scholarly journals A cell-specific enhancer of the mouse alpha 1-antitrypsin gene has multiple functional regions and corresponding protein-binding sites.

1988 ◽  
Vol 8 (3) ◽  
pp. 1055-1066 ◽  
Author(s):  
D R Grayson ◽  
R H Costa ◽  
K G Xanthopoulos ◽  
J E Darnell
Keyword(s):  
Protein Binding ◽  
Dna Sequences ◽  
Binding Sites ◽  
Hepatoma Cell ◽  
Regulatory Elements ◽  
Start Site ◽  
Specific Expression ◽  
Isolation And Characterization ◽  
A Cell ◽  
Alpha 1 Antitrypsin

We have previously described the isolation and characterization of genomic clones corresponding to the mouse alpha 1-antitrypsin gene (Krauter et al., DNA 5:29-36, 1986). In this report, we have analyzed the DNA sequences upstream of the RNA start site that direct hepatoma cell-specific expression of this gene when incorporated into recombinant plasmids. The 160 nucleotides 5' to the cap site direct low-level expression in hepatoma cells, and sequences between -520 and -160 bp upstream of the RNA start site functioned as a cell-specific enhancer of expression both with the alpha 1-antitrypsin promoter and when combined with a functional beta-globin promoter. Within the enhancer region, three binding sites for proteins present in hepatoma nuclear extracts were identified. The location of each site was positioned, using both methylation protection and methylation interference experiments. Each protein-binding site correlated with a functionally important region necessary for full enhancer activity. These experiments demonstrated a complex arrangement of regulatory elements comprising the alpha 1-antitrypsin enhancer. Significant qualitative differences exist between the findings presented here and the cis-acting elements operative in regulating expression of the human alpha 1-antitrypsin gene (Ciliberto et al., Cell 41:531-540, 1985; De Simone et al., EMBO J. 6:2759-2766, 1987).

A cell-specific enhancer of the mouse alpha 1-antitrypsin gene has multiple functional regions and corresponding protein-binding sites

1988 ◽  
Vol 8 (3) ◽  
pp. 1055-1066
Author(s):  
D R Grayson ◽  
R H Costa ◽  
K G Xanthopoulos ◽  
J E Darnell
Keyword(s):  
Protein Binding ◽  
Dna Sequences ◽  
Binding Sites ◽  
Hepatoma Cell ◽  
Regulatory Elements ◽  
Start Site ◽  
Specific Expression ◽  
Isolation And Characterization ◽  
A Cell ◽  
Alpha 1 Antitrypsin

We have previously described the isolation and characterization of genomic clones corresponding to the mouse alpha 1-antitrypsin gene (Krauter et al., DNA 5:29-36, 1986). In this report, we have analyzed the DNA sequences upstream of the RNA start site that direct hepatoma cell-specific expression of this gene when incorporated into recombinant plasmids. The 160 nucleotides 5' to the cap site direct low-level expression in hepatoma cells, and sequences between -520 and -160 bp upstream of the RNA start site functioned as a cell-specific enhancer of expression both with the alpha 1-antitrypsin promoter and when combined with a functional beta-globin promoter. Within the enhancer region, three binding sites for proteins present in hepatoma nuclear extracts were identified. The location of each site was positioned, using both methylation protection and methylation interference experiments. Each protein-binding site correlated with a functionally important region necessary for full enhancer activity. These experiments demonstrated a complex arrangement of regulatory elements comprising the alpha 1-antitrypsin enhancer. Significant qualitative differences exist between the findings presented here and the cis-acting elements operative in regulating expression of the human alpha 1-antitrypsin gene (Ciliberto et al., Cell 41:531-540, 1985; De Simone et al., EMBO J. 6:2759-2766, 1987).

Localization of transcriptional regulatory elements and nuclear factor binding sites in mouse ribosomal protein gene rpL32

1989 ◽  
Vol 9 (5) ◽  
pp. 2067-2074
Author(s):  
M L Atchison ◽  
O Meyuhas ◽  
R P Perry
Keyword(s):  
Ribosomal Protein ◽  
Dna Sequences ◽  
Binding Sites ◽  
Protein Gene ◽  
Transcriptional Start Site ◽  
Ribosomal Protein Gene ◽  
Regulatory Elements ◽  
Sequence Motif ◽  
Start Site ◽  
Nuclear Factors

The DNA sequences required for expression of the ribosomal protein gene rpL32 were identified by transient-expression assays of chimeric rpL32-chloramphenicol acetyltransferase genes. These studies showed that maximal rpL32 expression requires sequences in a 150- to 200-base-pair region spanning the transcriptional start site. Three discrete regions of importance were identified: one between positions -79 and -69 and two others located downstream of the transcriptional start site. Progressive 5' or 3' deletions caused stepwise decreases in expression, which suggested a complex interplay of redundant or compensatory elements. Gel mobility shift assays were used to identify trans-acting nuclear factors which bind to segments of the rpL32 promoter that are known to be important for transcription. Evidence for several distinct nuclear factors is presented. The binding sites for these factors were localized to the following regions: -79 to -69, -36 to -19, -19 to +11, +11 to +46 in exon I, and within the first 31 base pairs of intron 1. One of these factors may bind to multiple sites within the promoter region. Interestingly, the factor that binds to a sequence motif in the first exon also binds to similar motifs in a comparable region of the c-myc gene.

scholarly journals Localization of transcriptional regulatory elements and nuclear factor binding sites in mouse ribosomal protein gene rpL32.

1989 ◽  
Vol 9 (5) ◽  
pp. 2067-2074 ◽  
Author(s):  
M L Atchison ◽  
O Meyuhas ◽  
R P Perry
Keyword(s):  
Ribosomal Protein ◽  
Dna Sequences ◽  
Binding Sites ◽  
Protein Gene ◽  
Transcriptional Start Site ◽  
Ribosomal Protein Gene ◽  
Regulatory Elements ◽  
Sequence Motif ◽  
Start Site ◽  
Nuclear Factors

The DNA sequences required for expression of the ribosomal protein gene rpL32 were identified by transient-expression assays of chimeric rpL32-chloramphenicol acetyltransferase genes. These studies showed that maximal rpL32 expression requires sequences in a 150- to 200-base-pair region spanning the transcriptional start site. Three discrete regions of importance were identified: one between positions -79 and -69 and two others located downstream of the transcriptional start site. Progressive 5' or 3' deletions caused stepwise decreases in expression, which suggested a complex interplay of redundant or compensatory elements. Gel mobility shift assays were used to identify trans-acting nuclear factors which bind to segments of the rpL32 promoter that are known to be important for transcription. Evidence for several distinct nuclear factors is presented. The binding sites for these factors were localized to the following regions: -79 to -69, -36 to -19, -19 to +11, +11 to +46 in exon I, and within the first 31 base pairs of intron 1. One of these factors may bind to multiple sites within the promoter region. Interestingly, the factor that binds to a sequence motif in the first exon also binds to similar motifs in a comparable region of the c-myc gene.

E-box- and MEF-2-independent muscle-specific expression, positive autoregulation, and cross-activation of the chicken MyoD (CMD1) promoter reveal an indirect regulatory pathway

1994 ◽  
Vol 14 (8) ◽  
pp. 5474-5486
Author(s):  
C A Dechesne ◽  
Q Wei ◽  
J Eldridge ◽  
L Gannoun-Zaki ◽  
P Millasseau ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Primary Cultures ◽  
Regulatory Elements ◽  
The Other ◽  
Indirect Pathway ◽  
Specific Expression ◽  
Fibroblast Cultures ◽  
E Box ◽  
Myogenic Factors

Members of the MyoD family of gene-regulatory proteins (MyoD, myogenin, myf5, and MRF4) have all been shown not only to regulate the transcription of numerous muscle-specific genes but also to positively autoregulate and cross activate each other's transcription. In the case of muscle-specific genes, this transcriptional regulation can often be correlated with the presence of a DNA consensus in the regulatory region CANNTG, known as an E box. Little is known about the regulatory interactions of the myogenic factors themselves; however, these interactions are thought to be important for the activation and maintenance of the muscle phenotype. We have identified the minimal region in the chicken MyoD (CMD1) promoter necessary for muscle-specific transcription in primary cultures of embryonic chicken skeletal muscle. The CMD1 promoter is silent in primary chick fibroblast cultures and in muscle cell cultures treated with the thymidine analog bromodeoxyuridine. However, CMD1 and chicken myogenin, as well as, to a lesser degree, chicken Myf5 and MRF4, expressed in trans can activate transcription from the minimal CMD1 promoter in these primary fibroblast cultures. Here we show that the CMD1 promoter contains numerous E-box binding sites for CMD1 and the other myogenic factors, as well as a MEF-2 binding site. Surprisingly, neither muscle-specific and the other myogenic factors, as well as a MEF-2 binding site. Surprisingly, neither muscle-specific expression, autoregulation, or cross activation depends upon the presence of of these E-box or MEF-2 binding sites in the CMD1 promoter. These results demonstrate that the autoregulation and cross activation of the chicken MyoD promoter through the putative direct binding of the myogenic basic helix-loop-helix regulatory factors is mediated through an indirect pathway that involves unidentified regulatory elements and/or ancillary factors.

scholarly journals Localization of DNA sequences involved in dexamethasone-dependent expression of the rat alpha 1-acid glycoprotein gene.

1986 ◽  
Vol 6 (7) ◽  
pp. 2551-2561 ◽  
Author(s):  
H Baumann ◽  
L E Maquat
Keyword(s):  
Glucocorticoid Receptor ◽  
Receptor Binding ◽  
Dna Sequences ◽  
Base Pair ◽  
Binding Sites ◽  
Gene Region ◽  
Start Site ◽  
Base Pairs ◽  
Acid Glycoprotein ◽  
Cat Gene

Synthesis of rat alpha 1-acid glycoprotein (AGP), one of the major inflammation-induced plasma proteins, is positively regulated by dexamethasone. To define the dexamethasone-responsive genetic element, we isolated and tested AGP gene sequences for the ability to confer glucocorticoid induction to the bacterial chloramphenicol acetyltransferase (CAT) gene in L cells. A 141-base-pair region of the AGP gene, including 120 base pairs of DNA upstream from the start site of transcription and 21 base pairs of the 5' untranslated region, was sufficient for maximal CAT gene induction by dexamethasone. To localize more precisely the AGP glucocorticoid-responsive element, parts of this 141-base-pair region were inserted 5' to either an AGP promoter-CAT gene or a human triosephosphate isomerase promoter-CAT gene, both of which lacked a response to the steroid. The AGP gene region between 120 and 42 base pairs upstream from the start site of transcription was found to mediate maximal dexamethasone induction of CAT enzyme levels. This result was unexpected because this region does not contain sequence homologies to known glucocorticoid receptor-binding sites and those AGP gene regions that lay further upstream and were homologous to other glucocorticoid receptor-binding sites were inactive in the CAT assay. The fact that the AGP gene region mediating dexamethasone regulation was distinct from the transcribed region indicates that glucocorticoids increase AGP gene expression primarily at the transcriptional rather than the posttranscriptional level.

scholarly journals Isolation and Characterization of Point Mutations in Mismatch Repair Genes That Destabilize Microsatellites in Yeast

2001 ◽  
Vol 21 (23) ◽  
pp. 8157-8167 ◽  
Author(s):  
Elaine Ayres Sia ◽  
Margaret Dominska ◽  
Lela Stefanovic ◽  
Thomas D. Petes
Keyword(s):  
Mismatch Repair ◽  
Dna Sequences ◽  
Point Mutations ◽  
Mismatch Repair Genes ◽  
Isolation And Characterization ◽  
Dna Mismatches ◽  
A Cell ◽  
The Stability ◽  
Yeast Mutants ◽  
Repair Genes

ABSTRACT The stability of simple repetitive DNA sequences (microsatellites) is a sensitive indicator of the ability of a cell to repair DNA mismatches. In a genetic screen for yeast mutants with elevated microsatellite instability, we identified strains containing point mutations in the yeast mismatch repair genes, MSH2,MSH3, MLH1, and PMS1. Some of these mutations conferred phenotypes significantly different from those of null mutations in these genes. One semidominant MSH2mutation was identified. Finally we showed that strains heterozygous for null mutations of mismatch repair genes in diploid strains in yeast confer subtle defects in the repair of small DNA loops.

scholarly journals Identification of cis-regulatory elements required for larval expression of the Drosophila melanogaster alcohol dehydrogenase gene.

Genetics ◽  
1990 ◽  
Vol 124 (3) ◽  
pp. 637-646 ◽  
Author(s):  
V Corbin ◽  
T Maniatis
Keyword(s):  
Drosophila Melanogaster ◽  
Alcohol Dehydrogenase ◽  
Dna Sequences ◽  
Regulatory Elements ◽  
Malpighian Tubules ◽  
Proximal Promoter ◽  
Start Site ◽  
Wild Type ◽  
Tissue Specific ◽  
Adh Gene

Abstract The Alcohol dehydrogenase (Adh) genes of two distantly related species, Drosophila melanogaster and Drosophila mulleri, display similar, but not identical, patterns of tissue-specific expression in larvae and adults. The regulatory DNA sequences necessary for wild-type Adh expression in D. mulleri larvae were previously reported. In this paper we present an analysis of the DNA sequences necessary for wild-type Adh expression in D. melanogaster larvae. We show that transcription from the proximal promoter of the melanogaster Adh gene is regulated by a far upstream enhancer and two or more elements near the transcription start site. The enhancer is tissue specific and stimulates transcription to high levels in fat body and to lower levels in midgut and malpighian tubules whether linked to the proximal promoter or to a heterologous promoter. The enhancer activity localized to at least two discrete regions dispersed over more than 1.7 kb of DNA. Deletion of any one of these subregions reduces Adh transcription in all three larval tissues. Similarly, two regions immediately upstream of the proximal promoter start site are necessary for wild-type transcription levels in all three tissues. Thus, each of the identified regulatory elements is sufficient for low levels of Adh gene expression in all three larval tissues, but maximal levels of expression requires the entire set.

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.

Sequences downstream of the transcription initiation site modulate the activity of the murine dihydrofolate reductase promoter

1990 ◽  
Vol 10 (4) ◽  
pp. 1390-1398
Author(s):  
P J Farnham ◽  
A L Means
Keyword(s):  
Protein Binding ◽  
Dihydrofolate Reductase ◽  
Dna Sequences ◽  
Binding Sites ◽  
Transcription Initiation ◽  
Untranslated Region ◽  
Simian Virus 40 ◽  
Initiation Site ◽  
Transcription Initiation Site ◽  
Transcription Analysis

The murine dihydrofolate reductase gene is regulated by a bidirectional promoter that lacks a TATA box. To identify the DNA sequences required for dihydrofolate reductase transcription, the activities of various templates were determined by in vitro transcription analysis. Our data indicate that sequences both upstream and downstream of the transcription initiation site modulate the activity of the dihydrofolate reductase promoter. We have focused on two regions downstream of the transcription initiation site that are important in determining the overall efficiency of the promoter. Region 1, which included exon 1 and part of intron 1, could stimulate transcription when placed in either orientation in the normal downstream position and when inserted upstream of the transcription start site. This region could also stimulate transcription in trans when the enhancer was physically separate from the promoter. Deletion of region 2, spanning 46 nucleotides of the 5' untranslated region, reduced transcriptional activity by fivefold. DNase I footprinting reactions identified protein-binding sites in both downstream stimulatory regions. Protein bound to two sites in region 1, both of which contain an inverted CCAAT box. The protein-binding site in the 5' untranslated region has extensive homology to binding sites in promoters that both lack (simian virus 40 late) and contain (adenovirus type 2 major late promoter and c-myc) TATA boxes.

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