scholarly journals Evolutionary changes of sequences and factors that direct transcription termination of human and mouse ribsomal genes.

1987 ◽  
Vol 7 (7) ◽  
pp. 2521-2529 ◽  
Author(s):  
I Bartsch ◽  
C Schoneberg ◽  
I Grummt
Keyword(s):  
Base Pair ◽  
Signal Sequence ◽  
Transcription Termination ◽  
Proximal Part ◽  
In Vitro Transcription ◽  
Transcription Unit ◽  
Rdna Transcription ◽  
Human Sequence ◽  
Sequence Elements

We have analyzed the sequences required for termination of human rDNA transcription. The human ribosomal transcription unit is shown to extend about 350 nucleotides into the 3'-terminal spacer and ends immediately upstream of a region with a distinct sequence heterogeneity. This heterogeneous region contains a cluster of conserved 10-base pair sequence elements which exert a striking homology to the proximal part of the 18-base pair murine rDNA transcription termination signal sequence, termed SalI box. Exonuclease III protection assays and in vitro transcription experiments with both homologous and heterologous human-mouse minigene constructs, and extracts from HeLa or Ehrlich ascites cells, reveal a functional analogy of the human sequence to the mouse SalI box. It mediates binding of a nuclear protein which functions as a transcription termination factor. The murine signal sequence is recognized by the human factor but not vice versa. The different sequence specificities and electrophoretic properties of the functionally equivalent protein factors suggest that a molecular coevolution has taken place between the termination signal sequences and the genes coding for the termination factors.

Evolutionary changes of sequences and factors that direct transcription termination of human and mouse ribsomal genes

1987 ◽  
Vol 7 (7) ◽  
pp. 2521-2529
Author(s):  
I Bartsch ◽  
C Schoneberg ◽  
I Grummt
Keyword(s):  
Base Pair ◽  
Signal Sequence ◽  
Transcription Termination ◽  
Proximal Part ◽  
In Vitro Transcription ◽  
Transcription Unit ◽  
Rdna Transcription ◽  
Human Sequence ◽  
Sequence Elements

We have analyzed the sequences required for termination of human rDNA transcription. The human ribosomal transcription unit is shown to extend about 350 nucleotides into the 3'-terminal spacer and ends immediately upstream of a region with a distinct sequence heterogeneity. This heterogeneous region contains a cluster of conserved 10-base pair sequence elements which exert a striking homology to the proximal part of the 18-base pair murine rDNA transcription termination signal sequence, termed SalI box. Exonuclease III protection assays and in vitro transcription experiments with both homologous and heterologous human-mouse minigene constructs, and extracts from HeLa or Ehrlich ascites cells, reveal a functional analogy of the human sequence to the mouse SalI box. It mediates binding of a nuclear protein which functions as a transcription termination factor. The murine signal sequence is recognized by the human factor but not vice versa. The different sequence specificities and electrophoretic properties of the functionally equivalent protein factors suggest that a molecular coevolution has taken place between the termination signal sequences and the genes coding for the termination factors.

In vitro transcription termination activity of the Drosophila mitochondrial DNA-binding protein DmTTF

2005 ◽  
Vol 331 (1) ◽  
pp. 357-362 ◽  
Author(s):  
Marina Roberti ◽  
Patricio Fernandez-Silva ◽  
Paola Loguercio Polosa ◽  
Erika Fernandez-Vizarra ◽  
Francesco Bruni ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Binding ◽  
Binding Protein ◽  
Transcription Termination ◽  
Dna Binding Protein ◽  
In Vitro Transcription ◽  
Termination Activity

scholarly journals Termination-altering mutations in the second-largest subunit of yeast RNA polymerase III.

1995 ◽  
Vol 15 (3) ◽  
pp. 1467-1478 ◽  
Author(s):  
S A Shaaban ◽  
B M Krupp ◽  
B D Hall
Keyword(s):  
Amino Acid ◽  
Rna Polymerase ◽  
Transcription Initiation ◽  
Transcription Termination ◽  
Rna Polymerase Iii ◽  
In Vitro Transcription ◽  
The Other ◽  
Polymerase Iii

In order to identify catalytically important amino acid changes within the second-largest subunit of yeast RNA polymerase III, we mutagenized selected regions of its gene (RET1) and devised in vivo assays for both increased and decreased transcription termination by this enzyme. Using as the reporter gene a mutant SUP4-o tRNA gene that in one case terminates prematurely and in the other case fails to terminate, we screened mutagenized RET1 libraries for reduced and increased transcription termination, respectively. The gain in suppression phenotype was in both cases scored as a reduction in the accumulation of red pigment in yeast strains harboring the ade2-1 ochre mutation. Termination-altering mutations were obtained in regions of the RET1 gene encoding amino acids 300 to 325, 455 to 486, 487 to 521, and 1061 to 1082 of the protein. In degree of amino acid sequence conservation, these range from highly variable in the first to highly conserved in the last two regions. Residues 300 to 325 yielded mainly reduced-termination mutants, while in region 1061 to 1082, increased-termination mutants were obtained exclusively. All mutants recovered, while causing gain of suppression with one SUP4 allele, brought about a reduction in suppression with the other allele, thus confirming that the phenotype is due to altered termination rather than an elevated level of transcription initiation. In vitro transcription reactions performed with extracts from several strong mutants demonstrated that the mutant polymerases respond to RNA terminator sequences in a manner that matches their in vivo termination phenotypes.

scholarly journals Transcription Termination and 3′-End Processing of the Spliced Leader RNA in Kinetoplastids

1999 ◽  
Vol 19 (2) ◽  
pp. 1595-1604 ◽  
Author(s):  
Nancy R. Sturm ◽  
Michael C. Yu ◽  
David A. Campbell
Keyword(s):  
Binding Site ◽  
Transcription Termination ◽  
Small Nuclear Rna ◽  
Stem Loop ◽  
Spliced Leader ◽  
Nuclear Extracts ◽  
Sequence Elements ◽  
Rna Genes

ABSTRACT Addition of a 39-nucleotide (nt) spliced leader (SL) bytrans splicing is a basic requirement for all trypanosome nuclear mRNAs. The SL RNA in Leishmania tarentolae is a 96-nt precursor transcript synthesized by a polymerase that resembles polymerase II most closely. To analyze SL RNA genesis, we mutated SL RNA intron structures and sequence elements: stem-loops II and III, the Sm-binding site, and the downstream T tract. Using an exon-tagged SL RNA gene, we examined the phenotypes produced by a second-site 10-bp linker scan mutagenic series and directed mutagenesis. Here we report that transcription is terminated by the T tract, which is common to the 3′ end of all kinetoplastid SL RNA genes, and that more than six T’s are required for efficient termination in vivo. We describe mutants whose SL RNAs end in the T tract or appear to lack efficient termination but can generate wild-type 3′ ends. Transcriptionally active nuclear extracts show staggered products in the T tract, directed by eight or more T’s. The in vivo and in vitro data suggest that SL RNA transcription termination is staggered in the T tract and is followed by nucleolytic processing to generate the mature 3′ end. We show that the Sm-binding site and stem-loop III structures are necessary for correct 3′-end formation. Thus, we have defined the transcription termination element for the SL RNA gene. The termination mechanism differs from that of vertebrate small nuclear RNA genes and the SL RNA homologue in Ascaris.

scholarly journals Delineation of DNA sequences that are important for in vitro transcription from the adenovirus EIIa late promoter.

1988 ◽  
Vol 8 (5) ◽  
pp. 1906-1914 ◽  
Author(s):  
D H Huang ◽  
R G Roeder
Keyword(s):  
Dna Sequences ◽  
Nuclear Extract ◽  
In Vitro Transcription ◽  
Initiation Site ◽  
Late Promoter ◽  
Fold Reduction ◽  
Sequence Elements ◽  
A Cell ◽  
Circular Template

Late in infection, transcription of the EIIa gene is initiated primarily at map unit 72 of the adenovirus genome. A cell-free nuclear extract system was used to determine sequence elements important for the function of this late promoter. In such a system, the transcriptional activity of a circular template was found to be much higher (5- to 10-fold) than that of a linear template. The effect of template topology appeared to be dependent on two distal upstream elements with 5' boundaries located near -265 to -223 and -147 to -133 (in relation to the initiation site), since deletions of these regions reduced transcription of the circular template, in a stepwise fashion, to a level similar to that observed with the linear template. Further deletions revealed an element in the -116 region that appeared to be more important for transcription of the circular template (10-fold reduction) than for transcription of the linear template (3-fold reduction). Lastly, deletion of the TACAAA sequence in the -29 region resulted in further reduction in transcription, indicating that this element functions as a promoter in vitro.

scholarly journals A tridecamer DNA sequence supports human mitochondrial RNA 3'-end formation in vitro.

1988 ◽  
Vol 8 (10) ◽  
pp. 4502-4509 ◽  
Author(s):  
T W Christianson ◽  
D A Clayton
Keyword(s):  
Dna Sequence ◽  
Transcription Termination ◽  
In Vitro Transcription ◽  
Mitochondrial Rna ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Transcription System ◽  
Flanking Regions

Vertebrate mitochondrial genomes contain a putative transcription termination site at the boundary between the genes for 16S rRNA and leucyl-tRNA. We have described previously an in vitro transcription system from human cells with the capacity to generate RNA 3' ends with the same map positions as those synthesized in vivo. By assaying the ability of variously truncated templates to support 3'-end formation, we demonstrated that the tridecamer sequence 5'-TGGCAGAGCCCCGG-3', contained entirely within the gene for leucyl-tRNA, is necessary to direct accurate termination. When two tridecamer sequences and their immediate flanking regions were placed in tandem, termination occurred at both promoter-proximal and promoter-distal sites. Furthermore, termination was competitively inhibited, in a concentration-dependent manner, by DNA containing the tridecamer sequence. These results suggest a modest sequence requirement for transcription termination that is contingent on a factor capable of recognizing the presence of the tridecamer DNA sequence.

An in vitro transcription termination system to analyze chloroplast promoters: identification of multiple promoters for the spinach atpB gene

1990 ◽  
Vol 17 (1) ◽  
pp. 55-64 ◽  
Author(s):  
Liang-Jwu Chen ◽  
Sharon A. Rogers ◽  
D. Clark Bennett ◽  
Meng-Chun Hu ◽  
Emil M. Orozco
Keyword(s):  
Transcription Termination ◽  
In Vitro Transcription ◽  
Multiple Promoters

Regulatory region of the Klebsiella aerogenes tryptophan operon

1982 ◽  
Vol 152 (1) ◽  
pp. 49-56
Author(s):  
M Blumenberg ◽  
C Yanofsky
Keyword(s):  
Transcription Termination ◽  
Regulatory Region ◽  
Enteric Bacteria ◽  
In Vitro Transcription ◽  
Regulatory Sequences ◽  
Klebsiella Aerogenes ◽  
Transcription Termination Site ◽  
Tryptophan Operon ◽  
Trp Promoter

The trp operon of Klebsiella aerogenes was cloned, and its regulatory region was sequenced. Comparison with previously reported trp regulatory sequences of other enteric bacteria indicates that the K. aerogenes trp promoter-operator region is most similar to the corresponding region of Salmonella typhimurium. The trp leader regions of K. aerogenes and other enteric bacteria are organized similarly, but there are significant differences in the stabilities of the predicted secondary structures in their leader transcripts. These differences should make the K. aerogenes attenuator a weaker transcription termination site than any of the other attenuator regions studied; this was confirmed in in vitro transcription experiments. The sequence of the leader transcript and the precise site of in vitro termination were determined.

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