Pausing and termination of human RNA polymerase II transcription at a procaryotic terminator

1983 ◽  
Vol 3 (10) ◽  
pp. 1687-1693
Author(s):  
G W Hatfield ◽  
J A Sharp ◽  
M Rosenberg
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Sequence Specificity ◽  
Late Promoter ◽  
Transcription System ◽  
A Cell ◽  
Major Late Promoter ◽  
Dyad Symmetry ◽  
Rna Polymerase Ii Transcription ◽  
Terminator Sequence

Kinetic analyses of runoff transcription in a cell-free eucaryotic transcription system revealed that the bacteriophage lambda 4S RNA terminator caused human RNA polymerase II to pause on the template and partially terminate transcription of transcripts initiated by the adenovirus 2 major late promoter. Analogous to the procaryotic RNA polymerase, the eucaryotic enzyme terminated just beyond the guanine-plus-cytosine-rich region of dyad symmetry in the terminator sequence. These results suggest that the eucaryotic RNA polymerase II may respond to transcription termination sequences similar to those used by the procaryotic enzyme. However, similar templates containing lambda tint or lambda tR1 terminators did not elicit pausing or termination, suggesting that other features, such as sequence specificity, may also be involved.

A family of complex tandem DNA repeats in the telomeres of Chironomus pallidivittatus

1994 ◽  
Vol 14 (12) ◽  
pp. 8028-8036
Author(s):  
Y J Zhang ◽  
I Kamnert ◽  
C C López ◽  
M Cohn ◽  
J E Edström
Keyword(s):  
Special Kind ◽  
Single Strand ◽  
Dna Repeats ◽  
Interspecies Comparison ◽  
Functional Roles ◽  
Paired Chromosome ◽  
Selective Forces ◽  
Small Clusters ◽  
Dyad Symmetry ◽  
Complex Block

A family of 340-bp tandem telomere-associated DNA repeats is present in 50- to 200-kb blocks in seven of the eight paired chromosome ends in Chironomus pallidivittatus. It consists of four main subfamilies, differing from each other by small clusters of mutations. This differentiation may reflect different functional roles for the repeats. Here we find that one subfamily, D3, is consistently localized most peripherally and extends close to the ends of the chromosomes, as shown by its sensitivity to the exonuclease Bal 31. The amounts of D3 are highly variable between individuals. The repeat characteristic for D3 forms a segment with pronounced dyad symmetry, which in single-strand form would give rise to a hairpin. Evidence from an interspecies comparison suggests that a similar structure is the result of selective forces. Another subfamily, M1, is present more proximally in a subgroup of telomeres characterized by a special kind of repeat variability. Thus, a complex block with three kinds of subfamilies may occupy different M1 telomeres depending on the stock of animals. We conclude that subfamilies are differentially distributed between and within telomeres and are likely to serve different functions.

Evolutionary divergence of the Citrobacter freundii tryptophan operon regulatory region: comparison with other enteric bacteria

1982 ◽  
Vol 152 (1) ◽  
pp. 57-62
Author(s):  
M Blumenberg ◽  
C Yanofsky
Keyword(s):  
Regulatory Region ◽  
Enteric Bacteria ◽  
Evolutionary Divergence ◽  
Citrobacter Freundii ◽  
Initial Portion ◽  
Trp Repressor ◽  
E Coli ◽  
Weak Expression ◽  
Dyad Symmetry ◽  
Trp Operon

The regulatory region of the trp operon of Citrobacter freundii was sequenced and compared with the corresponding regions of other enteric bacteria. Significant differences were noted in the promoter region. These differences are presumably responsible for the weak expression of the cloned trp operon in Escherichia coli. The presumed operator region, although nonfunctional in E. coli, has dyad symmetry, but the sequence of the symmetrical region differs appreciably from those of operators that can be regulated by the E. coli trp repressor. The sequence of the trp leader region of C. freundii resembles that of other enteric bacteria, suggesting that the C. freundii operon is also regulated by attenuation. Comparison of the sequence of the initial portion of trpE with the homologous regions of E. coli and Salmonella typhimurium indicates that the three organisms probably are evolutionary equidistant.

Interactions between DNA-bound trimers of the yeast heat shock factor

1994 ◽  
Vol 14 (1) ◽  
pp. 501-508
Author(s):  
J J Bonner ◽  
C Ballou ◽  
D L Fackenthal
Keyword(s):  
Heat Shock ◽  
Protein Complexes ◽  
Consensus Sequence ◽  
The Other ◽  
Inverted Repeats ◽  
Electrophoretic Mobilities ◽  
Naturally Occurring ◽  
Initial Identification ◽  
Dyad Symmetry ◽  
Chemical Cross Linking

The heat shock transcription factor (HSF) is a trimer that binds to DNA containing inverted repeats of the sequence nGAAn. HSF can bind DNA with the sequence nGAAnnTTCn or with the sequence nTTCnnGAAn, with little preference for either sequence over the other. However, (nGAAnnTTCn)2 is considerably less active as a heat shock response element (HSE) than is (nTTCnnGAAn)2. The electrophoretic mobilities of DNA-protein complexes and chemical cross-linking between protein monomers indicate that the sequence (nGAAnnTTCn)2 is capable of binding a single HSF trimer. In contrast, the sequence with higher biological activity, (nTTCnnGAAn)2, is capable of binding two trimers. Thus, the ability of four-nGAAn-element HSEs to bind one or two trimers depends on the permutation with which the elements are presented. A survey of naturally occurring HSEs shows the sequence (nTTCnnGAAn)2 to be the more prevalent. We suggest that the greater ability of one permutation over the other to bind two HSF trimers accounts for the initial identification of the naturally occurring heat shock consensus sequence as a region of dyad symmetry.

scholarly journals Molecular interactions in paracrystals of a fragment corresponding to the alpha-helical coiled-coil rod portion of glial fibrillary acidic protein: evidence for an antiparallel packing of molecules and polymorphism related to intermediate filament structure.

1989 ◽  
Vol 109 (1) ◽  
pp. 225-234 ◽  
Author(s):  
M Stewart ◽  
R A Quinlan ◽  
R D Moir
Keyword(s):  
Glial Fibrillary Acidic Protein ◽  
Molecular Interactions ◽  
Divalent Cations ◽  
Coiled Coil ◽  
Unit Cell ◽  
Acidic Protein ◽  
Filament Structure ◽  
Solution Studies ◽  
Dyad Symmetry ◽  
Fundamental Pattern

We have expressed in Escherichia coli a fragment of c-DNA that broadly corresponds to the alpha-helical coiled-coil rod section of glial fibrillary acidic protein (GFAP) and have used the resultant protein to prepare paracrystals in which molecular interactions can be investigated. An engineered fragment of mouse GFAP c-DNA was inserted into a modified version of the E. coli expression vector pLcII, from which large quantities of a lambda cII-GFAP rod fusion protein were prepared. A protein fragment corresponding to the GFAP rod was then obtained by proteolysis with thrombin. Paracrystals of this material were produced using divalent cations (Mg, Ca, Ba) in the presence of a chaotrophic agent such as thiocyanate. These paracrystals showed a number of polymorphic patterns that were based on a fundamental pattern that had dyad symmetry and an axial repeat of 57 nm. Analysis of both positive and negative staining patterns showed that this fundamental pattern was consistent with a unit cell containing two 48-nm-long molecules in an antiparallel arrangement with their NH2 termini overlapping by approximately 34 nm. More complicated patterns were produced by stacking the fundamental pattern with staggers of approximately 1/5, 2/5, and 1/2 the axial repeat. The molecular packing the unit cell was consistent with a range of solution studies on intermediate filaments that have indicated that a molecular dimer (i.e., a tetramer containing four chains or two coiled-coil molecules) is an intermediate in filament assembly. Moreover, these paracrystals allow the molecular interactions involved in the tetramer to be investigated in some detail.

scholarly journals The cis-Acting Family of Repeats Can Inhibit as well as Stimulate Establishment of an oriPReplicon

2001 ◽  
Vol 75 (22) ◽  
pp. 10709-10720 ◽  
Author(s):  
Elizabeth R. Leight ◽  
Bill Sugden
Keyword(s):  
Inhibitory Activity ◽  
Binding Sites ◽  
Replication Fork ◽  
Epigenetic Modification ◽  
Cell Generation ◽  
Dna Looping ◽  
Proliferating Cells ◽  
Cis Acting ◽  
The Family ◽  
Dyad Symmetry

ABSTRACT Previously we have shown that the establishment of anoriP replicon is dependent on its epigenetic modification, which occurs in only 1 to 10% of proliferating cells (E. R. Leight and B. Sugden, Mol. Cell. Biol. 21:4149–4161, 2001). To gain insights into the cis-acting requirements for the establishment of oriP replicons, we monitored the replication of oriP plasmid derivatives for several weeks following their introduction into cells. In EBNA-1-positive 143B and H1299 cells, plasmids containing only the region of dyad symmetry (DS) of oriP replicated but were lost more rapidly from cells than were oriP plasmids, demonstrating that the family of repeats (FR) of oriP acts in cis to stimulate replication in these cells. Unexpectedly, we found that the DS plasmid was established efficiently in 293/EBNA-1 cells, being lost at a rate of only 8% per cell generation over 24 days posttransfection. However, plasmids containing the FR in addition to the DS of oriPreplicated but were lost at a rate of approximately 30% per cell generation in 293/EBNA-1 cells, indicating that the FR inhibitsoriP's establishment in this cell line. FR's enhancement of transcription of a promoter in cis and FR's ability to inhibit replication fork movement do not account solely fororiP's inefficient establishment. In addition, DNA looping between FR and DS neither stimulates nor inhibits replication. Deletion of 11 EBNA-1 binding sites in the FR or replacement of the FR with DS sequences, however, does overcome the inhibitory activity of the FR, thereby allowing efficient establishment of the oriPderivative in 293/EBNA-1 cells.

Mutation of the c-fos gene dyad symmetry element inhibits serum inducibility of transcription in vivo and the nuclear regulatory factor binding in vitro

1987 ◽  
Vol 7 (3) ◽  
pp. 1217-1225
Author(s):  
M E Greenberg ◽  
Z Siegfried ◽  
E B Ziff
Keyword(s):  
Growth Factor ◽  
Nuclear Protein ◽  
Symmetry Element ◽  
Regulatory Sequence ◽  
In Vitro Mutagenesis ◽  
Regulatory Factor ◽  
Mobility Shift ◽  
Sequence Element ◽  
Dyad Symmetry

In vitro mutagenesis of a 61-base-pair DNA sequence element that is necessary for induction of the c-fos proto-oncogene by growth factors revealed that a small region of dyad symmetry within the sequence element is critical for c-fos transcriptional activation. The same c-fos dyad symmetry element was found to bind a nuclear protein in vitro, causing a specific mobility shift of this c-fos regulatory sequence. An analysis of insertion and deletion mutants established a strict correlation between the ability of the dyad symmetry element to promote serum activation of c-fos transcription and in vitro nuclear protein binding. These experiments suggest that the DNA mobility shift assay detects a nuclear protein that mediates growth factor stimulation of c-fos expression. In vitro competition experiments indicate that the c-fos regulatory factor also binds to sequences within another growth factor-inducible gene, the beta-actin gene.

scholarly journals The dyad symmetry element is the molecular target for c-fos induction and inhibition during K 562 differentiation along mutually exclusive lineages

Blood ◽  
1991 ◽  
Vol 77 (1) ◽  
pp. 55-63 ◽  
Author(s):  
D Trouche ◽  
P Robin ◽  
P Sassone-Corsi ◽  
WL Farrar ◽  
A Harel-Bellan
Keyword(s):  
Transcriptional Activation ◽  
Regulatory Element ◽  
Regulatory Region ◽  
Myeloid Cell ◽  
Leukemic Cell ◽  
Erythroid Differentiation ◽  
Symmetry Element ◽  
Differentiation Markers ◽  
K 562 Cells ◽  
Dyad Symmetry

Abstract The c-fos proto-oncogene seems to play an important role during differentiation and activation of cells from the hematopoietic lineage. Therefore, it is of interest to investigate the mechanism underlying its transcriptional activation in these cells. To delineate the sequences and factors involved in c-fos transcriptional activation during the course of myeloid cell differentiation, we have used the K 562 chronic leukemic cell line as a model. K 562 cells were transfected with chloramphenicol transacetylase (CAT) reporter constructs, including various regions of the human c-fos promoter, and induced to differentiate by two distinct agents: 12-O-tetradecanoyl phorbol-13- acetate (TPA), which activates a differentiation program along the megakaryoblastic pathway; and hemin, which induces erythroid differentiation. We show here that TPA treatment of K 562 cells induces fos CAT reporter constructs activation, whereas treatment with hemin does not. Furthermore, predifferentiation of the cells with hemin blocks a subsequent induction by TPA, in correlation with the inhibition by hemin of megakaryoblastic differentiation markers appearance. Both the induction by TPA and the inhibition by hemin are mediated by a dyad symmetry element (DSE) located in the upstream regulatory region, between -318 and -296. These results suggest that the protein complex binding to the DSE regulatory element is the target for c-fos activation by TPA and inhibition by hemin in K 562 cells. However, no modulation of protein affinity for the DSE sequence was detected by gel shift assay during the course of induction or inhibition, suggesting that the structural change responsible for the transcriptional modulation is too unstable or too subtle to be detected by this method.

scholarly journals Binding Site Determinants for the LysR-Type Transcriptional Regulator PcaQ in the Legume Endosymbiont Sinorhizobium meliloti

2007 ◽  
Vol 190 (4) ◽  
pp. 1237-1246 ◽  
Author(s):  
Allyson M. MacLean ◽  
Michelle I. Anstey ◽  
Turlough M. Finan
Keyword(s):  
Binding Site ◽  
Sinorhizobium Meliloti ◽  
Rhizobium Leguminosarum ◽  
Transcriptional Start Site ◽  
Mesorhizobium Loti ◽  
Equilibrium Dissociation ◽  
Dyad Symmetry

ABSTRACT LysR-type transcriptional regulators represent one of the largest groups of prokaryotic regulators described to date. In the gram-negative legume endosymbiont Sinorhizobium meliloti, enzymes involved in the protocatechuate branch of the β-ketoadipate pathway are encoded within the pcaDCHGB operon, which is subject to regulation by the LysR-type protein PcaQ. In this work, purified PcaQ was shown to bind strongly (equilibrium dissociation constant, 0.54 nM) to a region at positions −78 to −45 upstream of the pcaD transcriptional start site. Within this region, we defined a PcaQ binding site with dyad symmetry that is required for regulation of pcaD expression in vivo and for binding of PcaQ in vitro. We also demonstrated that PcaQ participates in negative autoregulation by monitoring expression of pcaQ via a transcriptional fusion to lacZ. Although pcaQ homologues are present in many α-proteobacteria, this work describes the first reported purification of this regulator, as well as characterization of its binding site, which is conserved in Agrobacterium tumefaciens, Rhizobium leguminosarum, Rhizobium etli, and Mesorhizobium loti.

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