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)

A new affinity chromatographic procedure for the separation of transcriptionally active nucleosomes has been used to study the changes that take place in chromatin structure along the c-fos and c-myc genes when RNA synthesis is inhibited. Mercury-affinity chromatography separates the sulfhydryl-reactive nucleosomes of transcriptionally active genes from the compactly beaded, non-reactive nucleosomes of transcriptionally inert DNA sequences. The new procedure also discriminates between nucleosomes that have "unfolded" to reveal the previously shielded SH groups of histone H3 and nucleosomes that bind to the mercury column because of their association with thiol-containing non-histone proteins located in the transcription unit. Both classes of Hg-bound nucleosomes contain the c-fos and c-myc sequences, but only when they are being transcribed. We compared the effects of alpha-amanitin and actinomycin D on the transcription of c-fos and c-myc with the effects of each inhibitor on the distribution of the corresponding oncogenic DNA sequences in the chromatographically separated nucleosome fractions. It was found that the inhibition of RNA polymerase II by alpha-amanitin (added at the peaks of c-fos or c-myc expression in serum-stimulated BALB/c 3T3 cells) resulted in a rapid loss of affinity of the oncogene-containing nucleosomes for the mercury column. There was no corresponding effect on the mercury-binding properties of nucleosomes containing 28 S ribosomal gene sequences, which continue to be transcribed by amanitin-resistant RNA polymerase I. Therefore, the binding of the c-fos and c-myc nucleosomes to the mercury column seems to depend upon reversible structural changes associated with their transcription. Surprisingly, there was no corresponding loss of affinity of the c-fos and c-myc nucleosomes for the mercury column when actinomycin D was employed to inhibit RNA synthesis, despite the fact that transcription of both genes had been arrested abruptly. Measurements of [3H]actinomycin D binding show its preferential intercalation into the transcriptionally active nucleosomes. We suggest that the intercalation of actinomycin D into the DNA of active nucleosomes can lock the transcription complex into an "unfolded" but potentially active configuration. This was confirmed by run-off transcription assays showing a restoration of c-fos and c-myc RNA synthesis when actinomycin D was displaced by proflavine.
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PMID:Reversible and irreversible changes in nucleosome structure along the c-fos and c-myc oncogenes following inhibition of transcription. 232 30

The core histone mRNA levels in terminally differentiated L6 myotubes decrease to less than 5% of the amount present in proliferating myoblasts in parallel with the cessation of DNA synthesis (Bird, RC., Jacobs, F.A., Stein, G., Stein, J. and Sells, B.H. (1985) Biochim. Biophys. Acta 824, 209-217). The role of gene transcription in the down-shift of histone mRNA levels was assessed using a cell-free system. The level of transcription from the differentiation-independent adenovirus major late promoter was directly related to the RNA polymerase II activity of myoblast and myotube nuclear extracts. In addition, both extracts actively transcribed the histone H4 gene template containing only the 5 proximal promoter region (-210 bp). In contrast, inclusion of the distal-proximal promoter region (-410 to -210 bp) in the template resulted in a 60% decrease in transcription by the myotube extract. A similar down-shift in transcription of the histone H3 gene template (containing 900 bp 5 of the initiation site) by myotube nuclear extracts was also observed. The decrease in histone mRNA levels in myotubes may therefore be controlled in part by a transcriptional mechanism involving a negative regulatory factor.
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PMID:Down-regulation of histone H3 and H4 gene transcription in differentiated L6 myotubes. 255 1

The histone H3 and H4 genes are shown to be expressed in both Arabidopsis plantlets and transitory multicellular suspension. The 5'- and 3'-ends of the H4 mRNAs have been localized on two H4 genes previously sequenced, H4A748 and H4A777. S1-nuclease mapping and reverse-transcriptase-primer-elongation experiments revealed the existence of two start points for transcription, located 31 and 37 nucleotides downstream from the TATA-box. The 3'-end of the mRNA corresponding to H4A748 was localized at 177 nt after the stop codon. The other gene, H4A777, most probably is not expressed. In addition to a long 3'-untranslated region, the H4 mRNA was shown to be polyadenylated in both plantlets and cell-suspension. This observation was extended to the H3 mRNAs of Arabidopsis and of two other dicots, tobacco and sunflower. Previous results on maize H3 and H4 mRNAs suggest that polyadenylation is a common feature for histone mRNAs in higher plants.
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PMID:Polyadenylation of histone H3 and H4 mRNAs in dicotyledonous plants. 290 89

We have examined the process by which the 3' terminus of the Drosophila histone H3 mRNA is produced in vitro. When a template containing a portion of DNA that flanks the normal 3' end of the histone H3 gene and an oligo dC tail on the template strand is transcribed in vitro by Drosophila RNA polymerase II, transcription continues beyond the 3' end of the H3 gene. A processing activity was identified that cleaves the precursor transcript generating an RNA species with the same 3' end as the mature H3 mRNA. The processing activity was partially purified by ion exchange chromatography and sucrose gradient sedimentation. The isolated activity was found to require Mg++ but did not require addition of a nucleoside triphosphate for activity. The activity sedimented with a molecular weight of approximately 140,000 daltons. Transcription of the template and processing of the RNA can be uncoupled in vitro.
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PMID:The 3' end of drosophila histone H3 mRNA is produced by a processing activity in vitro. 643 43

Drosophila RNA polymerase II requires at least two chromatographically distinct transcription factors (designated A and B) to initiate transcription accurately in vitro. We describe the partial purification and concentration of one of these transcription factors, the B factor. Footprint analysis of the B fraction demonstrated the presence of a sequence-specific DNA-binding component in the transcription factor preparation. This component binds specifically to a 65 bp region of DNA surrounding the start point of transcription of the histone H3, H4, and actin 5C genes. Included in this binding region is the TATA box, the start point of transcription, and a portion of the leader region. The pattern of protection from DNAase I cleavage on the coding strand of the histone H3 gene is asymmetric with regard to the complementary noncoding strand. Sequence-specific binding of the B fraction occurs in the apparent absence of RNA polymerase II. The potential function of the binding component in the initiation of transcription by RNA polymerase II is discussed.
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PMID:A Drosophila RNA polymerase II transcription factor contains a promoter-region-specific DNA-binding activity. 653 4

We have adapted the oocyte injection procedure for the detection of regulatory components involved in the transcription of a eukaryotic mRNA gene. Injection of the histone gene repeat h22 DNA of Psammechinus miliaris into the Xenopus oocyte nucleus results in correct initiation of the histone mRNAs, but readthrough by RNA polymerase occurs at the 3' end of the H3 histone gene (Hentschel, C. C., Probst, E. & Birnstiel, M. L. (1980) Nature (London) 288, 100-102). Coinjection into the oocyte of a chromosomal salt wash fraction derived from sea urchin embryos results in the generation of authentic 3' termini of the histone H3 mRNA. We have partially purified the protein component by column chromatography and density gradient centrifugation. The regulatory factor binds to heparin columns and, hence, has the properties anticipated of an RNA- or DNA-binding protein. The sedimentation coefficient of the active component was determined to be about 12 S, suggesting a molecular weight of 200,000-250,000.
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PMID:Bioassay for components regulating eukaryotic gene expression: a chromosomal factor involved in the generation of histone mRNA 3' termini. 695 9

Histone octamers or histone H3/H4 tetramers were reconstituted onto either closed circular plasmids containing a single Xenopus 5S rRNA gene or a reiterated array of Lytechinus 5S rRNA genes. All "reconstitutes" were found to undergo both Na(+)-dependent and Mg(2+)-dependent compaction. However, in each case, the compaction of nucleosomal templates containing H2A/H2B was much more extensive than compaction of templates containing only H3/H4 tetramers. Inclusion of 5 mM MgCl2 in the transcription buffer increased the level of compaction of nucleosomal templates and led to a marked inhibition of both transcription initiation and elongation by RNA polymerase III. The inhibitory effect of Mg2+ was reduced significantly when DNA templates contained only H3/H4 tetramers, consistent with their lesser extent of Mg(2+)-dependent compaction. Thus, the removal of histones H2A/H2B from nucleosomal arrays enhances gene activity, in part because of decreased levels of chromatin folding.
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PMID:A role for histones H2A/H2B in chromatin folding and transcriptional repression. 813 97

Mutant a and alpha yeast cells were created with histone H3 containing cysteine in place of alanine 110. Because transcriptionally active nucleosomes "unfold" to reveal the histone H3-thiol groups at the center of the core, the active nucleosomes of the mutant strain can be isolated by mercury-affinity chromatography. We compared the unbound and mercury-bound nucleosomes of haploid H3-mutant strains expressing either the MAT alpha or the MATa mating-type locus. In a MAT alpha strain, the Hg-bound nucleosomes are enriched in MAT alpha DNA but lack the DNA of the transcriptionally silent HMRa mating-type locus. Conversely, in a MATa strain, the Hg-bound nucleosomes are enriched in MATa DNA sequences but deficient in HML alpha DNA. When the SIR3 gene, known to be required for silencing of the repressed mating-type loci, is mutated in the MAT alpha strain, transcription of the HMRa ensues, and its nucleosomes, as well as those of the MAT alpha locus, are retained by the organomercurial column. It follows that derepression of the silent mating-type locus, caused by the sir3 null mutation, is accompanied by an unfolding of its nucleosomes to reveal the histone H3 SH groups at their centers. Nucleosomes of the pheromone-encoding gene MFA2, a gene that is expressed in MATa cells but not in MAT alpha cells, are bound to the organomercurial column when isolated from MATa cells but not from MAT alpha cells. Thus, there is a good correlation between nucleosome unfolding and the renewed transcriptional activity at mating-type loci, and at MFA2, which had been silenced for prolonged periods. A close temporal correlation between nucleosome refolding and the cessation of transcription is not always observed in yeast, however, in contrast to observations in mammalian cells. For example, nucleosomes of the GAL1 gene are maintained in a "poised" or "primed" thiol-reactive state even when the gene is not being transcribed (Chen, T. A., Smith, M. M., Le, S., Sternglanz, R., and Allfrey, V. G. (1991) J. Biol. Chem. 266, 6489-6498). It follows that the unfolding of the nucleosome cores of the yeast H3 mutant is regulated by factors that are not temporally linked to the recruitment or traverse of the RNA polymerase complex, but which may determine the rate at which different domains of chromatin adapt to the need for transcription of the associated DNA sequences.
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PMID:Nucleosome structural changes during derepression of silent mating-type loci in yeast. 841 18

Analyses of Drosophila cells have revealed that RNA polymerase II is paused in a region 20 to 40 nucleotides downstream from the transcription start site of the hsp70 heat shock gene when the gene is not transcriptionally active. We have developed a cell-free system that reconstitutes this promoter-proximal pausing. The paused polymerase has been detected by monitoring the hyperreactivity of thymines in the transcription bubble toward potassium permanganate. The pattern of permanganate reactivity for the hsp70 promoter in the reconstituted system matches the pattern found on the promoter after it has been introduced back into files by P-element-mediated transposition. Matching patterns of permanganate reactivity are also observed for a non-heat shock promoter, the histone H3 promoter. Further analysis of the hsp70 promoter in the reconstituted system reveals that pausing does not depend on sequence-specific interactions located immediately downstream from the pause site. Sequences upstream from the TATA box influence the recruitment of polymerase rather than the efficiency of pausing. Kinetic analysis indicates that the polymerase rapidly enters the paused state and remains stably in this state for at least 25 min. Further analysis shows that the paused polymerase will initially resume elongation when Sarkosyl is added but loses this capacity within minutes of pausing. Using an alpha-amanitin-resistant polymerase, we provide evidence that promoter-proximal pausing does not require the carboxy-terminal domain of the polymerase.
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PMID:Analyses of promoter-proximal pausing by RNA polymerase II on the hsp70 heat shock gene promoter in a Drosophila nuclear extract. 881 56

The highly expressed mouse histone H2a-614 gene is located 800 nt 5' of the histone H3-614 gene. There is a 140 nt sequence located 500 nt from the end of the H2-614 mRNA which has been defined as a transcription termination site for RNA polymerase II. We established an in vitro transcription system in which both 3' end processing and transcription termination occur. A template containing the adenovirus major late promoter, a portion of the histone H2a-614 coding region, its 3' processing signal, followed by the transcription termination site was transcribed in a nuclear extract prepared from mouse myeloma cells. Some of the transcripts synthesized in the extract were cleaved at the histone processing site in a reaction which was dependent both on the hairpin binding factor and the U7 snRNP. The efficiency of histone 3' end formation was similar both on synthetic transcripts and transcripts synthesized by RNA polymerase II. Defined transcripts, which were not processed and which mapped to the transcription termination site, were released from the template, suggesting that they were formed by transcription termination. Termination in vitro was dependent on a functional histone processing signal.
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PMID:3' Processing and termination of mouse histone transcripts synthesized in vitro by RNA polymerase II. 887 61


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