scholarly journals A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number‐dependent manner

2020 ◽  
Vol 41 (4) ◽  
pp. 807-824
Author(s):  
Maria Bertuzzi ◽  
Dave Tang ◽  
Raffaella Calligaris ◽  
Christina Vlachouli ◽  
Sara Finaurini ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Dependent Manner ◽  
Start Site ◽  
Transcription Start ◽  
Repeat Number ◽  
Alternative Transcription Start Site ◽  
Alternative Transcription

scholarly journals Isolation and characterization of a TATA-less promoter for the human beta 3 integrin gene

Blood ◽  
1994 ◽  
Vol 83 (3) ◽  
pp. 668-676 ◽  
Author(s):  
M Villa-Garcia ◽  
L Li ◽  
G Riely ◽  
PF Bray
Keyword(s):  
Transcription Start Site ◽  
Phorbol Esters ◽  
K562 Cells ◽  
Start Codon ◽  
Dependent Manner ◽  
Start Site ◽  
Transcription Start ◽  
Specific Expression ◽  
Rnase Protection ◽  
Isolation And Characterization

Proper expression of the human platelet fibrinogen receptor is necessary for the maintenance of normal hemostasis. This receptor is formed by the heterodimer alpha IIb beta 3, a prototypic member of the integrin family of adhesive molecules. beta 3 is also expressed in other tissues with alpha v as the vitronectin receptor. It was not possible to study the basis for tissue-specific expression of this gene, because the beta 3 gene promoter had not been isolated previously. We have now isolated a 6.0-kb human genomic DNA fragment containing 2.0 kb of sequence 5′ to the beta 3 ATG start codon. This clone also contains sequence encoding the signal peptide of the immature beta 3 protein and 3.0 kb of 3′ intronic sequence. Primer extension and RNase protection studies of poly A+ RNA from a human erythroleukemia (HEL) cell line indicated a major transcription start site 30 bp upstream of the ATG start codon. In an orientation-dependent manner, a 584-bp fragment 5′ to the start codon promotes expression of the chloramphenicol acetyl transferase (CAT) reporter gene in K562 cells. CAT expression from this beta 3 promoter is fivefold above expression from a “promoter-less” control CAT construct. This beta 3 promoter lacks TATA and CAAT cis-acting elements, but there are two Sp1 sites flanking the transcription start site. Other potential transcription factor binding sites are also identified. Phorbol esters (TPA), which increase beta 3 transcription in K562 cells, stimulated transcription from the 584-bp 5′ beta 3 region. The isolation of this beta 3 promoter region should permit a more detailed analysis of its transcriptional regulation.

scholarly journals Transcription factor abundance controlled by an auto-regulatory mechanism involving a transcription start site switch

2013 ◽  
Vol 42 (4) ◽  
pp. 2171-2184 ◽  
Author(s):  
Richard Patryk Ngondo ◽  
Philippe Carbon
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Start Site ◽  
Regulatory Mechanism ◽  
Start Site ◽  
Transcription Start ◽  
Aberrant Expression ◽  
Alternative Transcription ◽  
Activating Transcription Factor

Abstract A transcriptional feedback loop is the simplest and most direct means for a transcription factor to provide an increased stability of gene expression. In this work performed in human cells, we reveal a new negative auto-regulatory mechanism involving an alternative transcription start site (TSS) usage. Using the activating transcription factor ZNF143 as a model, we show that the ZNF143 low-affinity binding sites, located downstream of its canonical TSS, play the role of protein sensors to induce the up- or down-regulation of ZNF143 gene expression. We uncovered that the TSS switch that mediates this regulation implies the differential expression of two transcripts with an opposite protein production ability due to their different 5′ untranslated regions. Moreover, our analysis of the ENCODE data suggests that this mechanism could be used by other transcription factors to rapidly respond to their own aberrant expression level.

scholarly journals Isolation and characterization of a TATA-less promoter for the human beta 3 integrin gene

Blood ◽  
1994 ◽  
Vol 83 (3) ◽  
pp. 668-676 ◽  
Author(s):  
M Villa-Garcia ◽  
L Li ◽  
G Riely ◽  
PF Bray
Keyword(s):  
Transcription Start Site ◽  
Phorbol Esters ◽  
K562 Cells ◽  
Start Codon ◽  
Dependent Manner ◽  
Start Site ◽  
Transcription Start ◽  
Specific Expression ◽  
Rnase Protection ◽  
Isolation And Characterization

Abstract Proper expression of the human platelet fibrinogen receptor is necessary for the maintenance of normal hemostasis. This receptor is formed by the heterodimer alpha IIb beta 3, a prototypic member of the integrin family of adhesive molecules. beta 3 is also expressed in other tissues with alpha v as the vitronectin receptor. It was not possible to study the basis for tissue-specific expression of this gene, because the beta 3 gene promoter had not been isolated previously. We have now isolated a 6.0-kb human genomic DNA fragment containing 2.0 kb of sequence 5′ to the beta 3 ATG start codon. This clone also contains sequence encoding the signal peptide of the immature beta 3 protein and 3.0 kb of 3′ intronic sequence. Primer extension and RNase protection studies of poly A+ RNA from a human erythroleukemia (HEL) cell line indicated a major transcription start site 30 bp upstream of the ATG start codon. In an orientation-dependent manner, a 584-bp fragment 5′ to the start codon promotes expression of the chloramphenicol acetyl transferase (CAT) reporter gene in K562 cells. CAT expression from this beta 3 promoter is fivefold above expression from a “promoter-less” control CAT construct. This beta 3 promoter lacks TATA and CAAT cis-acting elements, but there are two Sp1 sites flanking the transcription start site. Other potential transcription factor binding sites are also identified. Phorbol esters (TPA), which increase beta 3 transcription in K562 cells, stimulated transcription from the 584-bp 5′ beta 3 region. The isolation of this beta 3 promoter region should permit a more detailed analysis of its transcriptional regulation.

Cloning and characterization of the groE heat-shock operon of the marine bacterium Vibrio harveyi

Microbiology ◽  
2003 ◽  
Vol 149 (6) ◽  
pp. 1483-1492 ◽  
Author(s):  
Dorota Kuchanny-Ardigò ◽  
Barbara Lipińska
Keyword(s):  
Heat Shock ◽  
Transcription Start Site ◽  
Vibrio Harveyi ◽  
Regulatory Elements ◽  
Northern Hybridization ◽  
Dependent Manner ◽  
Start Site ◽  
Transcription Start ◽  
Transcriptional Regulatory Elements ◽  
E Coli

The DNA region of the Vibrio harveyi chromosome containing the heat-shock genes groES and groEL was cloned, and the genes were sequenced. These genes are arranged in the chromosome in the order groES–groEL. Northern hybridization experiments with RNA from V. harveyi and a DNA probe carrying both groES and groEL genes showed a single, heat-inducible transcript of approximately 2200 nt, indicating that these genes form an operon. Primer extension analysis revealed a strong, heat-inducible transcription start site 59 nt upstream of groES, preceded by a sequence typical for the Escherichia coli heat-shock promoters recognized by the σ 32 factor, and a weak transcription start site 25 nt upstream the groES gene, preceded by a sequence typical for σ 70 promoters. Transcription from the latter promoter occurred only at low temperatures. The V. harveyi groE operon cloned in a plasmid in E. coli cells was transcribed in a σ 32-dependent manner; the transcript size and the σ 32-dependent transcription start site were as in V. harveyi cells. Comparison of V. harveyi groE transcription regulation with the other well-characterized groE operons of the γ subdivision of proteobacteria (those of E. coli and Pseudomonas aeruginosa) indicates a high conservation of the transcriptional regulatory elements among these bacteria, with two promoters, σ 32 and σ 70, involved in the regulation. The ability of the cloned groESL genes to complement E. coli groE mutants was tested: V. harveyi groES restored a thermoresistant phenotype to groES bacteria and enabled λ phage to grow in the mutant cells. V. harveyi groEL did not abolish thermosensitivity of groEL bacteria but it complemented the groEL mutant with respect to growth of λ phage. The results suggest that the GroEL chaperone may be more species-specific than the GroES co-chaperone.

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