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At least 1,009 records · Page 56Linked to original sources
PubMed1988

Nuclear matrix associated DNA is preferentially repaired in normal human fibroblasts, exposed to a low dose of ultraviolet light but not in Cockayne's syndrome fibroblasts.

In this study we addressed the questions as to whether repair is confined to the nuclear matrix compartment, analogous to replication and transcription and how repair events are distributed in DNA loops associated with the nuclear matrix. Pulse labelling of ultraviolet (254 nm) irradiated confluent human fibroblasts revealed that repair was preferentially located in nuclear matrix associated DNA in cells exposed to 5 J/m2. However, in cells exposed to 30 J/m2 repair approached a random distribution. The non-random distribution of repair label at 5 J/m2 was most pronounced directly after irradiation and gradually changed to a more random distribution within two hours after treatment. The results of pulse-chase experiments exclude the possibility of transient binding of repair sites to the matrix and favour the model of preferential repair of DNA sequences permanently associated with the nuclear matrix. Pronounced differences in distribution pattern of repair events in DNA loops were found among normal and UV-sensitive cell lines exposed to 5 J/m2. Repair in nuclear matrix associated DNA was 1.7 fold more efficient than in loop DNA in normal and xeroderma pigmentosum group D cells and over 3 fold in xeroderma pigmentosum group C cells. In Cockayne's syndrome fibroblasts repair in nuclear matrix DNA was found to be 2 fold less efficient than in loop DNA. This heterogeneity in distribution of repair correlates well with preferential removal of pyrimidine dimers from transcriptionally active DNA in normal and xeroderma pigmentosum group C cells and its absence in Cockayne's syndrome cells as recently reported by Mayne et al., 1988. The results suggest that Cockayne's syndrome cells have a defect in excision of UV-damage from transcriptionally active genes located proximal to the nuclear matrix. Xeroderma pigmentosum group C cells may possess a defect in DNA repair associated with chromatin regions outside transcriptionally active DNA.

Cell Nucleus↗
PubMed1993

The centromere and promoter factor, 1, CPF1, of Saccharomyces cerevisiae modulates gene activity through a family of factors including SPT21, RPD1 (SIN3), RPD3 and CCR4.

In Saccharomyces cerevisiae, the CPF1 gene encodes a centromere binding protein that also plays a role in transcription; cpf1 strains are methionine auxotrophs. In this paper we describe four strains that are methionine prototrophs despite containing a defective CPF1 gene. These strains, which contain mutations at either the SPT21, RPD1 (SIN3), RPD3 or CCR4 loci, have defective centromere function and a chromatin structure around the CDEI elements in the MET25 promoter characteristic of strains lacking CPF1. This indicates that the roles of CPF1 in transcription, centromere function and chromatin modulation around CDEI sites are different. We propose that CPF1 functions to overcome the repressing action, mediated via inactive chromatin, of proteins such as SPT21 or RPD1 (SIN3) on gene expression. The absence of proteins such as SPT21 or RPD1 (SIN3) relieves this repression and explains how methionine prototrophy is restored in the absence of CPF1.

Base Sequence↗
PubMed2004

NSCL-1 and NSCL-2 synergistically determine the fate of GnRH-1 neurons and control necdin gene expression.

To study the role of the bHLH genes NSCL-1 and NSCL-2 in the development of GnRH-1 neurons, we have generated compound mutant mice. Mutant animals die at birth and show a virtually complete absence of GnRH-1 neurons in the posterior parts of the brain at E18.5 and an aberrant morphology of the remaining GnRH-1 neurons in the anterior parts of the brain indicating that NSCL-1 and NSCL-2 might concomitantly control differentiation/migration of GnRH-1 neurons in a cell autonomous manner. To gain further insights into this process, we screened for NSCL target genes using DNA array hybridization and detected necdin, which is deleted in the human Prader-Willi syndrome phenotypically resembling the NSCL-2 mutation. Using chromatin immunoprecipitation and site-directed mutagenesis of the necdin promoter, we demonstrate that NSCLs together with additional cofactors directly control transcription of the necdin gene. NSCL-dependent control of necdin expression might be instrumental for proper neuronal cell differentiation and enable GnRH-1 neurons to migrate.

Animals↗
PubMed2003

Hepatocyte nuclear factor-4 alpha mediates the stimulatory effect of peroxisome proliferator-activated receptor gamma co-activator-1 alpha (PGC-1 alpha) on glucose-6-phosphatase catalytic subunit gene transcription in H4IIE cells.

It has recently been shown that adenoviral-mediated expression of peroxisome proliferator-activated receptor gamma co-activator-1 alpha (PGC-1 alpha) in hepatocytes stimulates glucose-6-phosphatase catalytic subunit (G6Pase) gene expression. A combination of fusion gene, gel retardation and chromatin immunoprecipitation assays revealed that, in H4IIE cells, PGC-1 alpha mediates this stimulation through an evolutionarily conserved region of the G6Pase promoter that binds hepatocyte nuclear factor-4 alpha.

Animals↗
PubMed2006

Polycomb complexes and the propagation of the methylation mark at the Drosophila ubx gene.

Polycomb group proteins are transcriptional repressors that control many developmental genes. The Polycomb group protein Enhancer of Zeste has been shown in vitro to methylate specifically lysine 27 and lysine 9 of histone H3 but the role of this modification in Polycomb silencing is unknown. We show that H3 trimethylated at lysine 27 is found on the entire Ubx gene silenced by Polycomb. However, Enhancer of Zeste and other Polycomb group proteins stay primarily localized at their response elements, which appear to be the least methylated parts of the silenced gene. Our results suggest that, contrary to the prevailing view, the Polycomb group proteins and methyltransferase complexes are recruited to the Polycomb response elements independently of histone methylation and then loop over to scan the entire region, methylating all accessible nucleosomes. We propose that the Polycomb chromodomain is required for the looping mechanism that spreads methylation over a broad domain, which in turn is required for the stability of the Polycomb group protein complex. Both the spread of methylation from the Polycomb response elements, and the silencing effect can be blocked by the gypsy insulator.

Animals↗
PubMed2002

Caenorhabditis elegans unc-37/groucho interacts genetically with components of the transcriptional mediator complex.

Groucho functions as a general corepressor by modulating chromatin structure and has a widespread role in many developmental processes. Here we show that Groucho may also interact with the basal transcriptional machinery. Mutations in Caenorhabditis elegans groucho interact with mutations in components of the transcriptional Mediator complex, resulting in synthetic lethality and loss of male sensory neurons.

Animals↗
PubMed2004

A novel E2 box-GATA element modulates Cdc6 transcription during human cells polyploidization.

Cdc6 is a key regulator of the strict alternation of S and M phases during the mitotic cell cycle. In mammalian and plant cells that physiologically become polyploid, cdc6 is transcriptionally and post-translationally regulated. We have recently reported that Cdc6 levels are maintained in megakaryoblastic HEL cells, but severely downregulated by ectopic expression of transcriptional repressor Drosophila melanogaster escargot. Here, we show that cdc6 promoter activity is upregulated during megakaryocytic differentiation of HEL endoreplicating cells, and that Escargot interferes with such activation. Transactivation experiments showed that a 1.7 kb region located at 2800 upstream cdc6 transcription initiation site behaved as a potent enhancer in endoreplicating cells only. This activity was mainly dependent on a novel cis-regulatory element composed by an E2 box overlapping a GATA motif. Ectopic Escargot could bind this regulatory element in vitro and endogenous GATA-1 and E2A formed specific complexes in megakaryoblastic cells as well as in primary megakaryocytes. Chromatin Immunoprecipitation analysis revealed that both transcription factors were occupying the E2 box/GATA site in vivo. Altogether, these data suggest that cdc6 expression could be actively maintained during megakaryocytic differentiation through transcriptional mechanisms involving specific cis- and trans-regulatory elements.

5' Flanking Region↗
PubMed2000

Groucho/TLE family proteins and transcriptional repression.

The Drosophila Groucho (Gro) protein is the prototype for a large family of corepressors, examples of which are found in most metazoans. This family includes the human transducin-like Enhancer of split (TLE) proteins. As corepressors, Gro/TLE family proteins do not bind to DNA directly, but rather are recruited to the template by DNA-bound repressor proteins. Gro/TLE family proteins are required for many developmental processes, including lateral inhibition, segmentation, sex determination, dorsal/ventral pattern formation, terminal pattern formation, and eye development. These proteins are characterized by a conserved N-terminal glutamine-rich domain and a conserved C-terminal WD-repeat domain. The primary role of the glutamine-rich domain is apparently to mediate tetramerization, while the WD-repeat domain may mediate interactions with DNA-bound repressors. The glutamine rich and WD-repeat domains are separated by a less conserved region containing domains that have been implicated in transcriptional repression and nuclear localization. In addition to encoding full-length Gro/TLE family proteins, most metazoan genomes encode truncated family members that contain the N-terminal oligomerization domain, but lack the C-terminal WD-repeat domain. These truncated proteins may negatively regulate full-length Gro/TLE proteins, perhaps by sequestering them in non-productive complexes. Gro/TLE family proteins probably repress transcription by multiple mechanisms. For example, a glycine/proline-rich domain in the central variable region functions to recruit the histone deacetylase Rpd3 to the template. This histone deacetylase then presumably silences transcription by altering local chromatin structure. Other repression domains in Gro may function in a histone deacetylase-independent manner. Many aspects of Gro/TLE protein function remain to be explored, including the possible post-translational regulation of Gro/TLE activity as well as the mechanisms by which Gro/TLE proteins direct repression at a distance.

Animals↗
PubMed1984

Preferential repair of nuclear matrix associated DNA in xeroderma pigmentosum complementation group C.

The distribution of ultraviolet-induced DNA repair patches in the genome of xeroderma pigmentosum cells of complementation group C was investigated by determining the molecular weight distribution of repair labeled DNA and prelabeled DNA in alkaline sucrose gradients after treatment with the dimerspecific endonuclease V of bacteriophage T4. The results were consistent with the data reported by Mansbridge and Hanawalt (1983) and suggest that DNA-repair synthesis in xeroderma pigmentosum cells of complementation group C occurs in localized regions of the genome. Analysis of the spatial distribution of ultraviolet-induced repair patches in DNA loops attached to the nuclear matrix revealed that in xeroderma pigmentosum cells of complementation group C repair patches are preferentially situated near the attachment sites of DNA loops at the nuclear matrix. In normal human fibroblasts we observed no enrichment of repair-labeled DNA at the nuclear matrix and repair patches appeared to be distributed randomly along the DNA loops. The enrichment of repair-labeled DNA at the nuclear matrix in xeroderma pigmentosum cells of complementation group C may indicate that the residual DNA-repair synthesis in these cells occurs preferentially in transcribing regions of the genome.

Cell Nucleus↗
PubMed2004

The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis.

Asymmetric division during sporulation by Bacillus subtilis generates a mother cell that undergoes a 5-h program of differentiation. The program is governed by a hierarchical cascade consisting of the transcription factors: sigma(E), sigma(K), GerE, GerR, and SpoIIID. The program consists of the activation and repression of 383 genes. The sigma(E) factor turns on 262 genes, including those for GerR and SpoIIID. These DNA-binding proteins downregulate almost half of the genes in the sigma(E) regulon. In addition, SpoIIID turns on ten genes, including genes involved in the appearance of sigma(K). Next, sigma(K) activates 75 additional genes, including that for GerE. This DNA-binding protein, in turn, represses half of the genes that had been activated by sigma(K) while switching on a final set of 36 genes. Evidence is presented that repression and activation contribute to proper morphogenesis. The program of gene expression is driven forward by its hierarchical organization and by the repressive effects of the DNA-binding proteins. The logic of the program is that of a linked series of feed-forward loops, which generate successive pulses of gene transcription. Similar regulatory circuits could be a common feature of other systems of cellular differentiation.

Amino Acid Motifs↗
PubMed1988

Electron microscopy of nucleic acid.

Electron microscopy (EM) of nucleic acids was first described by Kleinschmidt and Zahn 1959 (1). By complexing duplex DNA with basic proteins and spreading the complexed DNA onto the surface of an aquous phase it was possible to obtain well stretched DNA molecules that could be examined by EM. Addition of formamide to DNA spreading solution as well as to hypophase prevented single-stranded DNA and RNA from forming secondary structures thus providing conditions for analysis of these molecules. EM studies have provided information about molecular weight, molecular configuration and homogeneity/heterogeneity of the DNA preparations examined. Furthermore, intramolecular heterogeneity in base sequence could be analyzed by partial denaturation of duplex DNA. By partial denaturation mapping information of the orientation of DNA molecules was obtained. Sequence homology between two DNA molecules were studied by heteroduplex analyses where the two DNAs to be studied were denatured to full strand separation followed by reassociation. This method has been widely used to analyze DNA mutations, and to discover sequence homologies within a DNA molecule or between two DNA molecules. Heteroduplex analyses between DNA and RNA (R-loop formation) provided information about distribution of ribosomal RNA genes and gave the first information of eukaryotic post transcriptional processing of mRNA. Also the various modes for DNA replication and transcription were studied by EM. It is possible to study duplex DNA not complexed by basic proteins by EM. The DNA is then adsorbed to an activated carbon film and rotary shadowed with finely grained metals to enhance the contrast. Using this method it was possible to study binding of proteins to DNA. This method was also used in the study of chromatin structure where it provided information of the size and distribution of nucleosomes as well as packaging of DNA in chromatin fibres. The complicated nature of DNA strand exchange and repair reactions was studied by in-vitro systems where EM analysis was used in the description of the presynoptic filament and structure of the joined molecules. Furthermore, EM provided the first direct evidence for the existence of the paranemic joint, where the DNA strands are joined without Watson-Crick base-pairing.

Animals↗
PubMed2005

Regulation of skeletal muscle gene expression by p38 MAP kinases.

The formation of skeletal muscle is a multistep process orchestrated by the basic helix-loop-helix myogenic regulatory factors (MRFs). A wide array of proteins can interact with the MRFs, resulting in either induction or repression of their myogenic potential and subsequent MRF-mediated muscle-specific transcription. Findings published over the past few years have unambiguously established a key role for the p38 MAP kinase pathway in the control of muscle gene expression at different stages of the myogenic process. Here, we discuss the mechanisms by which p38 MAP kinase controls skeletal muscle differentiation by regulating the sequential activation of MRFs and their transcriptional coactivators, including chromatin remodeling enzymes.

Animals↗
PubMed1979

Ultrastructural radioautography and cytochemistry of lead absorption.

Lead is a universal environmental contaminant absorbed largely through the gastrointestinal tract by unknown mechanisms. Because lead absorption is influenced by iron content in the body and diet, we used ultrastructural radioautography and cytochemistry to study absorption of physiologic lead doses in the rat duodenal epithelial cell and compared these findings to those previously reported for iron absorption. Rat duodenal loops exposed in vivo to 210Pb for 1 minute demonstrated the majority of labels on the microvilli, terminal web, and apical cytoplasm. Specimens exposed to radiolead for 10 minutes demonstrated more abundant labeling with a relative increase in labeling of epithelial cell mitochondria, nuclei and basal cytoplasm, as well as phagocytic cells, endothelial cells, and circulating erythrocytes of the lamina propria. Timm's sulfide-silver method localized trace metals in epithelial cells. After administration of lead, a significant increase in staining was observed in microvilli, mitochondria, non-membrane-bound cytoplasm, and nuclear chromatin. The rapid appearance of absorbed lead in epithelial cell mitochondria and nuclei, as well as phagocytic cells in the lamina propria, was distinctly different from that reported for absorbed iron and suggests different mechanisms for the subcellular transport of these cations. The combination of radioautography and Timm's sulfide-silver staining provides the specificity and resolution needed for ultrastructural evaluation of lead absorption and should be useful in further studies of lead metabolism.

Animals↗
PubMed2003

A paradigm for gene regulation: inflammation, NF-kappaB and PPAR.

The onset of inflammatory gene expression is driven by the transcription factor NF-kappaB, whose transcriptional activity is regulated at multiple levels. First, NF-kappaB activity is regulated by cytoplasmic degradation of the IkappaB inhibitor and nuclear translocation. Second, the nuclear p65 transactivation potential can be further influenced by posttranslational modifications, such as phosphorylation and/or acetylation. The p65 phosphorylation is a process highly regulated by both cell- and stimulus-dependent activating kinases. Ser276 phosphorylation seems to be highly important considering its crucial role in the interaction with and the engagement of the cofactor CBP/p300. We have identified MSK1 as an acting kinase in the TNF-signalling pathway, where it is responsible for p65 phosphorylation at Ser276, as well as for H3 phosphorylation of Ser10 in IL-6 promoter-associated chromatin (Fig. 1) (Saccani et al., 2002; Vermeulen et al., 2002, 2003). To our knowledge, this was the first report that identifies one particular kinase involved in transcription factor phosphorylation and histone modification at the level of a single promoter in order to establish gene activation. The question of which element takes the initial step to recruit and to assemble the activated transcription complex still remains unanswered (Vanden Berghe et al., 2002). PPAR alpha negatively interferes with inflammatory gene expression by up-regulation of the cytoplasmic inhibitor molecule IkappaB alpha, thus establishing an autoregulatory loop (Fig. 1). This induction takes place in the absence of a PPRE, but requires the presence of NF-kappaB and Sp1 elements in the IkappaB alpha promoter sequence as well as DRIP250 cofactors. The detailed mechanism how PPAR can activate genes in a non-DNA-binding way needs further investigation; moreover, it is at present not clear whether this upregulation, unlike the inhibitory effect of glucocorticoids, is a cell type- or a PPAR-specific phenomenon.

Animals↗
PubMed1977

The structure of nuclear ribonucleoprotein of amphibian oocytes.

Nuclear RNP from Triturus oocytes is organized as strings of beads which can be converted into 20-nm-diameter monoparticles with mild RNase treatment or into 5-nm-thick linear fibrils with low salt treatment. The protein component comprises a heterogeneous size-range of polypeptides which differ from the polypeptides of the other nucleoproteins of oocytes. The RNA is of high molecular weight, sediments mostly in excess of 50 S, and is capable of assuming considerable secondary structure. Duplex regions in the form of hairpin loops are present and may serve as focal points in the condensation of the RNP transcript fibres to generate the periodic beaded structure. The structure of the beads may be maintained by means of protein-protein interaction since at salt concentrations between 1 and 2 M NaC1 all of the proteins are released in a cooperative manner as various sized aggregates which sediment at 15-30 s. There are no specific proteins obviously peculiar to either the beaded or the fibrillar RNP configuration. The various properties of nuclear RNP are compared with those of chromatin.

Animals↗
PubMed1992

Differential radioprotection of cultured human diploid fibroblasts and fibrosarcoma cells by WR1065.

The present studies were performed to determine whether WR1065, the dephosphorylated, free-thiol active metabolite of WR2721, could provide differential radioprotection of normal and tumor cell lines in vitro and secondly to investigate potential mechanisms for the selective nature of the radioprotection at the cellular and molecular level. When 4 mM WR1065 was administered 30 min prior to and during irradiation, a protection factor of 1.9 was obtained in clonogenic assays performed with normal human diploid fibroblasts (AG1522) while no protection of fibrosarcoma cells (HT1080) was observed. Some radioprotection of fibrosarcoma cells was observed with higher drug concentrations (10-40 mM), but the increase in survival was considerably less than the plateau level reached with the diploid fibroblasts (3-fold vs 24-fold at 6 Gy). The observation of such a selective effect in vitro with WR1065 indicates that differences in tissue-specific variables such as blood flow, pH, pO2, and drug dephosphorylation cannot solely account for the selective nature of the radioprotection afforded by WR2721 in vivo. Incubation of nucleoids with increasing concentrations of the DNA intercalating dye propidium iodide was used to titrate the ability of DNA to undergo supercoiling changes. The relaxation and rewinding of supercoiled DNA loops in isolated nucleoids serves as an indicator of both the presence of DNA damage and inherent differences in DNA loop characteristics. Fibrosarcoma cells had a much larger propidium iodide-relaxable DNA loop size than fibroblasts. The rewinding phase of the DNA supercoiling response is impaired by the presence of radiation-induced DNA strand breaks. Four mM WR1065 resulted in a significant reduction in the amount of rewinding inhibition observed after a dose of 10 Gy in diploid fibroblasts (protection factor = 1.43) but did not alter the response of irradiated fibrosarcoma cells. These results, indicating that WR1065 had a preferential radioprotective effect in vitro on both survival and the manifestation of DNA damage at the nucleoid level, are consistent with the hypothesis that cell type differences in chromatin organization and DNA-drug associations could play a role in the selective radioprotection.

Cell Survival↗
PubMed2004

Structure and DNA-binding sites of the SWI1 AT-rich interaction domain (ARID) suggest determinants for sequence-specific DNA recognition.

ARID (AT-rich interaction domain) is a homologous family of DNA-binding domains that occur in DNA-binding proteins from a wide variety of species, ranging from yeast to nematodes, insects, mammals, and plants. SWI1, a member of the SWI/SNF protein complex that is involved in chromatin remodeling during transcription, contains the ARID motif. The ARID domain of human SWI1 (also known as p270) does not select for a specific DNA sequence from a random sequence pool. The lack of sequence specificity shown by the SWI1 ARID domain stands in contrast to the other characterized ARID domains, which recognize specific AT-rich sequences. We have solved the three-dimensional structure of human SWI1 ARID using solution NMR methods. In addition, we have characterized nonspecific DNA binding by the SWI1 ARID domain. Results from this study indicate that a flexible, long, internal loop in the ARID motif is likely to be important for sequence-specific DNA recognition. The structure of the human SWI1 ARID domain also represents a distinct structural subfamily. Studies of ARID indicate that the boundary of DNA binding structural and functional domains can extend beyond the sequence homologous region in a homologous family of proteins. Structural studies of homologous domains such as the ARID family of DNA-binding domains should provide information to better predict the boundary of structural and functional domains in structural genomic studies.

Amino Acid Sequence↗
PubMed2000

Reversible and irreversible unfolding of mitotic newt chromosomes by applied force.

The force-extension behavior of individual mitotic newt chromosomes was studied, using micropipette surgery and manipulation, for elongations up to 80 times native length. After elongations up to five times, chromosomes return to their native length. In this regime chromosomes have linear elasticity, requiring approximately 1 nN of force to be stretched to two times native length. After more than five times stretching, chromosomes are permanently elongated, with force hysteresis during relaxation. If a chromosome is repeatedly stretched to approximately 10 times native length and relaxed, a series of hysteresis loops are obtained that converge to a single reversible elastic response. For further elongations, the linear dependence of force on extension terminates at a force "plateau" of approximately 15-20 nN, near 30 times extension. After >30 times extensions, the elastic moduli of chromosomes can be reduced by more than 20-fold, and they appear as "ghosts": swollen, elongated, and with reduced optical contrast under both phase and differential interference contrast imaging. Antibody labeling indicates that histone proteins are not being lost during even extreme extensions. Results are interpreted in terms of extension and failure of chromatin-tethering elements; the force data allow estimates of the number and size of such connectors in a chromosome.

Animals↗