scholarly journals Transition mutations within the Xenopus borealis somatic 5S RNA gene can have independent effects on transcription and TFIIIA binding.

1987 ◽  
Vol 7 (1) ◽  
pp. 486-494 ◽  
Author(s):  
G A McConkey ◽  
D F Bogenhagen
Keyword(s):  
Fine Structure ◽  
Control Region ◽  
Tight Binding ◽  
Sequence Determination ◽  
5S Rna ◽  
Distal Half ◽  
Transcription Efficiency ◽  
Transcription Complexes ◽  
Independent Effects ◽  
Xenopus Borealis

Base-pair changes were introduced into the Xenopus borealis somatic 5S RNA gene by treatment with sodium bisulfite. Mutants were screened by sequence determination. The collection of mutants permitted a detailed investigation of the fine structure of the intragenic control region that binds the transcription factor TFIIIA. Selected mutants were recloned in tandem with a somatic 5S RNA maxigene to permit sensitive measurement of their relative transcription activities. The transcription efficiencies of a number of mutations at the borders of the control region were correlated with TFIIIA binding by using DNase I protection (footprinting) assays. Mutations affecting transcription and TFIIIA binding extended from gene residues 46 to 91. The results reinforce a model in which the distal half of the protected region constitutes a tight binding domain for TFIIIA. A number of transitions in the 5' domain led to significant increases or decreases in transcription efficiency, but resulted in barely detectable changes in TFIIIA binding. Two mutants with C----T transitions at gene residues 52 and 53 were transcribed with increased efficiencies (up phenotype). These results suggest that TFIIIA must make appropriate contacts within the 5' domain of the control region to permit subsequent binding of other factors in stable transcription complexes.

Transition mutations within the Xenopus borealis somatic 5S RNA gene can have independent effects on transcription and TFIIIA binding

1987 ◽  
Vol 7 (1) ◽  
pp. 486-494
Author(s):  
G A McConkey ◽  
D F Bogenhagen
Keyword(s):  
Fine Structure ◽  
Control Region ◽  
Tight Binding ◽  
Sequence Determination ◽  
5S Rna ◽  
Distal Half ◽  
Transcription Efficiency ◽  
Transcription Complexes ◽  
Independent Effects ◽  
Xenopus Borealis

Base-pair changes were introduced into the Xenopus borealis somatic 5S RNA gene by treatment with sodium bisulfite. Mutants were screened by sequence determination. The collection of mutants permitted a detailed investigation of the fine structure of the intragenic control region that binds the transcription factor TFIIIA. Selected mutants were recloned in tandem with a somatic 5S RNA maxigene to permit sensitive measurement of their relative transcription activities. The transcription efficiencies of a number of mutations at the borders of the control region were correlated with TFIIIA binding by using DNase I protection (footprinting) assays. Mutations affecting transcription and TFIIIA binding extended from gene residues 46 to 91. The results reinforce a model in which the distal half of the protected region constitutes a tight binding domain for TFIIIA. A number of transitions in the 5' domain led to significant increases or decreases in transcription efficiency, but resulted in barely detectable changes in TFIIIA binding. Two mutants with C----T transitions at gene residues 52 and 53 were transcribed with increased efficiencies (up phenotype). These results suggest that TFIIIA must make appropriate contacts within the 5' domain of the control region to permit subsequent binding of other factors in stable transcription complexes.

scholarly journals Fine-Structure Analysis of Ribosomal Protein Gene Transcription

2006 ◽  
Vol 26 (13) ◽  
pp. 4853-4862 ◽  
Author(s):  
Yu Zhao ◽  
Kerri B. McIntosh ◽  
Dipayan Rudra ◽  
Stephan Schawalder ◽  
David Shore ◽  
...  
Keyword(s):  
Fine Structure ◽  
Ribosomal Protein ◽  
Transcription Initiation ◽  
Tight Binding ◽  
Ribosomal Protein Gene ◽  
Initiation Site ◽  
Glycolytic Enzyme ◽  
Yeast Genome ◽  
Ribosomal Protein Genes ◽  
Active Transcription

ABSTRACT The ribosomal protein genes of Saccharomyces cerevisiae, responsible for nearly 40% of the polymerase II transcription initiation events, are characterized by the constitutive tight binding of the transcription factor Rap1. Rap1 binds at many places in the yeast genome, including glycolytic enzyme genes, the silent MAT loci, and telomeres, its specificity arising from specific cofactors recruited at the appropriate genes. At the ribosomal protein genes two such cofactors have recently been identified as Fhl1 and Ifh1. We have now characterized the interaction of these factors at a bidirectional ribosomal protein promoter by replacing the Rap1 sites with LexA operator sites. LexA-Gal4(AD) drives active transcription at this modified promoter, although not always at the correct initiation site. Tethering Rap1 to the promoter neither drives transcription nor recruits Fhl1 or Ifh1, showing that Rap1 function requires direct DNA binding. Tethering Fhl1 also fails to activate transcription, even though it does recruit Ifh1, suggesting that Fhl1 does more than simply provide a platform for Ifh1. Tethering Ifh1 to the promoter leads to low-level transcription, at the correct initiation sites. Remarkably, activation by tethered LexA-Gal4(AD) is strongly reduced when TOR kinase is inhibited by rapamycin. Thus, TOR can act independently of Fhl1/Ifh1 at ribosomal protein promoters. We also show that, in our strain background, the response of ribosomal protein promoters to TOR inhibition is independent of the Ifh1-related protein Crf1, indicating that the role of this corepressor is strain specific. Fine-structure chromatin mapping of several ribosomal protein promoters revealed that histones are essentially absent from the Rap1 sites, while Fhl1 and Ifh1 are coincident with each other but distinct from Rap1.

TFIIIA binds to different domains of 5S RNA and the Xenopus borealis 5S RNA gene

1987 ◽  
Vol 7 (11) ◽  
pp. 3985-3993
Author(s):  
M S Sands ◽  
D F Bogenhagen
Keyword(s):  
Control Region ◽  
Polyacrylamide Gels ◽  
Wild Type ◽  
Base Pairing ◽  
5S Rna ◽  
Ribonucleoprotein Particles ◽  
In Vitro Transcripts ◽  
Mutant Genes ◽  
Entire Gene

We have established the conditions for the reassociation of 5S RNA and TFIIIA to form 7S particles. We tested the ability of altered 5S RNAs to bind TFIIIA, taking advantage of the slower mobility of 7S particles compared with free 5S RNA in native polyacrylamide gels. Linker substitution mutants were constructed encompassing the entire gene, including the intragenic control region. In vitro transcripts of the linker substitution mutants were tested for their ability to bind TFIIIA to form 7S ribonucleoprotein particles. Altered 5S RNAs with base changes in or around helices IV and V, which would interfere with the normal base pairing of that region, showed decreased ability to bind TFIIIA. The transcripts of some mutant genes that were efficiently transcribed (greater than 50% of wild-type efficiency) failed to bind TFIIIA in this gel assay. In contrast, the RNA synthesized from a poorly transcribed mutant, LS 86/97, in which residues 87 to 96 of the RNA were replaced in the single-stranded loop at the base of helix V, bound TFIIIA well. The data indicate that TFIIIA binds to different domains in the 5S RNA gene and 5S RNA.

A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5′ border of the region

Cell ◽  
1980 ◽  
Vol 19 (1) ◽  
pp. 13-25 ◽  
Author(s):  
Shigeru Sakonju ◽  
Daniel F. Bogenhagen ◽  
Donald D. Brown
Keyword(s):  
Control Region ◽  
5S Rna ◽  
Initiation Of Transcription

Exciton fine structure in semiconductor nanocrystals in the tight-binding method

2003 ◽  
Vol 0 (5) ◽  
pp. 1536-1539 ◽  
Author(s):  
J. Pérez-Conde ◽  
A. K. Bhattacharjee ◽  
M. Pons
Keyword(s):  
Fine Structure ◽  
Semiconductor Nanocrystals ◽  
Tight Binding ◽  
Tight Binding Method
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