangement of the bacterial nucleoid. The long-range architecture of the chromosome has been studied by means of an assay based on in vivo genomic fragmentation mediated by endogenous DNA gyrase in the presence of oxolinic acid. The fragmentation products were analysed by CHEF electrophoresis. The results indicate that in vivo a large fraction of the bacterial chromatin constitutes an adequate substrate for the enzyme. DNA fragments released upon oxo-treatment span a size range from about 1000 kb to a limit-size of about 50 kb. The latter value is in excellent agreement with the average size reported for bacterial chromosomal domains. The DNA gyrase-mediated fragmentation does not appear to be significantly altered in strains depleted in histone-like proteins as compared to an E. coli wild type strain. This suggests that these proteins may not represent critical determinants for the maintenance of the supercoiled loop organisation of the E. coli chromosome.

Amino Acid Motifs↗
PubMed1993

A nucleosome-dependent static loop potentiates estrogen-regulated transcription from the Xenopus vitellogenin B1 promoter in vitro.

We describe the transcriptional potentiation in estrogen responsive transcription extracts of the Xenopus vitellogenin B1 gene promoter through the formation of a positioned nucleosome. Nuclease digestion and hydroxyl radical cleavage indicate that strong, DNA sequence-directed positioning of a nucleosome occurs between -300 and -140 relative to the start site of transcription. Deletion of this DNA sequence abolishes the potentiation of transcription due to nucleosome assembly. The wrapping of DNA around the histone core of the nucleosome positioned between -300 and -140 creates a static loop in which distal estrogen receptor binding sites are brought close to proximal promoter elements. This might facilitate interactions between the trans-acting factors themselves and/or RNA polymerase. Such a nucleosome provides an example of how chromatin structure might have a positive effect on the transcription process.

Animals↗
PubMed1988

The effect of heat shock on the morphology of amphibian lampbrush chromosomes.

Isolated oocytes of Triturus cristatus carnifex cultured in Barthe's medium respond to a sudden increase in temperature of 35 or 37 degrees C by the rapid condensation of their lampbrush chromosomes. The degree of condensation depends on the severity of the heat shock and is accompanied by the retraction of the transcriptionally active lampbrush loops. The oocytes were kept at 20 degrees C for 12 h after the period of heat shock, before the chromosomes were isolated. The minimum period required to effect loop retraction in immature oocytes of 0.7 mm in diameter was 10 min at 35 degrees C; although more extensive and complete retraction occurred if the oocytes were incubated for periods of up to 40 min. Chromosomes from more mature oocytes (1.4 mm in diameter) require longer periods of heat shock before undergoing condensation. The oocytes themselves do not show any obvious morphological changes after heat shock, although the germinal vesicles are initially too fragile to isolate manually for several hours. When the oocytes are returned to ambient temperatures, they can be cultured in Barthe's medium for several days, enabling the chromosomes to be isolated and studied. Generally, the chromosomes and loops from immature oocytes remain in a condensed state for about 48 h but then the chromosomal axis begins to relax and the loops begin to re-form. Depending on the severity of the initial heat shock, complete recovery of the normal lampbrush morphology is attained after a few days. The re-formed loops are morphologically indistinguishable from untreated loops in control preparations and are of the same length on average. This response of lampbrushes to heat shock is a reliable and repeatable process and should therefore become a valuable model system for the study of chromatin and chromosome structure during changes in transcriptional activity. The time taken for the lampbrushes to recover their normal morphology, is discussed in terms of the return to normal cellular transcription.

Animals↗
PubMed1991

The remote control of transcription, DNA looping and DNA compaction.

mRNA synthesis can be controlled at some distance from the start of transcription in eukaryotes and prokaryotes. It is generally assumed that the distal elements of the transcriptional machinery directly interact with the proximal elements, forcing the DNA to bend in a loop. DNA loop formation and transcription can be affected by the distance between the sites, their helical positioning, their orientation, their concentration (responsible for a cis- or a trans-effect of the DNA sequences), and DNA compaction in chromatin. The corresponding in vitro and in vivo situations have been critically examined for a number of systems, mostly prokaryotic.

Binding Sites↗
PubMed2005

E47 phosphorylation by p38 MAPK promotes MyoD/E47 association and muscle-specific gene transcription.

Selective recognition of the E-box sequences on muscle gene promoters by heterodimers of myogenic basic helix-loop-helix (bHLH) transcription factors, such as MyoD, with the ubiquitous bHLH proteins E12 and E47 is a key event in skeletal myogenesis. However, homodimers of MyoD or E47 are unable of binding to and activating muscle chromatin targets, suggesting that formation of functional MyoD/E47 heterodimers is pivotal in controlling muscle transcription. Here we show that p38 MAPK, whose activity is essential for myogenesis, regulates MyoD/E47 heterodimerization. Phosphorylation of E47 at Ser140 by p38 induces MyoD/E47 association and activation of muscle-specific transcription, while the nonphosphorylatable E47 mutant Ser140Ala fails to heterodimerize with MyoD and displays impaired myogenic potential. Moreover, inhibition of p38 activity in myocytes precludes E47 phosphorylation at Ser140, which results in reduced MyoD/E47 heterodimerization and inefficient muscle differentiation, as a consequence of the impaired binding of the transcription factors to the E regulatory regions of muscle genes. These findings identify a novel pro-myogenic role of p38 in regulating the formation of functional MyoD/E47 heterodimers that are essential for myogenesis.

Animals↗
PubMed2005

Cross-regulation between Egr-1 and APE/Ref-1 during early response to oxidative stress in the human osteoblastic HOBIT cell line: evidence for an autoregulatory loop.

The Early Growth Response protein (Egr-1) is a C(2)H(2)-zinc finger-containing transcriptional regulator involved in the control of cell proliferation and apoptosis. Its DNA-binding activity is redox regulated in vitro through the oxidation-reduction of Cys residues within its DNA-binding domain. APE/Ref-1 is a DNA-repair enzyme with redox modulating activities on several transcription factors. In this study, by evaluating the effects of different stimuli, we found a similar timing of activation being suggestive for a common and co-linear regulation for the two proteins. Indeed, we show that APE/Ref-1 increases the Egr-1 DNA-binding activity in unstimulated osteoblastic HOBIT cells. H(2)O(2) stimulation induces a strong interaction between Egr-1 and APE/Ref-1 at early times upon activation, as assayed by immunoprecipitation experiments. By using a cell transfection approach, we demonstrated the functional role of this interaction showing that two specific Egr-1 target genes, the PTEN phosphatase and the thymidine kinase (TK) genes promoters, are activated by contransfection of APE/Ref-1. Interestingly, by using a cell transfection approach and Chromatin immunoprecipitation assays, we were able to demonstrate that Egr-1 stimulates the transcriptional activity of APE/Ref-1 gene promoter by a direct interaction with specific DNA-binding site on its promoter. Taken together, our data delineate a new molecular mechanism of Egr-1 activation occurring soon after H(2)O(2) stimulation in osteoblastic cells and suggest a model for a positive loop between APE/Ref-1 and Egr-1 that could explain the early transcriptional activation of APE/Ref-1 gene expression.

Base Sequence↗
PubMed1986

Factors controlling the size of DNA loops in frog embryos and Friend erythroleukemia cells.

Measurements were made of the average size of fluorescent halos of nucleoids of developing frog embryos, mouse fibroblasts (A9 cells) and Friend erythroleukemia cells cultured with various compounds. These halos are thought to represent relaxed lengths of loops of DNA attached to the nuclear matrix. Measurement of transcription of RNA from nuclei in vitro suggested that cells with more loops (smaller halos) had more initiation sites for transcription. DNA loop number decreases during development of the frog embryos, and red blood cells of adults have even fewer and larger loops. One or two days of culture of Friend cells in various compounds that induce differentiation resulted in more DNA loops than for control cells, but after 5 days of culture the differentiated erythrocytes had fewer DNA loops than control cells at stationary phase. Stationary phase cells have almost twice as many DNA loops as log phase cells. Various compounds that stall cells at the G1/S border induced more DNA loops, but subsequently the number of DNA loops decreased as the cells entered S phase. A number of compounds which slow the rate of cell division cause the formation of more DNA loops, perhaps due to longer G1 periods.

Animals↗
PubMed2003

BETA2 activates transcription from the upstream glucokinase gene promoter in islet beta-cells and gut endocrine cells.

Glucokinase (GK) gene transcription initiates in the islet (beta-cell), gut, and brain from promoter sequences residing approximately 35 kbp upstream from those used in liver. Expression of betaGK is controlled in beta-cells by cell-enriched (i.e. pancreatic duodenal homeobox 1 [PDX-1]) and ubiquitously (i.e., Pal) distributed factors that bind to and activate from conserved sequence motifs within the upstream promoter region (termed betaGK). Here, we show that a conserved E-box element also contributes to control in the islet and gut. betaGK promoter-driven reporter gene activity was diminished by mutating the specific sequences involved in E-box-mediated basic helix-loop-helix factor activator binding in islet beta-cells and enteroendocrine cells. Gel shift assays demonstrated that the betaGK and insulin gene E-box elements formed the same cell-enriched (BETA2:E47) and generally distributed (upstream stimulatory factor [USF]) protein-DNA complexes. betaGK E-box-driven activity was stimulated in cotransfection assays performed in baby hamster kidney (BHK) cells with BETA2 and E47, but not USF. Chromatin immunoprecipitation assays performed with BETA2 antisera showed that BETA2 occupies the upstream promoter region of the endogenous betaGK gene in beta-cells. We propose that BETA2 (also termed NeuroD1) regulates betaGK promoter activity.

Animals↗
PubMed2001

The 5' boundary of the human apolipoprotein B chromatin domain in intestinal cells.

The 5' boundary of the chromosomal domain of the human apolipoprotein B (apoB) gene in intestinal cells has been localized and characterized. It is composed of two kinds of boundary elements; the first, functional boundary is an insulator activity exhibited by a 1.8 kb DNA fragment located between -58 and -56 kb upstream of the human apoB promoter. In this region, an enhancer-blocking activity has been mapped to a CTCF binding site that is located upstream of two apoB intestinal enhancers (IEs), the 315 IE and the 485 IE. The CTCF site represents a boundary between two types of chromatin structure: an open, DNaseI-sensitive region 3' of the CTCF site containing the intestinal regulatory elements and a closed, DNaseI-resistant region 5' of the CTCF site. The 1.8 kb fragment harboring the CTCF site also insulated mini-white transgenes against position effects in Drosophila melanogaster. The second, structural boundary is represented by a nuclear matrix attachment region (MAR), situated about 3 kb 5' of the CTCF site. This MAR may represent the 5' anchorage site for a chromosomal loop that functions to bring the intestinal regulatory elements closer to the apoB promoter.

5' Untranslated Regions↗
PubMed1992

Code domains in tandem repetitive DNA sequence structures.

Traditionally, many people doing research in molecular biology attribute coding properties to a given DNA sequence if this sequence contains an open reading frame for translation into a sequence of amino acids. This protein coding capability of DNA was detected about 30 years ago. The underlying genetic code is highly conserved and present in every biological species studied so far. Today, it is obvious that DNA has a much larger coding potential for other important tasks. Apart from coding for specific RNA molecules such as rRNA, snRNA and tRNA molecules, specific structural and sequence patterns of the DNA chain itself express distinct codes for the regulation and expression of its genetic activity. A chromatin code has been defined for phasing of the histone-octamer protein complex in the nucleosome. A translation frame code has been shown to exist that determines correct triplet counting at the ribosome during protein synthesis. A loop code seems to organize the single stranded interaction of the nascent RNA chain with proteins during the splicing process, and a splicing code phases successive 5' and 3' splicing sites. Most of these DNA codes are not exclusively based on the primary DNA sequence itself, but also seem to include specific features of the corresponding higher order structures. Based on the view that these various DNA codes are genetically instructive for specific molecular interactions or processes, important in the nucleus during interphase and during cell division, the coding capability of tandem repetitive DNA sequences has recently been reconsidered.

Animals↗