Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Actively transcribing eukaryotic RNA polymerase II is highly phosphorylated on its repetitive carboxyl-terminal domain. We have isolated a protein kinase that phosphorylates serine residues in this repetitive domain. A component of this kinase is cdc2, the product of a cell-cycle control gene previously shown to be a component of M-phase-promoting factor and M-phase-specific histone H1 kinase. This observation suggests a role for the cdc2 protein kinase in transcriptional regulation.
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PMID:Phosphorylation of RNA polymerase by the murine homologue of the cell-cycle control protein cdc2. 266 13

To investigate the chromatin surrounding an active gene, we have determined the distribution of RNA polymerase molecules, the intactness of nucleosomal structure, and the subnuclear compartmentalization along 15 kilobase pairs (kb) of the mouse kappa immunoglobulin locus of MPC-11 plasmacytoma cells. Hybridization of in vitro nuclear transcripts to probes specific for the template strand reveals that transcription terminates within the region between 1.1 and 2.3 kb downstream from the poly(A) addition site. Ten different short sequences (8-13 base pairs) reside within 460 base pairs of this termination region that exhibit homology with sequences found in the termination regions of mouse beta-globin and chicken ovalbumin genes. Transcription of the nontemplate strand occurs on either side of this termination region. We find that both within the transcription unit and 6.5 kb downstream of the termination region of the kappa gene, the canonical nucleosomal structure is perturbed, the chromatin exhibits pronounced insolubility, and the nucleosomes liberated by micrococcal nuclease appear to lack histone H1. The insolubility is characterized by interactions that are disrupted by 0.3 to 0.6 M NaCl treatment. We conclude that the active chromatin phenotype spreads a considerable distance along the kappa locus, well beyond the region of transcription termination.
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PMID:Transcription termination and chromatin structure of the active immunoglobulin kappa gene locus. 308 10

An intervening sequence of 254 base pairs interrupts the coding region of the single gene for macronuclear histone H1 of the ciliated protozoan, Tetrahymena thermophila. The intervening sequence has splice junctions similar to those found in RNA polymerase II genes of other organisms. No obvious similarities are observed between this intron and the self-splicing intervening sequence of the Tetrahymena ribosomal gene. The derived amino acid sequence describes a small extremely basic H1 protein missing most of the central hydrophobic domain that is conserved in all other H1 proteins. Macronuclei divide amitotically, without chromosome condensation, suggesting the conserved globular domain of H1 plays a role in higher-order chromatin structure.
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PMID:An intervening sequence in an unusual histone H1 gene of Tetrahymena thermophila. 346 76

Facilitated diffusion accounts for the rapid rate of association of many bacterial DNA binding proteins with specific DNA sequences in vitro. In this mechanism the proteins bind at random to non-specific sites on the DAN and diffuse (by 'sliding' or 'hopping') along the DNA chain until they arrive at their specific functional sites. We have investigated whether such a mechanism can operate in chromatin by using a bacterial DNA binding protein, Escherichia coli RNA polymerase, that depends on linear diffusion to locate initiation sites on DNA. We have measured the competition between chromatin and its free DNA for the formation of initiation complexes. Only the short linker segments exposed by the removal of histone H1 are available for interaction with the polymerase, but the sparsely distributed promoter sites on the linker DNA of such a polynucleosome chain are located at the same rate as those on DNA. We conclude that the polymerase is free to migrate between the separate linker DNA segments of a polynucleosome chain to reach a promoter site. This chain thus permits the 'hopping' of proteins between neighboring linker segments in their search for a target site on the accessible DNA.
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PMID:Facilitated diffusion of a DNA binding protein on chromatin. 354 17

The dependence of chromatin conformation upon salt concentration has been studied for chicken ovalbumin and beta-globin genes isolated from oviduct and adult erythrocytes. At NaCl concentrations of 25 or 50 mM, the sedimentation properties, as a function of DNA size, of ovalbumin and globin chromatin are similar regardless of the source of the chromatin. In 100 mM NaCl, however, beta-globin chromatin isolated from erythrocytes sediments more slowly than an ovalbumin chromatin fraction from erythrocytes containing DNA of the same size. When the same experiment is carried out with material isolated from oviduct nuclei, the relative sedimentation rates are reversed, so that the ovalbumin chromatin sediments more slowly. This behavior cannot be accounted for by differences in binding of RNA polymerase or other molecules associated with transcription, or by partial aggregation of the chromatin. The most reasonable explanation is that transcriptionally active chromatin with a history of transcriptional activity, although largely covered with histones and capable of considerable compaction, is not able to form a fully compact structure as the ionic strength is raised. This behavior is consistent with a slight depletion in active chromatin of core histones or histone H1/H5 or both.
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PMID:Comparison of the folding of beta-globin and ovalbumin gene containing chromatin isolated from chicken oviduct and erythrocytes. 380 55

Light treatment of nuclei of Physarum polycephalum microplasmodia with DNase I, at low MgCl2 concentration (less than or equal to 3% DNA acid solubility, 0.1 mM MgCl2) selectively solubilizes a defined fraction of chromatin, in the form of a macromolecular complex. This fraction (up to 15% of the total chromatin) contains a full complement of the core histones and a reduced amount of histone H1, and is enriched in the high-mobility-group type of proteins. It is preferentially associated with nascent RNA and RNA polymerase B actively engaged in transcription. Digestion of DNAase-I-solubilized chromatin by micrococcal nuclease releases a size-heterogeneous population of cleavage products, indicative of lack of a typical nucleosomal packaging. It is concluded that the procedure used allows the isolation of structurally and functionally distinct regions of Physarum chromatin.
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PMID:Lack of nucleosomal structure in a DNase-I-solubilized transcriptionally active chromatin fraction of Physarum polycephalum. 397 88

This paper reports three experiments concerning the structural relationship between the Xenopus transcription factor IIIA (TFIIIA), the histone octamer and the Xenopus somatic gene for 5S RNA. Quantitative footprinting methods have been used in order to discover where and how TFIIIA and the histone octamer bind to the same gene independently and also in a triple complex. First, DNaseI and DNaseII protection experiments show that TFIIIA binds to positions 45-97 within the gene, in agreement with other workers. Second, the histone octamer takes up a unique, well-defined position with respect to DNA sequence. The nucleosome core extends to position 78 of the gene and therefore overlaps the TFIIIA binding region by approximately 35 bp. Third, it is shown that a triple complex can be formed between TFIIIA, the histone octamer and the 5S RNA gene. TFIIIA displaces the DNA from the histone surface in the 35-bp region of overlap. This has led to a three-dimensional model which explains how RNA polymerase III could interact simultaneously with transcription factors bound at the internal control region of the 5S RNA gene and the start point of transcription. The model also explains how histone H1 could repress transcription of 5S RNA genes.
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PMID:Structural analysis of a triple complex between the histone octamer, a Xenopus gene for 5S RNA and transcription factor IIIA. 409 86

The regulatory effects of host cellular histones on the transcription of simian virus 40 (SV40) DNA were investigated by using reconstituted and native SV40 nucleoprotein complexes (NPCs). Reconstituted NPCs were prepared from SV40 DNA and the combination fraction of five histones, H1, H2A, H2B, H3, and H4, isolated from the nuclei of permissive (CV-1) or nonpermissive (BALB/c 3T3, rat liver, and calf thymus) cells. Native NPCs were prepared by alkali disruption of purified SV40 virions. Nuclease digestion of these NPCs gave regular patterns of bands similar to those of SV40 NPCs from SV40-infected CV-1 cells, suggesting the presence of a nucleosomal structure. Transcription of NPCs was analyzed in vitro by using Escherichia coli DNA-dependent RNA polymerase. Both histone H1 and the fraction consisting of all five histones inhibited transcription of SV40 DNA by about 90 to 95%. The fraction consisting of four histones lacking H1 reduced the transcription by 30 to 35%, to a level similar to that of transcription with native NPCs. Transcription was inhibited regardless of whether the origin of histones was permissive or nonpermissive cells. Gel electrophoretic patterns of RNA products transcribed from SV40 DNA and reconstituted and native NPCs showed several identical peaks between 13S and 28S. The patterns were identical whether NPCs reconstituted with H1 alone, all five histones, or four histones lacking H1 were used.
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PMID:Transcription of reconstituted simian virus 40 nucleoprotein complexes. 624 6

Rat liver and simian virus 40 (SV40) chromatin were reconstituted in vitro under physiological conditions of ionic strength and temperature. The nucleosome assembly under the conditions was mediated in the presence of chromatin extracts, rich in nicking-closing activity, from rat liver or cultured CV-1 cells. The frequency of nucleosome assembly on DNA was dependent on both the incubation time and the weight ratio of histone to DNA. The regulatory effects of host cellular histones on the transcription of SV40 DNA were investigated by using reconstituted SV40 chromatin containing or lacking histone H1. The cellular histones composing the chromatin were prepared from permissive CV-1 cells. Transcription of chromatin was analyzed in vitro using Escherichia coli DNA-dependent RNA polymerase. The rate of incorporation of ribonucleoside triphosphates into RNA synthesized on SV40 chromatin containing Hl as the template was 5 to 10% of the rate for RNA synthesized on supercoiled SV40 DNA. The rate of incorporation for SV40 chromatin lacking Hl was approximately 40 to 50% of that for SV40 DNA. RNA products transcribed from both these chromatin and SV40 DNA were fairly homogeneous 16 to 28S species with several identical peaks.
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PMID:Reconstitution of chromatin at physiological ionic strength and regulation of transcription of the reconstituted chromatin. 626 4

Nuclear protein kinases include enzymes that transfer the gamma-phosphate of ATP to serine, threonine, lysine or histidine in proteins. Nuclear kinases with a preference for basic proteins are known as histone kinases; those preferring acidic protein substrates are casein kinases. Histone kinases include both cyclic AMP-independent protein kinases and cyclic AMP-dependent protein kinases. The best-characterized cyclic AMP-independent nuclear protein kinase is associated with cell proliferation and is activated (or transported to the nucleus) in G2 phase of the cell cycle. It phosphorylates specific serine and threonine residues in the non globular domains of histone H1 and appears to promote chromosome condensation. The cyclic AMP-dependent protein kinase has unknown nuclear function(s), although it may be translocated from cytoplasm to nucleus in response to specific hormonal stimuli which are also associated with changes in transcriptional activity. There is a massive peak of nuclear cyclic AMP-dependent protein kinase activity in G2 phase of the cell cycle. Nuclear casein kinases are apparently very heterogeneous. Two of these enzymes have been purified to homogeneity. They phosphorylate non-histone chromosomal proteins, including RNA polymerase and ornithine decarboxylase. Phosphorylated ornithine decarboxylase is inactive enzymatically but, in Physarum, it binds to the rDNA minichromosome and stimulates rRNA transcription. Kinases forming phosphoramidate bonds occur in a variety of rat tissues and form phosphohistide in histone H4 and phospholysine in histone H1.
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PMID:Nuclear protein kinases. 632 62


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