scholarly journals A 12-base-pair sequence is an essential element of the ribosomal gene terminator in Xenopus laevis.

1987 ◽  
Vol 7 (5) ◽  
pp. 1900-1905 ◽  
Author(s):  
P Labhart ◽  
R H Reeder
Keyword(s):  
Xenopus Laevis ◽  
Base Pair ◽  
Transcription Initiation ◽  
Gene Promoter ◽  
Essential Element ◽  
Ribosomal Gene ◽  
Pulse Label ◽  
Conserved Sequence ◽  
Rrna Transcription ◽  
Pair Sequence

rRNA transcription in Xenopus laevis terminates near a 7-base-pair (bp) conserved sequence (T3 box) located 200 bp upstream of the site of transcription initiation for the adjacent gene promoter. We present evidence here that a 12-bp element containing the T3 box is an essential part of the terminator. Using an oocyte injection assay, we found that the 12-bp element (but not the T3 box alone) severely reduced the amount of RNA detectable at sites downstream from itself and that the T3 box within the 12-bp element was required to specify the formation of correct 3' ends. This requirement for the 12-bp element was also seen in pulse-label experiments by using a homogenate of oocyte nuclei, but the present data did not allow us to determine the exact mechanism by which the 12-bp element acts. Removal of the T3 region from its normal location allowed a significant amount of readthrough transcripts to accumulate, indicating that additional sequences may be required for complete terminator function.

A 12-base-pair sequence is an essential element of the ribosomal gene terminator in Xenopus laevis

1987 ◽  
Vol 7 (5) ◽  
pp. 1900-1905
Author(s):  
P Labhart ◽  
R H Reeder
Keyword(s):  
Xenopus Laevis ◽  
Base Pair ◽  
Transcription Initiation ◽  
Gene Promoter ◽  
Essential Element ◽  
Ribosomal Gene ◽  
Pulse Label ◽  
Conserved Sequence ◽  
Rrna Transcription ◽  
Pair Sequence

rRNA transcription in Xenopus laevis terminates near a 7-base-pair (bp) conserved sequence (T3 box) located 200 bp upstream of the site of transcription initiation for the adjacent gene promoter. We present evidence here that a 12-bp element containing the T3 box is an essential part of the terminator. Using an oocyte injection assay, we found that the 12-bp element (but not the T3 box alone) severely reduced the amount of RNA detectable at sites downstream from itself and that the T3 box within the 12-bp element was required to specify the formation of correct 3' ends. This requirement for the 12-bp element was also seen in pulse-label experiments by using a homogenate of oocyte nuclei, but the present data did not allow us to determine the exact mechanism by which the 12-bp element acts. Removal of the T3 region from its normal location allowed a significant amount of readthrough transcripts to accumulate, indicating that additional sequences may be required for complete terminator function.

scholarly journals Genetic analysis of the human thymidine kinase gene promoter.

1986 ◽  
Vol 6 (8) ◽  
pp. 2903-2909 ◽  
Author(s):  
J A Kreidberg ◽  
T J Kelly
Keyword(s):  
Thymidine Kinase ◽  
Base Pair ◽  
Promoter Region ◽  
Genomic Sequence ◽  
Gene Promoter ◽  
Thymidine Kinase Gene ◽  
Rich Region ◽  
Kinase Gene ◽  
Inverted Orientation ◽  
Pair Sequence

The promoter of the human thymidine kinase gene was defined by DNA sequence and genetic analyses. Mutant plasmids with deletions extending into the promoter region from both the 5' and 3' directions were constructed. The mutants were tested in a gene transfer system for the ability to transform TK- cells to the TK+ phenotype. This analysis delimited the functional promoter to within an 83-base-pair region upstream of the mRNA cap site. This region contains sequences common to other eucaryotic promoters including G X C-rich hexanucleotides, a CAAT box, and an A X T-rich region. The CAAT box is in an inverted orientation and is part of a 9-base-pair sequence repeated twice in the promoter region. Comparison of the genomic sequence with the cDNA sequence defined the first exon of the thymidine kinase gene.

Genetic analysis of the human thymidine kinase gene promoter

1986 ◽  
Vol 6 (8) ◽  
pp. 2903-2909
Author(s):  
J A Kreidberg ◽  
T J Kelly
Keyword(s):  
Thymidine Kinase ◽  
Base Pair ◽  
Promoter Region ◽  
Genomic Sequence ◽  
Gene Promoter ◽  
Thymidine Kinase Gene ◽  
Rich Region ◽  
Kinase Gene ◽  
Inverted Orientation ◽  
Pair Sequence

The promoter of the human thymidine kinase gene was defined by DNA sequence and genetic analyses. Mutant plasmids with deletions extending into the promoter region from both the 5' and 3' directions were constructed. The mutants were tested in a gene transfer system for the ability to transform TK- cells to the TK+ phenotype. This analysis delimited the functional promoter to within an 83-base-pair region upstream of the mRNA cap site. This region contains sequences common to other eucaryotic promoters including G X C-rich hexanucleotides, a CAAT box, and an A X T-rich region. The CAAT box is in an inverted orientation and is part of a 9-base-pair sequence repeated twice in the promoter region. Comparison of the genomic sequence with the cDNA sequence defined the first exon of the thymidine kinase gene.

scholarly journals DNase I footprinting shows three protected regions in the promoter of the rRNA genes of Xenopus laevis.

1985 ◽  
Vol 5 (2) ◽  
pp. 313-319 ◽  
Author(s):  
M Dunaway ◽  
R H Reeder
Keyword(s):  
Xenopus Laevis ◽  
Base Pair ◽  
Transcription Initiation ◽  
Protein S ◽  
Dnase I ◽  
Rrna Genes ◽  
Xenopus Laevis Oocytes ◽  
Dnase I Footprinting ◽  
Region I ◽  
Region Ii

Extracts prepared from Xenopus laevis oocytes contain a protein(s) which specifically protects three discrete regions of the RNA polymerase I promoter from digestion by DNase I. Protected region I, from nucleotide +15 to nucleotide -10, spans the site of transcription initiation. Protected region II extends from nucleotide -70 to nucleotide -100 relative to initiation, falling within a 42-base-pair sequence which is homologous to the 60/81-base-pair repeated elements which occur outside of the promoter in the spacer. Protected region III is upstream of region II, from nucleotide -120 to nucleotide -140. All three regions correlate with sequences known from deletion studies to be important for promoter function. Deletion mutants which retain either region I or regions II and III together footprint normally. Deletion of region III, however, reduces but does not eliminate footprinting on region II, suggesting either that one protein binds to both regions or that the proteins which bind to these sites interact with each other.

Conserved sequence blocks in kinetoplast minicircles from diverse species of trypanosomes

1989 ◽  
Vol 9 (3) ◽  
pp. 1365-1367
Author(s):  
D S Ray
Keyword(s):  
Base Pair ◽  
Common Mechanism ◽  
Sequence Motif ◽  
Kinetoplast Dna ◽  
Base Pairs ◽  
Conserved Sequence ◽  
Diverse Species ◽  
Pair Sequence ◽  
Sequence Region ◽  
Minicircle Sequence

Kinetoplast DNA minicircles from various species of trypanosomes are heterogeneous in nucleotide sequence to various degrees but in all instances contain a conserved sequence region of 100 to 200 base pairs present in one, two, or four copies per minicircle. Comparison of the conserved sequence regions of minicircles from eight species of trypanosomes revealed a common sequence motif consisting of three conserved sequence blocks (CSBs) present in the same order and with similar spacing in all species. In addition to the invariant 12-base-pair universal minicircle sequence (CSB-3), a 10-base-pair sequence (CSB-1) and an 8-base-pair sequence (CSB-2) are highly conserved in all minicircles. The overlap of CSB-1 and CSB-3 with previously identified 5' termini of newly synthesized minicircle H and L strands, respectively, and the presence of this conserved sequence motif in minicircles from diverse species suggest that these CSBs may determine a common mechanism of minicircle replication.

Spacer promoters are orientation-dependent activators of pre-rRNA transcription in Drosophila melanogaster

1990 ◽  
Vol 10 (9) ◽  
pp. 4667-4677
Author(s):  
G Grimaldi ◽  
P Fiorentini ◽  
P P Di Nocera
Keyword(s):  
Drosophila Melanogaster ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Gene Promoter ◽  
Large Set ◽  
Gene Promoters ◽  
Stimulatory Action ◽  
Rrna Transcription ◽  
Tandem Arrays

In Drosophila melanogaster, 240-base-pair (bp) repeats, clustered in tandem arrays within the ribosomal DNA nontranscribed spacer region, include sites of RNA polymerase I-dependent transcription initiation and elements that stimulate the rate of transcription from the downstream precursor rRNA (pre-rRNA) promoter. We have analyzed the in vivo transcriptional activity of a large set of recombinant constructs in which tandem arrays of distinct segments derived from a 240-bp repeat were inserted upstream of the pre-rRNA promoter. The results indicate that activating spacer elements are confined to a region of 70 bp. Enhancing units overlap with spacer promoters, since DNA segments that stimulate transcription at the gene promoter also efficiently drive transcription initiation. The finding that artificial spacer arrays invariably stimulate pre-rRNA transcription initiation in an orientation-dependent fashion suggest that spacer-initiated transcription is involved in the enhancement process. The minimal spacer activating segment includes a perfect copy of a core domain of the gene promoter extending from -24 to +10 flanked by poorly homologous upstream DNA sequences. Spacer and gene promoters are functionally interchangeable as activating units. However, the different combination of DNA elements within the two determines a functional hierarchy, as only the pre-rRNA promoter is responsive to the stimulatory action of upstream units.

scholarly journals Conserved sequence blocks in kinetoplast minicircles from diverse species of trypanosomes.

1989 ◽  
Vol 9 (3) ◽  
pp. 1365-1367 ◽  
Author(s):  
D S Ray
Keyword(s):  
Base Pair ◽  
Common Mechanism ◽  
Sequence Motif ◽  
Kinetoplast Dna ◽  
Base Pairs ◽  
Conserved Sequence ◽  
Diverse Species ◽  
Pair Sequence ◽  
Sequence Region ◽  
Minicircle Sequence

Kinetoplast DNA minicircles from various species of trypanosomes are heterogeneous in nucleotide sequence to various degrees but in all instances contain a conserved sequence region of 100 to 200 base pairs present in one, two, or four copies per minicircle. Comparison of the conserved sequence regions of minicircles from eight species of trypanosomes revealed a common sequence motif consisting of three conserved sequence blocks (CSBs) present in the same order and with similar spacing in all species. In addition to the invariant 12-base-pair universal minicircle sequence (CSB-3), a 10-base-pair sequence (CSB-1) and an 8-base-pair sequence (CSB-2) are highly conserved in all minicircles. The overlap of CSB-1 and CSB-3 with previously identified 5' termini of newly synthesized minicircle H and L strands, respectively, and the presence of this conserved sequence motif in minicircles from diverse species suggest that these CSBs may determine a common mechanism of minicircle replication.

Effect of intercalating agents on RNA polymerase I promoter selection in Xenopus laevis

1984 ◽  
Vol 4 (12) ◽  
pp. 2851-2857
Author(s):  
S C Pruitt ◽  
R H Reeder
Keyword(s):  
Xenopus Laevis ◽  
Rna Polymerase ◽  
Transcription Initiation ◽  
Large Range ◽  
Gene Promoter ◽  
Rna Polymerase I ◽  
Polymerase I ◽  
Template Dna ◽  
Intercalating Agents ◽  
Transcription Signals

We have analyzed the effect of DNA intercalating agents on the transcription signals from two different Xenopus laevis RNA polymerase I promoters. The transcription signal from the promoter for the 7.5-kilobase rRNA precursor (the gene promoter) is unaffected over a large range of intercalating agent concentrations regardless of whether the template is injected plasmid DNA in oocytes, the amplified endogenous nucleoli of oocytes, or the endogenous chromosomes of cultured Xenopus kidney cells. The transcription signal from a closely related promoter located in the spacer DNA between genes (the spacer promoter) ranges between undetectable to equivalent to the gene promoter signal on different templates. The transcription signal from the spacer promoter is also differentially affected by intercalating agents relative to the gene promoter. Depending on the template, these agents can either increase or decrease the transcription signal from the spacer promoter. Fusions between the gene and spacer promoters demonstrate that intercalating agents affect transcription initiation. One explanation for these results is that the degree of supercoiling of the template DNA can differentially inhibit transcription from the spacer promoters. The different effects of intercalating agents on transcription from the spacer promoters of various templates could then be explained as differences in the degree of supercoiling present on these templates initially.

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