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

---

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

Mammalian gene promoters for transcription by RNA polymerase II are typically organized in the following order: upstream sequence motif(s)/TATA box/initiation site. Here we report studies in which the order, orientation and DNA sequences of these three elements are varied to determine how these affect polarity of transcription. We have constructed promoters with an 'octamer' upstream sequence ATTTGCAT (or its complement ATGCAAAT) in combination with several different TATA boxes and initiation (cap) sites, and tested these promoters in transfection experiments with cultured cells. TATA boxes derived from the adenovirus major late promoter (TATAAAA), immunoglobulin kappa light chain (TTATATA) and heavy chain (TAAATATA) promoter functioned equally well or even better when inverted. Only the beta-globin TATA box (CATAAAA) was poorly active when inverted. In addition, a symmetrical TATA box (TATATATA) derived from a casein gene was very active. Our results suggest that the asymmetry of most TATA boxes (consensus TATAAAA) is not a primary determinant of the polarity of transcription. We also found that the initiation (cap) site, which usually consists of an adenine embedded in a pyrimidine-rich region (PyPyCAPyPyPyPyPy), was permissive towards sequence alterations; even a randomly composed sequence worked well. However, an inverted, hence purine-rich, cap site reduced transcript levels to 1/7th, as did an oligo G sequence. Irrespective of the presence of a cap site, the configuration: 'TATA box/octamer' yielded a strong leftward, rather than rightward transcription. From this, we conclude that the polarity of transcription is primarily determined by the linear order of an upstream sequence relative to a TATA box, rather than by the individual orientations of either of these two elements.
...
PMID:Upstream box/TATA box order is the major determinant of the direction of transcription. 176

Transcription initiation by mammalian RNA polymerase II is effected by multiple common factors interacting through minimal promoter elements and regulated by gene-specific factors interacting with distal control elements. Minimal promoter elements that can function independently or together, depending on the specific promoter, include the upstream TATA box and a pyrimidine-rich initiator (Inr) overlapping the transcription start site. The binding of TFIID to the TATA element promotes the assembly of other factors into a preinitiation complex but factors which function at the Inr have not been defined. We show here that a novel factor (TFII-I) binds specifically to Inr elements, supports basal transcription from the adenovirus major late promoter and is immunologically related to the helix-loop-helix activator USF. We further show that TFII-I also binds to the upstream high-affinity USF site (E box), that USF also binds to the Inr, and that TFII-I and USF interact cooperatively at both Inr and E box sites. Thus, TFII-I represents a novel type of transcription initiation factor whose interactions at multiple promoter elements may aid novel communication mechanisms between upstream regulatory factors and the general transcriptional machinery.
...
PMID:Cooperative interaction of an initiator-binding transcription initiation factor and the helix-loop-helix activator USF. 196 Dec 51

We have investigated whether DNA modified at a d(GG) or a d(AG) site by the chemotherapeutic drug cis-diamminedichloroplatinum(II) (cis-DDP) can be used as template by wheat germ RNA polymerase II. The templates used in the present study were obtained by ligation of double-helical oligodeoxyribonucleotides, containing 18 pyrimidine bases and 2 central dG, or dA and dG, bases on one strand and 18 purine bases and 2 central dC, or dT and dC, bases on the complementary strand. Therefore, the cis-DDP adducts are only present on one strand of each of the two templates and are regularly spaced by 18 pyrimidine bases. These constructs allowed us to investigate the effect of cis-DDP on transcription of the platinated strand and of the complementary unplatinated sequence. Transcription experiments were carried out in the presence of dinucleotide primers and either a single triphosphate substrate (abortive elongation) or the full set of triphosphate substrates dictated by the template sequence (productive elongation). The results show that the eucaryotic RNA polymerase can catalyze dinucleotide-primed reactions on platinated DNA. However, the eucaryotic enzyme behaved very differently depending on which strand was transcribed. Thus, transcription elongation was completely blocked on the strand carrying the metal complex, whereas transcription elongation was not blocked on the complementary template strand. However, on this latter strand and with the platinated polymers, productive elongation was slightly inhibited. Furthermore, abortive elongation leading to dinucleotide-primed trinucleotide formation was enhanced on the template strand complementary to that carrying the cis-DDP adducts.(ABSTRACT TRUNCATED AT 250 WORDS)
...
PMID:Transcription by eucaryotic and procaryotic RNA polymerases of DNA modified at a d(GG) or a d(AG) site by the antitumor drug cis-diamminedichloroplatinum(II). 198 23

Interaction of purified eukaryotic RNA polymerase II with various synthetic palindromic DNA sequences is associated with the formation of transcriptional complexes of different stabilities, i.e. having different propensities for releasing the nascent transcript. This phenomenon was observed by using wheat-germ RNA polymerase II and a series of double-stranded template polymers containing palindromic repeating motifs of 6-16 bp, with regulatory alternating purine and pyrimidine bases such as d[ATA(CG)nC].d[TAT(GC)nG], with n = 1, 3 or 6 referred to as d(GC), d(GC)3 or d(GC)6, respectively. We also synthesized two double-stranded methylated polymers, containing the repeating units d(ATAm5CGm5C).d(TATGm5CG) and d[ATA(m5CG)6m5C].d[TAT(Gm5C)6G] [designated d(GmC) and d(GmC)6, respectively]. All of these polymers served as templates for the reaction of single-step addition of CTP to a CpG primer catalysed by wheat-germ RNA polymerase II, to an extent that seems well correlated with the number of potential initiation sites within the DNA molecules. Furthermore, in these reactions, the enzyme appears to form relatively stable transcriptional complexes, as trinucleotide product was released only very slowly. In marked contrast to the results with the CpG primer, the single-step addition reaction primed by UpA, i.e. the synthesis of UpApU proceeded at a much higher velocity and was strongly enhanced by increasing the d(G-C) content of the repeating units of the DNA polymers. Thus, taking into account the number of potential sites at which UpApU synthesis could occur, the extent of UpApU synthesis was increased about 12-fold with d(GC)6 compared to that with the d(GC) template. The catalytic nature of the reaction necessarily implies that the stability of the transcription complexes with the plant RNA polymerase II decreased as the d(G-C) content of the repeating motif increased. Furthermore, although the synthesis of CpGpC could be demonstrated with d(GmC)6 as template, the UpA-primed synthesis of UpApU could not be detected with this polymer. The results obtained in transcription of these polymers are discussed in relation to the potential involvement of palindromic DNA in transcription termination and attenuation in the presence of RNA polymerase II.
...
PMID:Transcription of synthetic DNA containing sequences with dyad symmetry by wheat-germ RNA polymerase II. Increased rates of product release in single-step addition reactions. 199 1

The human T cell-specific transcription factor TCF-1 alpha plays a key role in the tissue-specific activation of the T cell receptor (TCR) C alpha enhancer and binds to pyrimidine-rich elements (5'-PyCTTTG-3') present in a variety of other T cell-specific control regions. Using amino acid sequence information derived from the DNA affinity-purified protein, we have now isolated cDNA clones encoding TCF-1 alpha. The TCF-1 alpha cDNA contains a single 68-amino-acid domain that is homologous to a region conserved among high-mobility group (HMG) and nonhistone chromosomal proteins. Expression of full-length and mutant cDNA clones in bacteria reveal that the single HMG motif, which is predicted to contain two extended alpha-helical segments, is sufficient to direct the sequence-specific binding of TCF-1 alpha to DNA. Northern blot experiments demonstrate further that TCF-1 alpha mRNA is highly tissue specific, found primarily in the thymus or T cell lines. The immature CEM T cell line expresses relatively low levels of TCF-1 alpha mRNA, which are increased upon activation of these cells by phorbol esters. Interestingly, the cloned TCF-1 alpha protein is a potent transcriptional activator of the human TCR alpha enhancer in nonlymphoid cell lines, whereas the activity of the endogenous protein in T cell lines is strongly dependent on an additional T cell-specific protein that interacts with the core enhancer. TCF-1 alpha is currently unique among the newly emerging family of DNA-binding regulatory proteins that share the HMG motif in that it is a highly tissue-specific RNA polymerase II transcription factor.
...
PMID:A thymus-specific member of the HMG protein family regulates the human T cell receptor C alpha enhancer. 201 90

Ribosomal protein S1 is known to play an important role in translational initiation, being directly involved in recognition and binding of mRNAs by 30S ribosomal particles. Using a specially developed procedure based on efficient crosslinking of S1 to mRNA induced by UV irradiation, we have identified S1 binding sites on several phage RNAs in preinitiation complexes. Targets for S1 on Q beta and fr RNAs are localized upstream from the coat protein gene and contain oligo(U)-sequences. In the case of Q beta RNA, this S1 binding site overlaps the S-site for Q beta replicase and the site for S1 binding within a binary complex. It is reasonable that similar U-rich sequences represent S1 binding sites on bacterial mRNAs. To test this idea we have used E. coli ssb mRNA prepared in vitro with the T7 promoter/RNA polymerase system. By the methods of toeprinting, enzymatic footprinting, and UV crosslinking we have shown that binding of the ssb mRNA to 30S ribosomes is S1-dependent. The oligo(U)-sequence preceding the SD domain was found to be the target for S1. We propose that S1 binding sites, represented by pyrimidine-rich sequences upstream from the SD region, serve as determinants involved in recognition of mRNA by the ribosome.
...
PMID:Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1. 201 95

Purine and pyrimidine adducts of alpha-methylene-gamma-lactone demonstrated potent cytotoxicity against murine L1210 lymphoid leukemia growth as well as a variety of human tissue cultured tumors. The most potent compound, 9-[(2-methyl-4-methylene-5-oxotetrahydrofuran-2-yl)-methyl 1] adenine 1 demonstrated significant inhibition of DNA synthesis in L1210 leukemic cells with moderate inhibition of protein synthesis. The major enzyme activities inhibited by 1 were DNA polymerase alpha, ribonucleoside reductase and t-RNA polymerase with marginal inhibition of thymidine kinase, TMP kinase, PRPP amidotransferase and IMP dehydrogenase. The inhibition of DNA polymerase alpha activity by 1 was evident at the lowest concentration 25 microM and was evident within 15 min incubation at 100 microM. The magnitude of enzyme inhibition was consistent with the observed DNA synthesis inhibition by 1. The only deoxyribonucleotide level reduced by 1 was the dATP pool level. U.V. absorption of DNA after interacting with 1 demonstrated a hyperchromic effect and L1210 DNA strand scission was observed after 24 hr incubation with 1 suggesting some type of interference with the DNA template by the drug.
...
PMID:The effects of alpha-methylene-gamma-lactone purines and pyrimidines on L1210 lymphoid leukemia nucleic acid metabolism. 201 69

It has been reported that pyrimidine dimers (pyrimidine mean value of pyrimidine) are removed preferentially from actively transcribing genes. Furthermore, the preferential repair is restricted to the transcribed strand of these genes. Currently there is no mechanistic explanation for these phenomena. In this study we investigated the effect of transcription on nucleotide excision repair using defined Escherichia coli systems consisting of DNA substrates containing a strong promoter and either (a) a T mean value of T at a defined position in the nontranscribed or transcribed strand or (b) photoproducts randomly distributed in both strands, as well as transcription and nucleotide excision repair enzymes. While a T mean value of T in the nontranscribed strand had no effect on transcription, a photodimer in the transcribed strand blocked transcription causing RNA polymerase to stall at the T mean value of T site. This stalled elongation complex inhibited the excision of the photodimer by (A)BC excinuclease resulting in a net effect of preferential repair of the nontranscribed strand in a mixture containing both substrates. Similarly, when we conducted transcription/repair experiments with a superhelical plasmid no enhanced repair of the transcribed gene was observed compared to nontranscribed regions. We conclude that RNA polymerase stalled at a photodimer does not direct the (A)BC excinuclease to the damaged template strand and therefore cannot account for the strand-specific repair observed in vivo.
...
PMID:Transcription preferentially inhibits nucleotide excision repair of the template DNA strand in vitro. 225 27

Mitochondrial promoters in Saccharomyces cerevisiae contain an identical octanucleotide [sequence: see text] sequence present just upstream of the initiation site (at the left end of the arrow). Studies have shown that the transcription rates of mitochondrial genes vary from 7- to 15-fold. The nucleotide at position +2 regulates the efficiency of mitochondrial promoters but does not affect the specificity of initiation. The data presented herein demonstrate that the variable transcription rates of mitochondrial genes are due to different levels of transcriptional initiation. The rate of first phosphodiester bond formation between a purine and a pyrimidine on a weak promoter is much lower than that of purine-purine on a strong promoter. A dinucleotide corresponding to positions +1 and +2 acts in vitro as a primer, bypassing the first phosphodiester bond formation at the initiation site. When these dinucleotides were used to prime transcription, the activities of the strong and weak promoters were found to be identical. In heparin-challenge experiments, there is no significant effect of dinucleotide on heparin-resistant DNA-RNA polymerase complex formation. These results indicate that the low level of transcription from the weak mitochondrial promoter is due to the slow rate of formation of the first phosphodiester bond.
...
PMID:Control of mitochondrial gene expression in the yeast Saccharomyces cerevisiae. 225 Dec 75

A low-molecular-weight RNA species from mouse ascites cells has been selected and purified by its intermolecular RNA X RNA hybridization capabilities. This 4.5S RNA is able to base pair with poly(A)+ mRNA sequences and with 18S rRNA. Melting experiments have shown that the intermolecular hybrids formed with this complementary low-molecular-weight RNA are of comparable stability to other RNA X RNA interactions. Analysis has shown that this hybridizing RNA is 87 nucleotides long and has an unusual sequence structure. Located near the 3' terminus is an alternating pyrimidine dinucleotide region of UUCCUUCCUU. This region along with the 3'-adjacent nucleotides form a 14-nucleotide sequence that exhibits perfect complementarity with 18S rRNA. An additional region of 10 nucleotides at the 3' terminus is perfectly homologous to a similarly located sequence in 5.8S rRNA. An obvious RNA polymerase III binding site is not found internally in this low-molecular-weight RNA sequence. The complementary and homologous character of hybridizing RNA with respect to rRNA and mRNA sequences suggests a potential regulatory role for this RNA in the coupling of ribosome and mRNA functions.
...
PMID:A low-molecular-weight RNA from mouse ascites cells that hybridizes to both 18S rRNA and mRNA sequences. 242 2


<< Previous 1 2 3 4 5 6 7 8 9 10 Next >>

---